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Difference between revisions of "Coexpression cluster:C737"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0000483!3.22e-21!309;UBERON:0000119!9.95e-21!312;UBERON:0000481!6.91e-18!347;UBERON:0000475!1.42e-14!365;UBERON:0000922!2.62e-13!612;UBERON:0000468!3.40e-12!659;UBERON:0002050!2.08e-11!605;UBERON:0005423!2.08e-11!605;UBERON:0000923!2.86e-11!604;UBERON:0005291!2.86e-11!604;UBERON:0006598!2.86e-11!604;UBERON:0002532!2.86e-11!604;UBERON:0003104!2.89e-10!238;UBERON:0009142!2.89e-10!238;UBERON:0000467!4.18e-10!625;UBERON:0000480!6.39e-10!626;UBERON:0000490!4.61e-09!138;UBERON:0001048!5.19e-09!168;UBERON:0005177!2.30e-08!107;UBERON:0002100!4.31e-08!216;UBERON:0000020!7.43e-08!23;UBERON:0004111!9.42e-08!241;UBERON:0003103!1.31e-07!69;UBERON:0004121!1.64e-07!169;UBERON:0000466!1.84e-07!126;UBERON:0000924!2.42e-07!173;UBERON:0006601!2.42e-07!173;UBERON:0000025!3.06e-07!194;UBERON:0001032!3.97e-07!24;UBERON:0004456!3.97e-07!24;UBERON:0000970!5.74e-07!20;UBERON:0005256!7.15e-07!143
 
|ontology_enrichment_uberon=UBERON:0000483!3.22e-21!309;UBERON:0000119!9.95e-21!312;UBERON:0000481!6.91e-18!347;UBERON:0000475!1.42e-14!365;UBERON:0000922!2.62e-13!612;UBERON:0000468!3.40e-12!659;UBERON:0002050!2.08e-11!605;UBERON:0005423!2.08e-11!605;UBERON:0000923!2.86e-11!604;UBERON:0005291!2.86e-11!604;UBERON:0006598!2.86e-11!604;UBERON:0002532!2.86e-11!604;UBERON:0003104!2.89e-10!238;UBERON:0009142!2.89e-10!238;UBERON:0000467!4.18e-10!625;UBERON:0000480!6.39e-10!626;UBERON:0000490!4.61e-09!138;UBERON:0001048!5.19e-09!168;UBERON:0005177!2.30e-08!107;UBERON:0002100!4.31e-08!216;UBERON:0000020!7.43e-08!23;UBERON:0004111!9.42e-08!241;UBERON:0003103!1.31e-07!69;UBERON:0004121!1.64e-07!169;UBERON:0000466!1.84e-07!126;UBERON:0000924!2.42e-07!173;UBERON:0006601!2.42e-07!173;UBERON:0000025!3.06e-07!194;UBERON:0001032!3.97e-07!24;UBERON:0004456!3.97e-07!24;UBERON:0000970!5.74e-07!20;UBERON:0005256!7.15e-07!143
 +
|tf_chipseq_enrich=USF1#7391;6:3.46990869665889:0.00339735017630123:0.0173351502375769
 
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}}
 
}}

Revision as of 02:45, 5 September 2012


Full id: C737_rhabdomyosarcoma_skeletal_mesenchymal_Skeletal_Pericytes_tongue_diaphragm



Phase1 CAGE Peaks

  Short description
Hg19::chr11:17741084..17741094,+ p3@MYOD1
Hg19::chr11:47470650..47470653,- p5@RAPSN
Hg19::chr11:47470657..47470674,- p2@RAPSN
Hg19::chr11:47470682..47470693,- p1@RAPSN
Hg19::chr11:47470703..47470715,- p3@RAPSN
Hg19::chr12:81102260..81102302,+ p@chr12:81102260..81102302
+
Hg19::chr16:31225409..31225428,+ p3@TRIM72
Hg19::chr16:31225432..31225453,+ p2@TRIM72
Hg19::chr17:7348374..7348435,+ p1@CHRNB1
Hg19::chr19:49223185..49223197,- p6@MAMSTR
Hg19::chr2:233390890..233390903,+ p3@CHRND


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


No results for this coexpression

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:0045211postsynaptic membrane6.79938374953971e-05
GO:0044456synapse part6.79938374953971e-05
GO:0005892nicotinic acetylcholine-gated receptor-channel complex6.79938374953971e-05
GO:0015464acetylcholine receptor activity0.000110207136155915
GO:0042166acetylcholine binding0.000110207136155915
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.000110207136155915
GO:0042391regulation of membrane potential0.000173536456370901
GO:0043176amine binding0.000308677077309302
GO:0030054cell junction0.000329255168161089
GO:0005231excitatory extracellular ligand-gated ion channel activity0.000666112422770907
GO:0043235receptor complex0.00141713184631989
GO:0005230extracellular ligand-gated ion channel activity0.00184280447188266
GO:0030594neurotransmitter receptor activity0.00193503853896072
GO:0042165neurotransmitter binding0.00193503853896072
GO:0015276ligand-gated ion channel activity0.00194818366524397
GO:0022834ligand-gated channel activity0.00194818366524397
GO:0003012muscle system process0.00194818366524397
GO:0006936muscle contraction0.00194818366524397
GO:0048625myoblast cell fate commitment0.00328069494872328
GO:0007518myoblast cell fate determination0.00328069494872328
GO:0055082cellular chemical homeostasis0.00328069494872328
GO:0006873cellular ion homeostasis0.00328069494872328
GO:0050801ion homeostasis0.00397762027942711
GO:0007268synaptic transmission0.00439703107944435
GO:0032501multicellular organismal process0.00439703107944435
GO:0048878chemical homeostasis0.00449427535592236
GO:0003008system process0.00484422787117751
GO:0019226transmission of nerve impulse0.00497613463498123
GO:0019725cellular homeostasis0.00618997073618544
GO:0005515protein binding0.00658133782506141
GO:0005261cation channel activity0.00724649481992225
GO:0007271synaptic transmission, cholinergic0.00832867358554158
GO:0042592homeostatic process0.00886226726540242
GO:0046873metal ion transmembrane transporter activity0.00923617233921631
GO:0022836gated channel activity0.00923617233921631
GO:0044459plasma membrane part0.0114977939322784
GO:0007267cell-cell signaling0.0139263162510835
GO:0005216ion channel activity0.0142062424824373
GO:0022838substrate specific channel activity0.0142062424824373
GO:0045445myoblast differentiation0.0142062424824373
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0142062424824373
GO:0022803passive transmembrane transporter activity0.0142062424824373
GO:0015267channel activity0.0142062424824373
GO:0001709cell fate determination0.0146236309168168
GO:0043234protein complex0.0179716781370358
GO:0048741skeletal muscle fiber development0.0196191815942839
GO:0048747muscle fiber development0.0196191815942839
GO:0008324cation transmembrane transporter activity0.0196191815942839
GO:0042692muscle cell differentiation0.0208083176960963
GO:0065008regulation of biological quality0.0224398321940344
GO:0007519skeletal muscle development0.0290832469142844
GO:0045165cell fate commitment0.0302197586792451
GO:0005886plasma membrane0.0338623366681617
GO:0032991macromolecular complex0.0348690262537573
GO:0014706striated muscle development0.0348690262537573
GO:0050877neurological system process0.0348690262537573
GO:0015075ion transmembrane transporter activity0.0368473140920722
GO:0005887integral to plasma membrane0.0368473140920722
GO:0031226intrinsic to plasma membrane0.0370642587046981
GO:0006811ion transport0.037387762057121
GO:0022891substrate-specific transmembrane transporter activity0.0453015648225363



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
uberon_data


Cell Type
Ontology termp-valuen
epithelial cell3.92e-11254
embryonic cell9.58e-10248
cell of skeletal muscle3.01e-079
general ecto-epithelial cell8.59e-0713
Uber Anatomy
Ontology termp-valuen
epithelium3.22e-21309
cell layer9.95e-21312
multi-tissue structure6.91e-18347
organism subdivision1.42e-14365
embryo2.62e-13612
multi-cellular organism3.40e-12659
embryonic structure2.08e-11605
developing anatomical structure2.08e-11605
germ layer2.86e-11604
embryonic tissue2.86e-11604
presumptive structure2.86e-11604
epiblast (generic)2.86e-11604
mesenchyme2.89e-10238
entire embryonic mesenchyme2.89e-10238
anatomical system4.18e-10625
anatomical group6.39e-10626
unilaminar epithelium4.61e-09138
primordium5.19e-09168
trunk region element2.30e-08107
trunk4.31e-08216
sense organ7.43e-0823
anatomical conduit9.42e-08241
compound organ1.31e-0769
ectoderm-derived structure1.64e-07169
immaterial anatomical entity1.84e-07126
ectoderm2.42e-07173
presumptive ectoderm2.42e-07173
tube3.06e-07194
sensory system3.97e-0724
entire sense organ system3.97e-0724
eye5.74e-0720
trunk mesenchyme7.15e-07143


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
USF1#739163.469908696658890.003397350176301230.0173351502375769



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


This analysis result is provided for C0 - C305 clusters.