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|full_id=C3999_anaplastic_Fibroblast_putamen_caudate_eye_frontal_testis
|full_id=C3999_anaplastic_Fibroblast_putamen_caudate_eye_frontal_testis
|id=C3999
|id=C3999
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:14566!4.98e-12!239;DOID:162!8.23e-11!235;DOID:0050687!1.47e-08!143;DOID:305!3.68e-08!106
|ontology_enrichment_uberon=UBERON:0002780!2.74e-19!41;UBERON:0001890!2.74e-19!41;UBERON:0006240!2.74e-19!41;UBERON:0001869!8.47e-19!32;UBERON:0003080!4.52e-18!42;UBERON:0001017!9.28e-18!82;UBERON:0001893!2.68e-17!34;UBERON:0005743!2.85e-17!86;UBERON:0000073!5.63e-17!94;UBERON:0001016!5.63e-17!94;UBERON:0002791!1.12e-16!33;UBERON:0000955!1.95e-16!69;UBERON:0006238!1.95e-16!69;UBERON:0002020!1.39e-15!34;UBERON:0003528!1.39e-15!34;UBERON:0000956!3.50e-15!25;UBERON:0000203!3.50e-15!25;UBERON:0002619!1.36e-13!22;UBERON:0001049!2.54e-13!57;UBERON:0005068!2.54e-13!57;UBERON:0006241!2.54e-13!57;UBERON:0007135!2.54e-13!57;UBERON:0002616!2.65e-13!59;UBERON:0001950!1.06e-12!20;UBERON:0003056!1.48e-12!61;UBERON:0000153!3.73e-12!129;UBERON:0007811!3.73e-12!129;UBERON:0000033!4.36e-12!123;UBERON:0004121!5.37e-11!169;UBERON:0003075!8.74e-11!86;UBERON:0007284!8.74e-11!86;UBERON:0000924!1.47e-10!173;UBERON:0006601!1.47e-10!173;UBERON:0002346!4.51e-10!90
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Revision as of 14:43, 21 May 2012


Full id: C3999_anaplastic_Fibroblast_putamen_caudate_eye_frontal_testis



Phase1 CAGE Peaks

Hg19::chr1:85155895..85155909,-p5@SSX2IP
Hg19::chr1:85155912..85155935,-p3@SSX2IP
Hg19::chr1:85155939..85155984,-p2@SSX2IP


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
regional part of forebrain2.74e-1941
forebrain2.74e-1941
future forebrain2.74e-1941
cerebral hemisphere8.47e-1932
anterior neural tube4.52e-1842
central nervous system9.28e-1882
telencephalon2.68e-1734
regional part of nervous system5.63e-1794
nervous system5.63e-1794
regional part of telencephalon1.12e-1633
brain1.95e-1669
future brain1.95e-1669
gray matter1.39e-1534
brain grey matter1.39e-1534
cerebral cortex3.50e-1525
pallium3.50e-1525
regional part of cerebral cortex1.36e-1322
neural tube2.54e-1357
neural rod2.54e-1357
future spinal cord2.54e-1357
neural keel2.54e-1357
regional part of brain2.65e-1359
neocortex1.06e-1220
pre-chordal neural plate1.48e-1261
anterior region of body3.73e-12129
craniocervical region3.73e-12129
head4.36e-12123
ectoderm-derived structure5.37e-11169
neural plate8.74e-1186
presumptive neural plate8.74e-1186
ectoderm1.47e-10173
presumptive ectoderm1.47e-10173
neurectoderm4.51e-1090
Disease
Ontology termp-valuen
disease of cellular proliferation4.98e-12239
cancer8.23e-11235
cell type cancer1.47e-08143
carcinoma3.68e-08106


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


No analysis results for this cluster

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.