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Coexpression cluster:C611: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0016972!thiol oxidase activity!0.0141274113637933!2671$GO:0016670!oxidoreductase activity, acting on sulfur group of donors, oxygen as acceptor!0.0141274113637933!2671
|gostat_on_coexpression_clusters=GO:0016972!thiol oxidase activity!0.0141274113637933!2671$GO:0016670!oxidoreductase activity, acting on sulfur group of donors, oxygen as acceptor!0.0141274113637933!2671
|id=C611
|id=C611
|ontology_enrichment_celltype=CL:0000066!1.89e-22!254;CL:0000223!5.13e-15!59;CL:0002076!1.85e-10!43
|ontology_enrichment_celltype=CL:0002563!2.36e-09!4;CL:0000181!4.59e-07!12;CL:0000417!4.59e-07!12;CL:0000668!4.59e-07!12;CL:0000412!4.59e-07!12;CL:0000182!4.59e-07!12
|ontology_enrichment_disease=DOID:305!2.58e-16!106;DOID:0050687!9.39e-11!143
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!5.43e-19!169;UBERON:0000925!5.43e-19!169;UBERON:0006595!5.43e-19!169;UBERON:0001007!4.17e-16!155;UBERON:0001555!4.17e-16!155;UBERON:0007026!4.17e-16!155;UBERON:0004921!2.22e-15!129;UBERON:0004185!2.22e-15!129;UBERON:0000481!1.32e-14!347;UBERON:0000064!5.70e-13!219;UBERON:0000077!7.92e-12!130;UBERON:0005911!3.63e-11!82;UBERON:0000062!5.43e-11!511;UBERON:0001041!1.46e-10!98;UBERON:0005177!1.64e-10!107;UBERON:0003104!2.54e-10!238;UBERON:0009142!2.54e-10!238;UBERON:0009569!1.23e-09!113;UBERON:0005172!4.71e-09!55;UBERON:0005173!4.71e-09!55;UBERON:0006554!1.37e-08!44;UBERON:0001004!1.87e-08!72;UBERON:0000466!1.91e-08!126;UBERON:0008947!3.16e-08!38;UBERON:0003258!3.16e-08!38;UBERON:0000922!3.52e-08!612;UBERON:0001008!5.06e-08!45;UBERON:0000065!7.92e-08!53;UBERON:0000468!1.34e-07!659;UBERON:0002417!2.27e-07!61;UBERON:0000916!2.27e-07!61;UBERON:0000475!2.47e-07!365;UBERON:0000467!2.77e-07!625;UBERON:0002050!3.02e-07!605;UBERON:0005423!3.02e-07!605;UBERON:0000923!3.54e-07!604;UBERON:0005291!3.54e-07!604;UBERON:0006598!3.54e-07!604;UBERON:0002532!3.54e-07!604;UBERON:0000480!4.15e-07!626;UBERON:0000483!5.51e-07!309
|ontology_enrichment_uberon=UBERON:0000160!9.34e-37!17;UBERON:0005409!7.88e-31!25;UBERON:0001155!3.27e-23!9;UBERON:0000059!5.57e-19!11;UBERON:0002108!4.04e-16!4;UBERON:0004921!2.65e-13!118;UBERON:0001007!5.89e-12!145;UBERON:0001555!5.89e-12!145;UBERON:0007026!5.89e-12!145;UBERON:0004119!1.41e-10!160;UBERON:0000925!1.41e-10!160;UBERON:0006595!1.41e-10!160;UBERON:0001154!1.48e-09!1;UBERON:0001153!1.48e-09!1;UBERON:0001045!1.48e-09!1;UBERON:0001242!2.36e-09!4;UBERON:0001262!2.36e-09!4;UBERON:0004786!2.36e-09!4;UBERON:0004808!2.36e-09!4;UBERON:0001277!2.36e-09!4;UBERON:0001882!2.67e-09!1;UBERON:0005403!2.67e-09!1;UBERON:0009854!4.59e-09!23;UBERON:0003929!6.13e-09!54;UBERON:0009497!2.41e-08!25;UBERON:0000015!2.41e-08!25;UBERON:0002423!2.41e-08!25;UBERON:0006235!2.41e-08!25;UBERON:0004161!2.41e-08!25;UBERON:0009856!5.37e-08!26;UBERON:0011216!1.05e-07!223;UBERON:0004907!1.66e-07!5;UBERON:0002107!2.26e-07!19;UBERON:0006925!2.26e-07!19;UBERON:0008836!2.26e-07!19
|tf_chipseq_enrich=CEBPB#1051;6:3.41620612535349:0.00475176856810538:0.0223343815249486!ELF1#1997;9:2.73734868780485:0.00133657072811265:0.00886962195154133!EP300#2033;8:3.87082384355611:0.000292351760388241:0.00310262427631212!FOSL2#2355;4:4.83720017273191:0.00754162287399241:0.0310877625251379!FOXA1#3169;9:7.12376983889065:5.19704363903544e-07:2.42743309757255e-05!FOXA2#3170;7:12.3152318763326:4.83510549852797e-07:2.27876165686265e-05!HDAC2#3066;8:7.66606870664358:1.89551452608875e-06:6.97799230138115e-05!HEY1#23462;14:4.04011104310571:3.23477172841824e-09:2.67487192829986e-07!HNF4A#3172;12:19.8276774539603:3.54543106940285e-15:6.31879309654204e-13!HNF4G#3174;9:18.4843430527158:1.26472046417331e-10:1.35612053960777e-08!NR2C2#7182;4:9.31846025864025:0.000690363193353926:0.00556548371676501!POLR2A#5430;14:2.14745317655807:2.25331953374171e-05:0.000492434481658192!RXRA#6256;9:12.9051110180142:2.9964879042402e-09:2.51163884615523e-07!SIN3A#25942;9:3.47714018152402:0.000204086532801336:0.00242211288627713!SP1#6667;9:3.66324517166201:0.000134181452530633:0.00175941955063989!SRF#6722;5:4.92756366505993:0.00229448556458705:0.0130179149217681!TAF1#6872;10:2.38789020410378:0.0016242233760895:0.010167971298652!TBP#6908;9:2.38292401313339:0.00381176112623516:0.0188243105855341!TCF7L2#6934;7:5.38508828156867:0.000113022621779428:0.00154887411048703
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}}
}}

Revision as of 16:29, 19 October 2012


Full id: C611_small_hepatocellular_colon_adenocarcinoma_Intestinal_signet_temporal



Phase1 CAGE Peaks

Hg19::chr10:102729876..102729890,-p1@AK000735
Hg19::chr10:102729908..102729938,-p2@AK000735
Hg19::chr13:76335013..76335032,+p14@LMO7
Hg19::chr16:2034715..2034726,+p10@GFER
Hg19::chr16:75284758..75284802,-p@chr16:75284758..75284802
-
Hg19::chr2:233742013..233742020,-p@chr2:233742013..233742020
-
Hg19::chr2:61245275..61245310,-p6@PUS10
Hg19::chr2:74753294..74753302,-p6@DQX1
Hg19::chr2:74753305..74753331,-p2@DQX1
Hg19::chr2:74753332..74753373,-p1@DQX1
Hg19::chr3:8693755..8693789,-p1@C3orf32
Hg19::chr6:158993336..158993351,+p10@TMEM181
Hg19::chr7:55256663..55256679,-p2@ENST00000442411
p2@uc003tqo.2
Hg19::chr9:86571432..86571453,-p5@C9orf64


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


GO IDGO nameFDR corrected p-value
GO:0016972thiol oxidase activity0.0141274113637933
GO:0016670oxidoreductase activity, acting on sulfur group of donors, oxygen as acceptor0.0141274113637933



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
intestinal epithelial cell2.36e-094
metabolising cell4.59e-0712
endopolyploid cell4.59e-0712
parenchymal cell4.59e-0712
polyploid cell4.59e-0712
hepatocyte4.59e-0712
Uber Anatomy
Ontology termp-valuen
intestine9.34e-3717
gastrointestinal system7.88e-3125
colon3.27e-239
large intestine5.57e-1911
small intestine4.04e-164
subdivision of digestive tract2.65e-13118
digestive system5.89e-12145
digestive tract5.89e-12145
primitive gut5.89e-12145
endoderm-derived structure1.41e-10160
endoderm1.41e-10160
presumptive endoderm1.41e-10160
vermiform appendix1.48e-091
caecum1.48e-091
midgut1.48e-091
intestinal mucosa2.36e-094
wall of intestine2.36e-094
gastrointestinal system mucosa2.36e-094
gastrointestinal system epithelium2.36e-094
intestinal epithelium2.36e-094
nucleus accumbens2.67e-091
ventral striatum2.67e-091
digestive tract diverticulum4.59e-0923
gut epithelium6.13e-0954
epithelium of foregut-midgut junction2.41e-0825
anatomical boundary2.41e-0825
hepatobiliary system2.41e-0825
foregut-midgut junction2.41e-0825
septum transversum2.41e-0825
sac5.37e-0826
organ system subdivision1.05e-07223
lower digestive tract1.66e-075
liver2.26e-0719
digestive gland2.26e-0719
liver bud2.26e-0719


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#105163.416206125353490.004751768568105380.0223343815249486
ELF1#199792.737348687804850.001336570728112650.00886962195154133
EP300#203383.870823843556110.0002923517603882410.00310262427631212
FOSL2#235544.837200172731910.007541622873992410.0310877625251379
FOXA1#316997.123769838890655.19704363903544e-072.42743309757255e-05
FOXA2#3170712.31523187633264.83510549852797e-072.27876165686265e-05
HDAC2#306687.666068706643581.89551452608875e-066.97799230138115e-05
HEY1#23462144.040111043105713.23477172841824e-092.67487192829986e-07
HNF4A#31721219.82767745396033.54543106940285e-156.31879309654204e-13
HNF4G#3174918.48434305271581.26472046417331e-101.35612053960777e-08
NR2C2#718249.318460258640250.0006903631933539260.00556548371676501
POLR2A#5430142.147453176558072.25331953374171e-050.000492434481658192
RXRA#6256912.90511101801422.9964879042402e-092.51163884615523e-07
SIN3A#2594293.477140181524020.0002040865328013360.00242211288627713
SP1#666793.663245171662010.0001341814525306330.00175941955063989
SRF#672254.927563665059930.002294485564587050.0130179149217681
TAF1#6872102.387890204103780.00162422337608950.010167971298652
TBP#690892.382924013133390.003811761126235160.0188243105855341
TCF7L2#693475.385088281568670.0001130226217794280.00154887411048703



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.