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Coexpression cluster:C1752

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Full id: C1752_left_heart_diaphragm_tongue_skeletal_nonsmall_chronic



Phase1 CAGE Peaks

  Short description
Hg19::chr15:75230368..75230470,- p1@COX5A
Hg19::chr16:23607619..23607645,- p1@NDUFAB1
Hg19::chr19:29704017..29704086,- p1@UQCRFS1
Hg19::chr1:17380510..17380541,- p1@SDHB
Hg19::chr2:176046426..176046445,- p1@ATP5G3


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
1.95890826360539e-124.13329643620737e-105132Oxidative phosphorylation (KEGG):00190
9.98425842405372e-087.90004447803251e-0651138Metabolic pathways (KEGG):01100
7.14406195160067e-050.00452219121536323277Cardiac muscle contraction (KEGG):04260
6.45306136521003e-121.02119696104449e-095167Alzheimer's disease (KEGG):05010
1.81277180396793e-124.13329643620737e-105130Parkinson's disease (KEGG):05012
1.02506741390146e-111.29773534599925e-095183Huntington's disease (KEGG):05016
7.39869346801531e-134.13329643620737e-105109Electron Transport Chain (Wikipathways):WP111
4.32675276711781e-050.00304314944620619260Oxidative phosphorylation (Wikipathways):WP623
3.00081089502779e-103.16585549425432e-08481Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305
1.15784794118768e-081.04702535253114e-06331{CYCS,35} (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:0005743mitochondrial inner membrane7.2853062072682e-09
GO:0019866organelle inner membrane7.2853062072682e-09
GO:0031966mitochondrial membrane1.38927723826689e-08
GO:0005740mitochondrial envelope1.38927723826689e-08
GO:0044429mitochondrial part5.02766866119338e-08
GO:0031967organelle envelope5.02766866119338e-08
GO:0031975envelope5.02766866119338e-08
GO:0006091generation of precursor metabolites and energy3.39472935653337e-07
GO:0005739mitochondrion4.15840126942672e-07
GO:0031090organelle membrane2.95776471166315e-06
GO:0044455mitochondrial membrane part6.8159481496038e-06
GO:0006118electron transport1.44109041859651e-05
GO:00515372 iron, 2 sulfur cluster binding2.07294526011205e-05
GO:0015078hydrogen ion transmembrane transporter activity2.5453239825651e-05
GO:0015077monovalent inorganic cation transmembrane transporter activity2.94318430339811e-05
GO:0009055electron carrier activity4.31458558391117e-05
GO:0022890inorganic cation transmembrane transporter activity5.15813345278657e-05
GO:0016491oxidoreductase activity0.00020066728170363
GO:0044446intracellular organelle part0.000226561805997089
GO:0044422organelle part0.000226561805997089
GO:0005506iron ion binding0.000256993805734495
GO:0022892substrate-specific transporter activity0.000271153402186825
GO:0044444cytoplasmic part0.00033485274735131
GO:0005746mitochondrial respiratory chain0.000350378200014024
GO:0051536iron-sulfur cluster binding0.000454123761373975
GO:0051540metal cluster binding0.000454123761373975
GO:0000036acyl carrier activity0.000898849472674975
GO:00515383 iron, 4 sulfur cluster binding0.000898849472674975
GO:0008324cation transmembrane transporter activity0.000952869621391505
GO:0006119oxidative phosphorylation0.00122936405546985
GO:0008177succinate dehydrogenase (ubiquinone) activity0.00157289396957018
GO:0016635oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor0.00157289396957018
GO:0005737cytoplasm0.00268233112191118
GO:0015075ion transmembrane transporter activity0.00278155976828436
GO:0005750mitochondrial respiratory chain complex III0.00279592670347524
GO:0045275respiratory chain complex III0.00279592670347524
GO:0006732coenzyme metabolic process0.00325469978139115
GO:0022891substrate-specific transmembrane transporter activity0.00376566803596882
GO:0051186cofactor metabolic process0.00436798411105563
GO:0022857transmembrane transporter activity0.00442111345383874
GO:0043231intracellular membrane-bound organelle0.0048177319164742
GO:0043227membrane-bound organelle0.0048177319164742
GO:0005753mitochondrial proton-transporting ATP synthase complex0.00701902077007293
GO:0016020membrane0.00755048581224576
GO:0045263proton-transporting ATP synthase complex, coupling factor F(o)0.00929238040428365
GO:0033177proton-transporting two-sector ATPase complex, proton-transporting domain0.00929238040428365
GO:0043229intracellular organelle0.0113906628961492
GO:0043226organelle0.0113906628961492
GO:0045259proton-transporting ATP synthase complex0.0117981586232232
GO:0016681oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor0.0125653841763755
GO:0008121ubiquinol-cytochrome-c reductase activity0.0125653841763755
GO:0016679oxidoreductase activity, acting on diphenols and related substances as donors0.0125653841763755
GO:0031177phosphopantetheine binding0.0128017131677387
GO:0043234protein complex0.0168600035498525
GO:0043169cation binding0.0168600035498525
GO:0006099tricarboxylic acid cycle0.0168600035498525
GO:00515394 iron, 4 sulfur cluster binding0.0168600035498525
GO:0046356acetyl-CoA catabolic process0.0168600035498525
GO:0030964NADH dehydrogenase complex (quinone)0.0168600035498525
GO:0045271respiratory chain complex I0.0168600035498525
GO:0005747mitochondrial respiratory chain complex I0.0168600035498525
GO:0006084acetyl-CoA metabolic process0.0168600035498525
GO:0004129cytochrome-c oxidase activity0.0168600035498525
GO:0009109coenzyme catabolic process0.0168600035498525
GO:0016676oxidoreductase activity, acting on heme group of donors, oxygen as acceptor0.0168600035498525
GO:0015002heme-copper terminal oxidase activity0.0168600035498525
GO:0016675oxidoreductase activity, acting on heme group of donors0.0168600035498525
GO:0046872metal ion binding0.0173435949224824
GO:0051187cofactor catabolic process0.0179616079764488
GO:0043167ion binding0.0179616079764488
GO:0009060aerobic respiration0.0180251282075584
GO:0006120mitochondrial electron transport, NADH to ubiquinone0.0188170305774173
GO:0044424intracellular part0.0189038473447777
GO:0045333cellular respiration0.0196600140575334
GO:0050136NADH dehydrogenase (quinone) activity0.022868458163971
GO:0008137NADH dehydrogenase (ubiquinone) activity0.022868458163971
GO:0003954NADH dehydrogenase activity0.022868458163971
GO:0006633fatty acid biosynthetic process0.022868458163971
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.022868458163971
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.022868458163971
GO:0042775organelle ATP synthesis coupled electron transport0.0229192437815628
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor0.0229192437815628
GO:0042773ATP synthesis coupled electron transport0.0230985066008147
GO:0015985energy coupled proton transport, down electrochemical gradient0.0230985066008147
GO:0015986ATP synthesis coupled proton transport0.0230985066008147
GO:0046394carboxylic acid biosynthetic process0.0230985066008147
GO:0006754ATP biosynthetic process0.0230985066008147
GO:0006753nucleoside phosphate metabolic process0.0230985066008147
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.0230985066008147
GO:0016053organic acid biosynthetic process0.0230985066008147
GO:0032991macromolecular complex0.0234562649297863
GO:0046034ATP metabolic process0.0252954145620041
GO:0019829cation-transporting ATPase activity0.0252954145620041
GO:0006810transport0.0252954145620041
GO:0051234establishment of localization0.0268075628635383
GO:0016310phosphorylation0.027561748733795
GO:0016469proton-transporting two-sector ATPase complex0.027561748733795
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.027561748733795
GO:0005622intracellular0.0280800180736992
GO:0015980energy derivation by oxidation of organic compounds0.0292458890931553
GO:0009145purine nucleoside triphosphate biosynthetic process0.0293578898059736
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0293578898059736
GO:0009201ribonucleoside triphosphate biosynthetic process0.0293578898059736
GO:0009142nucleoside triphosphate biosynthetic process0.0302681620625602
GO:0051179localization0.0303555756583221
GO:0009205purine ribonucleoside triphosphate metabolic process0.0305242924512726
GO:0009144purine nucleoside triphosphate metabolic process0.0305242924512726
GO:0009199ribonucleoside triphosphate metabolic process0.0305242924512726
GO:0015992proton transport0.0306450127356899
GO:0006818hydrogen transport0.0306450127356899
GO:0006752group transfer coenzyme metabolic process0.0310383140586656
GO:0009141nucleoside triphosphate metabolic process0.032460169643806
GO:0009152purine ribonucleotide biosynthetic process0.032460169643806
GO:0006793phosphorus metabolic process0.0334633945678108
GO:0006796phosphate metabolic process0.0334633945678108
GO:0009150purine ribonucleotide metabolic process0.0334633945678108
GO:0009260ribonucleotide biosynthetic process0.0334633945678108
GO:0006164purine nucleotide biosynthetic process0.0335985227240659
GO:0046914transition metal ion binding0.0343342368163303
GO:0006163purine nucleotide metabolic process0.034805727032307
GO:0009259ribonucleotide metabolic process0.034805727032307
GO:0006631fatty acid metabolic process0.0389637183680753
GO:0009108coenzyme biosynthetic process0.0394470093840013
GO:0044249cellular biosynthetic process0.0399590195081676
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0411754249305958
GO:0051188cofactor biosynthetic process0.043380794214328
GO:0019842vitamin binding0.0478595387983076
GO:0009165nucleotide biosynthetic process0.0493947362250097



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


Cell Type
Ontology termp-valuen
epithelial cell8.27e-09253
embryonic cell1.69e-07250
Uber Anatomy
Ontology termp-valuen
epithelial vesicle1.31e-0778
mesenchyme3.94e-07160
entire embryonic mesenchyme3.94e-07160
multi-tissue structure5.76e-07342
Disease
Ontology termp-valuen
hematologic cancer3.31e-1051
immune system cancer3.31e-1051
leukemia1.20e-0739
cancer2.75e-07235
disease of cellular proliferation3.28e-07239
myeloid leukemia8.58e-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)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.11.33654
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.12656
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.11.29278
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.11.35428
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.21.12758
MA0138.21.95446
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.11.60707
MA0161.10
MA0162.10.81299
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.27276
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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#90545.068961261570110.002709998091280770.0148939373075447
E2F1#186954.907389214879320.0003512818099256460.00352628997951024
E2F4#1874410.13444825222760.0001818201509632970.0022031691317387
EGR1#195843.990543275848110.0067800983001440.0287649464341203
ELF1#199754.258097958807540.0007142416939776840.0057301189335793
EP300#203345.419153380978560.00209386927943890.01211599610368
ESRRA#2101196.7680628272250.01029147057516070.0382311622465393
GABPB1#255345.654147068945740.001776696502096670.01090738337541
HDAC2#306638.049372141975760.003691673992246690.0186258328539252
HEY1#2346254.040111043105710.0009288852205177990.0067411467963073
HMGN3#932458.178547723350592.73180911341838e-050.000581666487250361
HNF4G#3174211.50136901057870.01127438304921050.0413777028947708
IRF1#365946.109731002851120.001315525264767990.00880944749468482
MXI1#460135.976942977255580.008653004889366880.0329508924976514
MYC#460944.177825497287520.005691969036823440.0256776620550647
NANOG#79923211.69791139240510.01091164951956080.0402202923757115
NR2C2#7182319.56876654314450.0002750171700966610.00293116830571743
NRF1#489949.768223558168730.0002101297748106790.00244466342335441
PAX5#507956.669565531177837.57493746384605e-050.00116994808309172
POU2F2#545235.463674434645510.01115650094469780.0410113618726299
PPARGC1A#10891170.01022727272730.01420240419464220.0498197995393223
RXRA#6256312.044770283480.001145262162836830.00783506059377152
SIN3A#2594244.327107781452110.004977052855762880.0232426409945904
SP1#666744.558705102512720.00407573565781680.0194839454555192
SP2#6668210.46141219753790.01353191183347140.0477807606997065
SRF#672238.278306957300690.003404846073776150.0173589806736201
TAF1#687253.343046285745290.002394600090870310.0135300605329152
TAF7#687936.859841642954350.005843286407019040.0262446561330866
TBP#690853.706770687096390.001428755106721120.00918602281401424
TCF7L2#693436.462105937882410.006930108755689190.0293203819459357
USF1#739145.089199421766370.00266867775360040.0147179614462836
YY1#752854.911170749853860.00034993140821360.00352731264766143



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.