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Coexpression cluster:C2408

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Full id: C2408_Alveolar_Renal_Mesenchymal_Mammary_chronic_Smooth_Trabecular



Phase1 CAGE Peaks

  Short description
Hg19::chr17:40761660..40761748,+ p1@TUBG1
Hg19::chr17:76183121..76183140,- p1@TK1
Hg19::chr17:79849438..79849493,- p1@ALYREF
Hg19::chr2:242626195..242626243,- p1@DTYMK


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
3.63651983036618e-050.01150958526310892100Pyrimidine metabolism (KEGG):00240
2.15074464693702e-050.0115095852631089277Metabolism of nucleotides (Reactome):REACT_1698



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:0000212meiotic spindle organization and biogenesis0.00482736289747114
GO:0005827polar microtubule0.00482736289747114
GO:0005816spindle pole body0.00482736289747114
GO:0004797thymidine kinase activity0.0055165801495387
GO:0000242pericentriolar material0.0055165801495387
GO:0019136deoxynucleoside kinase activity0.0055165801495387
GO:0005881cytoplasmic microtubule0.0055165801495387
GO:0000930gamma-tubulin complex0.00603358190524557
GO:0019206nucleoside kinase activity0.00750801537250585
GO:0005876spindle microtubule0.00833620862192411
GO:0007051spindle organization and biogenesis0.00833620862192411
GO:0044450microtubule organizing center part0.00924972184269641
GO:0000794condensed nuclear chromosome0.010684755395396
GO:0000922spindle pole0.010684755395396
GO:0000793condensed chromosome0.0167227884531008
GO:0051321meiotic cell cycle0.0213999825167229
GO:0005819spindle0.0221246261206918
GO:0005200structural constituent of cytoskeleton0.0223487963212117
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0223487963212117
GO:0051258protein polymerization0.0223487963212117
GO:0000228nuclear chromosome0.0223487963212117
GO:0000226microtubule cytoskeleton organization and biogenesis0.0223487963212117
GO:0005813centrosome0.0270249962186935
GO:0005815microtubule organizing center0.0295049287144001
GO:0032553ribonucleotide binding0.0336590258312562
GO:0032555purine ribonucleotide binding0.0336590258312562
GO:0017076purine nucleotide binding0.0348772877197093
GO:0000166nucleotide binding0.0454283255281328
GO:0003924GTPase activity0.0454283255281328
GO:0005874microtubule0.0477435948549856
GO:0007017microtubule-based process0.0488269739331223



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
unilaminar epithelium1.06e-09148
epithelial tube8.68e-09117
trunk1.40e-08199
organism subdivision1.92e-08264
nephron epithelium2.28e-0815
renal tubule2.28e-0815
nephron tubule2.28e-0815
nephron2.28e-0815
uriniferous tubule2.28e-0815
nephrogenic mesenchyme2.28e-0815
parenchyma5.08e-0815
cortex of kidney1.71e-0712
renal parenchyma1.71e-0712
simple squamous epithelium1.90e-0722
excretory tube2.42e-0716
kidney epithelium2.42e-0716
cortex3.37e-0715
epithelial vesicle4.09e-0778
segment of respiratory tract4.87e-0747
Disease
Ontology termp-valuen
cancer4.91e-27235
disease of cellular proliferation2.00e-26239
cell type cancer1.24e-13143
organ system cancer7.86e-13137
carcinoma7.18e-12106
hematologic cancer1.96e-1151
immune system cancer1.96e-1151
leukemia6.39e-0939
myeloid leukemia5.26e-0731


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)
MA0003.10.720743
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.12.32784
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
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.13.69367
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
MA0073.10.100363
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0105.10.232357
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
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.569905
MA0146.11.25938
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.22.01147
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.11128
MA0102.21.75932
MA0258.10.418966
MA0259.13.06353
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
CCNT2#90546.336201576962630.0006203100587215640.00511969039219389
E2F1#186944.907389214879320.001724022357361790.0106465924184312
E2F4#1874412.66806031528443.88145892637771e-050.000726609945889876
E2F6#187645.017155731697390.00157802193473060.00996595711684882
ELF1#199744.258097958807540.003041525565781240.0160821126247786
GABPB1#255347.067683836182170.0004006876864423170.00390185746241017
GATA1#2623310.17023110785030.001515158168498270.00966242925809313
HEY1#2346244.040111043105710.00375304636917980.0185914912370521
HMGN3#932448.178547723350590.0002234570284440470.00248061528419089
IRF1#365935.727872815172930.008097114790333330.0320044874385052
MAX#414934.839416631755340.01315737137836840.0466158731727191
MXI1#460137.471178721569470.003741314738550960.0186332460648318
MYC#460945.22228187160940.001344309395272740.00887193231803408
NANOG#79923214.62238924050630.006698757715363760.0284858125828532
NFYB#4801312.56984494015230.000811456397697350.00618776976629042
NRF1#489939.157709585783180.002061953791733420.0119611415271521
PAX5#507935.002174148383370.01196533174786410.0434856555108458
SIN3A#2594245.408884726815140.001168172384885160.00795791244569962
SP2#6668213.07676524692230.008330036536614940.0328059386043036
TAF1#687243.343046285745290.008005664898701650.0321974598103628
TAF7#687938.574802053692940.00250055433515240.0140300523374332
TBP#690843.706770687096390.005296377814784350.0244000177590764
THAP1#55145215.68457230142570.005840469678357920.026245549362679
USF1#739146.361499277207960.0006105011399140830.00507725183560176
YY1#752844.911170749853860.00171871838055440.0106776056716865
ZBTB7A#5134147.35190930787590.000342223540015990.00346332212167926



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.