Personal tools

Coexpression cluster:C459: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C459_diffuse_acute_testicular_iPS_CD14_Renal_chronic |id=C459 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C459_diffuse_acute_testicular_iPS_CD14_Renal_chronic
|full_id=C459_diffuse_acute_testicular_iPS_CD14_Renal_chronic
|gostat_on_coexpression_clusters=GO:0030530!heterogeneous nuclear ribonucleoprotein complex!1.45832616951182e-05!3181;3192$GO:0005681!spliceosome!0.000457085172934245!3181;3192$GO:0008380!RNA splicing!0.000800649661692765!3181;3192$GO:0006397!mRNA processing!0.000884717876170506!3181;3192$GO:0016071!mRNA metabolic process!0.00111158767673731!3181;3192$GO:0043047!single-stranded telomeric DNA binding!0.00187294831574558!3181$GO:0006396!RNA processing!0.00187294831574558!3181;3192$GO:0003723!RNA binding!0.00539548910907402!3181;3192$GO:0042162!telomeric DNA binding!0.00539548910907402!3181$GO:0044428!nuclear part!0.00560587338291255!3181;3192$GO:0030529!ribonucleoprotein complex!0.00560587338291255!3181;3192$GO:0003697!single-stranded DNA binding!0.0150951373577981!3181$GO:0000375!RNA splicing, via transesterification reactions!0.0150951373577981!3181$GO:0000398!nuclear mRNA splicing, via spliceosome!0.0150951373577981!3181$GO:0000377!RNA splicing, via transesterification reactions with bulged adenosine as nucleophile!0.0150951373577981!3181$GO:0050658!RNA transport!0.0156575469235196!3181$GO:0051236!establishment of RNA localization!0.0156575469235196!3181$GO:0050657!nucleic acid transport!0.0156575469235196!3181$GO:0006403!RNA localization!0.0156575469235196!3181$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.0168118700284401!3181$GO:0009986!cell surface!0.0227705399221662!3192$GO:0043566!structure-specific DNA binding!0.0233472040861499!3181$GO:0003677!DNA binding!0.0254627520372707!3181;3192$GO:0032991!macromolecular complex!0.0299326331208392!3181;3192$GO:0044446!intracellular organelle part!0.0304654080166691!3181;3192$GO:0044422!organelle part!0.0304654080166691!3181;3192$GO:0016070!RNA metabolic process!0.0304654080166691!3181;3192$GO:0000166!nucleotide binding!0.0309391045519627!3181;3192$GO:0010467!gene expression!0.0488748993612867!3181;3192
|id=C459
|id=C459
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C459_diffuse_acute_testicular_iPS_CD14_Renal_chronic



Phase1 CAGE Peaks

Hg19::chr10:112360803..112360817,+p@chr10:112360803..112360817
+
Hg19::chr10:70098368..70098404,+p3@HNRNPH3
Hg19::chr1:245019788..245019803,-p@chr1:245019788..245019803
-
Hg19::chr1:245022599..245022657,-p7@HNRNPU
Hg19::chr1:44588180..44588202,-p1@ENST00000402743
Hg19::chr6:114267231..114267258,-p@chr6:114267231..114267258
-
Hg19::chr7:26233209..26233239,-p@chr7:26233209..26233239
-
Hg19::chr7:26233242..26233284,-p@chr7:26233242..26233284
-
Hg19::chr7:26233292..26233320,-p@chr7:26233292..26233320
-
Hg19::chr7:26235486..26235540,-p@chr7:26235486..26235540
-
Hg19::chr7:26236054..26236075,-p@chr7:26236054..26236075
-
Hg19::chr7:26236076..26236108,-p@chr7:26236076..26236108
-
Hg19::chr7:26236464..26236483,-p3@HNRNPA2B1
Hg19::chr7:26236559..26236570,-p9@HNRNPA2B1
Hg19::chr7:26236592..26236600,-p11@HNRNPA2B1
Hg19::chr7:26236610..26236626,-p5@HNRNPA2B1
Hg19::chr7:26236630..26236642,-p8@HNRNPA2B1
Hg19::chr7:26236955..26236980,-p6@HNRNPA2B1
Hg19::chr7:26236987..26237030,-p4@HNRNPA2B1
Hg19::chr7:26237039..26237051,-p@chr7:26237039..26237051
-
Hg19::chr7:26237272..26237323,-p@chr7:26237272..26237323
-


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:0030530heterogeneous nuclear ribonucleoprotein complex1.45832616951182e-05
GO:0005681spliceosome0.000457085172934245
GO:0008380RNA splicing0.000800649661692765
GO:0006397mRNA processing0.000884717876170506
GO:0016071mRNA metabolic process0.00111158767673731
GO:0043047single-stranded telomeric DNA binding0.00187294831574558
GO:0006396RNA processing0.00187294831574558
GO:0003723RNA binding0.00539548910907402
GO:0042162telomeric DNA binding0.00539548910907402
GO:0044428nuclear part0.00560587338291255
GO:0030529ribonucleoprotein complex0.00560587338291255
GO:0003697single-stranded DNA binding0.0150951373577981
GO:0000375RNA splicing, via transesterification reactions0.0150951373577981
GO:0000398nuclear mRNA splicing, via spliceosome0.0150951373577981
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0150951373577981
GO:0050658RNA transport0.0156575469235196
GO:0051236establishment of RNA localization0.0156575469235196
GO:0050657nucleic acid transport0.0156575469235196
GO:0006403RNA localization0.0156575469235196
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0168118700284401
GO:0009986cell surface0.0227705399221662
GO:0043566structure-specific DNA binding0.0233472040861499
GO:0003677DNA binding0.0254627520372707
GO:0032991macromolecular complex0.0299326331208392
GO:0044446intracellular organelle part0.0304654080166691
GO:0044422organelle part0.0304654080166691
GO:0016070RNA metabolic process0.0304654080166691
GO:0000166nucleotide binding0.0309391045519627
GO:0010467gene expression0.0488748993612867



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.