Personal tools

Coexpression cluster:C327: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C327_Melanocyte_corpus_thalamus_substantia_melanoma_globus_optic |id=C327 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C327_Melanocyte_corpus_thalamus_substantia_melanoma_globus_optic
|full_id=C327_Melanocyte_corpus_thalamus_substantia_melanoma_globus_optic
|gostat_on_coexpression_clusters=GO:0032501!multicellular organismal process!0.0227175415179066!825;58473;6663;7077$GO:0030814!regulation of cAMP metabolic process!0.029251639102125!7077$GO:0048856!anatomical structure development!0.029251639102125!825;6663;7077$GO:0030799!regulation of cyclic nucleotide metabolic process!0.029251639102125!7077$GO:0006140!regulation of nucleotide metabolic process!0.0333906082972598!7077$GO:0043408!regulation of MAPKKK cascade!0.0333906082972598!7077$GO:0008191!metalloendopeptidase inhibitor activity!0.0333906082972598!7077$GO:0046058!cAMP metabolic process!0.0333906082972598!7077$GO:0045664!regulation of neuron differentiation!0.0333906082972598!7077$GO:0003705!RNA polymerase II transcription factor activity, enhancer binding!0.0333906082972598!6663$GO:0004198!calcium-dependent cysteine-type endopeptidase activity!0.0333906082972598!825$GO:0007602!phototransduction!0.0333906082972598!58473$GO:0032502!developmental process!0.0333906082972598!825;6663;7077$GO:0050962!detection of light stimulus during sensory perception!0.0333906082972598!58473$GO:0050908!detection of light stimulus during visual perception!0.0333906082972598!58473$GO:0009584!detection of visible light!0.0333906082972598!58473$GO:0009583!detection of light stimulus!0.0333906082972598!58473$GO:0007600!sensory perception!0.034757314032091!58473;6663$GO:0005178!integrin binding!0.034757314032091!7077$GO:0048469!cell maturation!0.034757314032091!6663$GO:0009582!detection of abiotic stimulus!0.034757314032091!58473$GO:0050906!detection of stimulus during sensory perception!0.034757314032091!58473$GO:0009187!cyclic nucleotide metabolic process!0.034757314032091!7077$GO:0009581!detection of external stimulus!0.034757314032091!58473$GO:0021700!developmental maturation!0.0353643566264006!6663$GO:0048468!cell development!0.0416643861860936!6663;7077$GO:0050877!neurological system process!0.0418400056854547!58473;6663$GO:0005604!basement membrane!0.0440454197736863!7077$GO:0051606!detection of stimulus!0.0449838416222539!58473$GO:0009416!response to light stimulus!0.0449838416222539!58473
|id=C327
|id=C327
}}
}}

Revision as of 17:38, 18 May 2012


Full id: C327_Melanocyte_corpus_thalamus_substantia_melanoma_globus_optic



Phase1 CAGE Peaks

Hg19::chr10:128358928..128358933,-p15@C10orf90
Hg19::chr10:128358986..128359007,-p2@C10orf90
Hg19::chr10:128359008..128359022,-p4@C10orf90
Hg19::chr10:128359027..128359032,-p13@C10orf90
Hg19::chr10:128359039..128359050,-p5@C10orf90
Hg19::chr10:14066761..14066793,-p@chr10:14066761..14066793
-
Hg19::chr11:73363887..73363920,+p13@PLEKHB1
Hg19::chr12:40704263..40704279,+p@chr12:40704263..40704279
+
Hg19::chr12:53438222..53438234,+p@chr12:53438222..53438234
+
Hg19::chr12:53438236..53438270,+p@chr12:53438236..53438270
+
Hg19::chr15:42696929..42696951,+p5@CAPN3
Hg19::chr15:42696954..42696986,+p1@CAPN3
Hg19::chr15:42696992..42697017,+p3@CAPN3
Hg19::chr15:42697018..42697035,+p6@CAPN3
Hg19::chr15:42697040..42697052,+p4@CAPN3
Hg19::chr16:19777384..19777399,-p@chr16:19777384..19777399
-
Hg19::chr16:48307127..48307152,+p@chr16:48307127..48307152
+
Hg19::chr17:76870126..76870201,-p10@TIMP2
Hg19::chr17:76870222..76870242,-p15@TIMP2
Hg19::chr17:79358943..79358954,-p@chr17:79358943..79358954
-
Hg19::chr17:79358956..79358981,-p@chr17:79358956..79358981
-
Hg19::chr17:79359021..79359029,-p@chr17:79359021..79359029
-
Hg19::chr17:79359048..79359058,-p@chr17:79359048..79359058
-
Hg19::chr17:79359154..79359164,-p@chr17:79359154..79359164
-
Hg19::chr17:79359173..79359188,-p@chr17:79359173..79359188
-
Hg19::chr17:79359195..79359212,-p@chr17:79359195..79359212
-
Hg19::chr19:3544836..3544874,-p@chr19:3544836..3544874
-
Hg19::chr22:38368890..38368901,-p@chr22:38368890..38368901
-
Hg19::chr22:38369134..38369144,-p@chr22:38369134..38369144
-
Hg19::chr22:38369664..38369689,+p2@CU678225
Hg19::chr22:38369881..38369891,-p@chr22:38369881..38369891
-
Hg19::chr22:38370098..38370111,-p@chr22:38370098..38370111
-
Hg19::chr22:38370123..38370134,-p@chr22:38370123..38370134
-
Hg19::chr22:38374029..38374049,+p@chr22:38374029..38374049
+
Hg19::chr22:38380543..38380569,-p1@SOX10


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:0032501multicellular organismal process0.0227175415179066
GO:0030814regulation of cAMP metabolic process0.029251639102125
GO:0048856anatomical structure development0.029251639102125
GO:0030799regulation of cyclic nucleotide metabolic process0.029251639102125
GO:0006140regulation of nucleotide metabolic process0.0333906082972598
GO:0043408regulation of MAPKKK cascade0.0333906082972598
GO:0008191metalloendopeptidase inhibitor activity0.0333906082972598
GO:0046058cAMP metabolic process0.0333906082972598
GO:0045664regulation of neuron differentiation0.0333906082972598
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0333906082972598
GO:0004198calcium-dependent cysteine-type endopeptidase activity0.0333906082972598
GO:0007602phototransduction0.0333906082972598
GO:0032502developmental process0.0333906082972598
GO:0050962detection of light stimulus during sensory perception0.0333906082972598
GO:0050908detection of light stimulus during visual perception0.0333906082972598
GO:0009584detection of visible light0.0333906082972598
GO:0009583detection of light stimulus0.0333906082972598
GO:0007600sensory perception0.034757314032091
GO:0005178integrin binding0.034757314032091
GO:0048469cell maturation0.034757314032091
GO:0009582detection of abiotic stimulus0.034757314032091
GO:0050906detection of stimulus during sensory perception0.034757314032091
GO:0009187cyclic nucleotide metabolic process0.034757314032091
GO:0009581detection of external stimulus0.034757314032091
GO:0021700developmental maturation0.0353643566264006
GO:0048468cell development0.0416643861860936
GO:0050877neurological system process0.0418400056854547
GO:0005604basement membrane0.0440454197736863
GO:0051606detection of stimulus0.0449838416222539
GO:0009416response to light stimulus0.0449838416222539



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C327&oldid=1702981"