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Coexpression cluster:C1927: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1927_Corneal_Esophageal_Urothelial_Endothelial_Bronchial_Sebocyte_Tracheal
|id=C1927
}}

Latest revision as of 11:55, 17 September 2013


Full id: C1927_Corneal_Esophageal_Urothelial_Endothelial_Bronchial_Sebocyte_Tracheal



Phase1 CAGE Peaks

Hg19::chr3:50192438..50192447,+p5@SEMA3F
Hg19::chr3:50192457..50192498,+p2@SEMA3F
Hg19::chr3:50192499..50192534,+p1@SEMA3F
Hg19::chr3:50192537..50192563,+p3@SEMA3F
Hg19::chr3:50211299..50211317,-p@chr3:50211299..50211317
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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><br>

Uber Anatomy
Ontology termp-valuen
anatomical cluster7.11e-33373
epithelium1.43e-26306
multi-cellular organism7.13e-26656
cell layer1.73e-25309
multi-tissue structure5.92e-23342
anatomical system1.83e-22624
anatomical group4.47e-22625
embryo6.96e-21592
anatomical conduit2.61e-20240
developing anatomical structure8.44e-19581
epithelial tube3.88e-15117
tube5.40e-15192
organism subdivision7.04e-15264
embryonic structure9.87e-15564
germ layer2.06e-13560
germ layer / neural crest2.06e-13560
embryonic tissue2.06e-13560
presumptive structure2.06e-13560
germ layer / neural crest derived structure2.06e-13560
epiblast (generic)2.06e-13560
organ part1.08e-12218
vasculature5.90e-1278
vascular system5.90e-1278
organ1.04e-11503
compound organ1.43e-1168
endoderm-derived structure1.43e-11160
endoderm1.43e-11160
presumptive endoderm1.43e-11160
splanchnic layer of lateral plate mesoderm1.47e-1183
blood vessel endothelium6.76e-1118
endothelium6.76e-1118
cardiovascular system endothelium6.76e-1118
vessel8.54e-1168
head9.53e-1156
primordium1.35e-10160
subdivision of trunk1.40e-10112
epithelial tube open at both ends3.99e-1059
blood vessel3.99e-1059
blood vasculature3.99e-1059
vascular cord3.99e-1059
subdivision of head5.34e-1049
anterior region of body9.65e-1062
craniocervical region9.65e-1062
respiratory system1.21e-0974
trunk region element1.92e-09101
renal system2.35e-0948
ecto-epithelium4.12e-09104
urinary system structure4.80e-0947
ectodermal placode5.78e-0931
squamous epithelium7.95e-0925
ectoderm-derived structure1.37e-08171
ectoderm1.37e-08171
presumptive ectoderm1.37e-08171
excretory tube1.39e-0816
kidney epithelium1.39e-0816
nephron epithelium2.46e-0815
renal tubule2.46e-0815
nephron tubule2.46e-0815
nephron2.46e-0815
uriniferous tubule2.46e-0815
nephrogenic mesenchyme2.46e-0815
kidney2.47e-0826
kidney mesenchyme2.47e-0826
upper urinary tract2.47e-0826
kidney rudiment2.47e-0826
kidney field2.47e-0826
simple squamous epithelium4.33e-0822
abdomen element1.46e-0754
abdominal segment element1.46e-0754
parenchyma1.63e-0715
digestive system1.86e-07145
digestive tract1.86e-07145
primitive gut1.86e-07145
structure with developmental contribution from neural crest2.35e-07132
sense organ3.35e-0724
sensory system3.35e-0724
entire sense organ system3.35e-0724
cavitated compound organ3.87e-0731
eye5.22e-0721
visual system5.22e-0721


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)
MA0003.17.64574
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.15.83725
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.12.31153
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.13.64286
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.112.1857
MA0074.12.90612
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
MA0103.11.12656
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
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
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.333008
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.224.0142
MA0138.21.95446
MA0002.20.83106
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.22.6393
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.12.98611
MA0155.10.130813
MA0156.10.480289
MA0157.12.04894
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.111.9702
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.215.6929
MA0102.21.66336
MA0258.10.914277
MA0259.11.02361
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
CHD2#110648.275218267293490.0004028373567101730.00387938503434336
CTCF#1066444.288205098460020.005152015588243280.023941948741681
E2F1#186943.925911371903460.007214984547106360.0298804731190119
E2F6#187644.013724585357910.006632118233933880.0283026926095624
EGR1#195843.990543275848110.0067800983001440.0287742974671355
FOXA1#316948.865135799508360.0003075468591372710.0031692043829736



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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