Personal tools

Coexpression cluster:C1393

From FANTOM5_SSTAR

Revision as of 17:34, 18 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1393_thyroid_lung_throat_Alveolar_small_nonsmall_papillary



Phase1 CAGE Peaks

Hg19::chr14:36983118..36983142,-p3@SFTA3
Hg19::chr14:36986015..36986024,-p@chr14:36986015..36986024
-
Hg19::chr14:36988729..36988748,-p2@ENST00000521945
Hg19::chr14:36988882..36988895,-p13@NKX2-1
Hg19::chr14:36989573..36989577,-p18@NKX2-1
Hg19::chr9:138336075..138336099,-p@chr9:138336075..138336099
-


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:0021798forebrain dorsal/ventral pattern formation0.00523960908983869
GO:0021871forebrain regionalization0.00523960908983869
GO:0030878thyroid gland development0.00589456022606853
GO:0007492endoderm development0.00589456022606853
GO:0009953dorsal/ventral pattern formation0.0109555462787536
GO:0035270endocrine system development0.0109555462787536
GO:0001764neuron migration0.0109555462787536
GO:0030324lung development0.0109555462787536
GO:0030323respiratory tube development0.0109555462787536
GO:0030900forebrain development0.0109555462787536
GO:0048732gland development0.0109555462787536
GO:0003002regionalization0.0189935829506652
GO:0035295tube development0.0227595519839868
GO:0007389pattern specification process0.0227595519839868
GO:0007420brain development0.0227595519839868
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0227595519839868
GO:0005667transcription factor complex0.030190128565261
GO:0045893positive regulation of transcription, DNA-dependent0.030190128565261
GO:0016477cell migration0.030190128565261
GO:0007417central nervous system development0.030190128565261
GO:0048699generation of neurons0.030190128565261
GO:0022008neurogenesis0.0311353693992338
GO:0045941positive regulation of transcription0.0311353693992338
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0311353693992338
GO:0009888tissue development0.0311353693992338
GO:0016563transcription activator activity0.0311353693992338
GO:0009887organ morphogenesis0.0330433411955956
GO:0031325positive regulation of cellular metabolic process0.0330433411955956
GO:0051674localization of cell0.0330433411955956
GO:0006928cell motility0.0330433411955956
GO:0009893positive regulation of metabolic process0.0330433411955956
GO:0006357regulation of transcription from RNA polymerase II promoter0.0346305413281526
GO:0044451nucleoplasm part0.0358833834637438
GO:0005654nucleoplasm0.0399905458474453
GO:0006366transcription from RNA polymerase II promoter0.0479049973928109



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>


Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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.