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Coexpression cluster:C538: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0724992894770213,0.

Latest revision as of 11:25, 17 September 2013


Full id: C538_left_skeletal_heart_seminal_ductus_adipose_mature



Phase1 CAGE Peaks

Hg19::chr12:10856713..10856723,-p23@CSDA
Hg19::chr17:58042483..58042495,+p2@ENST00000501190
p2@uc002iye.1
Hg19::chr5:79026919..79026926,+p@chr5:79026919..79026926
+
Hg19::chr5:79029312..79029328,+p9@CMYA5
Hg19::chr7:95214018..95214046,-p@chr7:95214018..95214046
-
Hg19::chr7:95218981..95219000,-p12@PDK4
Hg19::chr7:95222151..95222232,-p7@PDK4
Hg19::chr7:95223041..95223065,-p@chr7:95223041..95223065
-
Hg19::chr7:95224363..95224402,-p@chr7:95224363..95224402
-
Hg19::chr7:95224413..95224447,-p@chr7:95224413..95224447
-
Hg19::chr7:95224469..95224481,-p@chr7:95224469..95224481
-
Hg19::chr7:95225490..95225542,-p3@PDK4
Hg19::chr7:95225580..95225618,-p4@PDK4
Hg19::chr7:95225631..95225666,-p2@PDK4
Hg19::chr7:95225695..95225721,-p8@PDK4
Hg19::chr7:95225729..95225740,-p6@PDK4
Hg19::chr7:95225768..95225967,-p1@PDK4


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:0004740pyruvate dehydrogenase (acetyl-transferring) kinase activity0.0252486593058398
GO:0009409response to cold0.0252486593058398
GO:0018106peptidyl-histidine phosphorylation0.0252486593058398
GO:0018202peptidyl-histidine modification0.0252486593058398
GO:0004673protein histidine kinase activity0.0419458539477759
GO:0009266response to temperature stimulus0.0419458539477759
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0419458539477759



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>

Cell Type
Ontology termp-valuen
fat cell5.61e-0915
Uber Anatomy
Ontology termp-valuen
adult organism2.35e-67114
neural tube1.57e-1656
neural rod1.57e-1656
future spinal cord1.57e-1656
neural keel1.57e-1656
regional part of nervous system8.31e-1553
regional part of brain8.31e-1553
neural plate5.42e-1382
presumptive neural plate5.42e-1382
neurectoderm5.38e-1286
central nervous system1.11e-1181
neural nucleus6.98e-119
nucleus of brain6.98e-119
brain9.26e-1168
future brain9.26e-1168
organ system subdivision1.26e-10223
brain grey matter1.95e-1034
gray matter1.95e-1034
regional part of forebrain1.98e-1041
forebrain1.98e-1041
anterior neural tube1.98e-1041
future forebrain1.98e-1041
structure with developmental contribution from neural crest2.18e-10132
ecto-epithelium3.54e-10104
brainstem6.94e-106
nervous system9.46e-1089
telencephalon4.26e-0934
regional part of telencephalon1.15e-0832
basal ganglion2.53e-089
nuclear complex of neuraxis2.53e-089
aggregate regional part of brain2.53e-089
collection of basal ganglia2.53e-089
cerebral subcortex2.53e-089
telencephalic nucleus2.54e-087
anatomical cluster4.64e-08373
posterior neural tube8.50e-0815
chordal neural plate8.50e-0815
organ1.42e-07503
multi-tissue structure1.84e-07342
cerebral hemisphere2.17e-0732
male genital duct3.54e-073
internal male genitalia3.54e-073
anatomical conduit4.74e-07240
corpus striatum6.22e-074
striatum6.22e-074
ventral part of telencephalon6.22e-074
future corpus striatum6.22e-074
valve7.28e-073
cardiac mesenchyme7.28e-073
cardial valve7.28e-073
tunica intima7.28e-073
heart layer7.28e-073
endocardium7.28e-073
endocardial cushion7.28e-073
presumptive endocardium7.28e-073


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)
MA0003.10.000106454
MA0004.10.221943
MA0006.10.112549
MA0007.10.208008
MA0009.10.621697
MA0014.10.0173262
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.387666
MA0029.11.34042
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.664972
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.10.0663643
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.274153
MA0056.10
MA0057.10.0616251
MA0058.10.467197
MA0059.10.465036
MA0060.10.742387
MA0061.10.0397345
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.0264141
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.11.44731
MA0073.10.0135515
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.382364
MA0081.10.152999
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.176197
MA0089.10
MA0090.10.174619
MA0091.10.223914
MA0092.10.195947
MA0093.10.366841
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.116395
MA0103.10.34743
MA0105.10.0103933
MA0106.10.33677
MA0107.10.0748038
MA0108.20.471286
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.10.072201
MA0115.10.850405
MA0116.10.0765991
MA0117.10.656858
MA0119.10.142224
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.0351037
MA0140.10.269307
MA0141.10.151722
MA0142.11.97987
MA0143.10.925263
MA0144.10.231909
MA0145.10.577453
MA0146.11.00986
MA0147.10.0784275
MA0148.10.240905
MA0149.10.261654
MA0062.20.0377014
MA0035.20.268747
MA0039.20.0172323
MA0138.20.38342
MA0002.21.07772
MA0137.20.398112
MA0104.20.188874
MA0047.20.326636
MA0112.20.0286692
MA0065.20.211898
MA0150.10.170499
MA0151.10
MA0152.10.753898
MA0153.10.714423
MA0154.10.0498326
MA0155.10.00448085
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.0787617
MA0160.10.252705
MA0161.10
MA0162.10.155087
MA0163.10.000152387
MA0164.10.361105
MA0080.20.366978
MA0018.20.337929
MA0099.20.27482
MA0079.22.92288e-06
MA0102.21.14323
MA0258.10.0605489
MA0259.10.0828875
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
SMARCB1#659866.442134981584970.0001975136049639610.00237323094671319
ZNF263#1012762.901826460121420.01212951648882460.043984395422949



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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