Athurva Gore/LabNotes/ExomeReseq/2009-5-13: Difference between revisions
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Line 38: | Line 38: | ||
** 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 128: | Line 136: | ||
|Median: 0.03711173039552113 | |Median: 0.03711173039552113 | ||
|Geo: 0.039704364737313154 | |Geo: 0.039704364737313154 | ||
| | | | ||
| | | | ||
Line 142: | Line 148: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 156: | Line 160: | ||
|transmembrane region | |transmembrane region | ||
|18 | |18 | ||
|0 | |0 | ||
|34 | |34 | ||
|3211 | |3211 | ||
Line 170: | Line 172: | ||
|topological domain:Extracellular | |topological domain:Extracellular | ||
|14 | |14 | ||
|0 | |0 | ||
|34 | |34 | ||
|2092 | |2092 | ||
Line 184: | Line 184: | ||
|glycoprotein | |glycoprotein | ||
|18 | |18 | ||
|0 | |0 | ||
|43 | |43 | ||
|3807 | |3807 | ||
Line 198: | Line 196: | ||
|GO:0004888~transmembrane receptor activity | |GO:0004888~transmembrane receptor activity | ||
|9 | |9 | ||
|0.01 | |0.01 | ||
|36 | |36 | ||
|1388 | |1388 | ||
Line 212: | Line 208: | ||
|transmembrane | |transmembrane | ||
|19 | |19 | ||
|0.01 | |0.01 | ||
|43 | |43 | ||
|4452 | |4452 | ||
Line 226: | Line 220: | ||
|topological domain:Cytoplasmic | |topological domain:Cytoplasmic | ||
|14 | |14 | ||
|0.01 | |0.01 | ||
|34 | |34 | ||
|2554 | |2554 | ||
Line 240: | Line 232: | ||
|GO:0004872~receptor activity | |GO:0004872~receptor activity | ||
|10 | |10 | ||
|0.02 | |0.02 | ||
|36 | |36 | ||
|2113 | |2113 | ||
Line 254: | Line 244: | ||
|glycosylation site:N-linked (GlcNAc...) | |glycosylation site:N-linked (GlcNAc...) | ||
|15 | |15 | ||
|0.03 | |0.03 | ||
|34 | |34 | ||
|3085 | |3085 | ||
Line 268: | Line 256: | ||
|membrane | |membrane | ||
|20 | |20 | ||
|0.03 | |0.03 | ||
|43 | |43 | ||
|5272 | |5272 | ||
Line 282: | Line 268: | ||
|GO:0001584~rhodopsin-like receptor activity | |GO:0001584~rhodopsin-like receptor activity | ||
|6 | |6 | ||
|0.03 | |0.03 | ||
|36 | |36 | ||
|828 | |828 | ||
Line 296: | Line 280: | ||
|IPR000276:Rhodopsin-like GPCR superfamily | |IPR000276:Rhodopsin-like GPCR superfamily | ||
|6 | |6 | ||
|0.03 | |0.03 | ||
|42 | |42 | ||
|747 | |747 | ||
Line 310: | Line 292: | ||
|GO:0060089~molecular transducer activity | |GO:0060089~molecular transducer activity | ||
|11 | |11 | ||
|0.03 | |0.03 | ||
|36 | |36 | ||
|2557 | |2557 | ||
Line 324: | Line 304: | ||
|GO:0004871~signal transducer activity | |GO:0004871~signal transducer activity | ||
|11 | |11 | ||
|0.03 | |0.03 | ||
|36 | |36 | ||
|2557 | |2557 | ||
Line 338: | Line 316: | ||
|GO:0004930~G-protein coupled receptor activity | |GO:0004930~G-protein coupled receptor activity | ||
|6 | |6 | ||
|0.04 | |0.04 | ||
|36 | |36 | ||
|953 | |953 | ||
Line 352: | Line 328: | ||
|g-protein coupled receptor | |g-protein coupled receptor | ||
|6 | |6 | ||
|0.05 | |0.05 | ||
|43 | |43 | ||
|832 | |832 | ||
Line 366: | Line 340: | ||
|receptor | |receptor | ||
|9 | |9 | ||
|0.05 | |0.05 | ||
|43 | |43 | ||
|1731 | |1731 | ||
Line 380: | Line 352: | ||
|transducer | |transducer | ||
|6 | |6 | ||
|0.06 | |0.06 | ||
|43 | |43 | ||
|881 | |881 | ||
Line 394: | Line 364: | ||
|GO:0016021~integral to membrane | |GO:0016021~integral to membrane | ||
|18 | |18 | ||
|0.07 | |0.07 | ||
|37 | |37 | ||
|5357 | |5357 | ||
Line 408: | Line 376: | ||
|GO:0031224~intrinsic to membrane | |GO:0031224~intrinsic to membrane | ||
|18 | |18 | ||
|0.07 | |0.07 | ||
|37 | |37 | ||
|5378 | |5378 | ||
Line 422: | Line 388: | ||
|GO:0007186~G-protein coupled receptor protein signaling pathway | |GO:0007186~G-protein coupled receptor protein signaling pathway | ||
|6 | |6 | ||
|0.17 | |0.17 | ||
|40 | |40 | ||
|1155 | |1155 | ||
Line 436: | Line 400: | ||
|GO:0044425~membrane part | |GO:0044425~membrane part | ||
|18 | |18 | ||
|0.17 | |0.17 | ||
|37 | |37 | ||
|6065 | |6065 | ||
Line 450: | Line 412: | ||
|GO:0005886~plasma membrane | |GO:0005886~plasma membrane | ||
|11 | |11 | ||
|0.2 | |0.2 | ||
|37 | |37 | ||
|3314 | |3314 | ||
Line 464: | Line 424: | ||
|GO:0016020~membrane | |GO:0016020~membrane | ||
|20 | |20 | ||
|0.25 | |0.25 | ||
|37 | |37 | ||
|7262 | |7262 | ||
Line 478: | Line 436: | ||
|GO:0007166~cell surface receptor linked signal transduction | |GO:0007166~cell surface receptor linked signal transduction | ||
|7 | |7 | ||
|0.34 | |0.34 | ||
|40 | |40 | ||
|1868 | |1868 | ||
Line 492: | Line 448: | ||
|GO:0007165~signal transduction | |GO:0007165~signal transduction | ||
|12 | |12 | ||
|0.35 | |0.35 | ||
|40 | |40 | ||
|3758 | |3758 | ||
Line 506: | Line 460: | ||
|GO:0007154~cell communication | |GO:0007154~cell communication | ||
|12 | |12 | ||
|0.48 | |0.48 | ||
|40 | |40 | ||
|4123 | |4123 | ||
Line 517: | Line 469: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 534: | Line 484: | ||
|Median: 0.05315479858365215 | |Median: 0.05315479858365215 | ||
|Geo: 0.043640878080478424 | |Geo: 0.043640878080478424 | ||
| | | | ||
| | | | ||
Line 548: | Line 496: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 562: | Line 508: | ||
|leucine-rich repeat | |leucine-rich repeat | ||
|4 | |4 | ||
|0.02 | |0.02 | ||
|43 | |43 | ||
|256 | |256 | ||
Line 576: | Line 520: | ||
|repeat:LRR 3 | |repeat:LRR 3 | ||
|3 | |3 | ||
|0.05 | |0.05 | ||
|34 | |34 | ||
|132 | |132 | ||
Line 590: | Line 532: | ||
|repeat:LRR 2 | |repeat:LRR 2 | ||
|3 | |3 | ||
|0.06 | |0.06 | ||
|34 | |34 | ||
|140 | |140 | ||
Line 604: | Line 544: | ||
|repeat:LRR 1 | |repeat:LRR 1 | ||
|3 | |3 | ||
|0.06 | |0.06 | ||
|34 | |34 | ||
|140 | |140 | ||
Line 615: | Line 553: | ||
|71.3 | |71.3 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 632: | Line 568: | ||
|Median: 0.1336143269166979 | |Median: 0.1336143269166979 | ||
|Geo: 0.12431956759597426 | |Geo: 0.12431956759597426 | ||
| | | | ||
| | | | ||
Line 646: | Line 580: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 660: | Line 592: | ||
|GO:0005887~integral to plasma membrane | |GO:0005887~integral to plasma membrane | ||
|7 | |7 | ||
|0.06 | |0.06 | ||
|37 | |37 | ||
|1246 | |1246 | ||
Line 674: | Line 604: | ||
|GO:0031226~intrinsic to plasma membrane | |GO:0031226~intrinsic to plasma membrane | ||
|7 | |7 | ||
|0.06 | |0.06 | ||
|37 | |37 | ||
|1262 | |1262 | ||
Line 688: | Line 616: | ||
|GO:0005886~plasma membrane | |GO:0005886~plasma membrane | ||
|11 | |11 | ||
|0.2 | |0.2 | ||
|37 | |37 | ||
|3314 | |3314 | ||
Line 702: | Line 628: | ||
|GO:0044459~plasma membrane part | |GO:0044459~plasma membrane part | ||
|7 | |7 | ||
|0.31 | |0.31 | ||
|37 | |37 | ||
|2037 | |2037 | ||
Line 713: | Line 637: | ||
|99.71 | |99.71 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 730: | Line 652: | ||
|Median: 0.31357655372100196 | |Median: 0.31357655372100196 | ||
|Geo: 0.294106233156399 | |Geo: 0.294106233156399 | ||
| | | | ||
| | | | ||
Line 744: | Line 664: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 758: | Line 676: | ||
|cell adhesion | |cell adhesion | ||
|3 | |3 | ||
|0.23 | |0.23 | ||
|43 | |43 | ||
|386 | |386 | ||
Line 772: | Line 688: | ||
|GO:0007155~cell adhesion | |GO:0007155~cell adhesion | ||
|4 | |4 | ||
|0.31 | |0.31 | ||
|40 | |40 | ||
|774 | |774 | ||
Line 786: | Line 700: | ||
|GO:0022610~biological adhesion | |GO:0022610~biological adhesion | ||
|4 | |4 | ||
|0.31 | |0.31 | ||
|40 | |40 | ||
|774 | |774 | ||
Line 800: | Line 712: | ||
|GO:0009653~anatomical structure morphogenesis | |GO:0009653~anatomical structure morphogenesis | ||
|5 | |5 | ||
|0.32 | |0.32 | ||
|40 | |40 | ||
|1133 | |1133 | ||
Line 811: | Line 721: | ||
|99.94 | |99.94 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 828: | Line 736: | ||
|Median: 0.2994000556276062 | |Median: 0.2994000556276062 | ||
|Geo: 0.3722618330261535 | |Geo: 0.3722618330261535 | ||
| | | | ||
| | | | ||
Line 842: | Line 748: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 856: | Line 760: | ||
|GO:0009605~response to external stimulus | |GO:0009605~response to external stimulus | ||
|4 | |4 | ||
|0.22 | |0.22 | ||
|40 | |40 | ||
|644 | |644 | ||
Line 870: | Line 772: | ||
|GO:0009611~response to wounding | |GO:0009611~response to wounding | ||
|3 | |3 | ||
|0.3 | |0.3 | ||
|40 | |40 | ||
|431 | |431 | ||
Line 884: | Line 784: | ||
|GO:0006950~response to stress | |GO:0006950~response to stress | ||
|3 | |3 | ||
|0.77 | |0.77 | ||
|40 | |40 | ||
|1081 | |1081 | ||
Line 895: | Line 793: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 912: | Line 808: | ||
|Median: 0.3688618227951922 | |Median: 0.3688618227951922 | ||
|Geo: 0.37308799552587163 | |Geo: 0.37308799552587163 | ||
| | | | ||
| | | | ||
Line 926: | Line 820: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 940: | Line 832: | ||
|GO:0048856~anatomical structure development | |GO:0048856~anatomical structure development | ||
|9 | |9 | ||
|0.17 | |0.17 | ||
|40 | |40 | ||
|2153 | |2153 | ||
Line 954: | Line 844: | ||
|GO:0009888~tissue development | |GO:0009888~tissue development | ||
|3 | |3 | ||
|0.21 | |0.21 | ||
|40 | |40 | ||
|339 | |339 | ||
Line 968: | Line 856: | ||
|GO:0048731~system development | |GO:0048731~system development | ||
|7 | |7 | ||
|0.29 | |0.29 | ||
|40 | |40 | ||
|1760 | |1760 | ||
Line 982: | Line 868: | ||
|GO:0032502~developmental process | |GO:0032502~developmental process | ||
|11 | |11 | ||
|0.31 | |0.31 | ||
|40 | |40 | ||
|3262 | |3262 | ||
Line 996: | Line 880: | ||
|GO:0032501~multicellular organismal process | |GO:0032501~multicellular organismal process | ||
|12 | |12 | ||
|0.35 | |0.35 | ||
|40 | |40 | ||
|3759 | |3759 | ||
Line 1,010: | Line 892: | ||
|GO:0007275~multicellular organismal development | |GO:0007275~multicellular organismal development | ||
|8 | |8 | ||
|0.39 | |0.39 | ||
|40 | |40 | ||
|2349 | |2349 | ||
Line 1,024: | Line 904: | ||
|GO:0048513~organ development | |GO:0048513~organ development | ||
|5 | |5 | ||
|0.41 | |0.41 | ||
|40 | |40 | ||
|1282 | |1282 | ||
Line 1,038: | Line 916: | ||
|GO:0007399~nervous system development | |GO:0007399~nervous system development | ||
|3 | |3 | ||
|0.6 | |0.6 | ||
|40 | |40 | ||
|780 | |780 | ||
Line 1,052: | Line 928: | ||
|GO:0048869~cellular developmental process | |GO:0048869~cellular developmental process | ||
|5 | |5 | ||
|0.7 | |0.7 | ||
|40 | |40 | ||
|1835 | |1835 | ||
Line 1,066: | Line 940: | ||
|GO:0030154~cell differentiation | |GO:0030154~cell differentiation | ||
|5 | |5 | ||
|0.7 | |0.7 | ||
|40 | |40 | ||
|1835 | |1835 | ||
Line 1,077: | Line 949: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 1,094: | Line 964: | ||
|Median: 0.36781428439882924 | |Median: 0.36781428439882924 | ||
|Geo: 0.40941510044660673 | |Geo: 0.40941510044660673 | ||
| | | | ||
| | | | ||
Line 1,108: | Line 976: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 1,122: | Line 988: | ||
|GO:0005615~extracellular space | |GO:0005615~extracellular space | ||
|3 | |3 | ||
|0.33 | |0.33 | ||
|37 | |37 | ||
|521 | |521 | ||
Line 1,136: | Line 1,000: | ||
|GO:0005576~extracellular region | |GO:0005576~extracellular region | ||
|5 | |5 | ||
|0.37 | |0.37 | ||
|37 | |37 | ||
|1350 | |1350 | ||
Line 1,150: | Line 1,012: | ||
|GO:0044421~extracellular region part | |GO:0044421~extracellular region part | ||
|3 | |3 | ||
|0.56 | |0.56 | ||
|37 | |37 | ||
|819 | |819 | ||
Line 1,161: | Line 1,021: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 1,178: | Line 1,036: | ||
|Median: 0.4245273768008249 | |Median: 0.4245273768008249 | ||
|Geo: 0.4297118369268503 | |Geo: 0.4297118369268503 | ||
| | | | ||
| | | | ||
Line 1,192: | Line 1,048: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 1,206: | Line 1,060: | ||
|GO:0005576~extracellular region | |GO:0005576~extracellular region | ||
|5 | |5 | ||
|0.37 | |0.37 | ||
|37 | |37 | ||
|1350 | |1350 | ||
Line 1,220: | Line 1,072: | ||
|signal | |signal | ||
|9 | |9 | ||
|0.4 | |0.4 | ||
|43 | |43 | ||
|2919 | |2919 | ||
Line 1,234: | Line 1,084: | ||
|Secreted | |Secreted | ||
|5 | |5 | ||
|0.45 | |0.45 | ||
|43 | |43 | ||
|1440 | |1440 | ||
Line 1,248: | Line 1,096: | ||
|signal peptide | |signal peptide | ||
|8 | |8 | ||
|0.52 | |0.52 | ||
|34 | |34 | ||
|2447 | |2447 | ||
Line 1,259: | Line 1,105: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 1,276: | Line 1,120: | ||
|Median: 0.3631068152753514 | |Median: 0.3631068152753514 | ||
|Geo: 0.45212872922107583 | |Geo: 0.45212872922107583 | ||
| | | | ||
| | | | ||
Line 1,290: | Line 1,132: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 1,304: | Line 1,144: | ||
|GO:0009653~anatomical structure morphogenesis | |GO:0009653~anatomical structure morphogenesis | ||
|5 | |5 | ||
|0.32 | |0.32 | ||
|40 | |40 | ||
|1133 | |1133 | ||
Line 1,318: | Line 1,156: | ||
|GO:0032989~cellular structure morphogenesis | |GO:0032989~cellular structure morphogenesis | ||
|3 | |3 | ||
|0.36 | |0.36 | ||
|40 | |40 | ||
|499 | |499 | ||
Line 1,332: | Line 1,168: | ||
|GO:0000902~cell morphogenesis | |GO:0000902~cell morphogenesis | ||
|3 | |3 | ||
|0.36 | |0.36 | ||
|40 | |40 | ||
|499 | |499 | ||
Line 1,346: | Line 1,180: | ||
|GO:0016043~cellular component organization and biogenesis | |GO:0016043~cellular component organization and biogenesis | ||
|4 | |4 | ||
|0.98 | |0.98 | ||
|40 | |40 | ||
|2723 | |2723 | ||
Line 1,357: | Line 1,189: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 1,374: | Line 1,204: | ||
|Median: 0.5734687246608097 | |Median: 0.5734687246608097 | ||
|Geo: 0.5127166515642717 | |Geo: 0.5127166515642717 | ||
| | | | ||
| | | | ||
Line 1,388: | Line 1,216: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 1,402: | Line 1,228: | ||
|GO:0000074~regulation of progression through cell cycle | |GO:0000074~regulation of progression through cell cycle | ||
|3 | |3 | ||
|0.39 | |0.39 | ||
|40 | |40 | ||
|526 | |526 | ||
Line 1,416: | Line 1,240: | ||
|GO:0051726~regulation of cell cycle | |GO:0051726~regulation of cell cycle | ||
|3 | |3 | ||
|0.39 | |0.39 | ||
|40 | |40 | ||
|529 | |529 | ||
Line 1,430: | Line 1,252: | ||
|GO:0022402~cell cycle process | |GO:0022402~cell cycle process | ||
|3 | |3 | ||
|0.57 | |0.57 | ||
|40 | |40 | ||
|749 | |749 | ||
Line 1,444: | Line 1,264: | ||
|GO:0008283~cell proliferation | |GO:0008283~cell proliferation | ||
|3 | |3 | ||
|0.61 | |0.61 | ||
|40 | |40 | ||
|796 | |796 | ||
Line 1,458: | Line 1,276: | ||
|GO:0007049~cell cycle | |GO:0007049~cell cycle | ||
|3 | |3 | ||
|0.67 | |0.67 | ||
|40 | |40 | ||
|894 | |894 | ||
Line 1,469: | Line 1,285: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 1,486: | Line 1,300: | ||
|Median: 0.9605162482170493 | |Median: 0.9605162482170493 | ||
|Geo: 0.6129377540659845 | |Geo: 0.6129377540659845 | ||
| | | | ||
| | | | ||
Line 1,500: | Line 1,312: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 1,514: | Line 1,324: | ||
|GO:0016020~membrane | |GO:0016020~membrane | ||
|20 | |20 | ||
|0.25 | |0.25 | ||
|37 | |37 | ||
|7262 | |7262 | ||
Line 1,528: | Line 1,336: | ||
|GO:0044464~cell part | |GO:0044464~cell part | ||
|33 | |33 | ||
|0.96 | |0.96 | ||
|37 | |37 | ||
|15019 | |15019 | ||
Line 1,542: | Line 1,348: | ||
|GO:0005623~cell | |GO:0005623~cell | ||
|33 | |33 | ||
|0.96 | |0.96 | ||
|37 | |37 | ||
|15020 | |15020 | ||
Line 1,553: | Line 1,357: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 1,570: | Line 1,372: | ||
|Median: 0.7836410046532671 | |Median: 0.7836410046532671 | ||
|Geo: 0.7488370592269121 | |Geo: 0.7488370592269121 | ||
| | | | ||
| | | | ||
Line 1,584: | Line 1,384: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 1,598: | Line 1,396: | ||
|GO:0009056~catabolic process | |GO:0009056~catabolic process | ||
|3 | |3 | ||
|0.57 | |0.57 | ||
|40 | |40 | ||
|746 | |746 | ||
Line 1,612: | Line 1,408: | ||
|hydrolase | |hydrolase | ||
|4 | |4 | ||
|0.67 | |0.67 | ||
|43 | |43 | ||
|1422 | |1422 | ||
Line 1,626: | Line 1,420: | ||
|GO:0016787~hydrolase activity | |GO:0016787~hydrolase activity | ||
|4 | |4 | ||
|0.9 | |0.9 | ||
|36 | |36 | ||
|2438 | |2438 | ||
Line 1,640: | Line 1,432: | ||
|GO:0003824~catalytic activity | |GO:0003824~catalytic activity | ||
|10 | |10 | ||
|0.92 | |0.92 | ||
|36 | |36 | ||
|5976 | |5976 | ||
Line 1,651: | Line 1,441: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 1,668: | Line 1,456: | ||
|Median: 0.9968215046691112 | |Median: 0.9968215046691112 | ||
|Geo: 0.8265131236074682 | |Geo: 0.8265131236074682 | ||
| | | | ||
| | | | ||
Line 1,682: | Line 1,468: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 1,696: | Line 1,480: | ||
|GO:0005783~endoplasmic reticulum | |GO:0005783~endoplasmic reticulum | ||
|3 | |3 | ||
|0.57 | |0.57 | ||
|37 | |37 | ||
|827 | |827 | ||
Line 1,710: | Line 1,492: | ||
|GO:0005737~cytoplasm | |GO:0005737~cytoplasm | ||
|8 | |8 | ||
|1 | |1 | ||
|37 | |37 | ||
|6219 | |6219 | ||
Line 1,724: | Line 1,504: | ||
|GO:0044444~cytoplasmic part | |GO:0044444~cytoplasmic part | ||
|3 | |3 | ||
|1 | |1 | ||
|37 | |37 | ||
|3717 | |3717 | ||
Line 1,735: | Line 1,513: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 1,752: | Line 1,528: | ||
|Median: 0.8759330074668149 | |Median: 0.8759330074668149 | ||
|Geo: 0.8575501630938809 | |Geo: 0.8575501630938809 | ||
| | | | ||
| | | | ||
Line 1,766: | Line 1,540: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 1,780: | Line 1,552: | ||
|GO:0050794~regulation of cellular process | |GO:0050794~regulation of cellular process | ||
|12 | |12 | ||
|0.59 | |0.59 | ||
|40 | |40 | ||
|4422 | |4422 | ||
Line 1,794: | Line 1,564: | ||
|GO:0065007~biological regulation | |GO:0065007~biological regulation | ||
|14 | |14 | ||
|0.6 | |0.6 | ||
|40 | |40 | ||
|5238 | |5238 | ||
Line 1,808: | Line 1,576: | ||
|metal-binding | |metal-binding | ||
|7 | |7 | ||
|0.62 | |0.62 | ||
|43 | |43 | ||
|2649 | |2649 | ||
Line 1,822: | Line 1,588: | ||
|GO:0050789~regulation of biological process | |GO:0050789~regulation of biological process | ||
|12 | |12 | ||
|0.7 | |0.7 | ||
|40 | |40 | ||
|4759 | |4759 | ||
Line 1,836: | Line 1,600: | ||
|zinc | |zinc | ||
|5 | |5 | ||
|0.72 | |0.72 | ||
|43 | |43 | ||
|2007 | |2007 | ||
Line 1,850: | Line 1,612: | ||
|GO:0008270~zinc ion binding | |GO:0008270~zinc ion binding | ||
|5 | |5 | ||
|0.75 | |0.75 | ||
|36 | |36 | ||
|2400 | |2400 | ||
Line 1,864: | Line 1,624: | ||
|zinc-finger | |zinc-finger | ||
|4 | |4 | ||
|0.76 | |0.76 | ||
|43 | |43 | ||
|1629 | |1629 | ||
Line 1,878: | Line 1,636: | ||
|GO:0019222~regulation of metabolic process | |GO:0019222~regulation of metabolic process | ||
|7 | |7 | ||
|0.79 | |0.79 | ||
|40 | |40 | ||
|2975 | |2975 | ||
Line 1,892: | Line 1,648: | ||
|Transcription regulation | |Transcription regulation | ||
|4 | |4 | ||
|0.8 | |0.8 | ||
|43 | |43 | ||
|1754 | |1754 | ||
Line 1,906: | Line 1,660: | ||
|Transcription | |Transcription | ||
|4 | |4 | ||
|0.81 | |0.81 | ||
|43 | |43 | ||
|1783 | |1783 | ||
Line 1,920: | Line 1,672: | ||
|GO:0045449~regulation of transcription | |GO:0045449~regulation of transcription | ||
|6 | |6 | ||
|0.81 | |0.81 | ||
|40 | |40 | ||
|2598 | |2598 | ||
Line 1,934: | Line 1,684: | ||
|GO:0046872~metal ion binding | |GO:0046872~metal ion binding | ||
|8 | |8 | ||
|0.82 | |0.82 | ||
|36 | |36 | ||
|4312 | |4312 | ||
Line 1,948: | Line 1,696: | ||
|GO:0019219~regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | |GO:0019219~regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | ||
|6 | |6 | ||
|0.83 | |0.83 | ||
|40 | |40 | ||
|2658 | |2658 | ||
Line 1,962: | Line 1,708: | ||
|GO:0030528~transcription regulator activity | |GO:0030528~transcription regulator activity | ||
|3 | |3 | ||
|0.84 | |0.84 | ||
|36 | |36 | ||
|1534 | |1534 | ||
Line 1,976: | Line 1,720: | ||
|GO:0006350~transcription | |GO:0006350~transcription | ||
|6 | |6 | ||
|0.84 | |0.84 | ||
|40 | |40 | ||
|2695 | |2695 | ||
Line 1,990: | Line 1,732: | ||
|GO:0043167~ion binding | |GO:0043167~ion binding | ||
|8 | |8 | ||
|0.84 | |0.84 | ||
|36 | |36 | ||
|4397 | |4397 | ||
Line 2,004: | Line 1,744: | ||
|GO:0010468~regulation of gene expression | |GO:0010468~regulation of gene expression | ||
|6 | |6 | ||
|0.85 | |0.85 | ||
|40 | |40 | ||
|2760 | |2760 | ||
Line 2,018: | Line 1,756: | ||
|GO:0043169~cation binding | |GO:0043169~cation binding | ||
|7 | |7 | ||
|0.87 | |0.87 | ||
|36 | |36 | ||
|4006 | |4006 | ||
Line 2,032: | Line 1,768: | ||
|GO:0046914~transition metal ion binding | |GO:0046914~transition metal ion binding | ||
|5 | |5 | ||
|0.87 | |0.87 | ||
|36 | |36 | ||
|2908 | |2908 | ||
Line 2,046: | Line 1,780: | ||
|GO:0031323~regulation of cellular metabolic process | |GO:0031323~regulation of cellular metabolic process | ||
|6 | |6 | ||
|0.88 | |0.88 | ||
|40 | |40 | ||
|2873 | |2873 | ||
Line 2,060: | Line 1,792: | ||
|GO:0006355~regulation of transcription, DNA-dependent | |GO:0006355~regulation of transcription, DNA-dependent | ||
|5 | |5 | ||
|0.89 | |0.89 | ||
|40 | |40 | ||
|2432 | |2432 | ||
Line 2,074: | Line 1,804: | ||
|GO:0006351~transcription, DNA-dependent | |GO:0006351~transcription, DNA-dependent | ||
|5 | |5 | ||
|0.9 | |0.9 | ||
|40 | |40 | ||
|2487 | |2487 | ||
Line 2,088: | Line 1,816: | ||
|GO:0032774~RNA biosynthetic process | |GO:0032774~RNA biosynthetic process | ||
|5 | |5 | ||
|0.9 | |0.9 | ||
|40 | |40 | ||
|2490 | |2490 | ||
Line 2,102: | Line 1,828: | ||
|GO:0003677~DNA binding | |GO:0003677~DNA binding | ||
|4 | |4 | ||
|0.9 | |0.9 | ||
|36 | |36 | ||
|2450 | |2450 | ||
Line 2,116: | Line 1,840: | ||
|dna-binding | |dna-binding | ||
|3 | |3 | ||
|0.93 | |0.93 | ||
|43 | |43 | ||
|1748 | |1748 | ||
Line 2,130: | Line 1,852: | ||
|GO:0043283~biopolymer metabolic process | |GO:0043283~biopolymer metabolic process | ||
|10 | |10 | ||
|0.96 | |0.96 | ||
|40 | |40 | ||
|5361 | |5361 | ||
Line 2,144: | Line 1,864: | ||
|GO:0016070~RNA metabolic process | |GO:0016070~RNA metabolic process | ||
|5 | |5 | ||
|0.96 | |0.96 | ||
|40 | |40 | ||
|3020 | |3020 | ||
Line 2,158: | Line 1,876: | ||
|GO:0003676~nucleic acid binding | |GO:0003676~nucleic acid binding | ||
|5 | |5 | ||
|0.96 | |0.96 | ||
|36 | |36 | ||
|3690 | |3690 | ||
Line 2,172: | Line 1,888: | ||
|GO:0006139~nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | |GO:0006139~nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | ||
|7 | |7 | ||
|0.97 | |0.97 | ||
|40 | |40 | ||
|4051 | |4051 | ||
Line 2,186: | Line 1,900: | ||
|GO:0010467~gene expression | |GO:0010467~gene expression | ||
|6 | |6 | ||
|0.97 | |0.97 | ||
|40 | |40 | ||
|3686 | |3686 | ||
Line 2,200: | Line 1,912: | ||
|GO:0005634~nucleus | |GO:0005634~nucleus | ||
|7 | |7 | ||
|0.97 | |0.97 | ||
|37 | |37 | ||
|4664 | |4664 | ||
Line 2,214: | Line 1,924: | ||
|nucleus | |nucleus | ||
|5 | |5 | ||
|0.99 | |0.99 | ||
|43 | |43 | ||
|3710 | |3710 | ||
Line 2,228: | Line 1,936: | ||
|GO:0043231~intracellular membrane-bound organelle | |GO:0043231~intracellular membrane-bound organelle | ||
|10 | |10 | ||
|1 | |1 | ||
|37 | |37 | ||
|7191 | |7191 | ||
Line 2,242: | Line 1,948: | ||
|GO:0043227~membrane-bound organelle | |GO:0043227~membrane-bound organelle | ||
|10 | |10 | ||
|1 | |1 | ||
|37 | |37 | ||
|7194 | |7194 | ||
Line 2,256: | Line 1,960: | ||
|GO:0044424~intracellular part | |GO:0044424~intracellular part | ||
|15 | |15 | ||
|1 | |1 | ||
|37 | |37 | ||
|9906 | |9906 | ||
Line 2,270: | Line 1,972: | ||
|GO:0043229~intracellular organelle | |GO:0043229~intracellular organelle | ||
|11 | |11 | ||
|1 | |1 | ||
|37 | |37 | ||
|8288 | |8288 | ||
Line 2,284: | Line 1,984: | ||
|GO:0043226~organelle | |GO:0043226~organelle | ||
|11 | |11 | ||
|1 | |1 | ||
|37 | |37 | ||
|8292 | |8292 | ||
Line 2,298: | Line 1,996: | ||
|GO:0005622~intracellular | |GO:0005622~intracellular | ||
|15 | |15 | ||
|1 | |1 | ||
|37 | |37 | ||
|10544 | |10544 | ||
Line 2,309: | Line 2,005: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 2,326: | Line 2,020: | ||
|Median: 0.8662513767254609 | |Median: 0.8662513767254609 | ||
|Geo: 0.88361465668396 | |Geo: 0.88361465668396 | ||
| | | | ||
| | | | ||
Line 2,340: | Line 2,032: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 2,354: | Line 2,044: | ||
|GO:0044267~cellular protein metabolic process | |GO:0044267~cellular protein metabolic process | ||
|8 | |8 | ||
|0.81 | |0.81 | ||
|40 | |40 | ||
|3482 | |3482 | ||
Line 2,368: | Line 2,056: | ||
|GO:0044260~cellular macromolecule metabolic process | |GO:0044260~cellular macromolecule metabolic process | ||
|8 | |8 | ||
|0.83 | |0.83 | ||
|40 | |40 | ||
|3534 | |3534 | ||
Line 2,382: | Line 2,068: | ||
|GO:0006464~protein modification process | |GO:0006464~protein modification process | ||
|4 | |4 | ||
|0.85 | |0.85 | ||
|40 | |40 | ||
|1804 | |1804 | ||
Line 2,396: | Line 2,080: | ||
|GO:0019538~protein metabolic process | |GO:0019538~protein metabolic process | ||
|8 | |8 | ||
|0.86 | |0.86 | ||
|40 | |40 | ||
|3691 | |3691 | ||
Line 2,410: | Line 2,092: | ||
|GO:0043412~biopolymer modification | |GO:0043412~biopolymer modification | ||
|4 | |4 | ||
|0.87 | |0.87 | ||
|40 | |40 | ||
|1877 | |1877 | ||
Line 2,424: | Line 2,104: | ||
|GO:0043687~post-translational protein modification | |GO:0043687~post-translational protein modification | ||
|3 | |3 | ||
|0.91 | |0.91 | ||
|40 | |40 | ||
|1522 | |1522 | ||
Line 2,438: | Line 2,116: | ||
|GO:0043234~protein complex | |GO:0043234~protein complex | ||
|3 | |3 | ||
|0.96 | |0.96 | ||
|37 | |37 | ||
|2115 | |2115 | ||
Line 2,452: | Line 2,128: | ||
|GO:0032991~macromolecular complex | |GO:0032991~macromolecular complex | ||
|3 | |3 | ||
|0.99 | |0.99 | ||
|37 | |37 | ||
|2609 | |2609 | ||
Line 2,463: | Line 2,137: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 2,480: | Line 2,152: | ||
|Median: 0.9612032324365326 | |Median: 0.9612032324365326 | ||
|Geo: 0.8965362550566862 | |Geo: 0.8965362550566862 | ||
| | | | ||
| | | | ||
Line 2,494: | Line 2,164: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 2,508: | Line 2,176: | ||
|GO:0008152~metabolic process | |GO:0008152~metabolic process | ||
|23 | |23 | ||
|0.73 | |0.73 | ||
|40 | |40 | ||
|9181 | |9181 | ||
Line 2,522: | Line 2,188: | ||
|GO:0044237~cellular metabolic process | |GO:0044237~cellular metabolic process | ||
|20 | |20 | ||
|0.79 | |0.79 | ||
|40 | |40 | ||
|8269 | |8269 | ||
Line 2,536: | Line 2,200: | ||
|GO:0044238~primary metabolic process | |GO:0044238~primary metabolic process | ||
|19 | |19 | ||
|0.87 | |0.87 | ||
|40 | |40 | ||
|8291 | |8291 | ||
Line 2,550: | Line 2,212: | ||
|GO:0043283~biopolymer metabolic process | |GO:0043283~biopolymer metabolic process | ||
|10 | |10 | ||
|0.96 | |0.96 | ||
|40 | |40 | ||
|5361 | |5361 | ||
Line 2,564: | Line 2,224: | ||
|GO:0043170~macromolecule metabolic process | |GO:0043170~macromolecule metabolic process | ||
|14 | |14 | ||
|0.97 | |0.97 | ||
|40 | |40 | ||
|7216 | |7216 | ||
Line 2,578: | Line 2,236: | ||
|GO:0044424~intracellular part | |GO:0044424~intracellular part | ||
|15 | |15 | ||
|1 | |1 | ||
|37 | |37 | ||
|9906 | |9906 | ||
Line 2,592: | Line 2,248: | ||
|GO:0005622~intracellular | |GO:0005622~intracellular | ||
|15 | |15 | ||
|1 | |1 | ||
|37 | |37 | ||
|10544 | |10544 | ||
Line 2,603: | Line 2,257: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 2,620: | Line 2,272: | ||
|Median: 0.9355098519781113 | |Median: 0.9355098519781113 | ||
|Geo: 0.9267703680488794 | |Geo: 0.9267703680488794 | ||
| | | | ||
| | | | ||
Line 2,634: | Line 2,284: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 2,648: | Line 2,296: | ||
|transport | |transport | ||
|3 | |3 | ||
|0.87 | |0.87 | ||
|43 | |43 | ||
|1432 | |1432 | ||
Line 2,662: | Line 2,308: | ||
|GO:0006810~transport | |GO:0006810~transport | ||
|5 | |5 | ||
|0.93 | |0.93 | ||
|40 | |40 | ||
|2697 | |2697 | ||
Line 2,676: | Line 2,320: | ||
|GO:0051234~establishment of localization | |GO:0051234~establishment of localization | ||
|5 | |5 | ||
|0.94 | |0.94 | ||
|40 | |40 | ||
|2788 | |2788 | ||
Line 2,690: | Line 2,332: | ||
|GO:0051179~localization | |GO:0051179~localization | ||
|5 | |5 | ||
|0.97 | |0.97 | ||
|40 | |40 | ||
|3161 | |3161 | ||
Line 2,701: | Line 2,341: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 2,718: | Line 2,356: | ||
|Median: 0.9348568006971572 | |Median: 0.9348568006971572 | ||
|Geo: 0.9279057981361349 | |Geo: 0.9279057981361349 | ||
| | | | ||
| | | | ||
Line 2,732: | Line 2,368: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 2,746: | Line 2,380: | ||
|transferase | |transferase | ||
|3 | |3 | ||
|0.86 | |0.86 | ||
|43 | |43 | ||
|1398 | |1398 | ||
Line 2,760: | Line 2,392: | ||
|GO:0016740~transferase activity | |GO:0016740~transferase activity | ||
|3 | |3 | ||
|0.93 | |0.93 | ||
|36 | |36 | ||
|2040 | |2040 | ||
Line 2,774: | Line 2,404: | ||
|GO:0005737~cytoplasm | |GO:0005737~cytoplasm | ||
|8 | |8 | ||
|1 | |1 | ||
|37 | |37 | ||
|6219 | |6219 | ||
Line 2,785: | Line 2,413: | ||
|100 | |100 | ||
|---- | |---- | ||
| | | | ||
| | | | ||
Line 2,802: | Line 2,428: | ||
|Median: 0.9261389414215063 | |Median: 0.9261389414215063 | ||
|Geo: 0.9334226746370794 | |Geo: 0.9334226746370794 | ||
| | | | ||
| | | | ||
Line 2,816: | Line 2,440: | ||
|Term | |Term | ||
|Count | |Count | ||
|PValue | |PValue | ||
|List Total | |List Total | ||
|Pop Hits | |Pop Hits | ||
Line 2,830: | Line 2,452: | ||
|GO:0032553~ribonucleotide binding | |GO:0032553~ribonucleotide binding | ||
|3 | |3 | ||
|0.92 | |0.92 | ||
|36 | |36 | ||
|1933 | |1933 | ||
Line 2,844: | Line 2,464: | ||
|GO:0032555~purine ribonucleotide binding | |GO:0032555~purine ribonucleotide binding | ||
|3 | |3 | ||
|0.92 | |0.92 | ||
|36 | |36 | ||
|1933 | |1933 | ||
Line 2,858: | Line 2,476: | ||
|GO:0017076~purine nucleotide binding | |GO:0017076~purine nucleotide binding | ||
|3 | |3 | ||
|0.93 | |0.93 | ||
|36 | |36 | ||
|2016 | |2016 | ||
Line 2,872: | Line 2,488: | ||
|GO:0000166~nucleotide binding | |GO:0000166~nucleotide binding | ||
|3 | |3 | ||
|0.96 | |0.96 | ||
|36 | |36 | ||
|2314 | |2314 | ||
Line 2,884: | Line 2,498: | ||
|---- | |---- | ||
|} | |} | ||
** '''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