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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:45, 17 September 2013


Full id: C1459_rectum_colon_amniotic_Intestinal_small_chorionic_pancreatic



Phase1 CAGE Peaks

Hg19::chr19:959112..959138,+p@chr19:959112..959138
+
Hg19::chr19:959145..959162,+p@chr19:959145..959162
+
Hg19::chr7:100609502..100609528,+p12@MUC3A
p12@MUC3B
Hg19::chr7:100609529..100609542,+p22@MUC3A
p22@MUC3B
Hg19::chr7:100609612..100609625,+p11@MUC3A
p11@MUC3B
Hg19::chr7:100609627..100609654,+p3@MUC3A
p3@MUC3B


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

Cell Type
Ontology termp-valuen
germ line cell1.87e-177
germ cell1.87e-177
embryonic stem cell1.42e-135
Uber Anatomy
Ontology termp-valuen
intestine1.27e-1717
gastrointestinal system8.84e-1625
large intestine2.05e-1211
lower digestive tract9.77e-105
subdivision of digestive tract2.62e-08118
hindgut2.83e-0819
colon4.82e-089
endoderm-derived structure1.14e-07160
endoderm1.14e-07160
presumptive endoderm1.14e-07160
rectum3.02e-074
Disease
Ontology termp-valuen
carcinoma1.44e-08106
cell type cancer1.59e-07143


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)
MA0003.11.37104
MA0004.10.558729
MA0006.13.68107
MA0007.10.539222
MA0009.11.03681
MA0014.10.788761
MA0017.10.432438
MA0019.11.69574
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.12.08744
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.14.21208
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.14.94062
MA0074.12.68181
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.13.72097
MA0103.10.381434
MA0105.17.75496
MA0106.10.70837
MA0107.12.35015
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.13.45912
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.13.00011
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.22.28878
MA0138.25.77199
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.12.1986
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.16.43468
MA0163.11.18186
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.22.88163
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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
CCNT2#90566.336201576962631.54467812014647e-050.00036252727683141
CTCF#1066443.573504248716680.01316635007238510.0466097361266975
CTCFL#140690413.16431623931629.07806692187542e-050.00132435288623236
E2F4#187448.445373543522960.0005111193523770840.00443325255733828
EGR1#195864.988179094810146.48943962979974e-050.00105519318931442
FOSL1#8061213.23785990545770.00888833088009090.0337216066835881
HDAC2#3066613.41562023662631.71355402088576e-079.4240057075981e-06
HMGN3#932445.452365148900390.002729616882333770.0149883521332312
IRF1#365945.091442502375930.003535240765893810.0179449336743224
JUND#372766.994663941871038.53468650061654e-060.000232183934211485
MAX#414944.301703672671410.006644923910676370.0282995232356208
NR3C1#290849.982015554115360.0002673219180401920.00286053624981554
PAX5#507944.446377020785220.005874733519240790.0263643560508761
POLR2A#543062.147453176558070.01019570676818780.0380364143298006
RAD21#588546.903355930304220.00111085151625360.00771384451502727
REST#597846.433352477418680.001454954223032070.00932576188162799
SIN3A#2594243.605923151210090.01273893844487140.045943849445539
SMC3#9126410.02995522995520.0002623881821065520.00281062147190012
SRF#672249.19811884144520.0003672404582485860.00365835809033042
STAT1#6772413.80439166479957.53702299850546e-050.00116650732800965
TAF7#687947.622046269949280.000759279015141480.00596721657478825
TCF12#693847.089643268124280.001002991572657710.00718804891626969
TCF7L2#693447.180117708758230.0009553297120679730.00687667515326122
ZBTB7A#5134144.901272871917260.004079628118843750.0194882807073102
ZNF143#770249.000584368151940.0003994818197133810.00390066209508655



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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