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Coexpression cluster:C4870: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|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:0007023!1.45e-35!114;UBERON:0001017!3.00e-31!81;UBERON:0000955!1.04e-30!68;UBERON:0006238!1.04e-30!68;UBERON:0001049!4.37e-27!56;UBERON:0005068!4.37e-27!56;UBERON:0006241!4.37e-27!56;UBERON:0007135!4.37e-27!56;UBERON:0001016!6.39e-26!89;UBERON:0000073!1.93e-25!53;UBERON:0002616!1.93e-25!53;UBERON:0003075!1.26e-23!82;UBERON:0007284!1.26e-23!82;UBERON:0011216!3.64e-23!223;UBERON:0002780!4.76e-22!41;UBERON:0001890!4.76e-22!41;UBERON:0003080!4.76e-22!41;UBERON:0006240!4.76e-22!41;UBERON:0002346!2.89e-21!86;UBERON:0001893!1.35e-20!34;UBERON:0003528!2.81e-20!34;UBERON:0002020!2.81e-20!34;UBERON:0001869!8.32e-20!32;UBERON:0002791!2.24e-19!32;UBERON:0004121!3.74e-19!171;UBERON:0000924!3.74e-19!171;UBERON:0006601!3.74e-19!171;UBERON:0010314!1.23e-18!132;UBERON:0000477!1.32e-18!373;UBERON:0003056!3.07e-18!61;UBERON:0010371!6.79e-17!104;UBERON:0000481!2.33e-16!342;UBERON:0002619!9.65e-16!22;UBERON:0000956!2.92e-15!25;UBERON:0000203!2.92e-15!25;UBERON:0001950!2.63e-14!20;UBERON:0004111!5.82e-10!240;UBERON:0000062!1.26e-09!503;UBERON:0000025!7.11e-09!192;UBERON:0000064!1.83e-08!218;UBERON:0000468!2.00e-07!656;UBERON:0000119!4.58e-07!309;UBERON:0002420!6.97e-07!9;UBERON:0007245!6.97e-07!9;UBERON:0010009!6.97e-07!9;UBERON:0010011!6.97e-07!9;UBERON:0000454!6.97e-07!9;UBERON:0000922!9.22e-07!592
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0328338293271034
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0328338293271034
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}}
}}

Revision as of 16:19, 19 October 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
adult organism1.45e-35114
central nervous system3.00e-3181
brain1.04e-3068
future brain1.04e-3068
neural tube4.37e-2756
neural rod4.37e-2756
future spinal cord4.37e-2756
neural keel4.37e-2756
nervous system6.39e-2689
regional part of nervous system1.93e-2553
regional part of brain1.93e-2553
neural plate1.26e-2382
presumptive neural plate1.26e-2382
organ system subdivision3.64e-23223
regional part of forebrain4.76e-2241
forebrain4.76e-2241
anterior neural tube4.76e-2241
future forebrain4.76e-2241
neurectoderm2.89e-2186
telencephalon1.35e-2034
brain grey matter2.81e-2034
gray matter2.81e-2034
cerebral hemisphere8.32e-2032
regional part of telencephalon2.24e-1932
ectoderm-derived structure3.74e-19171
ectoderm3.74e-19171
presumptive ectoderm3.74e-19171
structure with developmental contribution from neural crest1.23e-18132
anatomical cluster1.32e-18373
pre-chordal neural plate3.07e-1861
ecto-epithelium6.79e-17104
multi-tissue structure2.33e-16342
regional part of cerebral cortex9.65e-1622
cerebral cortex2.92e-1525
pallium2.92e-1525
neocortex2.63e-1420
anatomical conduit5.82e-10240
organ1.26e-09503
tube7.11e-09192
organ part1.83e-08218
multi-cellular organism2.00e-07656
cell layer4.58e-07309
basal ganglion6.97e-079
nuclear complex of neuraxis6.97e-079
aggregate regional part of brain6.97e-079
collection of basal ganglia6.97e-079
cerebral subcortex6.97e-079
embryo9.22e-07592


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.