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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: C703_liver_hepatocellular_Hepatocyte_hepatoblastoma_colon_gastrointestinal_mature



Phase1 CAGE Peaks

Hg19::chr16:20911174..20911242,+p4@LYRM1
Hg19::chr17:53344980..53345011,+p3@HLF
Hg19::chr17:7018076..7018096,-p3@ASGR2
Hg19::chr20:22504822..22504839,-p@chr20:22504822..22504839
-
Hg19::chr20:22566100..22566105,-p9@FOXA2
Hg19::chr20:22566120..22566136,-p4@FOXA2
Hg19::chr2:20793055..20793071,-p@chr2:20793055..20793071
-
Hg19::chr4:186732197..186732211,-p33@SORBS2
Hg19::chr4:39408537..39408563,+p1@KLB
Hg19::chr4:74283279..74283295,-p@chr4:74283279..74283295
-
Hg19::chr8:40010642..40010656,+p2@C8orf4
Hg19::chr9:683039..683053,+p@chr9:683039..683053
+


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:0004873asialoglycoprotein receptor activity0.0418518401051033



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
metabolising cell5.96e-4112
endopolyploid cell5.96e-4112
parenchymal cell5.96e-4112
polyploid cell5.96e-4112
hepatocyte5.96e-4112
endodermal cell1.82e-1458
intestinal epithelial cell1.07e-084
Uber Anatomy
Ontology termp-valuen
liver6.24e-4019
digestive gland6.24e-4019
liver bud6.24e-4019
epithelium of foregut-midgut junction3.93e-3625
anatomical boundary3.93e-3625
hepatobiliary system3.93e-3625
foregut-midgut junction3.93e-3625
septum transversum3.93e-3625
hepatic diverticulum2.83e-3422
liver primordium2.83e-3422
digestive tract diverticulum1.02e-3223
epithelial sac5.66e-3025
sac9.25e-2926
gut epithelium7.84e-2654
exocrine gland7.28e-2431
exocrine system7.28e-2431
abdomen element5.22e-2254
abdominal segment element5.22e-2254
endo-epithelium2.32e-2182
endocrine gland5.93e-2135
abdominal segment of trunk1.42e-1960
abdomen1.42e-1960
endocrine system6.18e-1645
subdivision of digestive tract1.02e-15118
trunk region element1.69e-14101
gland2.76e-1459
digestive system6.82e-14145
digestive tract6.82e-14145
primitive gut6.82e-14145
subdivision of trunk8.39e-13112
foregut8.44e-1387
endoderm-derived structure2.74e-12160
endoderm2.74e-12160
presumptive endoderm2.74e-12160
immaterial anatomical entity3.99e-12117
primordium2.18e-09160
intestinal mucosa1.07e-084
wall of intestine1.07e-084
gastrointestinal system mucosa1.07e-084
gastrointestinal system epithelium1.07e-084
intestinal epithelium1.07e-084
unilaminar epithelium8.54e-08148
epithelial tube1.70e-07117
trunk mesenchyme3.86e-07122
trunk5.22e-07199
mesenchyme5.40e-07160
entire embryonic mesenchyme5.40e-07160
organ system subdivision9.77e-07223


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)
MA0003.10.050563
MA0004.10.861826
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.0339142
MA0017.11.8359
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.11.4626
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.835565
MA0043.10.756508
MA0046.11.76456
MA0048.10.0399193
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.400018
MA0056.10
MA0057.10.617373
MA0058.10.240796
MA0059.10.239727
MA0060.10.103131
MA0061.10.0856761
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.491198
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.11.72531
MA0073.10.052979
MA0074.10.40963
MA0076.10.254045
MA0077.11.70983
MA0078.11.25378
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.0806254
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.558691
MA0095.10
MA0098.10
MA0100.11.09213
MA0101.10.19375
MA0103.10.535462
MA0105.10.130274
MA0106.11.14663
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.761158
MA0113.11.17934
MA0114.11.34132
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.268952
MA0140.10.376643
MA0141.10.670251
MA0142.10.570448
MA0143.10.467429
MA0144.10.783809
MA0145.10.232227
MA0146.10.0677137
MA0147.10.440281
MA0148.12.46692
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.20.0300713
MA0138.20.503176
MA0002.20.316618
MA0137.20.595725
MA0104.20.102626
MA0047.22.92258
MA0112.20.681028
MA0065.20.452385
MA0150.10.723395
MA0151.10
MA0152.10.382565
MA0153.11.98449
MA0154.10.30107
MA0155.10.202876
MA0156.10.208455
MA0157.11.34413
MA0158.10
MA0159.10.867657
MA0160.10.357736
MA0161.10
MA0162.10.00310762
MA0163.10.0909552
MA0164.10.478818
MA0080.20.558855
MA0018.20.453345
MA0099.20.382887
MA0079.20.250032
MA0102.21.28978
MA0258.10.754226
MA0259.10.455773
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#105174.649836115064480.0002169608117053290.00248592103276938
EP300#203395.08045629466744.77520229064111e-060.000148031271009874
FOSL2#235557.05425025190070.0004002859722500580.0039077833852892
FOXA1#316987.387613166256971.5568251234609e-065.93189562455793e-05
FOXA2#3170918.47284781449895.87146030386133e-116.55838976122966e-09
HDAC2#3066910.06171517746971.26626514699338e-089.39925129259716e-07
HEY1#23462113.70343512284691.98027513061222e-067.26696958418869e-05
HNF4A#3172815.42152690863585.14574068083495e-094.13396931512093e-07
HNF4G#3174819.16894835096459.30701468536427e-108.69423351274382e-08
RAD21#588554.314597456440140.00371367380173060.0187286869563447
RXRA#6256610.03730856956661.08580868623514e-050.00028139149722509
SIN3A#2594262.704442363407570.01325491342780750.0468867029123382
SP1#666794.273786033605672.0740195727163e-050.00045843075165062
TBP#690882.471180458064260.004672713706606670.0220561125736371
TCF7L2#693476.282602995163453.08533765812745e-050.00062910890214208



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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