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Coexpression cluster:C1689: Difference between revisions

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|full_id=C1689_testicular_choriocarcinoma_Prostate_hepatoblastoma_hepatocellular_Intestinal_pancreas
|full_id=C1689_testicular_choriocarcinoma_Prostate_hepatoblastoma_hepatocellular_Intestinal_pancreas
|id=C1689
|id=C1689
|ontology_enrichment_celltype=CL:0000039!1.68e-13!7;CL:0000586!1.68e-13!7
|ontology_enrichment_celltype=CL:0000039!3.65e-38!7;CL:0000586!3.65e-38!7;CL:0000181!1.24e-07!12;CL:0000417!1.24e-07!12;CL:0000668!1.24e-07!12;CL:0000412!1.24e-07!12;CL:0000182!1.24e-07!12
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:3095!1.02e-18!22;DOID:2994!1.02e-18!22;DOID:1799!9.48e-07!1;DOID:10165!9.48e-07!1;DOID:1798!9.48e-07!1
|ontology_enrichment_uberon=UBERON:0003135!8.98e-10!11;UBERON:0000991!3.86e-09!21;UBERON:0009196!3.86e-09!21;UBERON:0009117!3.86e-09!21;UBERON:0005564!3.86e-09!21;UBERON:0004176!1.39e-08!22;UBERON:0003133!2.25e-08!48;UBERON:0005156!2.81e-08!59;UBERON:0000990!2.81e-08!59;UBERON:0000473!3.59e-08!8;UBERON:0003101!2.53e-07!22;UBERON:0000079!2.53e-07!22;UBERON:0002323!5.25e-07!46
|ontology_enrichment_uberon=UBERON:0000473!3.34e-17!8;UBERON:0003135!1.92e-12!11;UBERON:0000991!6.04e-12!21;UBERON:0009196!6.04e-12!21;UBERON:0009117!6.04e-12!21;UBERON:0005564!6.04e-12!21;UBERON:0004176!2.33e-11!22;UBERON:0000160!4.71e-10!17;UBERON:0002108!7.13e-10!4;UBERON:0003101!1.47e-08!22;UBERON:0000079!1.47e-08!22;UBERON:0002323!4.13e-08!46;UBERON:0002114!5.64e-08!2;UBERON:0004458!1.60e-07!49;UBERON:0005409!8.82e-07!25
|tf_chipseq_enrich=CEBPB#1051;5:7.97114762582482:3.10621793420244e-05:0.000628458533185138!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.0011074350972203!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388909690292711!FOSL1#8061;5:39.713579716373:1.01017090471068e-08:7.63948147118603e-07!FOSL2#2355;5:16.9302006045617:7.18315284751475e-07:3.20598846257091e-05!FOXA1#3169;5:11.0814197493855:5.98116883436141e-06:0.000178834037186336!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00673833739985125!HNF4A#3172;5:23.1322903629537:1.50794906621644e-07:8.47624825223781e-06!HNF4G#3174;5:28.7534225264468:5.08042423670912e-08:3.24721191467359e-06!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.000109093581141712!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000983554230352318!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204108500886716!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00917980649589956
|tf_chipseq_enrich=CEBPB#1051;5:7.97114762582482:3.10621793420244e-05:0.000628458533185138!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.0011074350972203!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388909690292711!FOSL1#8061;5:39.713579716373:1.01017090471068e-08:7.63948147118603e-07!FOSL2#2355;5:16.9302006045617:7.18315284751475e-07:3.20598846257091e-05!FOXA1#3169;5:11.0814197493855:5.98116883436141e-06:0.000178834037186336!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00673833739985125!HNF4A#3172;5:23.1322903629537:1.50794906621644e-07:8.47624825223781e-06!HNF4G#3174;5:28.7534225264468:5.08042423670912e-08:3.24721191467359e-06!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.000109093581141712!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000983554230352318!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204108500886716!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00917980649589956
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}}
}}

Revision as of 11:35, 19 October 2012


Full id: C1689_testicular_choriocarcinoma_Prostate_hepatoblastoma_hepatocellular_Intestinal_pancreas



Phase1 CAGE Peaks

Hg19::chr12:8043698..8043709,-p6@SLC2A14
Hg19::chr12:8043720..8043733,-p2@SLC2A14
Hg19::chr12:8043736..8043748,-p5@SLC2A14
Hg19::chr12:8043767..8043775,-p8@SLC2A14
Hg19::chr12:8043779..8043798,-p1@SLC2A14


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>disease_data<br>

Cell Type
Ontology termp-valuen
germ line cell3.65e-387
germ cell3.65e-387
metabolising cell1.24e-0712
endopolyploid cell1.24e-0712
parenchymal cell1.24e-0712
polyploid cell1.24e-0712
hepatocyte1.24e-0712
Uber Anatomy
Ontology termp-valuen
testis3.34e-178
male reproductive organ1.92e-1211
gonad6.04e-1221
indifferent external genitalia6.04e-1221
indifferent gonad6.04e-1221
gonad primordium6.04e-1221
external genitalia2.33e-1122
intestine4.71e-1017
small intestine7.13e-104
male organism1.47e-0822
male reproductive system1.47e-0822
body cavity4.13e-0846
duodenum5.64e-082
body cavity or lining1.60e-0749
gastrointestinal system8.82e-0725
Disease
Ontology termp-valuen
germ cell and embryonal cancer1.02e-1822
germ cell cancer1.02e-1822
islet cell tumor9.48e-071
endocrine pancreas cancer9.48e-071
pancreatic endocrine carcinoma9.48e-071


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
CEBPB#105157.971147625824823.10621793420244e-050.000628458533185138
EP300#203356.77394172622327.00901578206049e-050.0011074350972203
FOS#235358.99795530889441.69470025615156e-050.000388909690292711
FOSL1#8061539.7135797163731.01017090471068e-087.63948147118603e-07
FOSL2#2355516.93020060456177.18315284751475e-073.20598846257091e-05
FOXA1#3169511.08141974938555.98116883436141e-060.000178834037186336
HEY1#2346254.040111043105710.0009288852205177990.00673833739985125
HNF4A#3172523.13229036295371.50794906621644e-078.47624825223781e-06
HNF4G#3174528.75342252644685.08042423670912e-083.24721191467359e-06
JUN#3725512.51282919233633.25800591331781e-060.000109093581141712
JUND#372756.994663941871035.97069468343598e-050.000983554230352318
SP1#666755.69838137814090.000166391843712550.00204108500886716
TBP#690853.706770687096390.001428755106721120.00917980649589956



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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