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Coexpression cluster:C495: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0004687!myosin light chain kinase activity!0.0435818046170126!4638$GO:0005010!insulin-like growth factor receptor activity!0.0435818046170126!3480$GO:0043548!phosphoinositide 3-kinase binding!0.0435818046170126!3480$GO:0043560!insulin receptor substrate binding!0.0435818046170126!3480$GO:0030238!male sex determination!0.0435818046170126!3480$GO:0042346!positive regulation of NF-kappaB import into nucleus!0.0435818046170126!387$GO:0048009!insulin-like growth factor receptor signaling pathway!0.0435818046170126!3480$GO:0042993!positive regulation of transcription factor import into nucleus!0.0435818046170126!387$GO:0042307!positive regulation of protein import into nucleus!0.0435818046170126!387$GO:0046824!positive regulation of nucleocytoplasmic transport!0.0435818046170126!387$GO:0051222!positive regulation of protein transport!0.0435818046170126!387$GO:0042802!identical protein binding!0.0435818046170126!3480;7164$GO:0042345!regulation of NF-kappaB import into nucleus!0.0435818046170126!387$GO:0042348!NF-kappaB import into nucleus!0.0435818046170126!387$GO:0000287!magnesium ion binding!0.0465671813510537!387;4638$GO:0000086!G2/M transition of mitotic cell cycle!0.0465671813510537!7164$GO:0051262!protein tetramerization!0.0465671813510537!3480$GO:0007530!sex determination!0.0465671813510537!3480$GO:0042990!regulation of transcription factor import into nucleus!0.0465671813510537!387$GO:0042991!transcription factor import into nucleus!0.0465671813510537!387$GO:0043450!alkene biosynthetic process!0.0465671813510537!84909$GO:0019370!leukotriene biosynthetic process!0.0465671813510537!84909$GO:0042306!regulation of protein import into nucleus!0.0465671813510537!387$GO:0033157!regulation of intracellular protein transport!0.0465671813510537!387
|gostat_on_coexpression_clusters=GO:0004687!myosin light chain kinase activity!0.0435818046170126!4638$GO:0005010!insulin-like growth factor receptor activity!0.0435818046170126!3480$GO:0043548!phosphoinositide 3-kinase binding!0.0435818046170126!3480$GO:0043560!insulin receptor substrate binding!0.0435818046170126!3480$GO:0030238!male sex determination!0.0435818046170126!3480$GO:0042346!positive regulation of NF-kappaB import into nucleus!0.0435818046170126!387$GO:0048009!insulin-like growth factor receptor signaling pathway!0.0435818046170126!3480$GO:0042993!positive regulation of transcription factor import into nucleus!0.0435818046170126!387$GO:0042307!positive regulation of protein import into nucleus!0.0435818046170126!387$GO:0046824!positive regulation of nucleocytoplasmic transport!0.0435818046170126!387$GO:0051222!positive regulation of protein transport!0.0435818046170126!387$GO:0042802!identical protein binding!0.0435818046170126!3480;7164$GO:0042345!regulation of NF-kappaB import into nucleus!0.0435818046170126!387$GO:0042348!NF-kappaB import into nucleus!0.0435818046170126!387$GO:0000287!magnesium ion binding!0.0465671813510537!387;4638$GO:0000086!G2/M transition of mitotic cell cycle!0.0465671813510537!7164$GO:0051262!protein tetramerization!0.0465671813510537!3480$GO:0007530!sex determination!0.0465671813510537!3480$GO:0042990!regulation of transcription factor import into nucleus!0.0465671813510537!387$GO:0042991!transcription factor import into nucleus!0.0465671813510537!387$GO:0043450!alkene biosynthetic process!0.0465671813510537!84909$GO:0019370!leukotriene biosynthetic process!0.0465671813510537!84909$GO:0042306!regulation of protein import into nucleus!0.0465671813510537!387$GO:0033157!regulation of intracellular protein transport!0.0465671813510537!387
|id=C495
|id=C495
|ontology_enrichment_celltype=CL:0000055!1.46e-15!180;CL:0000222!8.73e-11!119;CL:0000057!5.80e-09!75;CL:0000359!1.31e-08!32;CL:0000192!5.22e-08!42;CL:0000514!5.22e-08!42;CL:0000077!5.37e-08!19;CL:0000680!4.21e-07!57;CL:0000056!4.21e-07!57;CL:0000355!4.21e-07!57;CL:0000393!9.00e-07!60;CL:0000211!9.00e-07!60
|ontology_enrichment_celltype=CL:0000077!5.37e-22!19;CL:0000213!4.33e-08!58;CL:0000215!4.33e-08!58;CL:0000076!1.52e-07!63
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!1.40e-11!84;UBERON:0000468!2.44e-10!659;UBERON:0001981!2.75e-10!60;UBERON:0007500!2.75e-10!60;UBERON:0004537!2.75e-10!60;UBERON:0006965!2.75e-10!60;UBERON:0002049!5.09e-10!79;UBERON:0007798!5.09e-10!79;UBERON:0001637!6.23e-10!42;UBERON:0003509!6.23e-10!42;UBERON:0004572!6.23e-10!42;UBERON:0000055!1.23e-08!69;UBERON:0004573!4.97e-08!33;UBERON:0004571!4.97e-08!33;UBERON:0001134!8.52e-08!61;UBERON:0002036!8.52e-08!61;UBERON:0003082!8.52e-08!61;UBERON:0000467!9.62e-08!625;UBERON:0002385!1.04e-07!63;UBERON:0001015!1.04e-07!63;UBERON:0000383!1.04e-07!63;UBERON:0000480!1.10e-07!626;UBERON:0003081!1.32e-07!216;UBERON:0001009!2.01e-07!113;UBERON:0004535!6.03e-07!110;UBERON:0003914!7.86e-07!118
|ontology_enrichment_uberon=
|pathway_enrichment=0.000339245429383648;0.0429484713599698;2;116;Vascular smooth muscle contraction (KEGG):04270!1.16148822114083e-05;0.00245074014660715;3;200;Focal adhesion (KEGG):04510!0.000134337357082296;0.0212588867582733;2;73;Adherens junction (KEGG):04520!9.48585957389088e-07;0.000600454911027293;3;87;MicroRNAs in cardiomyocyte hypertrophy (Wikipathways):WP1544!9.65003594215768e-06;0.00245074014660715;3;188;Focal Adhesion (Wikipathways):WP306
|pathway_enrichment=0.000339245429383648;0.0429484713599698;2;116;Vascular smooth muscle contraction (KEGG):04270!1.16148822114083e-05;0.00245074014660715;3;200;Focal adhesion (KEGG):04510!0.000134337357082296;0.0212588867582733;2;73;Adherens junction (KEGG):04520!9.48585957389088e-07;0.000600454911027293;3;87;MicroRNAs in cardiomyocyte hypertrophy (Wikipathways):WP1544!9.65003594215768e-06;0.00245074014660715;3;188;Focal Adhesion (Wikipathways):WP306
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}}
}}

Revision as of 16:20, 19 October 2012


Full id: C495_mesothelioma_Preadipocyte_Smooth_Multipotent_Placental_Sertoli_Adipocyte



Phase1 CAGE Peaks

Hg19::chr11:29181712..29181720,+p@chr11:29181712..29181720
+
Hg19::chr11:7506866..7506875,+p8@OLFML1
Hg19::chr12:116440921..116440925,-p@chr12:116440921..116440925
-
Hg19::chr14:72053507..72053516,+p@chr14:72053507..72053516
+
Hg19::chr15:37242699..37242705,-p@chr15:37242699..37242705
-
Hg19::chr15:99191698..99191705,+p13@IGF1R
Hg19::chr17:39724493..39724502,-p@chr17:39724493..39724502
-
Hg19::chr19:39627507..39627526,+p@chr19:39627507..39627526
+
Hg19::chr1:64506368..64506373,-p@chr1:64506368..64506373
-
Hg19::chr3:123512832..123512846,-p46@MYLK
Hg19::chr3:49449521..49449532,-p2@RHOA
Hg19::chr5:167087144..167087148,-p1@ENST00000522956
Hg19::chr5:167088934..167088938,-p@chr5:167088934..167088938
-
Hg19::chr5:174774305..174774318,+p@chr5:174774305..174774318
+
Hg19::chr5:174905496..174905507,+p3@SFXN1
Hg19::chr6:125550179..125550191,+p20@TPD52L1
Hg19::chr8:117695642..117695657,-p@chr8:117695642..117695657
-
Hg19::chr8:74498117..74498133,-p@chr8:74498117..74498133
-
Hg19::chr9:97562440..97562463,+p18@C9orf3


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


p.valueFDRnGenesnPathwayName
0.0003392454293836480.04294847135996982116Vascular smooth muscle contraction (KEGG):04270
1.16148822114083e-050.002450740146607153200Focal adhesion (KEGG):04510
0.0001343373570822960.0212588867582733273Adherens junction (KEGG):04520
9.48585957389088e-070.000600454911027293387MicroRNAs in cardiomyocyte hypertrophy (Wikipathways):WP1544
9.65003594215768e-060.002450740146607153188Focal Adhesion (Wikipathways):WP306



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:0004687myosin light chain kinase activity0.0435818046170126
GO:0005010insulin-like growth factor receptor activity0.0435818046170126
GO:0043548phosphoinositide 3-kinase binding0.0435818046170126
GO:0043560insulin receptor substrate binding0.0435818046170126
GO:0030238male sex determination0.0435818046170126
GO:0042346positive regulation of NF-kappaB import into nucleus0.0435818046170126
GO:0048009insulin-like growth factor receptor signaling pathway0.0435818046170126
GO:0042993positive regulation of transcription factor import into nucleus0.0435818046170126
GO:0042307positive regulation of protein import into nucleus0.0435818046170126
GO:0046824positive regulation of nucleocytoplasmic transport0.0435818046170126
GO:0051222positive regulation of protein transport0.0435818046170126
GO:0042802identical protein binding0.0435818046170126
GO:0042345regulation of NF-kappaB import into nucleus0.0435818046170126
GO:0042348NF-kappaB import into nucleus0.0435818046170126
GO:0000287magnesium ion binding0.0465671813510537
GO:0000086G2/M transition of mitotic cell cycle0.0465671813510537
GO:0051262protein tetramerization0.0465671813510537
GO:0007530sex determination0.0465671813510537
GO:0042990regulation of transcription factor import into nucleus0.0465671813510537
GO:0042991transcription factor import into nucleus0.0465671813510537
GO:0043450alkene biosynthetic process0.0465671813510537
GO:0019370leukotriene biosynthetic process0.0465671813510537
GO:0042306regulation of protein import into nucleus0.0465671813510537
GO:0033157regulation of intracellular protein transport0.0465671813510537



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><br><br>


Cell Type
Ontology termp-valuen
mesothelial cell5.37e-2219
lining cell4.33e-0858
barrier cell4.33e-0858
squamous epithelial cell1.52e-0763


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.