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Coexpression cluster:C1165: Difference between revisions

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|ontology_enrichment_disease=DOID:8692!3.40e-08!31
|ontology_enrichment_disease=DOID:8692!3.40e-08!31
|ontology_enrichment_uberon=UBERON:0007023!1.23e-40!115;UBERON:0001049!9.05e-24!57;UBERON:0005068!9.05e-24!57;UBERON:0006241!9.05e-24!57;UBERON:0007135!9.05e-24!57;UBERON:0003080!5.03e-22!42;UBERON:0002780!7.51e-22!41;UBERON:0001890!7.51e-22!41;UBERON:0006240!7.51e-22!41;UBERON:0001017!1.18e-20!82;UBERON:0002616!2.42e-20!59;UBERON:0005743!5.70e-19!86;UBERON:0001893!1.32e-18!34;UBERON:0002020!3.44e-18!34;UBERON:0003528!3.44e-18!34;UBERON:0001869!5.43e-18!32;UBERON:0002791!5.46e-18!33;UBERON:0000955!1.10e-17!69;UBERON:0006238!1.10e-17!69;UBERON:0000073!5.42e-16!94;UBERON:0001016!5.42e-16!94;UBERON:0002619!9.84e-16!22;UBERON:0000956!6.51e-15!25;UBERON:0000203!6.51e-15!25;UBERON:0001950!1.15e-14!20;UBERON:0003075!1.86e-12!86;UBERON:0007284!1.86e-12!86;UBERON:0002346!9.98e-12!90;UBERON:0002193!2.76e-11!112;UBERON:0003056!2.11e-10!61;UBERON:0002390!2.54e-10!102;UBERON:0003061!2.54e-10!102;UBERON:0000479!3.98e-10!787;UBERON:0001474!7.31e-08!86;UBERON:0002371!1.21e-07!80;UBERON:0000025!7.97e-07!194
|ontology_enrichment_uberon=UBERON:0007023!1.23e-40!115;UBERON:0001049!9.05e-24!57;UBERON:0005068!9.05e-24!57;UBERON:0006241!9.05e-24!57;UBERON:0007135!9.05e-24!57;UBERON:0003080!5.03e-22!42;UBERON:0002780!7.51e-22!41;UBERON:0001890!7.51e-22!41;UBERON:0006240!7.51e-22!41;UBERON:0001017!1.18e-20!82;UBERON:0002616!2.42e-20!59;UBERON:0005743!5.70e-19!86;UBERON:0001893!1.32e-18!34;UBERON:0002020!3.44e-18!34;UBERON:0003528!3.44e-18!34;UBERON:0001869!5.43e-18!32;UBERON:0002791!5.46e-18!33;UBERON:0000955!1.10e-17!69;UBERON:0006238!1.10e-17!69;UBERON:0000073!5.42e-16!94;UBERON:0001016!5.42e-16!94;UBERON:0002619!9.84e-16!22;UBERON:0000956!6.51e-15!25;UBERON:0000203!6.51e-15!25;UBERON:0001950!1.15e-14!20;UBERON:0003075!1.86e-12!86;UBERON:0007284!1.86e-12!86;UBERON:0002346!9.98e-12!90;UBERON:0002193!2.76e-11!112;UBERON:0003056!2.11e-10!61;UBERON:0002390!2.54e-10!102;UBERON:0003061!2.54e-10!102;UBERON:0000479!3.98e-10!787;UBERON:0001474!7.31e-08!86;UBERON:0002371!1.21e-07!80;UBERON:0000025!7.97e-07!194
|tf_chipseq_enrich=ZNF263#10127;4:4.69819522114896:0.0056412295360981:0.0254828880415463
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}}
}}

Revision as of 12:15, 5 September 2012


Full id: C1165_occipital_parietal_duodenum_temporal_brain_medial_frontal



Phase1 CAGE Peaks

Hg19::chr12:122459956..122459988,+p3@BCL7A
Hg19::chr5:88036490..88036495,-p@chr5:88036490..88036495
-
Hg19::chr5:88178983..88179012,-p1@MEF2C
Hg19::chr5:88179017..88179046,-p2@MEF2C
Hg19::chr5:88179195..88179224,-p3@MEF2C
Hg19::chr5:88179518..88179569,-p5@MEF2C
Hg19::chr6:62996066..62996137,-p1@KHDRBS2


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


GO IDGO nameFDR corrected p-value
GO:0001958endochondral ossification0.015700393513282
GO:0001974blood vessel remodeling0.015700393513282
GO:0002062chondrocyte differentiation0.015700393513282
GO:0045449regulation of transcription0.015700393513282
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.015700393513282
GO:0006350transcription0.015700393513282
GO:0010468regulation of gene expression0.015700393513282
GO:0031323regulation of cellular metabolic process0.015700393513282
GO:0019222regulation of metabolic process0.0163963732111183
GO:0001649osteoblast differentiation0.0178697429430301
GO:0051216cartilage development0.0233855421719481
GO:0010467gene expression0.0279180613752491
GO:0050794regulation of cellular process0.0294799521563611
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0295006278096016
GO:0050789regulation of biological process0.0318685023796382
GO:0031214biomineral formation0.034238230533469
GO:0001503ossification0.034238230533469
GO:0065007biological regulation0.034238230533469
GO:0007507heart development0.034238230533469
GO:0046849bone remodeling0.034238230533469
GO:0048771tissue remodeling0.0356553666608488
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.045010292622195
GO:0048514blood vessel morphogenesis0.0455204763418833
GO:0001568blood vessel development0.0470817168598508
GO:0001944vasculature development0.0470817168598508
GO:0007517muscle development0.0470817168598508
GO:0003713transcription coactivator activity0.0492700420420545



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism1.23e-40115
neural tube9.05e-2457
neural rod9.05e-2457
future spinal cord9.05e-2457
neural keel9.05e-2457
anterior neural tube5.03e-2242
regional part of forebrain7.51e-2241
forebrain7.51e-2241
future forebrain7.51e-2241
central nervous system1.18e-2082
regional part of brain2.42e-2059
telencephalon1.32e-1834
gray matter3.44e-1834
brain grey matter3.44e-1834
cerebral hemisphere5.43e-1832
regional part of telencephalon5.46e-1833
brain1.10e-1769
future brain1.10e-1769
regional part of nervous system5.42e-1694
nervous system5.42e-1694
regional part of cerebral cortex9.84e-1622
cerebral cortex6.51e-1525
pallium6.51e-1525
neocortex1.15e-1420
neural plate1.86e-1286
presumptive neural plate1.86e-1286
neurectoderm9.98e-1290
hemolymphoid system2.76e-11112
pre-chordal neural plate2.11e-1061
hematopoietic system2.54e-10102
blood island2.54e-10102
tissue3.98e-10787
bone element7.31e-0886
bone marrow1.21e-0780
tube7.97e-07194
Disease
Ontology termp-valuen
myeloid leukemia3.40e-0831


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
ZNF263#1012744.698195221148960.00564122953609810.0254828880415463



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.