Personal tools

Coexpression cluster:C277

From FANTOM5_SSTAR

Revision as of 06:33, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C277_mesothelioma_epithelioid_thyroid_extraskeletal_alveolar_glioblastoma_adenocarcinoma



Phase1 CAGE Peaks

  Short description
Hg19::chr11:28792916..28792929,+ p@chr11:28792916..28792929
+
Hg19::chr14:36642956..36642966,+ p@chr14:36642956..36642966
+
Hg19::chr14:36642986..36642989,+ p@chr14:36642986..36642989
+
Hg19::chr14:36643089..36643094,+ p@chr14:36643089..36643094
+
Hg19::chr19:21452679..21452684,- p@chr19:21452679..21452684
-
Hg19::chr19:21452690..21452695,- p@chr19:21452690..21452695
-
Hg19::chr19:21452713..21452724,- p@chr19:21452713..21452724
-
Hg19::chr19:23015117..23015128,+ p@chr19:23015117..23015128
+
Hg19::chr19:36909811..36909826,- p3@ZFP82
Hg19::chr19:36909838..36909849,- p5@ZFP82
Hg19::chr19:36914887..36914892,- p@chr19:36914887..36914892
-
Hg19::chr19:37264112..37264129,+ p2@uc002oes.1
Hg19::chr19:37264138..37264154,+ p4@uc002oes.1
Hg19::chr19:37464799..37464817,+ p@chr19:37464799..37464817
+
Hg19::chr19:38104849..38104860,+ p@chr19:38104849..38104860
+
Hg19::chr19:38145832..38145833,- p@chr19:38145832..38145833
-
Hg19::chr19:38182936..38182940,- -
p@chr19:38182936..38182940
Hg19::chr19:38182963..38182975,- p@chr19:38182963..38182975
-
Hg19::chr19:38183029..38183044,- p@chr19:38183029..38183044
-
Hg19::chr19:38210552..38210570,- p2@ZNF607
Hg19::chr19:38281159..38281170,+ p@chr19:38281159..38281170
+
Hg19::chr19:38281171..38281178,+ p@chr19:38281171..38281178
+
Hg19::chr19:41727698..41727705,+ p@chr19:41727698..41727705
+
Hg19::chr19:44331295..44331299,- p4@ENST00000499389
p4@uc002oxo.1
Hg19::chr19:44331304..44331307,- p5@ENST00000499389
p5@uc002oxo.1
Hg19::chr19:44331332..44331339,- p3@ENST00000499389
p3@uc002oxo.1
Hg19::chr19:44331593..44331618,+ p5@ZNF283
Hg19::chr19:44331766..44331774,+ p@chr19:44331766..44331774
+
Hg19::chr19:44331769..44331809,- p2@ENST00000499389
p2@uc002oxo.1
Hg19::chr19:44331884..44331893,+ p8@ZNF283
Hg19::chr19:44331916..44331929,+ p6@ZNF283
Hg19::chr19:44405623..44405636,- p1@uc002oxt.2
Hg19::chr19:44405761..44405769,- p2@uc002oxt.2
Hg19::chr19:44405872..44405879,+ p@chr19:44405872..44405879
+
Hg19::chr19:52932395..52932413,+ p1@ZNF534
Hg19::chr19:52932444..52932455,+ p2@ZNF534
Hg19::chr19:56879625..56879636,+ p5@ZNF542
Hg19::chr19:56879817..56879825,+ p4@ZNF542
Hg19::chr19:9406118..9406133,- p@chr19:9406118..9406133
-
Hg19::chr19:9420326..9420349,- p2@ZNF699
Hg19::chr1:240926680..240926686,+ p@chr1:240926680..240926686
+
Hg19::chr21:47460896..47460904,+ p@chr21:47460896..47460904
+
Hg19::chr21:47461437..47461440,+ p@chr21:47461437..47461440
+
Hg19::chr5:1380178..1380183,- p1@ENST00000504989
p1@uc003jcj.1
Hg19::chr5:178696464..178696469,- p@chr5:178696464..178696469
-
Hg19::chr6:2938437..2938442,- p@chr6:2938437..2938442
-
Hg19::chr8:90710257..90710295,+ p@chr8:90710257..90710295
+


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


p.valueFDRnGenesnPathwayName
1.69712115516446e-070.000107427769121914390{ASH2L,391} (Static Module):NA



Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0006355regulation of transcription, DNA-dependent0.000694105102075861
GO:0006351transcription, DNA-dependent0.000694105102075861
GO:0032774RNA biosynthetic process0.000694105102075861
GO:0045449regulation of transcription0.000694105102075861
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000694105102075861
GO:0006350transcription0.000694105102075861
GO:0010468regulation of gene expression0.000694105102075861
GO:0031323regulation of cellular metabolic process0.000694105102075861
GO:0019222regulation of metabolic process0.000694105102075861
GO:0016070RNA metabolic process0.000694105102075861
GO:0008270zinc ion binding0.000694105102075861
GO:0046914transition metal ion binding0.00122601820250566
GO:0010467gene expression0.00173584310847537
GO:0050794regulation of cellular process0.00192843172763104
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00198867441603267
GO:0050789regulation of biological process0.00226568844957581
GO:0003676nucleic acid binding0.00248129964629139
GO:0043169cation binding0.0025249278869468
GO:0065007biological regulation0.00275580653910112
GO:0046872metal ion binding0.00279506898691079
GO:0043167ion binding0.00284718050993229
GO:0043283biopolymer metabolic process0.00460895279211949
GO:0043170macromolecule metabolic process0.0171109407578659
GO:0044237cellular metabolic process0.0260519854613869
GO:0005634nucleus0.0260519854613869
GO:0044238primary metabolic process0.0260519854613869
GO:0005622intracellular0.0466634707599534



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data



Cell Type
Ontology termp-valuen
non-terminally differentiated cell2.55e-15180
fibroblast1.24e-0975
mesothelial cell4.16e-0819
preadipocyte2.03e-0712


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ELF1#1997201.811956578215970.002962197311299230.0157905739584922
SETDB1#986986.862983179235831.88787728036671e-050.000428253725639051
SIX5#147912134.726112757892921.99961092276306e-067.3199216671031e-05
ZNF143#7702144.021537696408314.85528166720061e-060.000150335239264976



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data