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Coexpression cluster:C3829

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Full id: C3829_Alveolar_Osteoblast_Mesenchymal_CD19_CD8_Bronchial_CD4



Phase1 CAGE Peaks

  Short description
Hg19::chr19:58898627..58898649,+ p1@RPS5
Hg19::chr6:34393834..34393854,- p1@RPS10
Hg19::chr9:127624220..127624249,- p1@RPL35


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
3.23952687815502e-081.05948726550059e-05392Ribosome (KEGG):03010
3.34751110742684e-081.05948726550059e-05393Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.1037505066909e-060.000116445678455893296Metabolism of proteins (Reactome):REACT_17015
6.2031341872007e-081.30886131349935e-053114Regulation of beta-cell development (Reactome):REACT_13698
3.18533613032144e-060.0002520397213116843421Gene Expression (Reactome):REACT_71
1.29326205516739e-060.0001169478401315653312Diabetes pathways (Reactome):REACT_15380
1.23098667822397e-071.55842913463155e-053143Influenza Infection (Reactome):REACT_6167
1.10547371417187e-071.55842913463155e-053138{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:0005830cytosolic ribosome (sensu Eukaryota)4.85723043455606e-07
GO:0044445cytosolic part4.04684082958443e-06
GO:0033279ribosomal subunit4.43156848706747e-06
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)3.42491428310507e-05
GO:0005829cytosol4.37069685763082e-05
GO:0003735structural constituent of ribosome9.37311511897516e-05
GO:0005840ribosome0.000104438776913281
GO:0003723RNA binding0.000139325905542654
GO:0030529ribonucleoprotein complex0.000176986787891312
GO:0015935small ribosomal subunit0.000176986787891312
GO:0006412translation0.000191170908466735
GO:0009059macromolecule biosynthetic process0.000381477014010147
GO:0044249cellular biosynthetic process0.000670221350290751
GO:0009058biosynthetic process0.00126397184777576
GO:0043232intracellular non-membrane-bound organelle0.00186361035824562
GO:0043228non-membrane-bound organelle0.00186361035824562
GO:0032991macromolecular complex0.00412563219299036
GO:0044446intracellular organelle part0.00444174770396845
GO:0044422organelle part0.00444174770396845
GO:0044444cytoplasmic part0.00580049058691586
GO:0003729mRNA binding0.00671329398745446
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.00734943622756971
GO:0010467gene expression0.00845184466754722
GO:0044267cellular protein metabolic process0.00867222765158901
GO:0044260cellular macromolecule metabolic process0.00867222765158901
GO:0019538protein metabolic process0.00926456805294909
GO:0003676nucleic acid binding0.0115094352670833
GO:0015934large ribosomal subunit0.0155166873431472
GO:0005737cytoplasm0.0173082764382631
GO:0005730nucleolus0.0227175953065135
GO:0043234protein complex0.0308951312220169
GO:0043229intracellular organelle0.0453464256071891
GO:0043226organelle0.0453464256071891
GO:0043170macromolecule metabolic process0.0487865755901209



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
animal cell1.75e-27679
eukaryotic cell1.75e-27679
native cell3.52e-27722
somatic cell1.29e-17588
lymphocyte9.00e-1353
common lymphoid progenitor9.00e-1353
lymphoid lineage restricted progenitor cell1.36e-1252
nucleate cell7.75e-1255
contractile cell8.80e-1159
embryonic cell7.11e-10250
smooth muscle cell3.91e-0943
smooth muscle myoblast3.91e-0943
mesodermal cell4.33e-09121
muscle cell4.35e-0955
electrically responsive cell9.26e-0961
electrically active cell9.26e-0961
muscle precursor cell2.10e-0858
myoblast2.10e-0858
multi-potent skeletal muscle stem cell2.10e-0858
lymphocyte of B lineage6.81e-0824
pro-B cell6.81e-0824
B cell8.46e-0814
epithelial cell1.01e-07253
mature alpha-beta T cell1.32e-0718
alpha-beta T cell1.32e-0718
immature T cell1.32e-0718
mature T cell1.32e-0718
immature alpha-beta T cell1.32e-0718
vascular associated smooth muscle cell2.62e-0732
T cell7.07e-0725
pro-T cell7.07e-0725
Uber Anatomy
Ontology termp-valuen
epithelial vesicle9.60e-1178
multilaminar epithelium4.75e-0983
somite6.83e-0971
presomitic mesoderm6.83e-0971
presumptive segmental plate6.83e-0971
dermomyotome6.83e-0971
trunk paraxial mesoderm6.83e-0971
dense mesenchyme tissue2.31e-0873
paraxial mesoderm2.57e-0872
presumptive paraxial mesoderm2.57e-0872
skeletal muscle tissue7.55e-0862
striated muscle tissue7.55e-0862
myotome7.55e-0862
unilaminar epithelium2.97e-07148
muscle tissue6.38e-0764
musculature6.38e-0764
musculature of body6.38e-0764


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)
MA0003.11.0927
MA0004.10.826076
MA0006.11.5435
MA0007.11.88666
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
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
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
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
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
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
MA0162.11.43223
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.11.29138
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
E2F1#186934.907389214879320.008460985347239390.0325400224142118
ELF1#199734.258097958807540.01295179875054610.0462310027584088
ELK4#2005316.2356816584680.0002336043955745990.00255711240639509
GABPB1#255337.067683836182170.002832212825417420.0154115289571078
GTF2B#2959221.29588662288280.002878180589911410.0155804852863607
GTF2F1#2962312.73966087675770.0004835525047438590.00433901022793572
IRF1#365937.63716375356390.002244692747297240.0128084721540172
MAX#414936.452555509007120.003721913834265510.0186513583291039
MYC#460935.22228187160940.007020843755740150.0294513355426656
NFKB1#479035.488063424193840.006049381815655430.0269616091599555
NFYB#4801211.17319550235760.01025467135054530.0381337945942531
NR2C2#7182221.74307393682720.002762207975496010.0151378621374208
PAX5#507936.669565531177830.003370290999677260.0172908494235542
POU2F2#545239.106124057742520.001324165192682130.00882261490006564
SIN3A#2594235.408884726815140.006318961977991520.0276776576924785
SIX5#147912211.3911435703060.009873820081429030.0370766150895037
SP1#666735.69838137814090.005403962701712170.0246520686906664
TAF7#6879311.43306940492390.0006690181981945830.00543071596465444
TFAP2A#7020211.01242291536330.01054990655215560.0390149672603868
USF1#739136.361499277207960.00388404057290560.0190274081051498
YY1#752834.911170749853860.008441455341808260.0329404107922251



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.