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Coexpression cluster:C3996

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Full id: C3996_Fibroblast_normal_Preadipocyte_tenocyte_cholangiocellular_medulloblastoma_liposarcoma



Phase1 CAGE Peaks

  Short description
Hg19::chr1:75599672..75599682,- p@chr1:75599672..75599682
-
Hg19::chr1:75599683..75599699,- -
p@chr1:75599683..75599699
Hg19::chr1:75600067..75600094,+ p2@LHX8


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


No GOStat results

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


Cell Type
Ontology termp-valuen
fibroblast of periodontium1.06e-356
fibroblast of gingiva2.60e-305
fibroblast9.56e-1976
preadipocyte of the breast1.34e-083
Uber Anatomy
Ontology termp-valuen
mouth1.82e-3729
stomodeum1.82e-3729
periodontium1.06e-356
dentition1.06e-356
skull1.56e-307
cranial skeletal system4.11e-2611
subdivision of head3.92e-2449
anterior region of body5.12e-2162
craniocervical region5.12e-2162
head1.03e-2056
axial skeletal system2.50e-2014
gingiva7.01e-198
subdivision of skeletal system1.13e-1716
oral opening3.70e-1622
surface structure1.58e-1399
orifice9.33e-1236
mouth mucosa1.59e-1113
digestive system2.00e-10145
digestive tract2.00e-10145
primitive gut2.00e-10145
mucosa3.40e-1020
endoderm-derived structure4.40e-09160
endoderm4.40e-09160
presumptive endoderm4.40e-09160
ectoderm-derived structure3.92e-08171
ectoderm3.92e-08171
presumptive ectoderm3.92e-08171
organism subdivision1.12e-07264
primary palate mesenchyme1.55e-071
pneumatized bone1.55e-071
subdivision of skeleton1.55e-071
intramembranous bone1.55e-071
head bone1.55e-071
dermal bone1.55e-071
irregular bone1.55e-071
mesenchyme derived from head neural crest1.55e-071
facial mesenchyme1.55e-071
head or neck bone1.55e-071
embryonic nasal process1.55e-071
cranial neural crest1.55e-071
roof of mouth1.55e-071
mesenchyme of upper jaw1.55e-071
mesenchyme from rhombencephalic neural crest1.55e-071
membrane bone1.55e-071
pharyngeal arch mesenchymal region1.55e-071
1st arch mesenchyme1.55e-071
1st arch maxillary mesenchyme1.55e-071
1st arch mesenchyme from neural crest1.55e-071
pharyngeal arch mesenchyme from neural crest1.55e-071
maxillary process mesenchyme1.55e-071
maxilla1.55e-071
dermatocranium1.55e-071
skeleton of upper jaw1.55e-071
upper jaw region1.55e-071
frontonasal prominence1.55e-071
premaxilla1.55e-071
primary palate1.55e-071
pharyngeal arch 11.55e-071
dermal skeleton1.55e-071
entire pharyngeal arch associated mesenchyme1.55e-071
maxillary prominence1.55e-071
1st arch maxillary component1.55e-071
skeleton1.55e-071
medial nasal prominence1.55e-071
maxillary process mesenchyme from neural crest1.55e-071
rhombencephalon neural crest1.55e-071
1st arch maxillary mesenchyme from neural crest1.55e-071
intralobular bile duct3.20e-071
acinus3.20e-071
intrahepatic bile duct3.20e-071
portal lobule3.20e-071
hepatic acinus3.20e-071


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.12.74347
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.12.63873
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.13.44314
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.12.07172
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.22.07067
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.12.22591
MA0259.10.575594
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
SPI1#668838.204323508522730.001810593189410520.0109146633251859
SUZ12#23512350.11578091106297.93834897779404e-060.000222809252591194



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.