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Coexpression cluster:C1236

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Full id: C1236_acute_Mesenchymal_iPS_Skeletal_Bronchial_chronic_embryonic



Phase1 CAGE Peaks

  Short description
Hg19::chr18:47018869..47018896,- p2@RPL17
Hg19::chr18:47018897..47018922,- p3@RPL17
Hg19::chr1:45241186..45241289,+ p1@RPS8
Hg19::chr2:3622817..3622828,+ p4@RPS7
Hg19::chr2:3622829..3622838,+ p5@RPS7
Hg19::chr2:3622840..3622882,+ p1@RPS7
Hg19::chr4:109541684..109541697,+ p4@RPL34


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
1.01011768964648e-103.34070889167409e-08492Ribosome (KEGG):03010
1.05551623749576e-103.34070889167409e-08493Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.133023502997e-081.19533979566183e-064296Metabolism of proteins (Reactome):REACT_17015
2.41231788802606e-105.08999074373498e-084114Regulation of beta-cell development (Reactome):REACT_13698
4.66478822294209e-083.69101368140293e-064421Gene Expression (Reactome):REACT_71
1.40005596835204e-081.2660506113812e-064312Diabetes pathways (Reactome):REACT_15380
6.03784237646204e-107.64390844860094e-084143Influenza Infection (Reactome):REACT_6167
5.22856572235584e-107.64390844860094e-084138{RPS27A,138} (Static Module):NA



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:0033279ribosomal subunit8.46541406768146e-08
GO:0005830cytosolic ribosome (sensu Eukaryota)9.49265585536572e-07
GO:0003735structural constituent of ribosome4.18593866862922e-06
GO:0005840ribosome4.45499684263136e-06
GO:0003723RNA binding5.25917983946982e-06
GO:0044445cytosolic part5.25917983946982e-06
GO:0030529ribonucleoprotein complex8.23244723203298e-06
GO:0006412translation9.11860074703107e-06
GO:0009059macromolecule biosynthetic process2.28763759932242e-05
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)2.6799510277966e-05
GO:0044249cellular biosynthetic process4.41598008983352e-05
GO:0005829cytosol7.04056771737254e-05
GO:0009058biosynthetic process9.61263843812998e-05
GO:0043232intracellular non-membrane-bound organelle0.000162564217958898
GO:0043228non-membrane-bound organelle0.000162564217958898
GO:0015934large ribosomal subunit0.000162564217958898
GO:0015935small ribosomal subunit0.000203313742897541
GO:0032991macromolecular complex0.000435587953843731
GO:0044446intracellular organelle part0.000501752069462546
GO:0044422organelle part0.000501752069462546
GO:0044444cytoplasmic part0.000730416704183392
GO:0010467gene expression0.00138774622843352
GO:0044267cellular protein metabolic process0.00145860309969479
GO:0044260cellular macromolecule metabolic process0.00147134878170099
GO:0019538protein metabolic process0.00162540887295163
GO:0003676nucleic acid binding0.00219499584095007
GO:0005737cytoplasm0.00400598022910381
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.00753137890643941
GO:0043229intracellular organelle0.0154713065329693
GO:0043226organelle0.0154713065329693
GO:0043170macromolecule metabolic process0.0171758779144423
GO:0005730nucleolus0.0269440353263539
GO:0044237cellular metabolic process0.0269440353263539
GO:0044238primary metabolic process0.026953438245518
GO:0044424intracellular part0.0278120385522976
GO:0005622intracellular0.0473496982711292
GO:0043234protein complex0.0478253109342925



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
multilaminar epithelium7.15e-1483
unilaminar epithelium7.99e-14148
somite2.67e-1371
presomitic mesoderm2.67e-1371
presumptive segmental plate2.67e-1371
dermomyotome2.67e-1371
trunk paraxial mesoderm2.67e-1371
epithelial vesicle3.04e-1378
paraxial mesoderm1.03e-1272
presumptive paraxial mesoderm1.03e-1272
dense mesenchyme tissue1.72e-1273
skeletal muscle tissue4.08e-1162
striated muscle tissue4.08e-1162
myotome4.08e-1162
trunk4.86e-10199
muscle tissue6.73e-1064
musculature6.73e-1064
musculature of body6.73e-1064
organism subdivision9.42e-10264
trunk mesenchyme1.66e-09122
mesenchyme6.21e-09160
entire embryonic mesenchyme6.21e-09160
vasculature1.08e-0778
vascular system1.08e-0778
artery1.50e-0742
arterial blood vessel1.50e-0742
arterial system1.50e-0742
epithelial tube open at both ends7.10e-0759
blood vessel7.10e-0759
blood vasculature7.10e-0759
vascular cord7.10e-0759
Disease
Ontology termp-valuen
disease of cellular proliferation4.31e-17239
cancer3.37e-16235
organ system cancer4.40e-08137
cell type cancer1.21e-07143
hematologic cancer2.51e-0751
immune system cancer2.51e-0751
carcinoma7.99e-07106


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)
MA0003.10.0462779
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.13.64702
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.11.39213
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.11.04059
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.581146
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.22.39331
MA0035.20.564239
MA0039.20.0553061
MA0138.20.704862
MA0002.20.213296
MA0137.20.95459
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.0015479
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
BATF#10538310.43905791098730.00213725079298980.0123505967780148
BCL3#602629.61180240320434.00448178379027e-093.2776181270946e-07
BCLAF1#9774515.46617686437274.07501217827014e-060.000129555615490519
BRCA1#672720.18423064322387.31084756176234e-106.92865343469054e-08
CHD2#1106710.34402283411697.88338195961115e-084.72365191325203e-06
CTBP2#1488326.87871443114060.0001350903031296680.0017700032829707
E2F4#187447.238891608733970.001117741430524870.007666368770118
E2F6#187653.583682665498130.004598101897827240.0217274981498135
ELF1#199774.258097958807543.93848941900192e-050.000735440544307423
ELK4#200549.277532376267440.0004328178589665770.00404284629036851
EP300#203365.806235765334176.3256174139893e-050.00103225180796817
ETS1#211356.949114944430240.0002014062633330390.0023935672207828
FAM48A#555782330.0482142857141.55944547998347e-050.000365500283850974
FOSL2#235537.255800259097870.006020775093849750.0269872845504967
FOXA1#316946.332239856791690.001854681016920170.0109435610579732
GABPB1#255344.038676477818380.00980113494696150.036850051577713
GATA3#2625311.67279272451690.001549108698473610.00984467344285538
GTF2B#2959731.94382993432422.93605109232773e-113.41467973309149e-09
GTF2F1#2962712.73966087675771.83364622006546e-081.31889929461031e-06
HDAC2#306647.666068706643580.0008986373447057820.00668657634965283
HEY1#2346274.040111043105715.68979821988558e-050.000950626837764566
HNF4A#3172413.21845163597350.0001099302546513230.00152855889569025
HNF4G#3174416.43052715796964.70133893497423e-050.000822175380157022
IRF1#365955.455116966831360.00064157947210550.00525949124703503
IRF3#3661213.42341491756850.00885816023056540.0336169112034891
IRF4#3662412.52257867813950.0001356731131035550.00177674786952003
JUNB#3726313.11884256849480.00110478999316960.00767890071187542
JUND#372765.995426235889455.24232039014691e-050.000891407846347368
KAT2A#26486528.0771428571431.21570198874926e-162.44166730774968e-14
MAX#414976.452555509007122.14589603858566e-067.77098600464106e-05
MEF2A#4205410.71041766265370.0002487360970091120.00268282032794946
MEF2C#4208317.70486621112460.0004611347670711750.00424807744007642
MYC#460975.22228187160949.4355989882785e-060.000251004717966586
NANOG#79923520.88912748643769.25196150281741e-073.96986691615755e-05
NFKB1#479075.488063424193846.66568321176054e-060.000194892858049569
NR2C2#7182523.29615064660065.39462754436063e-072.51185691531645e-05
NR3C1#290836.417009999074160.008497228015651550.0324333746336756
PAX5#507965.716770455295286.92762487228137e-050.00109906458155278
POLR2A#543072.147453176558070.004747636447610280.022346135605569
POU2F2#545279.106124057742521.92426562613847e-071.0483483449571e-05
REST#597879.650028716128021.28195528172884e-077.32018193922787e-06
RFX5#599346.884520472682910.001352207031528580.0089032373071374
RXRA#6256514.3390122422385.91222266390468e-060.000177483938716741
SETDB1#9869317.28001121914730.000495101030461790.00437831130570694
SIN3A#2594264.636186908698690.0002351678146357830.00256615728688188
SIX5#147912717.0867153554592.34744782955753e-092.00134778670334e-07
SMC3#912636.447828362114080.008384311283437850.0329463874682431
SP1#666754.070272412957780.002549206128991580.0141119759835552
SP2#6668311.20865592593340.001741515330916110.0107178620887182
SPI1#668867.032277293019482.05436318006376e-050.000455242173058941
SRF#6722611.82615279614389.50741412579311e-074.0661131199169e-05
STAT1#6772514.79041964085665.07663030596835e-060.000156539177007685
STAT2#6773327.97018765133170.000120105768178720.00162799822489517
TAF1#687273.343046285745290.0002142336319622450.00246657990172031
TAF7#6879711.43306940492393.91151708659369e-082.59045613828001e-06
TBP#690873.706770687096390.0001039672097505110.00145144117352408
TCF12#693869.11525563044554.4461156654571e-060.000139151295770055
TCF7L2#693446.154386607507050.002064676148138040.0119729434889166
THAP1#55145313.44391911550770.001029040833692380.00728969650885158
TRIM28#1015537.967367876541080.004622341263156460.0218331463607615
WRNIP1#56897578.44283167812581.2872343948194e-091.16699195278249e-07
YY1#752874.911170749853861.45048003565243e-050.000345465642972642
ZBTB33#10009522.61766073570086.24429259373417e-072.86155188326899e-05
ZEB1#693549.650532581453630.0003718916645689250.00369869474868241
ZNF143#7702611.57217990190961.08146108094101e-064.50166256805092e-05
ZZZ3#260094136.807549962991.04657769083544e-087.8976537177141e-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


This analysis result is provided for C0 - C305 clusters.