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Coexpression cluster:C1455

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Full id: C1455_Tracheal_Corneal_Keratinocyte_Mammary_Urothelial_Bronchial_Esophageal



Phase1 CAGE Peaks

  Short description
Hg19::chr19:45281118..45281181,+ p1@CBLC
Hg19::chr19:45281215..45281224,+ p2@CU688574
Hg19::chr19:45281245..45281260,+ p1@CU688574
Hg19::chr1:26856236..26856292,+ p2@RPS6KA1
Hg19::chr22:37915562..37915598,- p3@CARD10
Hg19::chr22:40390930..40390994,+ p1@FAM83F


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0007175negative regulation of epidermal growth factor receptor activity0.00847707066194942
GO:0042059negative regulation of epidermal growth factor receptor signaling pathway0.00847707066194942
GO:0032449CBM complex0.00847707066194942
GO:0007176regulation of epidermal growth factor receptor activity0.0158169451647997
GO:0007250activation of NF-kappaB-inducing kinase0.0158169451647997
GO:0042058regulation of epidermal growth factor receptor signaling pathway0.0158169451647997
GO:0065009regulation of a molecular function0.0158169451647997
GO:0030159receptor signaling complex scaffold activity0.0188285090913903
GO:0032947protein complex scaffold0.0188285090913903
GO:0007173epidermal growth factor receptor signaling pathway0.0277273132276541
GO:0006468protein amino acid phosphorylation0.0277273132276541
GO:0007165signal transduction0.0277273132276541
GO:0007154cell communication0.0323588363159623
GO:0016310phosphorylation0.032800513276824
GO:0019538protein metabolic process0.032800513276824
GO:0032147activation of protein kinase activity0.0370140841269794
GO:0006793phosphorus metabolic process0.0385749904955098
GO:0006796phosphate metabolic process0.0385749904955098
GO:0009968negative regulation of signal transduction0.0462629851426927



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.04e-25160
endoderm3.04e-25160
presumptive endoderm3.04e-25160
digestive system9.41e-20145
digestive tract9.41e-20145
primitive gut9.41e-20145
subdivision of digestive tract1.34e-17118
renal system5.17e-1548
urinary system structure1.18e-1447
immaterial anatomical entity7.09e-14117
trunk region element5.82e-13101
endo-epithelium6.87e-1382
organ1.47e-12503
anatomical space4.47e-1295
organism subdivision6.05e-12264
embryo4.22e-11592
respiratory system4.17e-1074
foregut4.33e-1087
organ part4.66e-10218
orifice5.53e-1036
multi-cellular organism9.43e-10656
multi-tissue structure2.08e-09342
developing anatomical structure2.85e-09581
subdivision of trunk3.12e-09112
anatomical system1.65e-08624
kidney1.66e-0826
kidney mesenchyme1.66e-0826
upper urinary tract1.66e-0826
kidney rudiment1.66e-0826
kidney field1.66e-0826
anterior region of body1.70e-0862
craniocervical region1.70e-0862
nephron tubule epithelium1.80e-0810
anatomical group2.06e-08625
excretory tube2.20e-0816
kidney epithelium2.20e-0816
reproductive structure2.56e-0859
reproductive system2.56e-0859
epithelial bud3.27e-0837
nephron epithelium4.00e-0815
renal tubule4.00e-0815
nephron tubule4.00e-0815
nephron4.00e-0815
uriniferous tubule4.00e-0815
nephrogenic mesenchyme4.00e-0815
head4.15e-0856
exocrine gland5.07e-0831
exocrine system5.07e-0831
primordium5.73e-08160
abdomen element6.61e-0854
abdominal segment element6.61e-0854
oral opening7.60e-0822
cavitated compound organ8.24e-0831
gland2.59e-0759
gut epithelium3.96e-0754
subdivision of head4.04e-0749
reproductive organ5.27e-0748
intestine6.93e-0717
gastrointestinal system7.05e-0725
anatomical cavity8.35e-0761
Disease
Ontology termp-valuen
carcinoma3.50e-14106
squamous cell carcinoma5.95e-1014
cell type cancer1.76e-08143


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.15.21839
MA0004.12.35384
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.12.54844
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
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
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.13.00536
MA0059.10.457555
MA0060.10.737586
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
MA0073.10.347876
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.12.7063
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.11.94389
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.13.26878
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
MA0139.11.86787
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.11.47313
MA0145.10.707171
MA0146.14.73432
MA0147.12.3862
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.210.2989
MA0138.21.80506
MA0002.20.255126
MA0137.21.06611
MA0104.22.90014
MA0047.20.695777
MA0112.21.65732
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.3291
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.16.43468
MA0163.13.77571
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.27.49373
MA0102.21.58513
MA0258.11.43672
MA0259.12.42942
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
HEY1#2346253.366759202588090.004423827045203030.0209523410627164
POLR2A#543062.147453176558070.01019570676818780.0380336971519365
STAT3#677435.259732498577120.01377662058078550.0484743776307749
TAF1#687252.785871904787740.01078636340290410.0397950052082767
USF1#739144.240999518138640.007005367750829420.0296076080502154
USF2#739248.661464923379730.0004635355081435620.0042679348439571



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.