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{{Coexpression_clusters
{
|full_id=C1781_anaplastic_Hair_Pericytes_mesothelioma_Fibroblast_lens_transitionalcell
|

Latest revision as of 11:52, 17 September 2013


Full id: C1781_anaplastic_Hair_Pericytes_mesothelioma_Fibroblast_lens_transitionalcell



Phase1 CAGE Peaks

Hg19::chr17:42634734..42634754,+p3@FZD2
Hg19::chr17:42634810..42634825,+p4@FZD2
Hg19::chr17:42634844..42634858,+p1@FZD2
Hg19::chr17:42635049..42635107,+p5@FZD2
Hg19::chr17:42635121..42635149,+p1@AB590852


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:0007164establishment of tissue polarity0.0065936653714824
GO:0004926non-G-protein coupled 7TM receptor activity0.00706464146944543
GO:0030855epithelial cell differentiation0.0113034263511127
GO:0002009morphogenesis of an epithelium0.0148357470858354
GO:0016055Wnt receptor signaling pathway0.0273166136818556



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
fibroblast2.09e-1676
non-terminally differentiated cell7.47e-13106
contractile cell1.07e-0859
skin fibroblast1.65e-0823
neurectodermal cell5.14e-0859
electrically responsive cell5.93e-0861
electrically active cell5.93e-0861
animal cell1.04e-07679
eukaryotic cell1.04e-07679
muscle precursor cell2.19e-0758
myoblast2.19e-0758
multi-potent skeletal muscle stem cell2.19e-0758
muscle cell5.64e-0755


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)
MA0003.12.24383
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.02528
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.19.26754
MA0056.10
MA0057.12.36624
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.15.50918
MA0074.11.73427
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.12.26263
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.14.84512
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.22.8814
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.24.30878
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.91168
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.216.3784
MA0102.21.66336
MA0258.10.914277
MA0259.10.395396
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
CTBP2#1488562.71700033932811.02712351233917e-099.518345386441e-08
EGR1#195854.988179094810140.0003237398000590710.00330735214500336
ELF1#199743.406478367046030.01235066105299550.0447350589482484
FOS#235335.398773185336640.01153895317278740.0421915320664058
GATA2#262437.64695904013240.004279061879252130.020329388327672
GATA3#2625316.34190981432360.0004678865195089230.00430154931434792
IRF3#3661328.18917132689379.33088977565955e-050.00135612134327875
MYC#460955.22228187160940.0002573944848850610.00276507124119635
NFYA#4800311.05534841989830.001470892907644430.0094123267190415
NFYB#4801310.05587595212190.001938165606725460.0113879087370352
RFX5#599337.228746496317060.00502918278958660.0234661493705774
SP2#6668315.69211829630680.0005272235913302770.0045638379324445
SRF#672238.278306957300690.003404846073776150.0173615232447567
TAF1#687253.343046285745290.002394600090870310.0135337214616811
TFAP2C#702236.485537165916130.006858951517940.0290593500297001
USF1#739156.361499277207969.59569864925045e-050.00136814357846972
YY1#752843.928936599883080.007193866269917620.0298427152591327



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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