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Coexpression cluster:C1334

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Full id: C1334_Alveolar_gall_Renal_nasal_Prostate_signet_colon



Phase1 CAGE Peaks

  Short description
Hg19::chr11:130029635..130029654,+ p3@ST14
Hg19::chr11:130029668..130029690,+ p1@ST14
Hg19::chr15:41136360..41136365,+ p8@SPINT1
Hg19::chr15:41136369..41136420,+ p3@SPINT1
Hg19::chr17:7165787..7165807,- p1@CLDN7
Hg19::chr19:6464243..6464325,+ p1@CRB3


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


p.valueFDRnGenesnPathwayName
0.0001284814348661150.04066437413512552133Tight junction (KEGG):04530
6.82636944046713e-050.0406643741351255297Cell junction organization (Reactome):REACT_20676



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:0005923tight junction0.00109318546569462
GO:0043296apical junction complex0.00109318546569462
GO:0016327apicolateral plasma membrane0.00109318546569462
GO:0005911intercellular junction0.00222815365861779
GO:0001892embryonic placenta development0.00546259906066675
GO:0030054cell junction0.00907390042342841
GO:0044459plasma membrane part0.00956535539574324
GO:0001890placenta development0.0127967491689525
GO:0016338calcium-independent cell-cell adhesion0.0166780129869154
GO:0001763morphogenesis of a branching structure0.0218233954500037
GO:0005886plasma membrane0.0262091988801033
GO:0019897extrinsic to plasma membrane0.0262091988801033
GO:0001701in utero embryonic development0.0262091988801033
GO:0016324apical plasma membrane0.0330721699696492
GO:0045177apical part of cell0.0380048061144456
GO:0009792embryonic development ending in birth or egg hatching0.0380048061144456
GO:0043009chordate embryonic development0.0380048061144456
GO:0019898extrinsic to membrane0.0404059085111664



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 structure6.11e-25160
endoderm6.11e-25160
presumptive endoderm6.11e-25160
digestive system1.92e-19145
digestive tract1.92e-19145
primitive gut1.92e-19145
subdivision of digestive tract2.22e-18118
respiratory system1.11e-1274
anatomical space1.44e-1295
immaterial anatomical entity2.01e-12117
endo-epithelium5.67e-1282
foregut2.29e-1187
renal system2.70e-1148
trunk region element3.00e-11101
urinary system structure7.70e-1147
epithelial bud1.15e-0937
respiratory tract5.16e-0954
orifice5.87e-0936
organ2.59e-08503
thoracic cavity element2.61e-0834
thoracic cavity2.61e-0834
reproductive structure2.85e-0859
reproductive system2.85e-0859
subdivision of trunk3.35e-08112
nephron tubule epithelium6.93e-0810
thoracic segment organ7.17e-0835
epithelial fold9.77e-0847
male organism3.03e-0722
male reproductive system3.03e-0722
organism subdivision3.57e-07264
reproductive organ5.88e-0748
Disease
Ontology termp-valuen
carcinoma1.63e-17106
squamous cell carcinoma1.67e-1014
cell type cancer1.73e-10143
adenocarcinoma9.09e-0825


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)
MA0003.11.73878
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.14.33274
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.13.78197
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
MA0048.12.79473
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.11.41984
MA0058.11.16137
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.11.59928
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0214749
MA0074.10.660398
MA0076.13.08133
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.12.86388
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.12.64519
MA0105.10.830067
MA0106.11.68738
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
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
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.13.48752
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.21.90691
MA0035.20.621793
MA0039.24.88217
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.11.3291
MA0155.10.0961854
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.11.87239
MA0163.12.08316
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.21.68161
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
E2F1#186954.089491012399440.001749817597761990.0107556471127458
POLR2A#543062.147453176558070.01019570676818780.0379943416528497
SUZ12#23512216.70526030368760.005660234682079570.0255576848232472
TAF1#687263.343046285745290.0007162474284635620.00572641546209186
ZEB1#6935616.88843201754394.30431371220266e-082.827284401187e-06



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.