Athurva Gore/LabNotes/ExomeReseq/2009-5-13: Difference between revisions

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* '''NOTICE GO TERM CLUSTER 1'''
** GPCRs!  Includes mas gene, an oncogene.
* Also, membrane proteins, cell-cell adhesion, stress response, and developmental genes.
* Only GPCRs, membrane proteins, and adhesion have good P Values.  Should pay attention to these.

Revision as of 23:51, 13 May 2009

iPS Cancer?

  • 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

  • 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

  • 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

  • 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

  • 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.
  • 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, membrane proteins, and adhesion have good P Values. Should pay attention to these.