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Coexpression cluster:C1842: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=BATF#10538;4:19.4862414338429:1.37275300118359e-05:0.000332180145251652!BCL11A#53335;4:22.6955640828856:7.49488101632307e-06:0.0002143954747915!BCL3#602;4:27.6376822429907:3.425174836939e-06:0.000114142257433016!BRCA1#672;4:16.147384514579:2.89130901545765e-05:0.000605141126784331!CEBPB#1051;4:6.37691810065985:0.00111394417667732:0.0076549030048692!EBF1#1879;4:7.1251734772552:0.000723053104677421:0.00577154870065769!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110877703614452!FOS#2353;4:7.19836424711553:0.000694785845338251:0.00559724922101833!FOSL1#8061;4:31.7708637730984:1.96715033715934e-06:7.22642328746341e-05!FOSL2#2355;4:13.5441604836494:5.7953819349229e-05:0.000964871503110812!GATA2#2624;4:10.1959453868432:0.000177544777760982:0.00215737045312149!GTF2F1#2962;4:10.1917287014061:0.00017783388942764:0.00215912503812291!IRF4#3662;4:17.5316101493953:2.08739444052064e-05:0.000460899340324598!JUN#3725;4:10.0102633538691:0.000190853134780107:0.00230593597215404!JUNB#3726;4:24.4885061278569:5.54076322307085e-06:0.000167828239632917!JUND#3727;4:5.59573115349682:0.00184959330175546:0.0109351641574887!MAX#4149;4:5.1620444072057:0.00252630900948518:0.0140000629651715!MEF2A#4205;4:14.9945847277152:3.876195075647e-05:0.000728104204146577!MXI1#4601;4:7.96925730300744:0.000466854638007017:0.00429546573331115!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256854283717941!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.0222053515795598!NR3C1#2908;4:11.9784186649384:9.4122920812787e-05:0.00136548183452794!PAX5#5079;4:5.33565242494226:0.00222338958618779:0.0127797790309227!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542629733646572!PRDM1#639;4:105.464764621969:1.63839404354338e-08:1.1899320967568e-06!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386753306385405!RFX5#5993;4:9.63832866175608:0.00022148012581572:0.00249715673756536!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232467988910116!SMARCA4#6597;4:125.41272264631:8.195036471498e-09:6.32113304318153e-07!SMARCC1#6599;4:34.9306874557052:1.34857873968749e-06:5.3108678353779e-05!SMC3#9126;4:12.0359462759463:9.2360978468394e-05:0.00134365346570004!SP1#6667;4:4.55870510251272:0.0040757356578168:0.0194875134535883!STAT1#6772;4:16.5652699977594:2.61308619905866e-05:0.000563976254481271!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.00022056245412547!TCF12#6938;5:10.6344649021864:7.34844389925727e-06:0.000211248040846278!TCF7L2#6934;4:8.61614125050988:0.000343896972598245:0.00347352571771645!TFAP2C#7022;4:8.64738288788818:0.000339051887817405:0.00344893738304879!USF2#7392;4:10.3937579080557:0.000164617972868753:0.0020267047587457
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}}
}}

Revision as of 11:34, 5 September 2012


Full id: C1842_Preadipocyte_epithelioid_Synoviocyte_tenocyte_renal_Fibroblast_spindle



Phase1 CAGE Peaks

Hg19::chr1:200379777..200379783,-p@chr1:200379777..200379783
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Hg19::chr1:200452510..200452521,-p@chr1:200452510..200452521
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Hg19::chr1:200452556..200452567,-p@chr1:200452556..200452567
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Hg19::chr1:200452599..200452614,-p@chr1:200452599..200452614
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Hg19::chr1:200452620..200452639,-p@chr1:200452620..200452639
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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>cell_data<br><br><br>

Cell Type
Ontology termp-valuen
fibroblast2.06e-1575
non-terminally differentiated cell2.84e-15180
preadipocyte1.76e-0912
skin fibroblast5.82e-0923


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
BATF#10538419.48624143384291.37275300118359e-050.000332180145251652
BCL11A#53335422.69556408288567.49488101632307e-060.0002143954747915
BCL3#602427.63768224299073.425174836939e-060.000114142257433016
BRCA1#672416.1473845145792.89130901545765e-050.000605141126784331
CEBPB#105146.376918100659850.001113944176677320.0076549030048692
EBF1#187947.12517347725520.0007230531046774210.00577154870065769
EP300#203356.77394172622327.00901578206049e-050.00110877703614452
FOS#235347.198364247115530.0006947858453382510.00559724922101833
FOSL1#8061431.77086377309841.96715033715934e-067.22642328746341e-05
FOSL2#2355413.54416048364945.7953819349229e-050.000964871503110812
GATA2#2624410.19594538684320.0001775447777609820.00215737045312149
GTF2F1#2962410.19172870140610.000177833889427640.00215912503812291
IRF4#3662417.53161014939532.08739444052064e-050.000460899340324598
JUN#3725410.01026335386910.0001908531347801070.00230593597215404
JUNB#3726424.48850612785695.54076322307085e-060.000167828239632917
JUND#372745.595731153496820.001849593301755460.0109351641574887
MAX#414945.16204440720570.002526309009485180.0140000629651715
MEF2A#4205414.99458472771523.876195075647e-050.000728104204146577
MXI1#460147.969257303007440.0004668546380070170.00429546573331115
MYC#460944.177825497287520.005691969036823440.0256854283717941
NFKB1#479044.390450739355070.004707732692524960.0222053515795598
NR3C1#2908411.97841866493849.4122920812787e-050.00136548183452794
PAX5#507945.335652424942260.002223389586187790.0127797790309227
POU2F2#545247.284899246194020.0006631223288743860.00542629733646572
PRDM1#6394105.4647646219691.63839404354338e-081.1899320967568e-06
RAD21#588548.284027116365060.0004011622639122450.00386753306385405
RFX5#599349.638328661756080.000221480125815720.00249715673756536
SIN3A#2594244.327107781452110.004977052855762880.0232467988910116
SMARCA4#65974125.412722646318.195036471498e-096.32113304318153e-07
SMARCC1#6599434.93068745570521.34857873968749e-065.3108678353779e-05
SMC3#9126412.03594627594639.2360978468394e-050.00134365346570004
SP1#666744.558705102512720.00407573565781680.0194875134535883
STAT1#6772416.56526999775942.61308619905866e-050.000563976254481271
STAT3#6774510.51946499715427.759040745861e-060.00022056245412547
TCF12#6938510.63446490218647.34844389925727e-060.000211248040846278
TCF7L2#693448.616141250509880.0003438969725982450.00347352571771645
TFAP2C#702248.647382887888180.0003390518878174050.00344893738304879
USF2#7392410.39375790805570.0001646179728687530.0020267047587457



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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