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Coexpression cluster:C2419: Difference between revisions

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|ontology_enrichment_disease=DOID:305!2.70e-08!106
|ontology_enrichment_disease=DOID:305!2.70e-08!106
|ontology_enrichment_uberon=UBERON:0000468!6.70e-20!659;UBERON:0004119!1.12e-19!169;UBERON:0000925!1.12e-19!169;UBERON:0006595!1.12e-19!169;UBERON:0000062!9.22e-19!511;UBERON:0001007!1.39e-18!155;UBERON:0001555!1.39e-18!155;UBERON:0007026!1.39e-18!155;UBERON:0000467!2.55e-18!625;UBERON:0000480!5.80e-18!626;UBERON:0004921!3.51e-16!129;UBERON:0004185!3.51e-16!129;UBERON:0000926!1.94e-15!448;UBERON:0004120!1.94e-15!448;UBERON:0006603!1.94e-15!448;UBERON:0003104!1.63e-14!238;UBERON:0009142!1.63e-14!238;UBERON:0000923!2.23e-14!604;UBERON:0005291!2.23e-14!604;UBERON:0006598!2.23e-14!604;UBERON:0002532!2.23e-14!604;UBERON:0000077!2.54e-14!130;UBERON:0002050!2.71e-14!605;UBERON:0005423!2.71e-14!605;UBERON:0002100!2.85e-14!216;UBERON:0000922!5.48e-13!612;UBERON:0000481!1.91e-12!347;UBERON:0000475!3.83e-12!365;UBERON:0000466!1.42e-11!126;UBERON:0001041!1.82e-11!98;UBERON:0005177!2.72e-11!107;UBERON:0001048!1.38e-10!168;UBERON:0009569!3.88e-10!113;UBERON:0005911!4.24e-09!82;UBERON:0003102!1.73e-08!95;UBERON:0005256!9.35e-08!143;UBERON:0000464!2.13e-07!104;UBERON:0009497!3.65e-07!25;UBERON:0000015!3.65e-07!25;UBERON:0002423!3.65e-07!25;UBERON:0006235!3.65e-07!25;UBERON:0004161!3.65e-07!25;UBERON:0002417!4.34e-07!61;UBERON:0000916!4.34e-07!61;UBERON:0009856!5.00e-07!26;UBERON:0007499!7.96e-07!25
|ontology_enrichment_uberon=UBERON:0000468!6.70e-20!659;UBERON:0004119!1.12e-19!169;UBERON:0000925!1.12e-19!169;UBERON:0006595!1.12e-19!169;UBERON:0000062!9.22e-19!511;UBERON:0001007!1.39e-18!155;UBERON:0001555!1.39e-18!155;UBERON:0007026!1.39e-18!155;UBERON:0000467!2.55e-18!625;UBERON:0000480!5.80e-18!626;UBERON:0004921!3.51e-16!129;UBERON:0004185!3.51e-16!129;UBERON:0000926!1.94e-15!448;UBERON:0004120!1.94e-15!448;UBERON:0006603!1.94e-15!448;UBERON:0003104!1.63e-14!238;UBERON:0009142!1.63e-14!238;UBERON:0000923!2.23e-14!604;UBERON:0005291!2.23e-14!604;UBERON:0006598!2.23e-14!604;UBERON:0002532!2.23e-14!604;UBERON:0000077!2.54e-14!130;UBERON:0002050!2.71e-14!605;UBERON:0005423!2.71e-14!605;UBERON:0002100!2.85e-14!216;UBERON:0000922!5.48e-13!612;UBERON:0000481!1.91e-12!347;UBERON:0000475!3.83e-12!365;UBERON:0000466!1.42e-11!126;UBERON:0001041!1.82e-11!98;UBERON:0005177!2.72e-11!107;UBERON:0001048!1.38e-10!168;UBERON:0009569!3.88e-10!113;UBERON:0005911!4.24e-09!82;UBERON:0003102!1.73e-08!95;UBERON:0005256!9.35e-08!143;UBERON:0000464!2.13e-07!104;UBERON:0009497!3.65e-07!25;UBERON:0000015!3.65e-07!25;UBERON:0002423!3.65e-07!25;UBERON:0006235!3.65e-07!25;UBERON:0004161!3.65e-07!25;UBERON:0002417!4.34e-07!61;UBERON:0000916!4.34e-07!61;UBERON:0009856!5.00e-07!26;UBERON:0007499!7.96e-07!25
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}}
}}

Revision as of 11:35, 5 September 2012


Full id: C2419_tubular_hepatoma_lung_signet_bile_pleomorphic_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr17:48712143..48712165,+p2@ABCC3
Hg19::chr17:48712178..48712189,+p3@ABCC3
Hg19::chr17:48712191..48712198,+p5@ABCC3
Hg19::chr17:48712206..48712285,+p1@ABCC3


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
epithelial cell5.59e-17254
endodermal cell1.40e-0959
embryonic cell1.22e-08248
endo-epithelial cell6.51e-0843
animal cell1.03e-07679
eukaryotic cell1.03e-07679
fibroblast2.89e-0775
Uber Anatomy
Ontology termp-valuen
multi-cellular organism6.70e-20659
endoderm-derived structure1.12e-19169
endoderm1.12e-19169
presumptive endoderm1.12e-19169
organ9.22e-19511
digestive system1.39e-18155
digestive tract1.39e-18155
primitive gut1.39e-18155
anatomical system2.55e-18625
anatomical group5.80e-18626
subdivision of digestive tract3.51e-16129
endodermal part of digestive tract3.51e-16129
mesoderm1.94e-15448
mesoderm-derived structure1.94e-15448
presumptive mesoderm1.94e-15448
mesenchyme1.63e-14238
entire embryonic mesenchyme1.63e-14238
germ layer2.23e-14604
embryonic tissue2.23e-14604
presumptive structure2.23e-14604
epiblast (generic)2.23e-14604
mixed endoderm/mesoderm-derived structure2.54e-14130
embryonic structure2.71e-14605
developing anatomical structure2.71e-14605
trunk2.85e-14216
embryo5.48e-13612
multi-tissue structure1.91e-12347
organism subdivision3.83e-12365
immaterial anatomical entity1.42e-11126
foregut1.82e-1198
trunk region element2.72e-11107
primordium1.38e-10168
subdivision of trunk3.88e-10113
endo-epithelium4.24e-0982
surface structure1.73e-0895
trunk mesenchyme9.35e-08143
anatomical space2.13e-07104
epithelium of foregut-midgut junction3.65e-0725
anatomical boundary3.65e-0725
hepatobiliary system3.65e-0725
foregut-midgut junction3.65e-0725
septum transversum3.65e-0725
abdominal segment of trunk4.34e-0761
abdomen4.34e-0761
sac5.00e-0726
epithelial sac7.96e-0725
Disease
Ontology termp-valuen
carcinoma2.70e-08106


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#105147.971147625824820.0002476385788090830.00267956128597615
CTCF#1066445.360256373075030.001211145381643620.00817018553891476
E2F1#186944.907389214879320.001724022357361790.0106472219845372
EP300#203346.77394172622320.0004748459821442640.0043403150296836
HDAC2#3066413.41562023662633.0859005065161e-050.000626289084726069
HEY1#2346244.040111043105710.00375304636917980.018593255051979
HNF4A#3172423.13229036295373.48990320893214e-060.000115488593548056
HNF4G#3174428.75342252644681.46167379934821e-065.66440630538508e-05
JUND#372746.994663941871030.000417684217818580.00391479153053528
NR3C1#2908414.9730233311731.98868032687801e-050.000442848154922841
SUZ12#23512450.11578091106291.5827390373096e-078.79721566352197e-06
TAF1#687243.343046285745290.008005664898701650.0322011799097054
TBP#690843.706770687096390.005296377814784350.0244021705751836
TFAP2C#7022410.80922860986027.32289634782688e-050.00114490414920762
USF1#739146.361499277207960.0006105011399140830.00507765617197475



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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