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Coexpression cluster:C4870: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!1.75e-27!86;UBERON:0001017!1.75e-26!82;UBERON:0000033!5.68e-26!123;UBERON:0007023!2.47e-25!115;UBERON:0000153!4.31e-25!129;UBERON:0007811!4.31e-25!129;UBERON:0000955!1.90e-24!69;UBERON:0006238!1.90e-24!69;UBERON:0002616!3.92e-23!59;UBERON:0000073!6.59e-23!94;UBERON:0001016!6.59e-23!94;UBERON:0004121!7.43e-23!169;UBERON:0001049!3.21e-21!57;UBERON:0005068!3.21e-21!57;UBERON:0006241!3.21e-21!57;UBERON:0007135!3.21e-21!57;UBERON:0003075!1.04e-20!86;UBERON:0007284!1.04e-20!86;UBERON:0000924!1.09e-20!173;UBERON:0006601!1.09e-20!173;UBERON:0000481!6.06e-19!347;UBERON:0000477!1.38e-18!286;UBERON:0000475!2.87e-18!365;UBERON:0002346!9.16e-18!90;UBERON:0003080!1.85e-17!42;UBERON:0002780!5.63e-17!41;UBERON:0001890!5.63e-17!41;UBERON:0006240!5.63e-17!41;UBERON:0003056!7.09e-17!61;UBERON:0001893!2.26e-15!34;UBERON:0002020!4.79e-15!34;UBERON:0003528!4.79e-15!34;UBERON:0001869!5.85e-15!32;UBERON:0002791!8.23e-15!33;UBERON:0004111!1.50e-13!241;UBERON:0000062!2.22e-13!511;UBERON:0000956!6.81e-12!25;UBERON:0000203!6.81e-12!25;UBERON:0000119!1.10e-11!312;UBERON:0002619!1.75e-11!22;UBERON:0000468!3.20e-11!659;UBERON:0000025!5.42e-11!194;UBERON:0000483!5.83e-11!309;UBERON:0001950!1.50e-10!20;UBERON:0000064!2.12e-10!219;UBERON:0000467!1.45e-09!625;UBERON:0000480!2.63e-09!626;UBERON:0000922!1.27e-08!612;UBERON:0002365!4.54e-08!31;UBERON:0002330!4.54e-08!31;UBERON:0001048!7.90e-08!168;UBERON:0002050!2.87e-07!605;UBERON:0005423!2.87e-07!605;UBERON:0000923!4.18e-07!604;UBERON:0005291!4.18e-07!604;UBERON:0006598!4.18e-07!604;UBERON:0002532!4.18e-07!604;UBERON:0002530!4.18e-07!59;UBERON:0002107!8.36e-07!19;UBERON:0006925!8.36e-07!19;UBERON:0008836!8.36e-07!19
|ontology_enrichment_uberon=UBERON:0005743!1.75e-27!86;UBERON:0001017!1.75e-26!82;UBERON:0000033!5.68e-26!123;UBERON:0007023!2.47e-25!115;UBERON:0000153!4.31e-25!129;UBERON:0007811!4.31e-25!129;UBERON:0000955!1.90e-24!69;UBERON:0006238!1.90e-24!69;UBERON:0002616!3.92e-23!59;UBERON:0000073!6.59e-23!94;UBERON:0001016!6.59e-23!94;UBERON:0004121!7.43e-23!169;UBERON:0001049!3.21e-21!57;UBERON:0005068!3.21e-21!57;UBERON:0006241!3.21e-21!57;UBERON:0007135!3.21e-21!57;UBERON:0003075!1.04e-20!86;UBERON:0007284!1.04e-20!86;UBERON:0000924!1.09e-20!173;UBERON:0006601!1.09e-20!173;UBERON:0000481!6.06e-19!347;UBERON:0000477!1.38e-18!286;UBERON:0000475!2.87e-18!365;UBERON:0002346!9.16e-18!90;UBERON:0003080!1.85e-17!42;UBERON:0002780!5.63e-17!41;UBERON:0001890!5.63e-17!41;UBERON:0006240!5.63e-17!41;UBERON:0003056!7.09e-17!61;UBERON:0001893!2.26e-15!34;UBERON:0002020!4.79e-15!34;UBERON:0003528!4.79e-15!34;UBERON:0001869!5.85e-15!32;UBERON:0002791!8.23e-15!33;UBERON:0004111!1.50e-13!241;UBERON:0000062!2.22e-13!511;UBERON:0000956!6.81e-12!25;UBERON:0000203!6.81e-12!25;UBERON:0000119!1.10e-11!312;UBERON:0002619!1.75e-11!22;UBERON:0000468!3.20e-11!659;UBERON:0000025!5.42e-11!194;UBERON:0000483!5.83e-11!309;UBERON:0001950!1.50e-10!20;UBERON:0000064!2.12e-10!219;UBERON:0000467!1.45e-09!625;UBERON:0000480!2.63e-09!626;UBERON:0000922!1.27e-08!612;UBERON:0002365!4.54e-08!31;UBERON:0002330!4.54e-08!31;UBERON:0001048!7.90e-08!168;UBERON:0002050!2.87e-07!605;UBERON:0005423!2.87e-07!605;UBERON:0000923!4.18e-07!604;UBERON:0005291!4.18e-07!604;UBERON:0006598!4.18e-07!604;UBERON:0002532!4.18e-07!604;UBERON:0002530!4.18e-07!59;UBERON:0002107!8.36e-07!19;UBERON:0006925!8.36e-07!19;UBERON:0008836!8.36e-07!19
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}}
}}

Revision as of 12:10, 5 September 2012


Full id: C4870_Lens_seminal_gall_Fibroblast_glioblastoma_Smooth_ductus



Phase1 CAGE Peaks

Hg19::chrX:31285018..31285028,-p9@DMD
Hg19::chrX:31285029..31285040,-p8@DMD
Hg19::chrX:31285042..31285103,-p1@DMD


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
central nervous system1.75e-2682
head5.68e-26123
adult organism2.47e-25115
anterior region of body4.31e-25129
craniocervical region4.31e-25129
brain1.90e-2469
future brain1.90e-2469
regional part of brain3.92e-2359
regional part of nervous system6.59e-2394
nervous system6.59e-2394
ectoderm-derived structure7.43e-23169
neural tube3.21e-2157
neural rod3.21e-2157
future spinal cord3.21e-2157
neural keel3.21e-2157
neural plate1.04e-2086
presumptive neural plate1.04e-2086
ectoderm1.09e-20173
presumptive ectoderm1.09e-20173
multi-tissue structure6.06e-19347
anatomical cluster1.38e-18286
organism subdivision2.87e-18365
neurectoderm9.16e-1890
anterior neural tube1.85e-1742
regional part of forebrain5.63e-1741
forebrain5.63e-1741
future forebrain5.63e-1741
pre-chordal neural plate7.09e-1761
telencephalon2.26e-1534
gray matter4.79e-1534
brain grey matter4.79e-1534
cerebral hemisphere5.85e-1532
regional part of telencephalon8.23e-1533
anatomical conduit1.50e-13241
organ2.22e-13511
cerebral cortex6.81e-1225
pallium6.81e-1225
cell layer1.10e-11312
regional part of cerebral cortex1.75e-1122
multi-cellular organism3.20e-11659
tube5.42e-11194
epithelium5.83e-11309
neocortex1.50e-1020
organ part2.12e-10219
anatomical system1.45e-09625
anatomical group2.63e-09626
embryo1.27e-08612
exocrine gland4.54e-0831
exocrine system4.54e-0831
primordium7.90e-08168
embryonic structure2.87e-07605
developing anatomical structure2.87e-07605
germ layer4.18e-07604
embryonic tissue4.18e-07604
presumptive structure4.18e-07604
epiblast (generic)4.18e-07604
gland4.18e-0759
liver8.36e-0719
digestive gland8.36e-0719
liver bud8.36e-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
E2F1#186934.907389214879320.008460985347239390.0328338293271034



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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