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

Latest revision as of 11:25, 17 September 2013


Full id: C541_bronchogenic_anaplastic_cervical_Hep2_small_testicular_large



Phase1 CAGE Peaks

Hg19::chr13:113350755..113350785,+p1@ENST00000419448
Hg19::chr13:44596593..44596601,+p2@LINC00284
Hg19::chr13:44596618..44596628,+p1@LINC00284
Hg19::chr19:46119136..46119150,-p@chr19:46119136..46119150
-
Hg19::chr19:54024369..54024390,+p22@ZNF331
Hg19::chr19:54024454..54024463,+p31@ZNF331
Hg19::chr19:54024465..54024474,+p29@ZNF331
Hg19::chr19:54024499..54024503,+p48@ZNF331
Hg19::chr21:44839491..44839501,-p@chr21:44839491..44839501
-
Hg19::chr21:44842554..44842566,-p@chr21:44842554..44842566
-
Hg19::chr2:149862509..149862533,+p@chr2:149862509..149862533
+
Hg19::chr2:149863676..149863719,+p@chr2:149863676..149863719
+
Hg19::chr2:233385210..233385225,+p5@PRSS56
Hg19::chr2:233385234..233385255,+p4@PRSS56
Hg19::chr2:233385266..233385306,+p2@PRSS56
Hg19::chr8:1616323..1616360,+p@chr8:1616323..1616360
+
Hg19::chr9:68418482..68418506,-p@chr9:68418482..68418506
-


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
larynx5.74e-239
respiratory primordium1.19e-1238
endoderm of foregut1.19e-1238
upper respiratory tract1.72e-1119
segment of respiratory tract2.10e-1047
respiratory tract3.61e-0954
respiratory system6.51e-0774
Disease
Ontology termp-valuen
bronchus cancer1.89e-087
bronchogenic carcinoma1.89e-087


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)
MA0003.10.985135
MA0004.10.221943
MA0006.10.112549
MA0007.10.599001
MA0009.11.50668
MA0014.10.249137
MA0017.10.840365
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.11.26611
MA0029.10.542771
MA0030.12.26745
MA0031.12.07467
MA0038.10.302644
MA0040.10.548121
MA0041.10.236024
MA0042.10.608306
MA0043.10.621991
MA0046.10.611559
MA0048.10.868597
MA0050.10.212584
MA0051.11.47078
MA0052.10.551663
MA0055.11.42965
MA0056.10
MA0057.10.327175
MA0058.10.467197
MA0059.10.15289
MA0060.10.0509127
MA0061.10.155208
MA0063.10
MA0066.10.818531
MA0067.10.924196
MA0068.11.169
MA0069.10.607975
MA0070.10.597583
MA0071.11.36955
MA0072.10.593415
MA0073.10.000143211
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.382364
MA0081.10.152999
MA0083.11.52135
MA0084.11.10674
MA0087.10.591148
MA0088.12.57883
MA0089.10
MA0090.10.174619
MA0091.10.223914
MA0092.10.570207
MA0093.10.366841
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.749201
MA0103.10.34743
MA0105.10.0516824
MA0106.10.33677
MA0107.10.259598
MA0108.21.18798
MA0109.10
MA0111.10.541878
MA0113.10.350573
MA0114.11.37492
MA0115.10.850405
MA0116.10.264652
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
MA0139.10.594545
MA0140.10.269307
MA0141.12.08024
MA0142.10.445733
MA0143.10.350722
MA0144.10.5008
MA0145.10.0322091
MA0146.11.00986
MA0147.10.269778
MA0148.10.240905
MA0149.10.261654
MA0062.20.148712
MA0035.20.268747
MA0039.20.243085
MA0138.20.997372
MA0002.21.52414
MA0137.22.53112
MA0104.20.188874
MA0047.20.87164
MA0112.20.540922
MA0065.21.52581
MA0150.10.508545
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.11.80419
MA0155.10.507754
MA0156.10.12788
MA0157.11.08073
MA0158.10
MA0159.10.571105
MA0160.11.30016
MA0161.10
MA0162.10.0130334
MA0163.10.166772
MA0164.10.361105
MA0080.20.11444
MA0018.20.337929
MA0099.20.27482
MA0079.20.00256632
MA0102.21.14323
MA0258.10.476351
MA0259.10.591641
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
ATF3#46745.285452829649120.005857629621042940.0262966377231819
ESR1#209947.239671363801050.001888460530473440.0111259056434882
GATA3#262558.010740105060590.0002845620244940660.00302672097730276
NANOG#7992346.881124348473570.002273120967201780.0129058157484962
NR2C2#718247.674026095350790.001525006888559970.0097127817071786
SETDB1#986949.487064983061290.000694182090311990.00559540660107231
SP1#666782.681591236772190.004828972477916040.0226574894029864
STAT1#677244.87213823463510.007795644485065150.0320249110795626
TRIM28#1015544.374241187120590.0113205059123520.0415250884019435



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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