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Coexpression cluster:C2966: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.84e-61!115;UBERON:0001049!1.30e-31!57;UBERON:0005068!1.30e-31!57;UBERON:0006241!1.30e-31!57;UBERON:0007135!1.30e-31!57;UBERON:0002616!2.83e-26!59;UBERON:0003075!1.03e-22!86;UBERON:0007284!1.03e-22!86;UBERON:0000955!4.38e-22!69;UBERON:0006238!4.38e-22!69;UBERON:0002346!3.26e-21!90;UBERON:0001017!4.04e-21!82;UBERON:0003080!4.86e-21!42;UBERON:0005743!5.53e-21!86;UBERON:0002780!1.05e-19!41;UBERON:0001890!1.05e-19!41;UBERON:0006240!1.05e-19!41;UBERON:0002020!1.16e-18!34;UBERON:0003528!1.16e-18!34;UBERON:0001893!2.97e-18!34;UBERON:0000073!5.09e-18!94;UBERON:0001016!5.09e-18!94;UBERON:0002791!4.79e-17!33;UBERON:0002298!4.69e-16!8;UBERON:0001869!1.38e-15!32;UBERON:0003056!7.92e-15!61;UBERON:0000033!3.71e-14!123;UBERON:0002308!1.03e-13!9;UBERON:0000125!1.03e-13!9;UBERON:0000153!5.24e-13!129;UBERON:0007811!5.24e-13!129;UBERON:0001950!6.79e-12!20;UBERON:0003076!6.95e-12!15;UBERON:0003057!6.95e-12!15;UBERON:0004121!1.81e-11!169;UBERON:0000924!6.13e-11!173;UBERON:0006601!6.13e-11!173;UBERON:0002619!1.38e-10!22;UBERON:0004733!5.63e-10!12;UBERON:0002028!5.63e-10!12;UBERON:0007277!5.63e-10!12;UBERON:0009663!5.72e-10!7;UBERON:0004732!4.44e-09!13;UBERON:0000956!5.19e-09!25;UBERON:0000203!5.19e-09!25;UBERON:0004111!7.39e-09!241;UBERON:0002420!1.48e-07!9;UBERON:0007245!1.48e-07!9;UBERON:0010009!1.48e-07!9;UBERON:0010011!1.48e-07!9;UBERON:0000454!1.48e-07!9;UBERON:0000988!1.91e-07!3;UBERON:0006331!2.55e-07!3;UBERON:0000025!3.05e-07!194;UBERON:0000200!3.64e-07!6;UBERON:0000064!4.26e-07!219;UBERON:0001896!8.70e-07!3;UBERON:0005290!8.70e-07!3;UBERON:0010096!8.70e-07!3
|ontology_enrichment_uberon=UBERON:0007023!5.84e-61!115;UBERON:0001049!1.30e-31!57;UBERON:0005068!1.30e-31!57;UBERON:0006241!1.30e-31!57;UBERON:0007135!1.30e-31!57;UBERON:0002616!2.83e-26!59;UBERON:0003075!1.03e-22!86;UBERON:0007284!1.03e-22!86;UBERON:0000955!4.38e-22!69;UBERON:0006238!4.38e-22!69;UBERON:0002346!3.26e-21!90;UBERON:0001017!4.04e-21!82;UBERON:0003080!4.86e-21!42;UBERON:0005743!5.53e-21!86;UBERON:0002780!1.05e-19!41;UBERON:0001890!1.05e-19!41;UBERON:0006240!1.05e-19!41;UBERON:0002020!1.16e-18!34;UBERON:0003528!1.16e-18!34;UBERON:0001893!2.97e-18!34;UBERON:0000073!5.09e-18!94;UBERON:0001016!5.09e-18!94;UBERON:0002791!4.79e-17!33;UBERON:0002298!4.69e-16!8;UBERON:0001869!1.38e-15!32;UBERON:0003056!7.92e-15!61;UBERON:0000033!3.71e-14!123;UBERON:0002308!1.03e-13!9;UBERON:0000125!1.03e-13!9;UBERON:0000153!5.24e-13!129;UBERON:0007811!5.24e-13!129;UBERON:0001950!6.79e-12!20;UBERON:0003076!6.95e-12!15;UBERON:0003057!6.95e-12!15;UBERON:0004121!1.81e-11!169;UBERON:0000924!6.13e-11!173;UBERON:0006601!6.13e-11!173;UBERON:0002619!1.38e-10!22;UBERON:0004733!5.63e-10!12;UBERON:0002028!5.63e-10!12;UBERON:0007277!5.63e-10!12;UBERON:0009663!5.72e-10!7;UBERON:0004732!4.44e-09!13;UBERON:0000956!5.19e-09!25;UBERON:0000203!5.19e-09!25;UBERON:0004111!7.39e-09!241;UBERON:0002420!1.48e-07!9;UBERON:0007245!1.48e-07!9;UBERON:0010009!1.48e-07!9;UBERON:0010011!1.48e-07!9;UBERON:0000454!1.48e-07!9;UBERON:0000988!1.91e-07!3;UBERON:0006331!2.55e-07!3;UBERON:0000025!3.05e-07!194;UBERON:0000200!3.64e-07!6;UBERON:0000064!4.26e-07!219;UBERON:0001896!8.70e-07!3;UBERON:0005290!8.70e-07!3;UBERON:0010096!8.70e-07!3
|tf_chipseq_enrich=SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245245930823498
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}}
}}

Revision as of 13:38, 5 September 2012


Full id: C2966_cervix_acute_smooth_penis_rectum_uterus_lung



Phase1 CAGE Peaks

Hg19::chr10:100995586..100995597,-p4@HPSE2
Hg19::chr10:100995603..100995614,-p2@HPSE2
Hg19::chr10:100995626..100995635,-p5@HPSE2


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
adult organism5.84e-61115
neural tube1.30e-3157
neural rod1.30e-3157
future spinal cord1.30e-3157
neural keel1.30e-3157
regional part of brain2.83e-2659
neural plate1.03e-2286
presumptive neural plate1.03e-2286
brain4.38e-2269
future brain4.38e-2269
neurectoderm3.26e-2190
central nervous system4.04e-2182
anterior neural tube4.86e-2142
regional part of forebrain1.05e-1941
forebrain1.05e-1941
future forebrain1.05e-1941
gray matter1.16e-1834
brain grey matter1.16e-1834
telencephalon2.97e-1834
regional part of nervous system5.09e-1894
nervous system5.09e-1894
regional part of telencephalon4.79e-1733
brainstem4.69e-168
cerebral hemisphere1.38e-1532
pre-chordal neural plate7.92e-1561
head3.71e-14123
nucleus of brain1.03e-139
neural nucleus1.03e-139
anterior region of body5.24e-13129
craniocervical region5.24e-13129
neocortex6.79e-1220
posterior neural tube6.95e-1215
chordal neural plate6.95e-1215
ectoderm-derived structure1.81e-11169
ectoderm6.13e-11173
presumptive ectoderm6.13e-11173
regional part of cerebral cortex1.38e-1022
segmental subdivision of hindbrain5.63e-1012
hindbrain5.63e-1012
presumptive hindbrain5.63e-1012
telencephalic nucleus5.72e-107
segmental subdivision of nervous system4.44e-0913
cerebral cortex5.19e-0925
pallium5.19e-0925
anatomical conduit7.39e-09241
basal ganglion1.48e-079
nuclear complex of neuraxis1.48e-079
aggregate regional part of brain1.48e-079
collection of basal ganglia1.48e-079
cerebral subcortex1.48e-079
pons1.91e-073
brainstem nucleus2.55e-073
tube3.05e-07194
gyrus3.64e-076
organ part4.26e-07219
medulla oblongata8.70e-073
myelencephalon8.70e-073
future myelencephalon8.70e-073


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)

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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
SP1#666735.69838137814090.005403962701712170.0245245930823498



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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