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Coexpression cluster:C4013: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!1.90e-28!347;UBERON:0000475!3.67e-28!365;UBERON:0004121!3.50e-24!169;UBERON:0000924!3.09e-23!173;UBERON:0006601!3.09e-23!173;UBERON:0000468!1.40e-22!659;UBERON:0000922!7.38e-22!612;UBERON:0000033!8.67e-22!123;UBERON:0004119!1.30e-21!169;UBERON:0000925!1.30e-21!169;UBERON:0006595!1.30e-21!169;UBERON:0000153!1.42e-21!129;UBERON:0007811!1.42e-21!129;UBERON:0000062!3.68e-21!511;UBERON:0002050!2.96e-19!605;UBERON:0005423!2.96e-19!605;UBERON:0000923!5.09e-19!604;UBERON:0005291!5.09e-19!604;UBERON:0006598!5.09e-19!604;UBERON:0002532!5.09e-19!604;UBERON:0001007!5.26e-18!155;UBERON:0001555!5.26e-18!155;UBERON:0007026!5.26e-18!155;UBERON:0000467!7.28e-18!625;UBERON:0000480!1.50e-17!626;UBERON:0000064!5.05e-17!219;UBERON:0005743!5.87e-17!86;UBERON:0000119!3.97e-16!312;UBERON:0000483!4.06e-16!309;UBERON:0000073!4.51e-16!94;UBERON:0001016!4.51e-16!94;UBERON:0001017!1.31e-15!82;UBERON:0000955!4.65e-14!69;UBERON:0006238!4.65e-14!69;UBERON:0004921!3.10e-13!129;UBERON:0004185!3.10e-13!129;UBERON:0002616!4.44e-13!59;UBERON:0001049!5.45e-13!57;UBERON:0005068!5.45e-13!57;UBERON:0006241!5.45e-13!57;UBERON:0007135!5.45e-13!57;UBERON:0003075!6.95e-13!86;UBERON:0007284!6.95e-13!86;UBERON:0001869!3.69e-12!32;UBERON:0000077!5.11e-12!130;UBERON:0001893!5.76e-12!34;UBERON:0002346!6.21e-12!90;UBERON:0003056!6.50e-12!61;UBERON:0000477!7.74e-12!286;UBERON:0002020!9.02e-12!34;UBERON:0003528!9.02e-12!34;UBERON:0005911!1.04e-11!82;UBERON:0000956!1.06e-11!25;UBERON:0000203!1.06e-11!25;UBERON:0002780!1.48e-11!41;UBERON:0001890!1.48e-11!41;UBERON:0006240!1.48e-11!41;UBERON:0002791!1.82e-11!33;UBERON:0003080!3.92e-11!42;UBERON:0002619!3.92e-11!22;UBERON:0001950!1.75e-10!20;UBERON:0003104!1.77e-09!238;UBERON:0009142!1.77e-09!238;UBERON:0001004!3.50e-09!72;UBERON:0007023!6.37e-09!115;UBERON:0003929!1.01e-08!54;UBERON:0004111!1.08e-08!241;UBERON:0002530!8.21e-08!59;UBERON:0000161!1.00e-07!35;UBERON:0000063!2.09e-07!97;UBERON:0002100!2.55e-07!216;UBERON:0001048!5.40e-07!168;UBERON:0003102!5.79e-07!95;UBERON:0001046!6.21e-07!19
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}}
}}

Revision as of 19:39, 8 August 2012


Full id: C4013_serous_Mammary_lung_colon_Prostate_small_Small



Phase1 CAGE Peaks

Hg19::chr20:14318211..14318232,-p1@FLRT3
Hg19::chr20:14318248..14318264,-p2@FLRT3
Hg19::chr20:14318270..14318289,-p3@FLRT3


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
endo-epithelial cell1.32e-1043
epithelial cell3.67e-10254
endodermal cell4.81e-1059
Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.90e-28347
organism subdivision3.67e-28365
ectoderm-derived structure3.50e-24169
ectoderm3.09e-23173
presumptive ectoderm3.09e-23173
multi-cellular organism1.40e-22659
embryo7.38e-22612
head8.67e-22123
endoderm-derived structure1.30e-21169
endoderm1.30e-21169
presumptive endoderm1.30e-21169
anterior region of body1.42e-21129
craniocervical region1.42e-21129
organ3.68e-21511
embryonic structure2.96e-19605
developing anatomical structure2.96e-19605
germ layer5.09e-19604
embryonic tissue5.09e-19604
presumptive structure5.09e-19604
epiblast (generic)5.09e-19604
digestive system5.26e-18155
digestive tract5.26e-18155
primitive gut5.26e-18155
anatomical system7.28e-18625
anatomical group1.50e-17626
organ part5.05e-17219
cell layer3.97e-16312
epithelium4.06e-16309
regional part of nervous system4.51e-1694
nervous system4.51e-1694
central nervous system1.31e-1582
brain4.65e-1469
future brain4.65e-1469
subdivision of digestive tract3.10e-13129
endodermal part of digestive tract3.10e-13129
regional part of brain4.44e-1359
neural tube5.45e-1357
neural rod5.45e-1357
future spinal cord5.45e-1357
neural keel5.45e-1357
neural plate6.95e-1386
presumptive neural plate6.95e-1386
cerebral hemisphere3.69e-1232
mixed endoderm/mesoderm-derived structure5.11e-12130
telencephalon5.76e-1234
neurectoderm6.21e-1290
pre-chordal neural plate6.50e-1261
anatomical cluster7.74e-12286
gray matter9.02e-1234
brain grey matter9.02e-1234
endo-epithelium1.04e-1182
cerebral cortex1.06e-1125
pallium1.06e-1125
regional part of forebrain1.48e-1141
forebrain1.48e-1141
future forebrain1.48e-1141
regional part of telencephalon1.82e-1133
anterior neural tube3.92e-1142
regional part of cerebral cortex3.92e-1122
neocortex1.75e-1020
mesenchyme1.77e-09238
entire embryonic mesenchyme1.77e-09238
respiratory system3.50e-0972
adult organism6.37e-09115
gut epithelium1.01e-0854
anatomical conduit1.08e-08241
gland8.21e-0859
orifice1.00e-0735
organ segment2.09e-0797
trunk2.55e-07216
primordium5.40e-07168
surface structure5.79e-0795
hindgut6.21e-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


No analysis results for this cluster

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.