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

Latest revision as of 11:30, 17 September 2013


Full id: C744_breast_salivary_parotid_submaxillary_seminal_small_ductus



Phase1 CAGE Peaks

Hg19::chr11:826136..826180,+p2@EFCAB4A
Hg19::chr13:34922173..34922187,+p@chr13:34922173..34922187
+
Hg19::chr15:41069078..41069092,-p2@DNAJC17
Hg19::chr17:36763272..36763286,-p@chr17:36763272..36763286
-
Hg19::chr18:20911089..20911104,-p4@TMEM241
Hg19::chr18:20911109..20911117,-p5@TMEM241
Hg19::chr22:31739395..31739404,-p24@PATZ1
Hg19::chr7:94138905..94138932,+p3@CASD1
Hg19::chr9:140063847..140063858,-p2@MIR3621
Hg19::chr9:140063873..140063890,-p1@MIR3621
Hg19::chr9:140064092..140064112,-p3@MIR3621


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

No GOStat results

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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract1.05e-15118
immaterial anatomical entity5.46e-15117
digestive system1.68e-13145
digestive tract1.68e-13145
primitive gut1.68e-13145
foregut3.60e-1387
anatomical space4.56e-1395
adult organism4.75e-13114
endoderm-derived structure1.64e-11160
endoderm1.64e-11160
presumptive endoderm1.64e-11160
male genital duct6.62e-113
internal male genitalia6.62e-113
organism subdivision7.03e-11264
thoracic segment of trunk1.80e-1052
trunk region element3.01e-10101
subdivision of trunk5.67e-10112
thoracic cavity element4.71e-0934
thoracic cavity4.71e-0934
thoracic segment organ9.95e-0935
respiratory system1.70e-0874
duct of male reproductive system2.90e-084
epithelial bud3.51e-0837
major salivary gland4.33e-082
lung6.14e-0822
respiratory tube6.14e-0822
respiration organ6.14e-0822
pair of lungs6.14e-0822
lung primordium6.14e-0822
lung bud6.14e-0822
open tracheal system trachea7.62e-082
endo-epithelium9.33e-0882
throat1.28e-072
trunk2.57e-07199
respiratory tract4.55e-0754
Disease
Ontology termp-valuen
carcinoma1.60e-10106
thoracic cancer1.97e-084
breast cancer1.97e-084
cell type cancer6.89e-08143
adenocarcinoma9.43e-0725


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)
MA0003.11.34363
MA0004.10.92264
MA0006.10.210781
MA0007.10.885261
MA0009.10.79061
MA0014.10.21986
MA0017.10.24363
MA0019.10.486183
MA0024.11.64584
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.11.6617
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.16.16093
MA0050.11.61016
MA0051.10.439895
MA0052.10.716602
MA0055.13.78104
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.10.2641
MA0060.11.24766
MA0061.10.6764
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.11.80505
MA0071.10.40788
MA0072.10.760818
MA0073.10.00132306
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.10094
MA0089.10
MA0090.10.291627
MA0091.12.50413
MA0092.11.53836
MA0093.10.61153
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.11.11087
MA0105.10.15707
MA0106.10.482519
MA0107.10.475157
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.12.86229
MA0117.10.827487
MA0119.11.29122
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.438224
MA0145.10.277793
MA0146.13.6373
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.0468759
MA0138.20.534556
MA0002.21.19327
MA0137.21.21272
MA0104.20.118985
MA0047.20.47109
MA0112.21.14277
MA0065.20.11899
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.353037
MA0155.12.9974
MA0156.10.654264
MA0157.10.576556
MA0158.10
MA0159.10.489747
MA0160.11.0031
MA0161.10
MA0162.10.0809571
MA0163.10.387319
MA0164.10.509774
MA0080.20.611699
MA0018.20.483823
MA0099.20.411824
MA0079.22.06734e-05
MA0102.21.32663
MA0258.10.135061
MA0259.10.504687
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
CTCF#1066462.923776203495470.00821204794325940.0324133815247947
E2F1#186962.676757753570540.01278816717532660.04601493166663
EP300#203363.694877305212650.002441288066552230.0137470040644119
FOXA1#316955.037008976993390.001733897915820090.0106722397707646
GATA3#2625512.38023470782092.5558774340898e-050.000553114967548496
MYC#460973.323270281933260.001501335996249240.00959126682849731
NR3C1#290845.44473575679020.004481600804046920.0212038555030288
SUZ12#23512313.66794024847170.00116159721365010.00794161111523978



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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