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Coexpression cluster:C2246: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000924!7.89e-37!173;UBERON:0006601!7.89e-37!173;UBERON:0004121!2.98e-35!169;UBERON:0000033!1.40e-29!123;UBERON:0000073!1.66e-29!94;UBERON:0001016!1.66e-29!94;UBERON:0000153!3.97e-27!129;UBERON:0007811!3.97e-27!129;UBERON:0000475!5.77e-26!365;UBERON:0005743!1.11e-25!86;UBERON:0002346!2.70e-25!90;UBERON:0001017!7.27e-24!82;UBERON:0003075!7.38e-24!86;UBERON:0007284!7.38e-24!86;UBERON:0002616!2.11e-23!59;UBERON:0003056!4.31e-23!61;UBERON:0001049!7.25e-23!57;UBERON:0005068!7.25e-23!57;UBERON:0006241!7.25e-23!57;UBERON:0007135!7.25e-23!57;UBERON:0000955!7.15e-22!69;UBERON:0006238!7.15e-22!69;UBERON:0000119!2.31e-21!312;UBERON:0000483!6.45e-21!309;UBERON:0000481!7.64e-19!347;UBERON:0002780!1.25e-18!41;UBERON:0001890!1.25e-18!41;UBERON:0006240!1.25e-18!41;UBERON:0003080!1.87e-18!42;UBERON:0000468!5.02e-16!659;UBERON:0000922!6.91e-16!612;UBERON:0002020!7.77e-16!34;UBERON:0003528!7.77e-16!34;UBERON:0001893!2.17e-15!34;UBERON:0000064!2.53e-15!219;UBERON:0002791!6.70e-15!33;UBERON:0001869!1.26e-14!32;UBERON:0002050!1.82e-14!605;UBERON:0005423!1.82e-14!605;UBERON:0000923!2.11e-14!604;UBERON:0005291!2.11e-14!604;UBERON:0006598!2.11e-14!604;UBERON:0002532!2.11e-14!604;UBERON:0000467!1.31e-13!625;UBERON:0000480!1.38e-13!626;UBERON:0000477!1.56e-13!286;UBERON:0004111!1.34e-12!241;UBERON:0002619!3.35e-12!22;UBERON:0000956!1.83e-11!25;UBERON:0000203!1.83e-11!25;UBERON:0001950!3.75e-11!20;UBERON:0000025!1.98e-09!194;UBERON:0000486!2.18e-09!82;UBERON:0000914!2.57e-09!83;UBERON:0002329!2.57e-09!83;UBERON:0003077!2.57e-09!83;UBERON:0003059!2.57e-09!83;UBERON:0007282!2.57e-09!83;UBERON:0009618!2.57e-09!83;UBERON:0007285!2.57e-09!83;UBERON:0004290!6.46e-09!70;UBERON:0001444!1.70e-07!48;UBERON:0001134!2.68e-07!61;UBERON:0002036!2.68e-07!61;UBERON:0003082!2.68e-07!61;UBERON:0000063!4.52e-07!97;UBERON:0001032!4.80e-07!24;UBERON:0004456!4.80e-07!24;UBERON:0005085!5.17e-07!29;UBERON:0002385!5.77e-07!63;UBERON:0001015!5.77e-07!63;UBERON:0000383!5.77e-07!63;UBERON:0003102!7.15e-07!95;UBERON:0000020!7.57e-07!23
|ontology_enrichment_uberon=UBERON:0000924!7.89e-37!173;UBERON:0006601!7.89e-37!173;UBERON:0004121!2.98e-35!169;UBERON:0000033!1.40e-29!123;UBERON:0000073!1.66e-29!94;UBERON:0001016!1.66e-29!94;UBERON:0000153!3.97e-27!129;UBERON:0007811!3.97e-27!129;UBERON:0000475!5.77e-26!365;UBERON:0005743!1.11e-25!86;UBERON:0002346!2.70e-25!90;UBERON:0001017!7.27e-24!82;UBERON:0003075!7.38e-24!86;UBERON:0007284!7.38e-24!86;UBERON:0002616!2.11e-23!59;UBERON:0003056!4.31e-23!61;UBERON:0001049!7.25e-23!57;UBERON:0005068!7.25e-23!57;UBERON:0006241!7.25e-23!57;UBERON:0007135!7.25e-23!57;UBERON:0000955!7.15e-22!69;UBERON:0006238!7.15e-22!69;UBERON:0000119!2.31e-21!312;UBERON:0000483!6.45e-21!309;UBERON:0000481!7.64e-19!347;UBERON:0002780!1.25e-18!41;UBERON:0001890!1.25e-18!41;UBERON:0006240!1.25e-18!41;UBERON:0003080!1.87e-18!42;UBERON:0000468!5.02e-16!659;UBERON:0000922!6.91e-16!612;UBERON:0002020!7.77e-16!34;UBERON:0003528!7.77e-16!34;UBERON:0001893!2.17e-15!34;UBERON:0000064!2.53e-15!219;UBERON:0002791!6.70e-15!33;UBERON:0001869!1.26e-14!32;UBERON:0002050!1.82e-14!605;UBERON:0005423!1.82e-14!605;UBERON:0000923!2.11e-14!604;UBERON:0005291!2.11e-14!604;UBERON:0006598!2.11e-14!604;UBERON:0002532!2.11e-14!604;UBERON:0000467!1.31e-13!625;UBERON:0000480!1.38e-13!626;UBERON:0000477!1.56e-13!286;UBERON:0004111!1.34e-12!241;UBERON:0002619!3.35e-12!22;UBERON:0000956!1.83e-11!25;UBERON:0000203!1.83e-11!25;UBERON:0001950!3.75e-11!20;UBERON:0000025!1.98e-09!194;UBERON:0000486!2.18e-09!82;UBERON:0000914!2.57e-09!83;UBERON:0002329!2.57e-09!83;UBERON:0003077!2.57e-09!83;UBERON:0003059!2.57e-09!83;UBERON:0007282!2.57e-09!83;UBERON:0009618!2.57e-09!83;UBERON:0007285!2.57e-09!83;UBERON:0004290!6.46e-09!70;UBERON:0001444!1.70e-07!48;UBERON:0001134!2.68e-07!61;UBERON:0002036!2.68e-07!61;UBERON:0003082!2.68e-07!61;UBERON:0000063!4.52e-07!97;UBERON:0001032!4.80e-07!24;UBERON:0004456!4.80e-07!24;UBERON:0005085!5.17e-07!29;UBERON:0002385!5.77e-07!63;UBERON:0001015!5.77e-07!63;UBERON:0000383!5.77e-07!63;UBERON:0003102!7.15e-07!95;UBERON:0000020!7.57e-07!23
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}}
}}

Revision as of 12:22, 5 September 2012


Full id: C2246_carcinoid_Fibroblast_neuroblastoma_salivary_anaplastic_epitheloid_melanoma



Phase1 CAGE Peaks

Hg19::chr12:85285909..85285928,-p3@SLC6A15
Hg19::chr12:85306494..85306558,-p1@SLC6A15
Hg19::chr12:85306562..85306591,-p2@SLC6A15
Hg19::chr12:85306594..85306622,-p4@SLC6A15


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>


Uber Anatomy
Ontology termp-valuen
ectoderm7.89e-37173
presumptive ectoderm7.89e-37173
ectoderm-derived structure2.98e-35169
head1.40e-29123
regional part of nervous system1.66e-2994
nervous system1.66e-2994
anterior region of body3.97e-27129
craniocervical region3.97e-27129
organism subdivision5.77e-26365
neurectoderm2.70e-2590
central nervous system7.27e-2482
neural plate7.38e-2486
presumptive neural plate7.38e-2486
regional part of brain2.11e-2359
pre-chordal neural plate4.31e-2361
neural tube7.25e-2357
neural rod7.25e-2357
future spinal cord7.25e-2357
neural keel7.25e-2357
brain7.15e-2269
future brain7.15e-2269
cell layer2.31e-21312
epithelium6.45e-21309
multi-tissue structure7.64e-19347
regional part of forebrain1.25e-1841
forebrain1.25e-1841
future forebrain1.25e-1841
anterior neural tube1.87e-1842
multi-cellular organism5.02e-16659
embryo6.91e-16612
gray matter7.77e-1634
brain grey matter7.77e-1634
telencephalon2.17e-1534
organ part2.53e-15219
regional part of telencephalon6.70e-1533
cerebral hemisphere1.26e-1432
embryonic structure1.82e-14605
developing anatomical structure1.82e-14605
germ layer2.11e-14604
embryonic tissue2.11e-14604
presumptive structure2.11e-14604
epiblast (generic)2.11e-14604
anatomical system1.31e-13625
anatomical group1.38e-13626
anatomical cluster1.56e-13286
anatomical conduit1.34e-12241
regional part of cerebral cortex3.35e-1222
cerebral cortex1.83e-1125
pallium1.83e-1125
neocortex3.75e-1120
tube1.98e-09194
multilaminar epithelium2.18e-0982
somite2.57e-0983
paraxial mesoderm2.57e-0983
presomitic mesoderm2.57e-0983
presumptive segmental plate2.57e-0983
trunk paraxial mesoderm2.57e-0983
presumptive paraxial mesoderm2.57e-0983
dermomyotome6.46e-0970
subdivision of head1.70e-0748
skeletal muscle tissue2.68e-0761
striated muscle tissue2.68e-0761
myotome2.68e-0761
organ segment4.52e-0797
sensory system4.80e-0724
entire sense organ system4.80e-0724
ectodermal placode5.17e-0729
muscle tissue5.77e-0763
musculature5.77e-0763
musculature of body5.77e-0763
surface structure7.15e-0795
sense organ7.57e-0723


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
ATF3#467316.84738089450660.0003409986823655640.00346334351722038
MAX#414934.839416631755340.01315737137836840.0466048061517861
REST#597837.237521537096020.004104697304192610.0195731203430085
USF1#739134.771124457905970.01370465887188020.0482862447851121
USF2#739239.74414803880220.001718341848410070.0107167027532605



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.