Athurva Gore/LabNotes/ExomeReseq/2009-5-13: Difference between revisions
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>Ajgore |
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(4 intermediate revisions by the same user not shown) | |||
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** In one way, this is decent news; means that iPS cells do not stray too far from fibroblasts... | ** In one way, this is decent news; means that iPS cells do not stray too far from fibroblasts... | ||
** However, several of the GO groups are interesting. | ** However, several of the GO groups are interesting. | ||
==Summary of Below Data== | |||
* It seems that for the most part, very few genes stray away from fibroblast expression levels if they are not matching the stem cell levels. | |||
* These genes are listed below (~50 of them) | |||
* GO Terms reveal that the only highly enriched GO clusters are GPCR-related. GPCRs have been implicated in cancer. | |||
* However, is not a very good result alone. | |||
* Difficult to do this, since stem cells tend to match cancer in some cases. | |||
* '''TOMORROW:''' Look at cancer data; what genes does it have that are differentially expressed from Fibroblasts and Stem Cells both? Are any of these genes also found below? | |||
==Data== | |||
* Differentially expressed genes (from SAM): | * Differentially expressed genes (from SAM): | ||
ILLUMINA_ID Gene Name Related Genes Species | ILLUMINA_ID Gene Name Related Genes Species | ||
Line 90: | Line 98: | ||
ILMN_1753648 tripartite motif-containing 51 RG Homo sapiens | ILMN_1753648 tripartite motif-containing 51 RG Homo sapiens | ||
* GO Terms associated with this set: | * GO Terms associated with this set: | ||
Category Term | Category Term | ||
UP_SEQ_FEATURE repeat:LRR 3 | UP_SEQ_FEATURE repeat:LRR 3 | ||
UP_SEQ_FEATURE disulfide bond | UP_SEQ_FEATURE disulfide bond | ||
SP_PIR_KEYWORDS transducer | |||
GOTERM_BP_ALL GO:0009620~response to fungus | GOTERM_BP_ALL GO:0009620~response to fungus | ||
GOTERM_CC_ALL GO:0005887~integral to plasma membrane | |||
UP_SEQ_FEATURE topological domain: | UP_SEQ_FEATURE topological domain:Extracellular | ||
SP_PIR_KEYWORDS g-protein coupled receptor | |||
UP_SEQ_FEATURE topological domain:Cytoplasmic | |||
GOTERM_MF_ALL GO:0001871~pattern binding | |||
GOTERM_MF_ALL GO:0060089~molecular transducer activity | |||
UP_SEQ_FEATURE repeat:LRR 2 | |||
GOTERM_MF_ALL GO:0004930~G-protein coupled receptor activity | |||
UP_SEQ_FEATURE transmembrane region | |||
GOTERM_MF_ALL GO:0001584~rhodopsin-like receptor activity | |||
GOTERM_BP_ALL GO:0009410~response to xenobiotic stimulus | |||
SP_PIR_KEYWORDS glycoprotein | |||
SP_PIR_KEYWORDS membrane | |||
UP_SEQ_FEATURE repeat:LRR 1 | |||
SP_PIR_KEYWORDS mitogen | |||
SP_PIR_KEYWORDS receptor | |||
GOTERM_BP_ALL GO:0006805~xenobiotic metabolic process | |||
SP_PIR_KEYWORDS leucine-rich repeat | |||
GOTERM_CC_ALL GO:0031226~intrinsic to plasma membrane | |||
GOTERM_MF_ALL GO:0004888~transmembrane receptor activity | |||
GOTERM_CC_ALL GO:0031224~intrinsic to membrane | |||
PIR_SUPERFAMILY PIRSF036848:conserved protein with F-box/LRR-repeat, Skp2 type | |||
UP_SEQ_FEATURE glycosylation site:N-linked (GlcNAc...) | |||
SP_PIR_KEYWORDS transmembrane | |||
GOTERM_CC_ALL GO:0016021~integral to membrane | |||
GOTERM_MF_ALL GO:0004872~receptor activity | |||
INTERPRO IPR000276:Rhodopsin-like GPCR superfamily | |||
GOTERM_MF_ALL GO:0004871~signal transducer activity | |||
* '''FUNCTIONAL CATEGORIES''' (Important info here...) | |||
{| | |||
|Functional Group 1 | |||
|Median: 0.03711173039552113 | |||
|Geo: 0.039704364737313154 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|UP_SEQ_FEATURE | |||
|transmembrane region | |||
|18 | |||
|0 | |||
|34 | |||
|3211 | |||
|12056 | |||
|1.99 | |||
|1 | |||
|1 | |||
|4.25 | |||
|---- | |||
|UP_SEQ_FEATURE | |||
|topological domain:Extracellular | |||
|14 | |||
|0 | |||
|34 | |||
|2092 | |||
|12056 | |||
|2.37 | |||
|1 | |||
|1 | |||
|4.8 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|glycoprotein | |||
|18 | |||
|0 | |||
|43 | |||
|3807 | |||
|17599 | |||
|1.94 | |||
|0.99 | |||
|0.99 | |||
|6.87 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0004888~transmembrane receptor activity | |||
|9 | |||
|0.01 | |||
|36 | |||
|1388 | |||
|16968 | |||
|3.06 | |||
|1 | |||
|1 | |||
|10.67 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|transmembrane | |||
|19 | |||
|0.01 | |||
|43 | |||
|4452 | |||
|17599 | |||
|1.75 | |||
|1 | |||
|0.99 | |||
|14.35 | |||
|---- | |||
|UP_SEQ_FEATURE | |||
|topological domain:Cytoplasmic | |||
|14 | |||
|0.01 | |||
|34 | |||
|2554 | |||
|12056 | |||
|1.94 | |||
|1 | |||
|1 | |||
|25.03 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0004872~receptor activity | |||
|10 | |||
|0.02 | |||
|36 | |||
|2113 | |||
|16968 | |||
|2.23 | |||
|1 | |||
|1 | |||
|35.83 | |||
|---- | |||
|UP_SEQ_FEATURE | |||
|glycosylation site:N-linked (GlcNAc...) | |||
|15 | |||
|0.03 | |||
|34 | |||
|3085 | |||
|12056 | |||
|1.72 | |||
|1 | |||
|1 | |||
|43.23 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|membrane | |||
|20 | |||
|0.03 | |||
|43 | |||
|5272 | |||
|17599 | |||
|1.55 | |||
|1 | |||
|1 | |||
|34.08 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0001584~rhodopsin-like receptor activity | |||
|6 | |||
|0.03 | |||
|36 | |||
|828 | |||
|16968 | |||
|3.42 | |||
|1 | |||
|1 | |||
|38.03 | |||
|---- | |||
|INTERPRO | |||
|IPR000276:Rhodopsin-like GPCR superfamily | |||
|6 | |||
|0.03 | |||
|42 | |||
|747 | |||
|17845 | |||
|3.41 | |||
|1 | |||
|1 | |||
|41.57 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0060089~molecular transducer activity | |||
|11 | |||
|0.03 | |||
|36 | |||
|2557 | |||
|16968 | |||
|2.03 | |||
|1 | |||
|1 | |||
|41.96 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0004871~signal transducer activity | |||
|11 | |||
|0.03 | |||
|36 | |||
|2557 | |||
|16968 | |||
|2.03 | |||
|1 | |||
|1 | |||
|41.96 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0004930~G-protein coupled receptor activity | |||
|6 | |||
|0.04 | |||
|36 | |||
|953 | |||
|16968 | |||
|2.97 | |||
|1 | |||
|1 | |||
|55.63 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|g-protein coupled receptor | |||
|6 | |||
|0.05 | |||
|43 | |||
|832 | |||
|17599 | |||
|2.95 | |||
|1 | |||
|1 | |||
|53.41 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|receptor | |||
|9 | |||
|0.05 | |||
|43 | |||
|1731 | |||
|17599 | |||
|2.13 | |||
|1 | |||
|1 | |||
|55.46 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|transducer | |||
|6 | |||
|0.06 | |||
|43 | |||
|881 | |||
|17599 | |||
|2.79 | |||
|1 | |||
|1 | |||
|60.93 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0016021~integral to membrane | |||
|18 | |||
|0.07 | |||
|37 | |||
|5357 | |||
|15857 | |||
|1.44 | |||
|1 | |||
|1 | |||
|64.96 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0031224~intrinsic to membrane | |||
|18 | |||
|0.07 | |||
|37 | |||
|5378 | |||
|15857 | |||
|1.43 | |||
|1 | |||
|1 | |||
|66.24 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0007186~G-protein coupled receptor protein signaling pathway | |||
|6 | |||
|0.17 | |||
|40 | |||
|1155 | |||
|15360 | |||
|1.99 | |||
|1 | |||
|1 | |||
|96.91 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0044425~membrane part | |||
|18 | |||
|0.17 | |||
|37 | |||
|6065 | |||
|15857 | |||
|1.27 | |||
|1 | |||
|1 | |||
|94.83 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005886~plasma membrane | |||
|11 | |||
|0.2 | |||
|37 | |||
|3314 | |||
|15857 | |||
|1.42 | |||
|1 | |||
|1 | |||
|97.13 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0016020~membrane | |||
|20 | |||
|0.25 | |||
|37 | |||
|7262 | |||
|15857 | |||
|1.18 | |||
|1 | |||
|1 | |||
|98.84 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0007166~cell surface receptor linked signal transduction | |||
|7 | |||
|0.34 | |||
|40 | |||
|1868 | |||
|15360 | |||
|1.44 | |||
|1 | |||
|1 | |||
|99.96 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0007165~signal transduction | |||
|12 | |||
|0.35 | |||
|40 | |||
|3758 | |||
|15360 | |||
|1.23 | |||
|1 | |||
|1 | |||
|99.97 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0007154~cell communication | |||
|12 | |||
|0.48 | |||
|40 | |||
|4123 | |||
|15360 | |||
|1.12 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 2 | |||
|Median: 0.05315479858365215 | |||
|Geo: 0.043640878080478424 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|leucine-rich repeat | |||
|4 | |||
|0.02 | |||
|43 | |||
|256 | |||
|17599 | |||
|6.39 | |||
|1 | |||
|1 | |||
|30.99 | |||
|---- | |||
|UP_SEQ_FEATURE | |||
|repeat:LRR 3 | |||
|3 | |||
|0.05 | |||
|34 | |||
|132 | |||
|12056 | |||
|8.06 | |||
|1 | |||
|1 | |||
|67.41 | |||
|---- | |||
|UP_SEQ_FEATURE | |||
|repeat:LRR 2 | |||
|3 | |||
|0.06 | |||
|34 | |||
|140 | |||
|12056 | |||
|7.6 | |||
|1 | |||
|1 | |||
|71.3 | |||
|---- | |||
|UP_SEQ_FEATURE | |||
|repeat:LRR 1 | |||
|3 | |||
|0.06 | |||
|34 | |||
|140 | |||
|12056 | |||
|7.6 | |||
|1 | |||
|1 | |||
|71.3 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 3 | |||
|Median: 0.1336143269166979 | |||
|Geo: 0.12431956759597426 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005887~integral to plasma membrane | |||
|7 | |||
|0.06 | |||
|37 | |||
|1246 | |||
|15857 | |||
|2.41 | |||
|1 | |||
|1 | |||
|61.39 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0031226~intrinsic to plasma membrane | |||
|7 | |||
|0.06 | |||
|37 | |||
|1262 | |||
|15857 | |||
|2.38 | |||
|1 | |||
|1 | |||
|63.31 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005886~plasma membrane | |||
|11 | |||
|0.2 | |||
|37 | |||
|3314 | |||
|15857 | |||
|1.42 | |||
|1 | |||
|1 | |||
|97.13 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0044459~plasma membrane part | |||
|7 | |||
|0.31 | |||
|37 | |||
|2037 | |||
|15857 | |||
|1.47 | |||
|1 | |||
|1 | |||
|99.71 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 4 | |||
|Median: 0.31357655372100196 | |||
|Geo: 0.294106233156399 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|cell adhesion | |||
|3 | |||
|0.23 | |||
|43 | |||
|386 | |||
|17599 | |||
|3.18 | |||
|1 | |||
|1 | |||
|98.59 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0007155~cell adhesion | |||
|4 | |||
|0.31 | |||
|40 | |||
|774 | |||
|15360 | |||
|1.98 | |||
|1 | |||
|1 | |||
|99.93 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0022610~biological adhesion | |||
|4 | |||
|0.31 | |||
|40 | |||
|774 | |||
|15360 | |||
|1.98 | |||
|1 | |||
|1 | |||
|99.93 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0009653~anatomical structure morphogenesis | |||
|5 | |||
|0.32 | |||
|40 | |||
|1133 | |||
|15360 | |||
|1.69 | |||
|1 | |||
|1 | |||
|99.94 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 5 | |||
|Median: 0.2994000556276062 | |||
|Geo: 0.3722618330261535 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0009605~response to external stimulus | |||
|4 | |||
|0.22 | |||
|40 | |||
|644 | |||
|15360 | |||
|2.39 | |||
|1 | |||
|1 | |||
|99.21 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0009611~response to wounding | |||
|3 | |||
|0.3 | |||
|40 | |||
|431 | |||
|15360 | |||
|2.67 | |||
|1 | |||
|1 | |||
|99.89 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0006950~response to stress | |||
|3 | |||
|0.77 | |||
|40 | |||
|1081 | |||
|15360 | |||
|1.07 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 6 | |||
|Median: 0.3688618227951922 | |||
|Geo: 0.37308799552587163 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0048856~anatomical structure development | |||
|9 | |||
|0.17 | |||
|40 | |||
|2153 | |||
|15360 | |||
|1.61 | |||
|1 | |||
|1 | |||
|97.25 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0009888~tissue development | |||
|3 | |||
|0.21 | |||
|40 | |||
|339 | |||
|15360 | |||
|3.4 | |||
|1 | |||
|1 | |||
|98.96 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0048731~system development | |||
|7 | |||
|0.29 | |||
|40 | |||
|1760 | |||
|15360 | |||
|1.53 | |||
|1 | |||
|1 | |||
|99.84 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0032502~developmental process | |||
|11 | |||
|0.31 | |||
|40 | |||
|3262 | |||
|15360 | |||
|1.29 | |||
|1 | |||
|1 | |||
|99.91 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0032501~multicellular organismal process | |||
|12 | |||
|0.35 | |||
|40 | |||
|3759 | |||
|15360 | |||
|1.23 | |||
|1 | |||
|1 | |||
|99.97 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0007275~multicellular organismal development | |||
|8 | |||
|0.39 | |||
|40 | |||
|2349 | |||
|15360 | |||
|1.31 | |||
|1 | |||
|1 | |||
|99.99 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0048513~organ development | |||
|5 | |||
|0.41 | |||
|40 | |||
|1282 | |||
|15360 | |||
|1.5 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0007399~nervous system development | |||
|3 | |||
|0.6 | |||
|40 | |||
|780 | |||
|15360 | |||
|1.48 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0048869~cellular developmental process | |||
|5 | |||
|0.7 | |||
|40 | |||
|1835 | |||
|15360 | |||
|1.05 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0030154~cell differentiation | |||
|5 | |||
|0.7 | |||
|40 | |||
|1835 | |||
|15360 | |||
|1.05 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 7 | |||
|Median: 0.36781428439882924 | |||
|Geo: 0.40941510044660673 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005615~extracellular space | |||
|3 | |||
|0.33 | |||
|37 | |||
|521 | |||
|15857 | |||
|2.47 | |||
|1 | |||
|1 | |||
|99.81 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005576~extracellular region | |||
|5 | |||
|0.37 | |||
|37 | |||
|1350 | |||
|15857 | |||
|1.59 | |||
|1 | |||
|1 | |||
|99.92 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0044421~extracellular region part | |||
|3 | |||
|0.56 | |||
|37 | |||
|819 | |||
|15857 | |||
|1.57 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 8 | |||
|Median: 0.4245273768008249 | |||
|Geo: 0.4297118369268503 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005576~extracellular region | |||
|5 | |||
|0.37 | |||
|37 | |||
|1350 | |||
|15857 | |||
|1.59 | |||
|1 | |||
|1 | |||
|99.92 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|signal | |||
|9 | |||
|0.4 | |||
|43 | |||
|2919 | |||
|17599 | |||
|1.26 | |||
|1 | |||
|1 | |||
|99.97 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|Secreted | |||
|5 | |||
|0.45 | |||
|43 | |||
|1440 | |||
|17599 | |||
|1.42 | |||
|1 | |||
|1 | |||
|99.99 | |||
|---- | |||
|UP_SEQ_FEATURE | |||
|signal peptide | |||
|8 | |||
|0.52 | |||
|34 | |||
|2447 | |||
|12056 | |||
|1.16 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 9 | |||
|Median: 0.3631068152753514 | |||
|Geo: 0.45212872922107583 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0009653~anatomical structure morphogenesis | |||
|5 | |||
|0.32 | |||
|40 | |||
|1133 | |||
|15360 | |||
|1.69 | |||
|1 | |||
|1 | |||
|99.94 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0032989~cellular structure morphogenesis | |||
|3 | |||
|0.36 | |||
|40 | |||
|499 | |||
|15360 | |||
|2.31 | |||
|1 | |||
|1 | |||
|99.98 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0000902~cell morphogenesis | |||
|3 | |||
|0.36 | |||
|40 | |||
|499 | |||
|15360 | |||
|2.31 | |||
|1 | |||
|1 | |||
|99.98 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0016043~cellular component organization and biogenesis | |||
|4 | |||
|0.98 | |||
|40 | |||
|2723 | |||
|15360 | |||
|0.56 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 10 | |||
|Median: 0.5734687246608097 | |||
|Geo: 0.5127166515642717 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0000074~regulation of progression through cell cycle | |||
|3 | |||
|0.39 | |||
|40 | |||
|526 | |||
|15360 | |||
|2.19 | |||
|1 | |||
|1 | |||
|99.99 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0051726~regulation of cell cycle | |||
|3 | |||
|0.39 | |||
|40 | |||
|529 | |||
|15360 | |||
|2.18 | |||
|1 | |||
|1 | |||
|99.99 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0022402~cell cycle process | |||
|3 | |||
|0.57 | |||
|40 | |||
|749 | |||
|15360 | |||
|1.54 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0008283~cell proliferation | |||
|3 | |||
|0.61 | |||
|40 | |||
|796 | |||
|15360 | |||
|1.45 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0007049~cell cycle | |||
|3 | |||
|0.67 | |||
|40 | |||
|894 | |||
|15360 | |||
|1.29 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 11 | |||
|Median: 0.9605162482170493 | |||
|Geo: 0.6129377540659845 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0016020~membrane | |||
|20 | |||
|0.25 | |||
|37 | |||
|7262 | |||
|15857 | |||
|1.18 | |||
|1 | |||
|1 | |||
|98.84 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0044464~cell part | |||
|33 | |||
|0.96 | |||
|37 | |||
|15019 | |||
|15857 | |||
|0.94 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005623~cell | |||
|33 | |||
|0.96 | |||
|37 | |||
|15020 | |||
|15857 | |||
|0.94 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 12 | |||
|Median: 0.7836410046532671 | |||
|Geo: 0.7488370592269121 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0009056~catabolic process | |||
|3 | |||
|0.57 | |||
|40 | |||
|746 | |||
|15360 | |||
|1.54 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|hydrolase | |||
|4 | |||
|0.67 | |||
|43 | |||
|1422 | |||
|17599 | |||
|1.15 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0016787~hydrolase activity | |||
|4 | |||
|0.9 | |||
|36 | |||
|2438 | |||
|16968 | |||
|0.77 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0003824~catalytic activity | |||
|10 | |||
|0.92 | |||
|36 | |||
|5976 | |||
|16968 | |||
|0.79 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 13 | |||
|Median: 0.9968215046691112 | |||
|Geo: 0.8265131236074682 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005783~endoplasmic reticulum | |||
|3 | |||
|0.57 | |||
|37 | |||
|827 | |||
|15857 | |||
|1.55 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005737~cytoplasm | |||
|8 | |||
|1 | |||
|37 | |||
|6219 | |||
|15857 | |||
|0.55 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0044444~cytoplasmic part | |||
|3 | |||
|1 | |||
|37 | |||
|3717 | |||
|15857 | |||
|0.35 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 14 | |||
|Median: 0.8759330074668149 | |||
|Geo: 0.8575501630938809 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0050794~regulation of cellular process | |||
|12 | |||
|0.59 | |||
|40 | |||
|4422 | |||
|15360 | |||
|1.04 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0065007~biological regulation | |||
|14 | |||
|0.6 | |||
|40 | |||
|5238 | |||
|15360 | |||
|1.03 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|metal-binding | |||
|7 | |||
|0.62 | |||
|43 | |||
|2649 | |||
|17599 | |||
|1.08 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0050789~regulation of biological process | |||
|12 | |||
|0.7 | |||
|40 | |||
|4759 | |||
|15360 | |||
|0.97 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|zinc | |||
|5 | |||
|0.72 | |||
|43 | |||
|2007 | |||
|17599 | |||
|1.02 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0008270~zinc ion binding | |||
|5 | |||
|0.75 | |||
|36 | |||
|2400 | |||
|16968 | |||
|0.98 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|zinc-finger | |||
|4 | |||
|0.76 | |||
|43 | |||
|1629 | |||
|17599 | |||
|1 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0019222~regulation of metabolic process | |||
|7 | |||
|0.79 | |||
|40 | |||
|2975 | |||
|15360 | |||
|0.9 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|Transcription regulation | |||
|4 | |||
|0.8 | |||
|43 | |||
|1754 | |||
|17599 | |||
|0.93 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|Transcription | |||
|4 | |||
|0.81 | |||
|43 | |||
|1783 | |||
|17599 | |||
|0.92 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0045449~regulation of transcription | |||
|6 | |||
|0.81 | |||
|40 | |||
|2598 | |||
|15360 | |||
|0.89 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0046872~metal ion binding | |||
|8 | |||
|0.82 | |||
|36 | |||
|4312 | |||
|16968 | |||
|0.87 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0019219~regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | |||
|6 | |||
|0.83 | |||
|40 | |||
|2658 | |||
|15360 | |||
|0.87 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0030528~transcription regulator activity | |||
|3 | |||
|0.84 | |||
|36 | |||
|1534 | |||
|16968 | |||
|0.92 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0006350~transcription | |||
|6 | |||
|0.84 | |||
|40 | |||
|2695 | |||
|15360 | |||
|0.85 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0043167~ion binding | |||
|8 | |||
|0.84 | |||
|36 | |||
|4397 | |||
|16968 | |||
|0.86 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0010468~regulation of gene expression | |||
|6 | |||
|0.85 | |||
|40 | |||
|2760 | |||
|15360 | |||
|0.83 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0043169~cation binding | |||
|7 | |||
|0.87 | |||
|36 | |||
|4006 | |||
|16968 | |||
|0.82 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0046914~transition metal ion binding | |||
|5 | |||
|0.87 | |||
|36 | |||
|2908 | |||
|16968 | |||
|0.81 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0031323~regulation of cellular metabolic process | |||
|6 | |||
|0.88 | |||
|40 | |||
|2873 | |||
|15360 | |||
|0.8 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0006355~regulation of transcription, DNA-dependent | |||
|5 | |||
|0.89 | |||
|40 | |||
|2432 | |||
|15360 | |||
|0.79 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0006351~transcription, DNA-dependent | |||
|5 | |||
|0.9 | |||
|40 | |||
|2487 | |||
|15360 | |||
|0.77 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0032774~RNA biosynthetic process | |||
|5 | |||
|0.9 | |||
|40 | |||
|2490 | |||
|15360 | |||
|0.77 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0003677~DNA binding | |||
|4 | |||
|0.9 | |||
|36 | |||
|2450 | |||
|16968 | |||
|0.77 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|dna-binding | |||
|3 | |||
|0.93 | |||
|43 | |||
|1748 | |||
|17599 | |||
|0.7 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0043283~biopolymer metabolic process | |||
|10 | |||
|0.96 | |||
|40 | |||
|5361 | |||
|15360 | |||
|0.72 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0016070~RNA metabolic process | |||
|5 | |||
|0.96 | |||
|40 | |||
|3020 | |||
|15360 | |||
|0.64 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0003676~nucleic acid binding | |||
|5 | |||
|0.96 | |||
|36 | |||
|3690 | |||
|16968 | |||
|0.64 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0006139~nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | |||
|7 | |||
|0.97 | |||
|40 | |||
|4051 | |||
|15360 | |||
|0.66 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0010467~gene expression | |||
|6 | |||
|0.97 | |||
|40 | |||
|3686 | |||
|15360 | |||
|0.63 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005634~nucleus | |||
|7 | |||
|0.97 | |||
|37 | |||
|4664 | |||
|15857 | |||
|0.64 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|nucleus | |||
|5 | |||
|0.99 | |||
|43 | |||
|3710 | |||
|17599 | |||
|0.55 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0043231~intracellular membrane-bound organelle | |||
|10 | |||
|1 | |||
|37 | |||
|7191 | |||
|15857 | |||
|0.6 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0043227~membrane-bound organelle | |||
|10 | |||
|1 | |||
|37 | |||
|7194 | |||
|15857 | |||
|0.6 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0044424~intracellular part | |||
|15 | |||
|1 | |||
|37 | |||
|9906 | |||
|15857 | |||
|0.65 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0043229~intracellular organelle | |||
|11 | |||
|1 | |||
|37 | |||
|8288 | |||
|15857 | |||
|0.57 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0043226~organelle | |||
|11 | |||
|1 | |||
|37 | |||
|8292 | |||
|15857 | |||
|0.57 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005622~intracellular | |||
|15 | |||
|1 | |||
|37 | |||
|10544 | |||
|15857 | |||
|0.61 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 15 | |||
|Median: 0.8662513767254609 | |||
|Geo: 0.88361465668396 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0044267~cellular protein metabolic process | |||
|8 | |||
|0.81 | |||
|40 | |||
|3482 | |||
|15360 | |||
|0.88 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0044260~cellular macromolecule metabolic process | |||
|8 | |||
|0.83 | |||
|40 | |||
|3534 | |||
|15360 | |||
|0.87 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0006464~protein modification process | |||
|4 | |||
|0.85 | |||
|40 | |||
|1804 | |||
|15360 | |||
|0.85 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0019538~protein metabolic process | |||
|8 | |||
|0.86 | |||
|40 | |||
|3691 | |||
|15360 | |||
|0.83 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0043412~biopolymer modification | |||
|4 | |||
|0.87 | |||
|40 | |||
|1877 | |||
|15360 | |||
|0.82 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0043687~post-translational protein modification | |||
|3 | |||
|0.91 | |||
|40 | |||
|1522 | |||
|15360 | |||
|0.76 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0043234~protein complex | |||
|3 | |||
|0.96 | |||
|37 | |||
|2115 | |||
|15857 | |||
|0.61 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0032991~macromolecular complex | |||
|3 | |||
|0.99 | |||
|37 | |||
|2609 | |||
|15857 | |||
|0.49 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 16 | |||
|Median: 0.9612032324365326 | |||
|Geo: 0.8965362550566862 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0008152~metabolic process | |||
|23 | |||
|0.73 | |||
|40 | |||
|9181 | |||
|15360 | |||
|0.96 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0044237~cellular metabolic process | |||
|20 | |||
|0.79 | |||
|40 | |||
|8269 | |||
|15360 | |||
|0.93 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0044238~primary metabolic process | |||
|19 | |||
|0.87 | |||
|40 | |||
|8291 | |||
|15360 | |||
|0.88 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0043283~biopolymer metabolic process | |||
|10 | |||
|0.96 | |||
|40 | |||
|5361 | |||
|15360 | |||
|0.72 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0043170~macromolecule metabolic process | |||
|14 | |||
|0.97 | |||
|40 | |||
|7216 | |||
|15360 | |||
|0.75 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0044424~intracellular part | |||
|15 | |||
|1 | |||
|37 | |||
|9906 | |||
|15857 | |||
|0.65 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005622~intracellular | |||
|15 | |||
|1 | |||
|37 | |||
|10544 | |||
|15857 | |||
|0.61 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 17 | |||
|Median: 0.9355098519781113 | |||
|Geo: 0.9267703680488794 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|transport | |||
|3 | |||
|0.87 | |||
|43 | |||
|1432 | |||
|17599 | |||
|0.86 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0006810~transport | |||
|5 | |||
|0.93 | |||
|40 | |||
|2697 | |||
|15360 | |||
|0.71 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0051234~establishment of localization | |||
|5 | |||
|0.94 | |||
|40 | |||
|2788 | |||
|15360 | |||
|0.69 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_BP_ALL | |||
|GO:0051179~localization | |||
|5 | |||
|0.97 | |||
|40 | |||
|3161 | |||
|15360 | |||
|0.61 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 18 | |||
|Median: 0.9348568006971572 | |||
|Geo: 0.9279057981361349 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|SP_PIR_KEYWORDS | |||
|transferase | |||
|3 | |||
|0.86 | |||
|43 | |||
|1398 | |||
|17599 | |||
|0.88 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0016740~transferase activity | |||
|3 | |||
|0.93 | |||
|36 | |||
|2040 | |||
|16968 | |||
|0.69 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_CC_ALL | |||
|GO:0005737~cytoplasm | |||
|8 | |||
|1 | |||
|37 | |||
|6219 | |||
|15857 | |||
|0.55 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Functional Group 19 | |||
|Median: 0.9261389414215063 | |||
|Geo: 0.9334226746370794 | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
|---- | |||
|Category | |||
|Term | |||
|Count | |||
|PValue | |||
|List Total | |||
|Pop Hits | |||
|Pop Total | |||
|Fold Enrichment | |||
|Bonferroni | |||
|Benjamini | |||
|FDR | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0032553~ribonucleotide binding | |||
|3 | |||
|0.92 | |||
|36 | |||
|1933 | |||
|16968 | |||
|0.73 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0032555~purine ribonucleotide binding | |||
|3 | |||
|0.92 | |||
|36 | |||
|1933 | |||
|16968 | |||
|0.73 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0017076~purine nucleotide binding | |||
|3 | |||
|0.93 | |||
|36 | |||
|2016 | |||
|16968 | |||
|0.7 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|GOTERM_MF_ALL | |||
|GO:0000166~nucleotide binding | |||
|3 | |||
|0.96 | |||
|36 | |||
|2314 | |||
|16968 | |||
|0.61 | |||
|1 | |||
|1 | |||
|100 | |||
|---- | |||
|} | |||
** '''NOTICE GO TERM CLUSTER 1''' | |||
** GPCRs! Includes mas gene, an oncogene. | |||
** Also, membrane proteins, cell-cell adhesion, stress response, and developmental genes. | |||
** Only GPCRs and membrane proteins have good P Values. Should pay attention to these. | |||
* Gene Functional Classification is more revealing. | |||
** Only two gene groups appear | |||
** The first is GPCR-heavy, including mas | |||
** The second is very low-scoring, but deals with DNA binding and transcription | |||
Gene Group 1: (Score 1.68) | |||
1 ILMN_1759087 olfactory receptor, family 10, subfamily v, member 1 | |||
2 ILMN_1743329 retinal pigment epithelium-derived rhodopsin homolog | |||
3 ILMN_1747683 aquaporin 4 | |||
4 ILMN_1731745 ninjurin 2 | |||
5 ILMN_1741371 transmembrane protein 8 (five membrane-spanning domains) | |||
6 ILMN_1772727 g protein-coupled receptor 75 | |||
7 ILMN_1780465 c-type lectin domain family 5, member a | |||
8 ILMN_1748338 g protein-coupled receptor 85 | |||
9 ILMN_1714980 mas-related gpr, member d | |||
10 ILMN_1750497 g protein-coupled receptor 109a | |||
Gene Group 2: (Score 0.1) | |||
1 ILMN_1726928 transcription elongation factor a (sii), 3 | |||
2 ILMN_1706590 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, drosophila); translocated to, 1 | |||
3 ILMN_1662021 hypothetical protein flj20403 similar to zinc finger protein 326 | |||
4 ILMN_1754553 mediator of rna polymerase ii transcription, subunit 19 homolog (yeast) | |||
5 ILMN_1700766 flj45850 protein |
Latest revision as of 23:58, 13 May 2009
iPS Cancer?[edit]
- Obtained Illumina Array data from Dr. Zhang
- Used SAM and DAVID to try and identify GO Terms in differentially expressed genes.
- Say we want a desired FDR of 15% or lower; since we are just doing preliminary.
- SAM's multiclass feature is not useful here; it will call everything that is fibroblast-only "significant," leading to numbers that are far too large.
Very Lenient[edit]
- Very lenient analysis results in a large amount of GO Terms and GO Clusters.
- Delta of 2.3 was used for IPS_HESC
- Delta of 0.1 (very low, since figured a lot of genes would need to be called as "not similar")
- Will upload DAVID results to Wiki.
- Lots of very interesting GO terms and GO clusters
- However, inspection of several reveals that these values may be too lenient. Lots of things are called as significant that are not very.
Very Stringent[edit]
- Limited ESC_IPS differences to 475, limited GO differences to 250.
- In this case, only 3 or 4 clusters were obtained at all (only 23 diff. expressed genes)
- Most of them have very low scores...probably too stringent here
New Method[edit]
- It seems SAM has issues finding differences between fibroblasts and IPS that are meaningful
- Because so many genes are differentially expressed already, very hard to choose a proper delta value.
- FDR is predicted to be very high.
- Instead, will find differentially expressed genes between IPS and HESC first.
- Only look at these in Fibroblasts, then run SAM!
- Should help find any genes that do not match normal Fibroblasts or hESC in iPS cells.
- Should help find some new behavior.
Procedure[edit]
- First, run SAM on Illumina sequencing data for just iPS and hESC.
- Extract differentially expressed genes such that the FDR is 0.05
- Turned out to be a delta of 1.7 with 4365 differentially expressed genes.
- Extracted data for just this gene subset from Illumina data, and only for FIBROBLASTS and IPS.
- Saved file in NewMethod folder as csv
- Imported into R, ran SAM again.
- Interesting results.
- Pulled out at Delta=4 in order to obtain FDR of 0.2...FDR never went below 0.04 even after just one gene was being called significant. Delta of 4 gave around 50 genes to work with.
- In one way, this is decent news; means that iPS cells do not stray too far from fibroblasts...
- However, several of the GO groups are interesting.
Summary of Below Data[edit]
- It seems that for the most part, very few genes stray away from fibroblast expression levels if they are not matching the stem cell levels.
- These genes are listed below (~50 of them)
- GO Terms reveal that the only highly enriched GO clusters are GPCR-related. GPCRs have been implicated in cancer.
- However, is not a very good result alone.
- Difficult to do this, since stem cells tend to match cancer in some cases.
- TOMORROW: Look at cancer data; what genes does it have that are differentially expressed from Fibroblasts and Stem Cells both? Are any of these genes also found below?
Data[edit]
- Differentially expressed genes (from SAM):
ILLUMINA_ID Gene Name Related Genes Species ILMN_1731745 ninjurin 2 RG Homo sapiens ILMN_1759087 olfactory receptor, family 10, subfamily v, member 1 RG Homo sapiens ILMN_1662021 hypothetical protein flj20403 similar to zinc finger protein 326 RG Homo sapiens ILMN_1702568 chromosome 9 open reading frame 28 RG Homo sapiens ILMN_1722855 vascular endothelial growth factor b RG Homo sapiens ILMN_1714980 mas-related gpr, member d RG Homo sapiens ILMN_1772387 toll-like receptor 2 RG Homo sapiens ILMN_1767233 ectodysplasin a2 receptor RG Homo sapiens ILMN_1795336 phosphotriesterase related RG Homo sapiens ILMN_1772727 g protein-coupled receptor 75 RG Homo sapiens ILMN_1679558 hypothetical protein flj20393 RG Homo sapiens ILMN_1780465 c-type lectin domain family 5, member a RG Homo sapiens ILMN_1743329 retinal pigment epithelium-derived rhodopsin homolog RG Homo sapiens ILMN_1752813 udp glucuronosyltransferase 1 family, polypeptide a6 RG Homo sapiens ILMN_1754553 mediator of rna polymerase ii transcription, subunit 19 homolog (yeast) RG Homo sapiens ILMN_1700766 flj45850 protein RG Homo sapiens ILMN_1736951 leucine-rich repeats and iq motif containing 2 RG Homo sapiens ILMN_1747683 aquaporin 4 RG Homo sapiens ILMN_1717579 chromosome 17 open reading frame 64 RG Homo sapiens ILMN_1708779 granulysin RG Homo sapiens ILMN_1764201 microtubule-associated protein 2 RG Homo sapiens ILMN_1724424 proline-rich transmembrane protein 2 RG Homo sapiens ILMN_1750234 protease, serine, 2 (trypsin 2) RG Homo sapiens ILMN_1726928 transcription elongation factor a (sii), 3 RG Homo sapiens ILMN_1752046 lymphocyte adaptor protein RG Homo sapiens ILMN_1717252 f-box and leucine-rich repeat protein 21 RG Homo sapiens ILMN_1680932 hypothetical protein flj12492 RG Homo sapiens ILMN_1709953 downstream neighbor of son RG Homo sapiens ILMN_1748338 g protein-coupled receptor 85 RG Homo sapiens ILMN_1700888 ectonucleotide pyrophosphatase/phosphodiesterase 1 RG Homo sapiens ILMN_1729433 lipase, member h RG Homo sapiens ILMN_1750497 g protein-coupled receptor 109a RG Homo sapiens ILMN_1757521 creatine kinase, muscle RG Homo sapiens ILMN_1706266 ring finger protein 157 RG Homo sapiens ILMN_1729203 protein disulfide isomerase-like protein of the testis RG Homo sapiens ILMN_1738849 solute carrier family 9 (sodium/hydrogen exchanger), member 2 RG Homo sapiens ILMN_1706590 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, drosophila); translocated to, 1 RG Homo sapiens ILMN_1741371 transmembrane protein 8 (five membrane-spanning domains) RG Homo sapiens ILMN_1769538 flj36268 protein RG Homo sapiens ILMN_1718525 inter-alpha (globulin) inhibitor h4 (plasma kallikrein-sensitive glycoprotein) RG Homo sapiens ILMN_1732049 dolichyl-phosphate mannosyltransferase polypeptide 2, regulatory subunit RG Homo sapiens ILMN_1798957 chromosome 12 open reading frame 47 RG Homo sapiens ILMN_1699735 fibroblast growth factor 1 (acidic) RG Homo sapiens ILMN_1777658 scavenger receptor class f, member 1 RG Homo sapiens ILMN_1780172 chromosome 20 open reading frame 195 RG Homo sapiens ILMN_1722502 chaperonin containing tcp1, subunit 6a (zeta 1) RG Homo sapiens ILMN_1748884 transducer of erbb2, 2 RG Homo sapiens ILMN_1754489 f-box and leucine-rich repeat protein 20 RG Homo sapiens ILMN_1753648 tripartite motif-containing 51 RG Homo sapiens
- GO Terms associated with this set:
Category Term UP_SEQ_FEATURE repeat:LRR 3 UP_SEQ_FEATURE disulfide bond SP_PIR_KEYWORDS transducer GOTERM_BP_ALL GO:0009620~response to fungus GOTERM_CC_ALL GO:0005887~integral to plasma membrane UP_SEQ_FEATURE topological domain:Extracellular SP_PIR_KEYWORDS g-protein coupled receptor UP_SEQ_FEATURE topological domain:Cytoplasmic GOTERM_MF_ALL GO:0001871~pattern binding GOTERM_MF_ALL GO:0060089~molecular transducer activity UP_SEQ_FEATURE repeat:LRR 2 GOTERM_MF_ALL GO:0004930~G-protein coupled receptor activity UP_SEQ_FEATURE transmembrane region GOTERM_MF_ALL GO:0001584~rhodopsin-like receptor activity GOTERM_BP_ALL GO:0009410~response to xenobiotic stimulus SP_PIR_KEYWORDS glycoprotein SP_PIR_KEYWORDS membrane UP_SEQ_FEATURE repeat:LRR 1 SP_PIR_KEYWORDS mitogen SP_PIR_KEYWORDS receptor GOTERM_BP_ALL GO:0006805~xenobiotic metabolic process SP_PIR_KEYWORDS leucine-rich repeat GOTERM_CC_ALL GO:0031226~intrinsic to plasma membrane GOTERM_MF_ALL GO:0004888~transmembrane receptor activity GOTERM_CC_ALL GO:0031224~intrinsic to membrane PIR_SUPERFAMILY PIRSF036848:conserved protein with F-box/LRR-repeat, Skp2 type UP_SEQ_FEATURE glycosylation site:N-linked (GlcNAc...) SP_PIR_KEYWORDS transmembrane GOTERM_CC_ALL GO:0016021~integral to membrane GOTERM_MF_ALL GO:0004872~receptor activity INTERPRO IPR000276:Rhodopsin-like GPCR superfamily GOTERM_MF_ALL GO:0004871~signal transducer activity
- FUNCTIONAL CATEGORIES (Important info here...)
Functional Group 1 | Median: 0.03711173039552113 | Geo: 0.039704364737313154 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
UP_SEQ_FEATURE | transmembrane region | 18 | 0 | 34 | 3211 | 12056 | 1.99 | 1 | 1 | 4.25 |
UP_SEQ_FEATURE | topological domain:Extracellular | 14 | 0 | 34 | 2092 | 12056 | 2.37 | 1 | 1 | 4.8 |
SP_PIR_KEYWORDS | glycoprotein | 18 | 0 | 43 | 3807 | 17599 | 1.94 | 0.99 | 0.99 | 6.87 |
GOTERM_MF_ALL | GO:0004888~transmembrane receptor activity | 9 | 0.01 | 36 | 1388 | 16968 | 3.06 | 1 | 1 | 10.67 |
SP_PIR_KEYWORDS | transmembrane | 19 | 0.01 | 43 | 4452 | 17599 | 1.75 | 1 | 0.99 | 14.35 |
UP_SEQ_FEATURE | topological domain:Cytoplasmic | 14 | 0.01 | 34 | 2554 | 12056 | 1.94 | 1 | 1 | 25.03 |
GOTERM_MF_ALL | GO:0004872~receptor activity | 10 | 0.02 | 36 | 2113 | 16968 | 2.23 | 1 | 1 | 35.83 |
UP_SEQ_FEATURE | glycosylation site:N-linked (GlcNAc...) | 15 | 0.03 | 34 | 3085 | 12056 | 1.72 | 1 | 1 | 43.23 |
SP_PIR_KEYWORDS | membrane | 20 | 0.03 | 43 | 5272 | 17599 | 1.55 | 1 | 1 | 34.08 |
GOTERM_MF_ALL | GO:0001584~rhodopsin-like receptor activity | 6 | 0.03 | 36 | 828 | 16968 | 3.42 | 1 | 1 | 38.03 |
INTERPRO | IPR000276:Rhodopsin-like GPCR superfamily | 6 | 0.03 | 42 | 747 | 17845 | 3.41 | 1 | 1 | 41.57 |
GOTERM_MF_ALL | GO:0060089~molecular transducer activity | 11 | 0.03 | 36 | 2557 | 16968 | 2.03 | 1 | 1 | 41.96 |
GOTERM_MF_ALL | GO:0004871~signal transducer activity | 11 | 0.03 | 36 | 2557 | 16968 | 2.03 | 1 | 1 | 41.96 |
GOTERM_MF_ALL | GO:0004930~G-protein coupled receptor activity | 6 | 0.04 | 36 | 953 | 16968 | 2.97 | 1 | 1 | 55.63 |
SP_PIR_KEYWORDS | g-protein coupled receptor | 6 | 0.05 | 43 | 832 | 17599 | 2.95 | 1 | 1 | 53.41 |
SP_PIR_KEYWORDS | receptor | 9 | 0.05 | 43 | 1731 | 17599 | 2.13 | 1 | 1 | 55.46 |
SP_PIR_KEYWORDS | transducer | 6 | 0.06 | 43 | 881 | 17599 | 2.79 | 1 | 1 | 60.93 |
GOTERM_CC_ALL | GO:0016021~integral to membrane | 18 | 0.07 | 37 | 5357 | 15857 | 1.44 | 1 | 1 | 64.96 |
GOTERM_CC_ALL | GO:0031224~intrinsic to membrane | 18 | 0.07 | 37 | 5378 | 15857 | 1.43 | 1 | 1 | 66.24 |
GOTERM_BP_ALL | GO:0007186~G-protein coupled receptor protein signaling pathway | 6 | 0.17 | 40 | 1155 | 15360 | 1.99 | 1 | 1 | 96.91 |
GOTERM_CC_ALL | GO:0044425~membrane part | 18 | 0.17 | 37 | 6065 | 15857 | 1.27 | 1 | 1 | 94.83 |
GOTERM_CC_ALL | GO:0005886~plasma membrane | 11 | 0.2 | 37 | 3314 | 15857 | 1.42 | 1 | 1 | 97.13 |
GOTERM_CC_ALL | GO:0016020~membrane | 20 | 0.25 | 37 | 7262 | 15857 | 1.18 | 1 | 1 | 98.84 |
GOTERM_BP_ALL | GO:0007166~cell surface receptor linked signal transduction | 7 | 0.34 | 40 | 1868 | 15360 | 1.44 | 1 | 1 | 99.96 |
GOTERM_BP_ALL | GO:0007165~signal transduction | 12 | 0.35 | 40 | 3758 | 15360 | 1.23 | 1 | 1 | 99.97 |
GOTERM_BP_ALL | GO:0007154~cell communication | 12 | 0.48 | 40 | 4123 | 15360 | 1.12 | 1 | 1 | 100 |
Functional Group 2 | Median: 0.05315479858365215 | Geo: 0.043640878080478424 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
SP_PIR_KEYWORDS | leucine-rich repeat | 4 | 0.02 | 43 | 256 | 17599 | 6.39 | 1 | 1 | 30.99 |
UP_SEQ_FEATURE | repeat:LRR 3 | 3 | 0.05 | 34 | 132 | 12056 | 8.06 | 1 | 1 | 67.41 |
UP_SEQ_FEATURE | repeat:LRR 2 | 3 | 0.06 | 34 | 140 | 12056 | 7.6 | 1 | 1 | 71.3 |
UP_SEQ_FEATURE | repeat:LRR 1 | 3 | 0.06 | 34 | 140 | 12056 | 7.6 | 1 | 1 | 71.3 |
Functional Group 3 | Median: 0.1336143269166979 | Geo: 0.12431956759597426 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_CC_ALL | GO:0005887~integral to plasma membrane | 7 | 0.06 | 37 | 1246 | 15857 | 2.41 | 1 | 1 | 61.39 |
GOTERM_CC_ALL | GO:0031226~intrinsic to plasma membrane | 7 | 0.06 | 37 | 1262 | 15857 | 2.38 | 1 | 1 | 63.31 |
GOTERM_CC_ALL | GO:0005886~plasma membrane | 11 | 0.2 | 37 | 3314 | 15857 | 1.42 | 1 | 1 | 97.13 |
GOTERM_CC_ALL | GO:0044459~plasma membrane part | 7 | 0.31 | 37 | 2037 | 15857 | 1.47 | 1 | 1 | 99.71 |
Functional Group 4 | Median: 0.31357655372100196 | Geo: 0.294106233156399 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
SP_PIR_KEYWORDS | cell adhesion | 3 | 0.23 | 43 | 386 | 17599 | 3.18 | 1 | 1 | 98.59 |
GOTERM_BP_ALL | GO:0007155~cell adhesion | 4 | 0.31 | 40 | 774 | 15360 | 1.98 | 1 | 1 | 99.93 |
GOTERM_BP_ALL | GO:0022610~biological adhesion | 4 | 0.31 | 40 | 774 | 15360 | 1.98 | 1 | 1 | 99.93 |
GOTERM_BP_ALL | GO:0009653~anatomical structure morphogenesis | 5 | 0.32 | 40 | 1133 | 15360 | 1.69 | 1 | 1 | 99.94 |
Functional Group 5 | Median: 0.2994000556276062 | Geo: 0.3722618330261535 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_BP_ALL | GO:0009605~response to external stimulus | 4 | 0.22 | 40 | 644 | 15360 | 2.39 | 1 | 1 | 99.21 |
GOTERM_BP_ALL | GO:0009611~response to wounding | 3 | 0.3 | 40 | 431 | 15360 | 2.67 | 1 | 1 | 99.89 |
GOTERM_BP_ALL | GO:0006950~response to stress | 3 | 0.77 | 40 | 1081 | 15360 | 1.07 | 1 | 1 | 100 |
Functional Group 6 | Median: 0.3688618227951922 | Geo: 0.37308799552587163 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_BP_ALL | GO:0048856~anatomical structure development | 9 | 0.17 | 40 | 2153 | 15360 | 1.61 | 1 | 1 | 97.25 |
GOTERM_BP_ALL | GO:0009888~tissue development | 3 | 0.21 | 40 | 339 | 15360 | 3.4 | 1 | 1 | 98.96 |
GOTERM_BP_ALL | GO:0048731~system development | 7 | 0.29 | 40 | 1760 | 15360 | 1.53 | 1 | 1 | 99.84 |
GOTERM_BP_ALL | GO:0032502~developmental process | 11 | 0.31 | 40 | 3262 | 15360 | 1.29 | 1 | 1 | 99.91 |
GOTERM_BP_ALL | GO:0032501~multicellular organismal process | 12 | 0.35 | 40 | 3759 | 15360 | 1.23 | 1 | 1 | 99.97 |
GOTERM_BP_ALL | GO:0007275~multicellular organismal development | 8 | 0.39 | 40 | 2349 | 15360 | 1.31 | 1 | 1 | 99.99 |
GOTERM_BP_ALL | GO:0048513~organ development | 5 | 0.41 | 40 | 1282 | 15360 | 1.5 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0007399~nervous system development | 3 | 0.6 | 40 | 780 | 15360 | 1.48 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0048869~cellular developmental process | 5 | 0.7 | 40 | 1835 | 15360 | 1.05 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0030154~cell differentiation | 5 | 0.7 | 40 | 1835 | 15360 | 1.05 | 1 | 1 | 100 |
Functional Group 7 | Median: 0.36781428439882924 | Geo: 0.40941510044660673 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_CC_ALL | GO:0005615~extracellular space | 3 | 0.33 | 37 | 521 | 15857 | 2.47 | 1 | 1 | 99.81 |
GOTERM_CC_ALL | GO:0005576~extracellular region | 5 | 0.37 | 37 | 1350 | 15857 | 1.59 | 1 | 1 | 99.92 |
GOTERM_CC_ALL | GO:0044421~extracellular region part | 3 | 0.56 | 37 | 819 | 15857 | 1.57 | 1 | 1 | 100 |
Functional Group 8 | Median: 0.4245273768008249 | Geo: 0.4297118369268503 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_CC_ALL | GO:0005576~extracellular region | 5 | 0.37 | 37 | 1350 | 15857 | 1.59 | 1 | 1 | 99.92 |
SP_PIR_KEYWORDS | signal | 9 | 0.4 | 43 | 2919 | 17599 | 1.26 | 1 | 1 | 99.97 |
SP_PIR_KEYWORDS | Secreted | 5 | 0.45 | 43 | 1440 | 17599 | 1.42 | 1 | 1 | 99.99 |
UP_SEQ_FEATURE | signal peptide | 8 | 0.52 | 34 | 2447 | 12056 | 1.16 | 1 | 1 | 100 |
Functional Group 9 | Median: 0.3631068152753514 | Geo: 0.45212872922107583 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_BP_ALL | GO:0009653~anatomical structure morphogenesis | 5 | 0.32 | 40 | 1133 | 15360 | 1.69 | 1 | 1 | 99.94 |
GOTERM_BP_ALL | GO:0032989~cellular structure morphogenesis | 3 | 0.36 | 40 | 499 | 15360 | 2.31 | 1 | 1 | 99.98 |
GOTERM_BP_ALL | GO:0000902~cell morphogenesis | 3 | 0.36 | 40 | 499 | 15360 | 2.31 | 1 | 1 | 99.98 |
GOTERM_BP_ALL | GO:0016043~cellular component organization and biogenesis | 4 | 0.98 | 40 | 2723 | 15360 | 0.56 | 1 | 1 | 100 |
Functional Group 10 | Median: 0.5734687246608097 | Geo: 0.5127166515642717 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_BP_ALL | GO:0000074~regulation of progression through cell cycle | 3 | 0.39 | 40 | 526 | 15360 | 2.19 | 1 | 1 | 99.99 |
GOTERM_BP_ALL | GO:0051726~regulation of cell cycle | 3 | 0.39 | 40 | 529 | 15360 | 2.18 | 1 | 1 | 99.99 |
GOTERM_BP_ALL | GO:0022402~cell cycle process | 3 | 0.57 | 40 | 749 | 15360 | 1.54 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0008283~cell proliferation | 3 | 0.61 | 40 | 796 | 15360 | 1.45 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0007049~cell cycle | 3 | 0.67 | 40 | 894 | 15360 | 1.29 | 1 | 1 | 100 |
Functional Group 11 | Median: 0.9605162482170493 | Geo: 0.6129377540659845 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_CC_ALL | GO:0016020~membrane | 20 | 0.25 | 37 | 7262 | 15857 | 1.18 | 1 | 1 | 98.84 |
GOTERM_CC_ALL | GO:0044464~cell part | 33 | 0.96 | 37 | 15019 | 15857 | 0.94 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0005623~cell | 33 | 0.96 | 37 | 15020 | 15857 | 0.94 | 1 | 1 | 100 |
Functional Group 12 | Median: 0.7836410046532671 | Geo: 0.7488370592269121 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_BP_ALL | GO:0009056~catabolic process | 3 | 0.57 | 40 | 746 | 15360 | 1.54 | 1 | 1 | 100 |
SP_PIR_KEYWORDS | hydrolase | 4 | 0.67 | 43 | 1422 | 17599 | 1.15 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0016787~hydrolase activity | 4 | 0.9 | 36 | 2438 | 16968 | 0.77 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0003824~catalytic activity | 10 | 0.92 | 36 | 5976 | 16968 | 0.79 | 1 | 1 | 100 |
Functional Group 13 | Median: 0.9968215046691112 | Geo: 0.8265131236074682 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_CC_ALL | GO:0005783~endoplasmic reticulum | 3 | 0.57 | 37 | 827 | 15857 | 1.55 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0005737~cytoplasm | 8 | 1 | 37 | 6219 | 15857 | 0.55 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0044444~cytoplasmic part | 3 | 1 | 37 | 3717 | 15857 | 0.35 | 1 | 1 | 100 |
Functional Group 14 | Median: 0.8759330074668149 | Geo: 0.8575501630938809 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_BP_ALL | GO:0050794~regulation of cellular process | 12 | 0.59 | 40 | 4422 | 15360 | 1.04 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0065007~biological regulation | 14 | 0.6 | 40 | 5238 | 15360 | 1.03 | 1 | 1 | 100 |
SP_PIR_KEYWORDS | metal-binding | 7 | 0.62 | 43 | 2649 | 17599 | 1.08 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0050789~regulation of biological process | 12 | 0.7 | 40 | 4759 | 15360 | 0.97 | 1 | 1 | 100 |
SP_PIR_KEYWORDS | zinc | 5 | 0.72 | 43 | 2007 | 17599 | 1.02 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0008270~zinc ion binding | 5 | 0.75 | 36 | 2400 | 16968 | 0.98 | 1 | 1 | 100 |
SP_PIR_KEYWORDS | zinc-finger | 4 | 0.76 | 43 | 1629 | 17599 | 1 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0019222~regulation of metabolic process | 7 | 0.79 | 40 | 2975 | 15360 | 0.9 | 1 | 1 | 100 |
SP_PIR_KEYWORDS | Transcription regulation | 4 | 0.8 | 43 | 1754 | 17599 | 0.93 | 1 | 1 | 100 |
SP_PIR_KEYWORDS | Transcription | 4 | 0.81 | 43 | 1783 | 17599 | 0.92 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0045449~regulation of transcription | 6 | 0.81 | 40 | 2598 | 15360 | 0.89 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0046872~metal ion binding | 8 | 0.82 | 36 | 4312 | 16968 | 0.87 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0019219~regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 6 | 0.83 | 40 | 2658 | 15360 | 0.87 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0030528~transcription regulator activity | 3 | 0.84 | 36 | 1534 | 16968 | 0.92 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0006350~transcription | 6 | 0.84 | 40 | 2695 | 15360 | 0.85 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0043167~ion binding | 8 | 0.84 | 36 | 4397 | 16968 | 0.86 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0010468~regulation of gene expression | 6 | 0.85 | 40 | 2760 | 15360 | 0.83 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0043169~cation binding | 7 | 0.87 | 36 | 4006 | 16968 | 0.82 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0046914~transition metal ion binding | 5 | 0.87 | 36 | 2908 | 16968 | 0.81 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0031323~regulation of cellular metabolic process | 6 | 0.88 | 40 | 2873 | 15360 | 0.8 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0006355~regulation of transcription, DNA-dependent | 5 | 0.89 | 40 | 2432 | 15360 | 0.79 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0006351~transcription, DNA-dependent | 5 | 0.9 | 40 | 2487 | 15360 | 0.77 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0032774~RNA biosynthetic process | 5 | 0.9 | 40 | 2490 | 15360 | 0.77 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0003677~DNA binding | 4 | 0.9 | 36 | 2450 | 16968 | 0.77 | 1 | 1 | 100 |
SP_PIR_KEYWORDS | dna-binding | 3 | 0.93 | 43 | 1748 | 17599 | 0.7 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0043283~biopolymer metabolic process | 10 | 0.96 | 40 | 5361 | 15360 | 0.72 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0016070~RNA metabolic process | 5 | 0.96 | 40 | 3020 | 15360 | 0.64 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0003676~nucleic acid binding | 5 | 0.96 | 36 | 3690 | 16968 | 0.64 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0006139~nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 7 | 0.97 | 40 | 4051 | 15360 | 0.66 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0010467~gene expression | 6 | 0.97 | 40 | 3686 | 15360 | 0.63 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0005634~nucleus | 7 | 0.97 | 37 | 4664 | 15857 | 0.64 | 1 | 1 | 100 |
SP_PIR_KEYWORDS | nucleus | 5 | 0.99 | 43 | 3710 | 17599 | 0.55 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0043231~intracellular membrane-bound organelle | 10 | 1 | 37 | 7191 | 15857 | 0.6 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0043227~membrane-bound organelle | 10 | 1 | 37 | 7194 | 15857 | 0.6 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0044424~intracellular part | 15 | 1 | 37 | 9906 | 15857 | 0.65 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0043229~intracellular organelle | 11 | 1 | 37 | 8288 | 15857 | 0.57 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0043226~organelle | 11 | 1 | 37 | 8292 | 15857 | 0.57 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0005622~intracellular | 15 | 1 | 37 | 10544 | 15857 | 0.61 | 1 | 1 | 100 |
Functional Group 15 | Median: 0.8662513767254609 | Geo: 0.88361465668396 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_BP_ALL | GO:0044267~cellular protein metabolic process | 8 | 0.81 | 40 | 3482 | 15360 | 0.88 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0044260~cellular macromolecule metabolic process | 8 | 0.83 | 40 | 3534 | 15360 | 0.87 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0006464~protein modification process | 4 | 0.85 | 40 | 1804 | 15360 | 0.85 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0019538~protein metabolic process | 8 | 0.86 | 40 | 3691 | 15360 | 0.83 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0043412~biopolymer modification | 4 | 0.87 | 40 | 1877 | 15360 | 0.82 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0043687~post-translational protein modification | 3 | 0.91 | 40 | 1522 | 15360 | 0.76 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0043234~protein complex | 3 | 0.96 | 37 | 2115 | 15857 | 0.61 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0032991~macromolecular complex | 3 | 0.99 | 37 | 2609 | 15857 | 0.49 | 1 | 1 | 100 |
Functional Group 16 | Median: 0.9612032324365326 | Geo: 0.8965362550566862 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_BP_ALL | GO:0008152~metabolic process | 23 | 0.73 | 40 | 9181 | 15360 | 0.96 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0044237~cellular metabolic process | 20 | 0.79 | 40 | 8269 | 15360 | 0.93 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0044238~primary metabolic process | 19 | 0.87 | 40 | 8291 | 15360 | 0.88 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0043283~biopolymer metabolic process | 10 | 0.96 | 40 | 5361 | 15360 | 0.72 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0043170~macromolecule metabolic process | 14 | 0.97 | 40 | 7216 | 15360 | 0.75 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0044424~intracellular part | 15 | 1 | 37 | 9906 | 15857 | 0.65 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0005622~intracellular | 15 | 1 | 37 | 10544 | 15857 | 0.61 | 1 | 1 | 100 |
Functional Group 17 | Median: 0.9355098519781113 | Geo: 0.9267703680488794 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
SP_PIR_KEYWORDS | transport | 3 | 0.87 | 43 | 1432 | 17599 | 0.86 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0006810~transport | 5 | 0.93 | 40 | 2697 | 15360 | 0.71 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0051234~establishment of localization | 5 | 0.94 | 40 | 2788 | 15360 | 0.69 | 1 | 1 | 100 |
GOTERM_BP_ALL | GO:0051179~localization | 5 | 0.97 | 40 | 3161 | 15360 | 0.61 | 1 | 1 | 100 |
Functional Group 18 | Median: 0.9348568006971572 | Geo: 0.9279057981361349 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
SP_PIR_KEYWORDS | transferase | 3 | 0.86 | 43 | 1398 | 17599 | 0.88 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0016740~transferase activity | 3 | 0.93 | 36 | 2040 | 16968 | 0.69 | 1 | 1 | 100 |
GOTERM_CC_ALL | GO:0005737~cytoplasm | 8 | 1 | 37 | 6219 | 15857 | 0.55 | 1 | 1 | 100 |
Functional Group 19 | Median: 0.9261389414215063 | Geo: 0.9334226746370794 | ||||||||
Category | Term | Count | PValue | List Total | Pop Hits | Pop Total | Fold Enrichment | Bonferroni | Benjamini | FDR |
GOTERM_MF_ALL | GO:0032553~ribonucleotide binding | 3 | 0.92 | 36 | 1933 | 16968 | 0.73 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0032555~purine ribonucleotide binding | 3 | 0.92 | 36 | 1933 | 16968 | 0.73 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0017076~purine nucleotide binding | 3 | 0.93 | 36 | 2016 | 16968 | 0.7 | 1 | 1 | 100 |
GOTERM_MF_ALL | GO:0000166~nucleotide binding | 3 | 0.96 | 36 | 2314 | 16968 | 0.61 | 1 | 1 | 100 |
- NOTICE GO TERM CLUSTER 1
- GPCRs! Includes mas gene, an oncogene.
- Also, membrane proteins, cell-cell adhesion, stress response, and developmental genes.
- Only GPCRs and membrane proteins have good P Values. Should pay attention to these.
- Gene Functional Classification is more revealing.
- Only two gene groups appear
- The first is GPCR-heavy, including mas
- The second is very low-scoring, but deals with DNA binding and transcription
Gene Group 1: (Score 1.68) 1 ILMN_1759087 olfactory receptor, family 10, subfamily v, member 1 2 ILMN_1743329 retinal pigment epithelium-derived rhodopsin homolog 3 ILMN_1747683 aquaporin 4 4 ILMN_1731745 ninjurin 2 5 ILMN_1741371 transmembrane protein 8 (five membrane-spanning domains) 6 ILMN_1772727 g protein-coupled receptor 75 7 ILMN_1780465 c-type lectin domain family 5, member a 8 ILMN_1748338 g protein-coupled receptor 85 9 ILMN_1714980 mas-related gpr, member d 10 ILMN_1750497 g protein-coupled receptor 109a Gene Group 2: (Score 0.1) 1 ILMN_1726928 transcription elongation factor a (sii), 3 2 ILMN_1706590 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, drosophila); translocated to, 1 3 ILMN_1662021 hypothetical protein flj20403 similar to zinc finger protein 326 4 ILMN_1754553 mediator of rna polymerase ii transcription, subunit 19 homolog (yeast) 5 ILMN_1700766 flj45850 protein