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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:29, 17 September 2013


Full id: C737_rhabdomyosarcoma_skeletal_mesenchymal_Skeletal_Pericytes_tongue_diaphragm



Phase1 CAGE Peaks

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 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: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 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><br>

Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue9.28e-2362
striated muscle tissue9.28e-2362
myotome9.28e-2362
muscle tissue6.41e-2264
musculature6.41e-2264
musculature of body6.41e-2264
somite2.35e-1971
presomitic mesoderm2.35e-1971
presumptive segmental plate2.35e-1971
dermomyotome2.35e-1971
trunk paraxial mesoderm2.35e-1971
paraxial mesoderm4.98e-1972
presumptive paraxial mesoderm4.98e-1972
dense mesenchyme tissue1.03e-1873
epithelial vesicle2.98e-1778
multilaminar epithelium5.72e-1683
trunk mesenchyme2.55e-15122
organism subdivision5.05e-13264
unilaminar epithelium5.54e-13148
muscle structure1.31e-112
muscle organ1.31e-112
throat2.85e-112
open tracheal system trachea9.16e-112
mesenchyme1.60e-10160
entire embryonic mesenchyme1.60e-10160
trunk2.02e-10199
chordate pharynx4.00e-0810
pharyngeal region of foregut4.00e-0810
tongue6.57e-083
gustatory system6.57e-083
future tongue6.57e-083
multi-tissue structure1.40e-07342
pharynx2.16e-0711


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)
MA0003.10.486434
MA0004.11.64978
MA0006.10.605586
MA0007.10.332734
MA0009.10.79061
MA0014.10.559573
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.637069
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.41425
MA0050.10.338274
MA0051.10.439895
MA0052.11.70446
MA0055.16.93632
MA0056.10
MA0057.10.397382
MA0058.15.75618
MA0059.13.77498
MA0060.10.119532
MA0061.10.330174
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.11.4122
MA0069.10.776171
MA0070.10.765217
MA0071.11.85155
MA0072.10.760818
MA0073.18.09724
MA0074.10.439193
MA0076.10.764079
MA0077.10.753278
MA0078.10.533387
MA0081.10.730303
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.11.10483
MA0089.10
MA0090.13.06338
MA0091.10.351901
MA0092.10.318032
MA0093.13.34956
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.11.74349
MA0105.13.03609
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.13.64606
MA0117.10.827487
MA0119.17.718
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.307853
MA0140.10.405425
MA0141.13.76281
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.11.62175
MA0146.10.700193
MA0147.10.946858
MA0148.10.372124
MA0149.10.396509
MA0062.21.09636
MA0035.20.404774
MA0039.20.396868
MA0138.20.534556
MA0002.20.358551
MA0137.20.229531
MA0104.23.15517
MA0047.20.47109
MA0112.22.53749
MA0065.20.839576
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.12.42238
MA0155.11.09568
MA0156.11.22
MA0157.10.576556
MA0158.10
MA0159.10.948902
MA0160.11.7766
MA0161.10
MA0162.10.178494
MA0163.15.09868
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.21.17095
MA0102.21.32663
MA0258.13.35614
MA0259.11.54967
MA0442.10



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

(#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 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.

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