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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: C725_Mast_cord_mycosis_mesenchymal_Endothelial_hepatic_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr10:64576035..64576046,-p2@EGR2
Hg19::chr12:93966545..93966557,+p25@SOCS2
Hg19::chr16:72128270..72128282,-p5@TXNL4B
Hg19::chr1:173174598..173174624,-p4@TNFSF4
Hg19::chr1:173174630..173174644,-p7@TNFSF4
Hg19::chr1:173174664..173174677,-p6@TNFSF4
Hg19::chr1:173174681..173174702,-p5@TNFSF4
Hg19::chr1:173174706..173174733,-p3@TNFSF4
Hg19::chr1:173174759..173174799,-p2@TNFSF4
Hg19::chr1:173176462..173176477,-p1@TNFSF4
Hg19::chr2:191185566..191185602,-p@chr2:191185566..191185602
-


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:0005148prolactin receptor binding0.012546365820773
GO:0008269JAK pathway signal transduction adaptor activity0.012546365820773
GO:0008268receptor signaling protein tyrosine kinase signaling protein activity0.012546365820773
GO:0032868response to insulin stimulus0.012546365820773
GO:0005131growth hormone receptor binding0.012546365820773
GO:0005125cytokine activity0.012546365820773
GO:0007638mechanosensory behavior0.0154378789766626
GO:0048168regulation of neuronal synaptic plasticity0.0202595321431702
GO:0005159insulin-like growth factor receptor binding0.0220084121224001
GO:0048167regulation of synaptic plasticity0.0249249009211236
GO:0009612response to mechanical stimulus0.0249249009211236
GO:0007267cell-cell signaling0.0249249009211236
GO:0050803regulation of synapse structure and activity0.0249249009211236
GO:0043434response to peptide hormone stimulus0.0282827880332297
GO:0007422peripheral nervous system development0.0287944772484493
GO:0065008regulation of biological quality0.0388055118302518
GO:0005164tumor necrosis factor receptor binding0.0388055118302518
GO:0007259JAK-STAT cascade0.0388055118302518
GO:0032813tumor necrosis factor receptor superfamily binding0.0388055118302518
GO:0007611learning and/or memory0.03905990040876
GO:0005102receptor binding0.03905990040876
GO:0005070SH3/SH2 adaptor activity0.0400389898549058
GO:0005126hematopoietin/interferon-class (D200-domain) cytokine receptor binding0.0449198938933818
GO:0060090molecular adaptor activity0.0449198938933818



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
circulating cell1.50e-106
endothelial cell of artery9.27e-079
Uber Anatomy
Ontology termp-valuen
blood8.34e-2215
haemolymphatic fluid8.34e-2215
organism substance8.34e-2215
cardiovascular system4.96e-15109
circulatory system2.56e-14112
lateral plate mesoderm9.05e-07203
endothelial tube9.27e-079
arterial system endothelium9.27e-079
endothelium of artery9.27e-079
Disease
Ontology termp-valuen
ovarian cancer2.36e-0914


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)
MA0003.10.000970254
MA0004.10.349539
MA0006.10.210781
MA0007.10.885261
MA0009.10.79061
MA0014.10.0144431
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.12.12648
MA0027.12.39404
MA0028.10.224112
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
MA0048.11.12059
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.00989454
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.11.12972
MA0067.11.1037
MA0068.10.556338
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.552437
MA0074.10.439193
MA0076.12.98143
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.11.87258
MA0084.11.28962
MA0087.10.758426
MA0088.10.0234479
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.11.15683
MA0101.10.617985
MA0103.10.203171
MA0105.10.0403209
MA0106.10.482519
MA0107.10.475157
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.14.5976
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.11.99564
MA0139.10.0922451
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.02761
MA0146.10.0109959
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.166893
MA0138.20.534556
MA0002.21.19327
MA0137.21.21272
MA0104.20.118985
MA0047.20.47109
MA0112.21.14277
MA0065.20.28513
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.10.245306
MA0156.10.654264
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.10.00253231
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.20.00352009
MA0102.21.32663
MA0258.11.34618
MA0259.10.168926
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
CEBPB#105164.347898704995350.001022434272625610.00724584467657907
EP300#203363.694877305212650.002441288066552230.0137462629061165
FOXA1#316977.051812567790741.15697264990643e-050.000294571103324177
FOXA2#3170613.43479841054471.73076139279195e-066.52324031403099e-05
HDAC2#306667.317611038159785.69712326977083e-050.000950330389988174
HEY1#2346272.570979754703630.007126829840213170.0296340718112045
HNF4A#3172612.61761292524752.49318000901648e-068.78196380983718e-05
HNF4G#3174615.68368501442557.0138286269284e-073.1438508496471e-05
SP1#666763.108208024440490.006011321202489790.0269483785494626
USF1#739174.04822681276870.0004339107367003340.0040508807929066



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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