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Coexpression cluster:C1453

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Full id: C1453_argyrophil_hepatocellular_Intestinal_small_liver_hepatoblastoma_gastrointestinal



Phase1 CAGE Peaks

  Short description
Hg19::chr19:36611472..36611485,+ p@chr19:36611472..36611485
+
Hg19::chr1:117008831..117008843,+ p@chr1:117008831..117008843
+
Hg19::chr1:117008851..117008867,+ p@chr1:117008851..117008867
+
Hg19::chr1:21996297..21996310,- p9@RAP1GAP
Hg19::chr1:235814345..235814362,- p9@GNG4
Hg19::chr9:139693833..139693853,+ p10@KIAA1984


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:0009966regulation of signal transduction0.0232625119888189
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.0304795437772065
GO:0005834heterotrimeric G-protein complex0.0304795437772065
GO:0019897extrinsic to plasma membrane0.0308855156143789



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
liver4.91e-1819
digestive gland4.91e-1819
liver bud4.91e-1819
hepatic diverticulum1.60e-1522
liver primordium1.60e-1522
digestive tract diverticulum7.88e-1523
exocrine gland1.50e-1431
exocrine system1.50e-1431
epithelial sac1.31e-1325
epithelium of foregut-midgut junction1.31e-1325
anatomical boundary1.31e-1325
hepatobiliary system1.31e-1325
foregut-midgut junction1.31e-1325
septum transversum1.31e-1325
gut epithelium2.91e-1354
sac4.52e-1326
endocrine gland6.90e-1335
gland5.50e-1259
intestinal mucosa1.69e-104
wall of intestine1.69e-104
gastrointestinal system mucosa1.69e-104
gastrointestinal system epithelium1.69e-104
intestinal epithelium1.69e-104
postcentral gyrus1.77e-101
endocrine system7.31e-1045
endo-epithelium2.62e-0882
abdomen element4.34e-0854
abdominal segment element4.34e-0854
abdominal segment of trunk3.32e-0760
abdomen3.32e-0760
Disease
Ontology termp-valuen
somatostatinoma1.10e-101
disease of anatomical entity1.77e-0839


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)
MA0003.10.321379
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.12.02362
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
MA0055.10.808182
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.11.15845
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.51617
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.13.21192
MA0115.11.28169
MA0116.10.323925
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
MA0139.10.226048
MA0140.10.622527
MA0141.12.01346
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.11.16614
MA0146.12.91645
MA0147.10.327615
MA0148.12.43826
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.200862
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.21.66123
MA0112.21.12726
MA0065.21.7308
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.65596
MA0156.10.417278
MA0157.11.89858
MA0158.10
MA0159.10.875329
MA0160.11.46233
MA0161.10
MA0162.10.150673
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.166826
MA0102.21.58513
MA0258.10.788656
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
EP300#203366.77394172622321.03454107484288e-050.000269644210919679
FOSL2#2355411.28680040304110.0001656657722157630.00203792315482239
FOXA1#316959.234516457821213.31890114386024e-050.000659982323997753
FOXA2#3170520.52538646055446.3869668268396e-072.91160379060803e-05
HDAC2#3066511.17968353052191.29408913564529e-050.000316963825604264
HEY1#2346253.366759202588090.004423827045203030.020951390929347
HNF4A#3172519.27690863579478.72194926701819e-073.78600024729058e-05
HNF4G#3174523.96118543870572.95997618535695e-071.49630664483298e-05
RXRA#6256413.38307809275558.51052088844461e-050.0012765047983172
SIN3A#2594243.605923151210090.01273893844487140.0459422629318664
SP1#666765.69838137814092.91961319085282e-050.000609842964078956
TCF7L2#693447.180117708758230.0009553297120679730.00687620122664831
TRIM28#1015539.295262522631260.00275136505059490.0150926947066065
USF1#739144.240999518138640.007005367750829420.0296064099437064



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.