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Coexpression cluster:C2631: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001032!6.19e-15!24;UBERON:0004456!6.19e-15!24;UBERON:0000020!1.01e-13!23;UBERON:0002104!3.06e-13!21;UBERON:0000970!4.96e-12!20;UBERON:0007625!9.52e-12!11;UBERON:0000019!8.19e-11!19;UBERON:0000047!8.19e-11!19;UBERON:0004088!8.19e-11!19;UBERON:0003072!8.19e-11!19;UBERON:0003071!8.19e-11!19;UBERON:0004128!8.19e-11!19;UBERON:0001456!1.68e-09!21;UBERON:0001801!7.86e-09!14;UBERON:0000488!1.09e-07!4;UBERON:0000476!7.97e-07!3;UBERON:0000920!7.97e-07!3
|ontology_enrichment_uberon=UBERON:0001032!6.19e-15!24;UBERON:0004456!6.19e-15!24;UBERON:0000020!1.01e-13!23;UBERON:0002104!3.06e-13!21;UBERON:0000970!4.96e-12!20;UBERON:0007625!9.52e-12!11;UBERON:0000019!8.19e-11!19;UBERON:0000047!8.19e-11!19;UBERON:0004088!8.19e-11!19;UBERON:0003072!8.19e-11!19;UBERON:0003071!8.19e-11!19;UBERON:0004128!8.19e-11!19;UBERON:0001456!1.68e-09!21;UBERON:0001801!7.86e-09!14;UBERON:0000488!1.09e-07!4;UBERON:0000476!7.97e-07!3;UBERON:0000920!7.97e-07!3
|tf_chipseq_enrich=ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161033097721092!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195058660062136!GTF2B#2959;4:31.9438299343242:9.59435337635006e-07:4.09156664872448e-05!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000718784905446953!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186294871554548!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00307792792326129!JUND#3727;4:6.99466394187103:0.00041768421781858:0.003919716239083!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142550495001707!NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000234730780360019!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.00031159169544185!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157241679931352!SIRT6#51548;4:153.638403990025:1.78585744852249e-09:1.55427638388534e-07!SP2#6668;4:26.1535304938446:2.13562021071447e-06:7.74989712254374e-05!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032263308367953!TAL1#6886;4:29.8686166774402:1.25525650806991e-06:5.04416061740335e-05!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244550334938884
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}}
}}

Revision as of 14:01, 5 September 2012


Full id: C2631_chronic_pineal_gall_teratocarcinoma_testicular_choriocarcinoma_cholangiocellular



Phase1 CAGE Peaks

Hg19::chr21:39493435..39493461,-p1@DSCR4
Hg19::chr21:39493560..39493573,+p2@DSCR8
Hg19::chr21:39493574..39493607,+p1@DSCR8
Hg19::chr21:39493611..39493629,+p3@DSCR8


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>uberon_data<br><br>

Cell Type
Ontology termp-valuen
germ line cell3.22e-077
germ cell3.22e-077
chorionic membrane mesenchymal stem cell7.97e-073
Uber Anatomy
Ontology termp-valuen
sensory system6.19e-1524
entire sense organ system6.19e-1524
sense organ1.01e-1323
visual system3.06e-1321
eye4.96e-1220
pigment epithelium of eye9.52e-1211
camera-type eye8.19e-1119
simple eye8.19e-1119
ocular region8.19e-1119
optic cup8.19e-1119
eye primordium8.19e-1119
optic vesicle8.19e-1119
face1.68e-0921
anterior segment of eyeball7.86e-0914
atypical epithelium1.09e-074
acellular anatomical structure7.97e-073
egg chorion7.97e-073


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
ELF1#199744.258097958807540.003041525565781240.0161033097721092
FOS#235348.99795530889440.0001525147711168630.00195058660062136
GTF2B#2959431.94382993432429.59435337635006e-074.09156664872448e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000718784905446953
HEY1#2346244.040111043105710.00375304636917980.0186294871554548
IRF1#365947.63716375356390.0002938853996185490.00307792792326129
JUND#372746.994663941871030.000417684217818580.003919716239083
MXI1#460149.96157162875930.0001015224754950450.00142550495001707
NFYA#4800418.42558069983058.67100748407158e-060.000234730780360019
NFYB#4801416.75979325353651.26678572070404e-050.00031159169544185
REST#597849.650028716128020.0001152825614219170.00157241679931352
SIRT6#515484153.6384039900251.78585744852249e-091.55427638388534e-07
SP2#6668426.15353049384462.13562021071447e-067.74989712254374e-05
TAF1#687243.343046285745290.008005664898701650.032263308367953
TAL1#6886429.86861667744021.25525650806991e-065.04416061740335e-05
TBP#690843.706770687096390.005296377814784350.0244550334938884



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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