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Coexpression cluster:C240

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Full id: C240_Adipocyte_Preadipocyte_Osteoblast_Chondrocyte_tenocyte_Synoviocyte_mesenchymal



Phase1 CAGE Peaks

  Short description
Hg19::chr13:114567443..114567462,- p11@GAS6
Hg19::chr14:23080048..23080060,+ p3@ABHD4
Hg19::chr15:68643106..68643126,- p4@ITGA11
Hg19::chr15:68653998..68654015,- p@chr15:68653998..68654015
-
Hg19::chr19:18709616..18709634,- p@chr19:18709616..18709634
-
Hg19::chr19:18893583..18893586,+ p@chr19:18893583..18893586
+
Hg19::chr19:18893717..18893745,+ p@chr19:18893717..18893745
+
Hg19::chr19:18893751..18893758,- p@chr19:18893751..18893758
-
Hg19::chr19:18893910..18893932,- p@chr19:18893910..18893932
-
Hg19::chr19:18895139..18895177,- p@chr19:18895139..18895177
-
Hg19::chr19:18895742..18895757,- p@chr19:18895742..18895757
-
Hg19::chr19:18895812..18895830,- p@chr19:18895812..18895830
-
Hg19::chr19:18895892..18895911,- p@chr19:18895892..18895911
-
Hg19::chr19:18896512..18896527,- p@chr19:18896512..18896527
-
Hg19::chr19:18896607..18896614,- p@chr19:18896607..18896614
-
Hg19::chr19:18896642..18896656,- p@chr19:18896642..18896656
-
Hg19::chr19:18896798..18896823,- p@chr19:18896798..18896823
-
Hg19::chr19:18896862..18896874,- p@chr19:18896862..18896874
-
Hg19::chr19:18896874..18896893,+ p@chr19:18896874..18896893
+
Hg19::chr19:18896885..18896896,- p@chr19:18896885..18896896
-
Hg19::chr19:18896916..18896933,+ p@chr19:18896916..18896933
+
Hg19::chr19:18896920..18896932,- p@chr19:18896920..18896932
-
Hg19::chr19:18896944..18896955,- p@chr19:18896944..18896955
-
Hg19::chr19:18897072..18897100,- p@chr19:18897072..18897100
-
Hg19::chr19:18897375..18897390,- p4@COMP
Hg19::chr19:18897380..18897392,+ p@chr19:18897380..18897392
+
Hg19::chr19:18897438..18897467,- p3@COMP
Hg19::chr19:18898324..18898353,+ p@chr19:18898324..18898353
+
Hg19::chr19:18898325..18898337,- p2@COMP
Hg19::chr19:18898355..18898369,+ p@chr19:18898355..18898369
+
Hg19::chr19:18898379..18898416,+ p@chr19:18898379..18898416
+
Hg19::chr19:18898393..18898405,- p@chr19:18898393..18898405
-
Hg19::chr19:18898451..18898462,- p@chr19:18898451..18898462
-
Hg19::chr19:18899076..18899101,- p@chr19:18899076..18899101
-
Hg19::chr19:18899082..18899091,+ p@chr19:18899082..18899091
+
Hg19::chr19:18899114..18899135,- p@chr19:18899114..18899135
-
Hg19::chr19:18899247..18899272,- p@chr19:18899247..18899272
-
Hg19::chr19:18899276..18899289,- p@chr19:18899276..18899289
-
Hg19::chr19:18899427..18899432,- p@chr19:18899427..18899432
-
Hg19::chr19:18899448..18899459,- p@chr19:18899448..18899459
-
Hg19::chr19:18899462..18899501,- p@chr19:18899462..18899501
-
Hg19::chr19:18899504..18899530,- p@chr19:18899504..18899530
-
Hg19::chr19:18899552..18899562,- p@chr19:18899552..18899562
-
Hg19::chr19:18899674..18899694,- p@chr19:18899674..18899694
-
Hg19::chr19:18899713..18899727,- p@chr19:18899713..18899727
-
Hg19::chr19:18899991..18900007,- p@chr19:18899991..18900007
-
Hg19::chr19:18900020..18900058,- p@chr19:18900020..18900058
-
Hg19::chr19:18900031..18900054,+ p@chr19:18900031..18900054
+
Hg19::chr19:18900083..18900109,- p@chr19:18900083..18900109
-
Hg19::chr19:18900774..18900802,- p@chr19:18900774..18900802
-
Hg19::chr19:18900805..18900820,- p@chr19:18900805..18900820
-
Hg19::chr19:18900836..18900848,- p@chr19:18900836..18900848
-
Hg19::chr19:18900850..18900868,- p@chr19:18900850..18900868
-
Hg19::chr19:18900893..18900901,- p@chr19:18900893..18900901
-
Hg19::chr19:18900904..18900922,- p@chr19:18900904..18900922
-
Hg19::chr19:18901737..18901749,- p7@COMP
Hg19::chr22:31501005..31501034,- p@chr22:31501005..31501034
-


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
0.0002903581890930110.0459491834239692200Focal adhesion (KEGG):04510
5.23707650350948e-050.0288361706736934285ECM-receptor interaction (KEGG):04512
0.0002566225776512870.0459491834239692188Focal Adhesion (Wikipathways):WP306
9.1109543992712e-050.02883617067369343816TGF beta receptor up reg. targets (Netpath):NetPath_7



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:0005509calcium ion binding0.0232138068983212
GO:0048856anatomical structure development0.0268361558672058
GO:0006929substrate-bound cell migration0.0268361558672058
GO:0005518collagen binding0.0424718208543621
GO:0032502developmental process0.049126762771572
GO:0022610biological adhesion0.049126762771572
GO:0007155cell adhesion0.049126762771572
GO:0009653anatomical structure morphogenesis0.049126762771572
GO:0008305integrin complex0.049126762771572
GO:0048513organ development0.049126762771572



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
fat cell4.49e-3615
GAG secreting cell8.22e-309
carbohydrate secreting cell8.22e-309
collagen secreting cell2.61e-236
chondroblast2.61e-236
chondrocyte2.61e-236
preadipocyte1.21e-2212
preadipocyte of the breast2.06e-183
stromal cell2.23e-1828
adipocyte of omentum tissue2.91e-183
fibrocyte7.71e-183
attachment cell7.71e-183
tendon cell7.71e-183
extracellular matrix secreting cell1.50e-1715
omentum preadipocyte2.02e-173
adipocyte of breast5.24e-132
fibroblast1.52e-1176
mesenchymal cell4.28e-11354
connective tissue cell9.33e-11361
motile cell1.46e-09386
synovial cell1.66e-083
subcutaneous fat cell2.51e-083
multi fate stem cell4.25e-08427
somatic stem cell6.77e-08433
stem cell1.24e-07441
perirenal preadipocyte4.25e-071
perirenal adipocyte cell4.51e-071
supportive cell5.58e-078
secretory cell8.52e-0736


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)
MA0003.16.72665
MA0004.10.0206186
MA0006.11.5208
MA0007.10.958891
MA0009.10.222068
MA0014.11.70951
MA0017.12.7124
MA0019.10.473319
MA0024.10.157836
MA0025.10.315513
MA0027.11.68322
MA0028.10.160181
MA0029.10.504821
MA0030.10.946735
MA0031.10.796801
MA0038.10.390349
MA0040.10.17242
MA0041.10.0242142
MA0042.10.0821999
MA0043.10.222275
MA0046.10.214982
MA0048.10.564781
MA0050.10.0183996
MA0051.10.0440688
MA0052.10.17471
MA0055.10.229886
MA0056.10
MA0057.11.24088
MA0058.10.00757512
MA0059.10.112128
MA0060.10.00227143
MA0061.10.904322
MA0063.10
MA0066.14.51523
MA0067.11.16495
MA0068.10.994852
MA0069.10.212494
MA0070.10.205336
MA0071.10.589458
MA0072.10.202487
MA0073.121.6942
MA0074.10.16816
MA0076.10.129579
MA0077.10.197639
MA0078.13.96785
MA0081.10.41442
MA0083.10.227008
MA0084.10.621693
MA0087.10.200944
MA0088.14.25485
MA0089.10
MA0090.10.767429
MA0091.10.0926003
MA0092.10.889337
MA0093.10.0194276
MA0095.10
MA0098.10
MA0100.115.3414
MA0101.10.272814
MA0103.10.395962
MA0105.11.06172
MA0106.10.0586346
MA0107.10.373767
MA0108.20.125525
MA0109.10
MA0111.10.321779
MA0113.10.230055
MA0114.13.07982
MA0115.10.398428
MA0116.15.17343
MA0117.10.247205
MA0119.10.585824
MA0122.10.26509
MA0124.10.365763
MA0125.10.302328
MA0130.10
MA0131.10.08643
MA0132.10
MA0133.10
MA0135.10.242288
MA0136.10.0474597
MA0139.12.14731
MA0140.10.136469
MA0141.12.02396
MA0142.10.111215
MA0143.10.0645373
MA0144.10.103225
MA0145.10.235354
MA0146.11.38216
MA0147.10.0270302
MA0148.10.108219
MA0149.10.0315445
MA0062.20.000103797
MA0035.20.0337499
MA0039.28.79037
MA0138.21.44779
MA0002.20.806291
MA0137.20.00432827
MA0104.20.126247
MA0047.20.443145
MA0112.20.614055
MA0065.27.76331
MA0150.10.0101119
MA0151.10
MA0152.10.0356056
MA0153.10.29008
MA0154.13.15625
MA0155.12.62602
MA0156.10.00447233
MA0157.10.666202
MA0158.10
MA0159.10.586167
MA0160.12.13931
MA0161.10
MA0162.11.61654
MA0163.113.3846
MA0164.10.0690971
MA0080.20.0619771
MA0018.20.0591151
MA0099.20.0356983
MA0079.216.226
MA0102.20.6549
MA0258.11.63912
MA0259.10.42884
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
NANOG#7992363.078397734843440.01305121351582760.0463025914932916
SUZ12#235121210.55069071811851.20506169961436e-091.10109745272112e-07



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