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Coexpression cluster:C2341

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Full id: C2341_Smooth_Fibroblast_mesenchymal_Hepatic_Adipocyte_Pericytes_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr15:64455164..64455227,-p1@PPIB
Hg19::chr19:13049413..13049432,+p1@CALR
Hg19::chr3:127771233..127771316,+p1@SEC61A1
Hg19::chr3:128369643..128369678,-p1@RPN1


Enriched pathways on this co-expression cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

p.valueFDRnGenesnPathwayName
7.83254338792028e-070.0004957999964553543167Protein processing in endoplasmic reticulum (KEGG):04141
0.0001767677946094820.02237880279756042156Phagosome (KEGG):04145
5.131046541619e-060.001623976230422413312Diabetes pathways (Reactome):REACT_15380
1.44809941098012e-050.002291617317876053441AR up reg. targets (Netpath):NetPath_2
8.74889515724365e-060.00184601687817841235{INS,35} (Static Module):NA



Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0044432endoplasmic reticulum part9.33494354018741e-06
GO:0005783endoplasmic reticulum4.32238704894574e-05
GO:0005788endoplasmic reticulum lumen0.00119892517736691
GO:0048770pigment granule0.00121336223236269
GO:0042470melanosome0.00121336223236269
GO:0051082unfolded protein binding0.00450023955118235
GO:0044446intracellular organelle part0.00450023955118235
GO:0044422organelle part0.00450023955118235
GO:0040020regulation of meiosis0.00450023955118235
GO:0044444cytoplasmic part0.00573535899024002
GO:0006457protein folding0.00838247864021421
GO:0016023cytoplasmic membrane-bound vesicle0.00838247864021421
GO:0031988membrane-bound vesicle0.00838247864021421
GO:0031410cytoplasmic vesicle0.0109134708244856
GO:0031982vesicle0.0109134708244856
GO:0005789endoplasmic reticulum membrane0.0112394684514031
GO:0042175nuclear envelope-endoplasmic reticulum network0.0112394684514031
GO:0030867rough endoplasmic reticulum membrane0.012370741454421
GO:0006886intracellular protein transport0.0127422358547018
GO:0030866cortical actin cytoskeleton organization and biogenesis0.0127422358547018
GO:0030865cortical cytoskeleton organization and biogenesis0.0127422358547018
GO:0006611protein export from nucleus0.0127422358547018
GO:0008250oligosaccharyl transferase complex0.0127422358547018
GO:0018279protein amino acid N-linked glycosylation via asparagine0.0127422358547018
GO:0018196peptidyl-asparagine modification0.0127422358547018
GO:0005791rough endoplasmic reticulum0.0127422358547018
GO:0004579dolichyl-diphosphooligosaccharide-protein glycotransferase activity0.0127422358547018
GO:0004576oligosaccharyl transferase activity0.013009355382734
GO:0005737cytoplasm0.0139458562098636
GO:0022884macromolecule transmembrane transporter activity0.0169667838835292
GO:0015450P-P-bond-hydrolysis-driven protein transmembrane transporter activity0.0169667838835292
GO:0008320protein transmembrane transporter activity0.0176993602305049
GO:0015031protein transport0.0196169772724579
GO:0046907intracellular transport0.0202639729663448
GO:0045184establishment of protein localization0.0202639729663448
GO:0043231intracellular membrane-bound organelle0.0202639729663448
GO:0043227membrane-bound organelle0.0202639729663448
GO:0008104protein localization0.0202639729663448
GO:0031974membrane-enclosed lumen0.0202639729663448
GO:0043233organelle lumen0.0202639729663448
GO:0005515protein binding0.02060231316098
GO:0033036macromolecule localization0.02060231316098
GO:0051168nuclear export0.02060231316098
GO:0012505endomembrane system0.02060231316098
GO:0009897external side of plasma membrane0.0224202744666166
GO:0051649establishment of cellular localization0.0224202744666166
GO:0006487protein amino acid N-linked glycosylation0.022571110402564
GO:0051641cellular localization0.022571110402564
GO:0009306protein secretion0.0235002266741561
GO:0051327M phase of meiotic cell cycle0.0267922280755042
GO:0065002intracellular protein transport across a membrane0.0267922280755042
GO:0007126meiosis0.0267922280755042
GO:0051321meiotic cell cycle0.0270462586568967
GO:0043229intracellular organelle0.0315541271581508
GO:0043226organelle0.0315541271581508
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.0329087021205927
GO:0016859cis-trans isomerase activity0.0329087021205927
GO:0031090organelle membrane0.0331285673484481
GO:0006874cellular calcium ion homeostasis0.0389554397810922
GO:0055074calcium ion homeostasis0.0389554397810922
GO:0018193peptidyl-amino acid modification0.0393270725751541
GO:0006875cellular metal ion homeostasis0.0393270725751541
GO:0055065metal ion homeostasis0.0393270725751541
GO:0044267cellular protein metabolic process0.0418384575583755
GO:0044260cellular macromolecule metabolic process0.0427315939816818
GO:0009986cell surface0.0448250058407225
GO:0019538protein metabolic process0.0448250058407225
GO:0006913nucleocytoplasmic transport0.0448250058407225
GO:0008565protein transporter activity0.0448250058407225
GO:0051169nuclear transport0.0448250058407225
GO:0006486protein amino acid glycosylation0.0483741220471638
GO:0043413biopolymer glycosylation0.0483741220471638
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0483741220471638
GO:0044424intracellular part0.0483741220471638
GO:0009101glycoprotein biosynthetic process0.0483741220471638
GO:0055066di-, tri-valent inorganic cation homeostasis0.0483741220471638



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
epithelial tube1.37e-21117
unilaminar epithelium1.48e-19148
trunk mesenchyme2.06e-19122
epithelial vesicle2.51e-1978
mesenchyme6.74e-19160
entire embryonic mesenchyme6.74e-19160
multilaminar epithelium3.17e-1783
vasculature6.26e-1778
vascular system6.26e-1778
trunk1.00e-16199
somite1.58e-1671
presomitic mesoderm1.58e-1671
presumptive segmental plate1.58e-1671
dermomyotome1.58e-1671
trunk paraxial mesoderm1.58e-1671
artery2.71e-1642
arterial blood vessel2.71e-1642
arterial system2.71e-1642
dense mesenchyme tissue6.19e-1673
paraxial mesoderm1.24e-1572
presumptive paraxial mesoderm1.24e-1572
vessel2.97e-1568
skeletal muscle tissue1.06e-1462
striated muscle tissue1.06e-1462
myotome1.06e-1462
splanchnic layer of lateral plate mesoderm1.18e-1483
epithelial tube open at both ends2.10e-1459
blood vessel2.10e-1459
blood vasculature2.10e-1459
vascular cord2.10e-1459
organism subdivision2.37e-14264
systemic artery2.16e-1333
systemic arterial system2.16e-1333
muscle tissue2.68e-1364
musculature2.68e-1364
musculature of body2.68e-1364
cardiovascular system1.51e-11109
circulatory system1.06e-10112
mesoderm1.37e-09315
mesoderm-derived structure1.37e-09315
presumptive mesoderm1.37e-09315
subdivision of trunk1.01e-07112
integument1.41e-0746
integumental system1.41e-0746
surface structure3.54e-0799
aorta4.39e-0721
aortic system4.39e-0721
abdominal segment of trunk6.01e-0760
abdomen6.01e-0760


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.14.10305
MA0004.10.71247
MA0006.11.31813
MA0007.11.65296
MA0009.11.20602
MA0014.13.76953
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.380957
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.12.47057
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.75643
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.11128
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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

TF#promotersEnrichmentp-valueq-value
ATF3#467211.23158726300440.01119559039922220.0411261041013107
BRCA1#672210.09211532161190.0137713969900260.0484674281462957
CCNT2#90534.752151182721970.01386206996689490.048712675816707
E2F1#186944.907389214879320.001724022357361790.0106396721019032
E2F4#1874412.66806031528443.88145892637771e-050.000725959328101651
ELF1#199744.258097958807540.003041525565781240.0160756016480074
ETS1#211349.728760922202340.0001115955317418140.00154390326395328
GABPB1#255335.300762877136630.01012678824234270.0378496094636235
HEY1#2346244.040111043105710.00375304636917980.0185800345919022
HMGN3#932436.133910792512940.006640696683324720.0282895954033998
IRF1#365935.727872815172930.008097114790333330.0320020651499573
MAX#414934.839416631755340.01315737137836840.0466095485172449
MXI1#460137.471178721569470.003741314738550960.018630580745698
NFKB1#479045.488063424193840.001102199566301980.00767366312279263
NFYA#4800313.81918552487290.0006132411806734510.00508626871572066
NFYB#4801312.56984494015230.000811456397697350.0061864146812989
PAX5#507935.002174148383370.01196533174786410.0434841423347197
POU2F2#545249.106124057742520.000145395665174930.00188259085980715
SIN3A#2594245.408884726815140.001168172384885160.00795324352705481
SIX5#147912312.81503651659420.0007664471136930380.0060144992190989
SP2#6668213.07676524692230.008330036536614940.0328047015779611
TAF1#687243.343046285745290.008005664898701650.0321776337883121
TAF7#687938.574802053692940.00250055433515240.0140292986413635
TBP#690843.706770687096390.005296377814784350.024384958675642
USF1#739134.771124457905970.01370465887188020.0482927615871615
ZNF143#7702310.12565741417090.001534861610688180.00976304353241143



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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