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Coexpression cluster:C2931: Difference between revisions

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|id=C2931
|id=C2931
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:162!2.25e-09!235;DOID:14566!5.11e-09!239;DOID:0050687!3.70e-07!143
|ontology_enrichment_disease=DOID:162!5.07e-08!235;DOID:14566!1.17e-07!239
|ontology_enrichment_uberon=UBERON:0007023!1.31e-29!115;UBERON:0000073!5.88e-16!94;UBERON:0001016!5.88e-16!94;UBERON:0001049!1.10e-15!57;UBERON:0005068!1.10e-15!57;UBERON:0006241!1.10e-15!57;UBERON:0007135!1.10e-15!57;UBERON:0005743!2.23e-15!86;UBERON:0001017!2.79e-15!82;UBERON:0003080!9.45e-13!42;UBERON:0002780!1.45e-12!41;UBERON:0001890!1.45e-12!41;UBERON:0006240!1.45e-12!41;UBERON:0000955!1.60e-12!69;UBERON:0006238!1.60e-12!69;UBERON:0002616!1.99e-12!59;UBERON:0003075!3.78e-10!86;UBERON:0007284!3.78e-10!86;UBERON:0002346!5.08e-10!90;UBERON:0000924!1.15e-09!173;UBERON:0006601!1.15e-09!173;UBERON:0004121!1.19e-09!169;UBERON:0002020!1.87e-09!34;UBERON:0003528!1.87e-09!34;UBERON:0000033!8.76e-09!123;UBERON:0001893!1.04e-08!34;UBERON:0002791!1.45e-08!33;UBERON:0000153!2.04e-08!129;UBERON:0007811!2.04e-08!129;UBERON:0001869!4.59e-08!32;UBERON:0003056!6.51e-07!61
|ontology_enrichment_uberon=UBERON:0007023!7.97e-29!114;UBERON:0001016!5.29e-16!89;UBERON:0001049!1.76e-15!56;UBERON:0005068!1.76e-15!56;UBERON:0006241!1.76e-15!56;UBERON:0007135!1.76e-15!56;UBERON:0001017!2.77e-15!81;UBERON:0000073!4.50e-14!53;UBERON:0002616!4.50e-14!53;UBERON:0002780!1.11e-12!41;UBERON:0001890!1.11e-12!41;UBERON:0003080!1.11e-12!41;UBERON:0006240!1.11e-12!41;UBERON:0000955!2.40e-12!68;UBERON:0006238!2.40e-12!68;UBERON:0011216!1.69e-11!223;UBERON:0003075!1.33e-10!82;UBERON:0007284!1.33e-10!82;UBERON:0002346!1.93e-10!86;UBERON:0004121!9.29e-10!171;UBERON:0000924!9.29e-10!171;UBERON:0006601!9.29e-10!171;UBERON:0003528!1.39e-09!34;UBERON:0002020!1.39e-09!34;UBERON:0001893!8.80e-09!34;UBERON:0002791!1.42e-08!32;UBERON:0001869!3.75e-08!32;UBERON:0010371!4.17e-08!104;UBERON:0003056!2.91e-07!61;UBERON:0010314!6.21e-07!132
|tf_chipseq_enrich=ATF3#467;4:22.4631745260087:3.92475754624726e-06:0.000127614493577994!BRCA1#672;4:20.1842306432238:6.02116732184487e-06:0.000179824047448143!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.0051391846916406!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268875408381763!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106864010315454!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.000728568815262332!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161335714645044!ELK4#2005;4:16.235681658468:1.43847748454449e-05:0.000343861638838045!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435632813854223!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00107394309257034!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.45817868374318e-05!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00391024306525408!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.000615653618930319!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000719829271455594!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186711956247687!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248695956880519!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00308194570245623!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392818748534486!MAFF#23764;4:56.3153564899452:9.92458849374232e-08:5.83622802757857e-06!MAFK#7975;4:27.1007331378299:1.85228494563408e-06:6.85995700131483e-05!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486797926733489!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00890174543069296!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00769572272396124!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.000312106237047911!NR2C2#7182;4:32.6146109052409:8.82887529809196e-07:3.82605355708476e-05!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000796068096113263!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00445096728649344!PBX3#5090;4:21.9145126867441:4.33289161192893e-06:0.000136920685948032!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188867884019956!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00130153539149363!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157632828388892!RXRA#6256;4:20.0746171391333:6.1537798808435e-06:0.000182687497718992!SETDB1#9869;4:40.3200261780105:3.77887289069054e-07:1.85461327928021e-05!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.0079844735409045!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00686030683608628!SP2#6668;4:26.1535304938446:2.13562021071447e-06:7.76338458708002e-05!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249953429987737!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000586134984697785!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323494403913759!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.00097251696089956!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245168160002776!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115847993244202!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509347567914099!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107126539118358!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613606061114287
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}}
}}

Revision as of 14:35, 19 October 2012


Full id: C2931_Mast_malignant_pituitary_occipital_pineal_cerebellum_small



Phase1 CAGE Peaks

Hg19::chr8:92082244..92082289,-p1@uc003yet.2
Hg19::chr8:92082301..92082316,-p3@uc003yet.2
Hg19::chr8:92082319..92082348,-p2@uc003yet.2
Hg19::chr8:92082349..92082360,-p2@ENST00000522817


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism7.97e-29114
nervous system5.29e-1689
neural tube1.76e-1556
neural rod1.76e-1556
future spinal cord1.76e-1556
neural keel1.76e-1556
central nervous system2.77e-1581
regional part of nervous system4.50e-1453
regional part of brain4.50e-1453
regional part of forebrain1.11e-1241
forebrain1.11e-1241
anterior neural tube1.11e-1241
future forebrain1.11e-1241
brain2.40e-1268
future brain2.40e-1268
organ system subdivision1.69e-11223
neural plate1.33e-1082
presumptive neural plate1.33e-1082
neurectoderm1.93e-1086
ectoderm-derived structure9.29e-10171
ectoderm9.29e-10171
presumptive ectoderm9.29e-10171
brain grey matter1.39e-0934
gray matter1.39e-0934
telencephalon8.80e-0934
regional part of telencephalon1.42e-0832
cerebral hemisphere3.75e-0832
ecto-epithelium4.17e-08104
pre-chordal neural plate2.91e-0761
structure with developmental contribution from neural crest6.21e-07132
Disease
Ontology termp-valuen
cancer5.07e-08235
disease of cellular proliferation1.17e-07239


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467422.46317452600873.92475754624726e-060.000127614493577994
BRCA1#672420.18423064322386.02116732184487e-060.000179824047448143
CCNT2#90546.336201576962630.0006203100587215640.0051391846916406
CEBPB#105147.971147625824820.0002476385788090830.00268875408381763
E2F1#186944.907389214879320.001724022357361790.0106864010315454
E2F4#1874412.66806031528443.88145892637771e-050.000728568815262332
ELF1#199744.258097958807540.003041525565781240.0161335714645044
ELK4#2005416.2356816584681.43847748454449e-050.000343861638838045
EP300#203346.77394172622320.0004748459821442640.00435632813854223
FOXA1#3169411.08141974938556.62943068949433e-050.00107394309257034
FOXA2#3170424.63046375266522.71504128667089e-069.45817868374318e-05
GABPB1#255347.067683836182170.0004006876864423170.00391024306525408
GATA1#2623413.56030814380042.95627390049268e-050.000615653618930319
GTF2F1#2962412.73966087675773.79492332235515e-050.000719829271455594
HEY1#2346244.040111043105710.00375304636917980.0186711956247687
HMGN3#932448.178547723350590.0002234570284440470.00248695956880519
IRF1#365947.63716375356390.0002938853996185490.00308194570245623
JUND#372746.994663941871030.000417684217818580.00392818748534486
MAFF#23764456.31535648994529.92458849374232e-085.83622802757857e-06
MAFK#7975427.10073313782991.85228494563408e-066.85995700131483e-05
MAX#414946.452555509007120.0005767613195645490.00486797926733489
MYC#460945.22228187160940.001344309395272740.00890174543069296
NFKB1#479045.488063424193840.001102199566301980.00769572272396124
NFYB#4801416.75979325353651.26678572070404e-050.000312106237047911
NR2C2#7182432.61461090524098.82887529809196e-073.82605355708476e-05
NRF1#4899412.21027944771094.49717228915276e-050.000796068096113263
PAX5#507946.669565531177830.0005052774169483260.00445096728649344
PBX3#5090421.91451268674414.33289161192893e-060.000136920685948032
POU2F2#545249.106124057742520.000145395665174930.00188867884019956
RAD21#5885410.35503389545638.6948481184721e-050.00130153539149363
REST#597849.650028716128020.0001152825614219170.00157632828388892
RXRA#6256420.07461713913336.1537798808435e-060.000182687497718992
SETDB1#9869440.32002617801053.77887289069054e-071.85461327928021e-05
SIN3A#2594245.408884726815140.001168172384885160.0079844735409045
SP1#666745.69838137814090.0009482606065333980.00686030683608628
SP2#6668426.15353049384462.13562021071447e-067.76338458708002e-05
SPI1#668848.204323508522730.000220661881527680.00249953429987737
SRF#6722413.79717826216782.75840773062708e-050.000586134984697785
TAF1#687243.343046285745290.008005664898701650.0323494403913759
TAF7#6879411.43306940492395.85061525419808e-050.00097251696089956
TBP#690843.706770687096390.005296377814784350.0245168160002776
TCF7L2#6934410.77017656313737.42969445082454e-050.00115847993244202
USF1#739146.361499277207960.0006105011399140830.00509347567914099
YY1#752844.911170749853860.00171871838055440.0107126539118358
ZEB1#6935312.66632401315790.000793336075912850.00613606061114287



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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