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Coexpression cluster:C2150

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Full id: C2150_left_heart_tongue_diaphragm_skeletal_throat_iPS



Phase1 CAGE Peaks

  Short description
Hg19::chr11:63742116..63742139,+ p1@ENST00000535431
Hg19::chr16:2009598..2009610,+ p2@NDUFB10
Hg19::chr16:58768148..58768173,- p2@GOT2
Hg19::chr17:46970196..46970219,+ p2@ATP5G1


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
6.34702985400389e-050.006696116495974112132Oxidative phosphorylation (KEGG):00190
6.31961929821581e-050.0066961164959741131138Metabolic pathways (KEGG):01100
0.0001016701891415990.009193889960947472167Alzheimer's disease (KEGG):05010
6.15571812123322e-050.006696116495974112130Parkinson's disease (KEGG):05012
0.0001221036367457750.009661450257509442183Huntington's disease (KEGG):05016
4.32324164114602e-050.006696116495974112109Electron Transport Chain (Wikipathways):WP111
1.30154892898757e-050.00669611649597411260Oxidative phosphorylation (Wikipathways):WP623
2.38132621447758e-050.00669611649597411281Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305



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 membrane6.82918866373343e-05
GO:0019866organelle inner membrane6.82918866373343e-05
GO:0031966mitochondrial membrane7.60730372543529e-05
GO:0005740mitochondrial envelope7.60730372543529e-05
GO:0044429mitochondrial part0.000131288369820187
GO:0031967organelle envelope0.000131288369820187
GO:0031975envelope0.000131288369820187
GO:0005739mitochondrion0.00047366066166673
GO:0044455mitochondrial membrane part0.00062342863819871
GO:0006119oxidative phosphorylation0.000970045477986535
GO:0031090organelle membrane0.00118959530382525
GO:0004069aspartate transaminase activity0.00219291790159512
GO:0006533aspartate catabolic process0.003759066507952
GO:0006531aspartate metabolic process0.003759066507952
GO:0009068aspartate family amino acid catabolic process0.00613926641404257
GO:0005753mitochondrial proton-transporting ATP synthase complex0.00986522591619858
GO:0045263proton-transporting ATP synthase complex, coupling factor F(o)0.0124210485008482
GO:0033177proton-transporting two-sector ATPase complex, proton-transporting domain0.0124210485008482
GO:0044446intracellular organelle part0.0133772210105688
GO:0044422organelle part0.0133772210105688
GO:0045259proton-transporting ATP synthase complex0.014401696749241
GO:0006091generation of precursor metabolites and energy0.0151895890322062
GO:0044444cytoplasmic part0.0153386794966899
GO:0009066aspartate family amino acid metabolic process0.0153386794966899
GO:0030964NADH dehydrogenase complex (quinone)0.0209292682243403
GO:0045271respiratory chain complex I0.0209292682243403
GO:0005747mitochondrial respiratory chain complex I0.0209292682243403
GO:0008483transaminase activity0.0215879191646015
GO:0006120mitochondrial electron transport, NADH to ubiquinone0.0236841567176141
GO:0016310phosphorylation0.0236841567176141
GO:0016769transferase activity, transferring nitrogenous groups0.0236841567176141
GO:0050136NADH dehydrogenase (quinone) activity0.0236841567176141
GO:0008137NADH dehydrogenase (ubiquinone) activity0.0236841567176141
GO:0003954NADH dehydrogenase activity0.0236841567176141
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.0236841567176141
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.0236841567176141
GO:0042775organelle ATP synthesis coupled electron transport0.0236841567176141
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor0.0236841567176141
GO:0005746mitochondrial respiratory chain0.0236841567176141
GO:0042773ATP synthesis coupled electron transport0.0236841567176141
GO:0015985energy coupled proton transport, down electrochemical gradient0.0236841567176141
GO:0015986ATP synthesis coupled proton transport0.0236841567176141
GO:0006793phosphorus metabolic process0.0236841567176141
GO:0006796phosphate metabolic process0.0236841567176141
GO:0006754ATP biosynthetic process0.0236841567176141
GO:0006753nucleoside phosphate metabolic process0.0236841567176141
GO:0009063amino acid catabolic process0.0242944952463599
GO:0046034ATP metabolic process0.024698602515066
GO:0009310amine catabolic process0.024698602515066
GO:0019829cation-transporting ATPase activity0.024698602515066
GO:0044270nitrogen compound catabolic process0.024698602515066
GO:0016469proton-transporting two-sector ATPase complex0.026727949683397
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.026727949683397
GO:0030170pyridoxal phosphate binding0.0272202797454679
GO:0009145purine nucleoside triphosphate biosynthetic process0.0272202797454679
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0272202797454679
GO:0009201ribonucleoside triphosphate biosynthetic process0.0272202797454679
GO:0005737cytoplasm0.0272202797454679
GO:0009142nucleoside triphosphate biosynthetic process0.0272202797454679
GO:0009205purine ribonucleoside triphosphate metabolic process0.0272202797454679
GO:0009144purine nucleoside triphosphate metabolic process0.0272202797454679
GO:0009199ribonucleoside triphosphate metabolic process0.0272202797454679
GO:0015992proton transport0.0272202797454679
GO:0006818hydrogen transport0.0272202797454679
GO:0006869lipid transport0.0272202797454679
GO:0006752group transfer coenzyme metabolic process0.027401158131206
GO:0009141nucleoside triphosphate metabolic process0.0283221990602095
GO:0009152purine ribonucleotide biosynthetic process0.0283221990602095
GO:0009150purine ribonucleotide metabolic process0.0293294340550967
GO:0009260ribonucleotide biosynthetic process0.0293294340550967
GO:0006164purine nucleotide biosynthetic process0.0293294340550967
GO:0006163purine nucleotide metabolic process0.029991643053738
GO:0009259ribonucleotide metabolic process0.029991643053738
GO:0009058biosynthetic process0.029991643053738
GO:0031980mitochondrial lumen0.0315133858777004
GO:0005759mitochondrial matrix0.0315133858777004
GO:0009108coenzyme biosynthetic process0.0330769873577077
GO:0043231intracellular membrane-bound organelle0.0330769873577077
GO:0043227membrane-bound organelle0.0330769873577077
GO:0015078hydrogen ion transmembrane transporter activity0.0331900151934134
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0334222348775195
GO:0015077monovalent inorganic cation transmembrane transporter activity0.0346519919713304
GO:0051188cofactor biosynthetic process0.0346519919713304
GO:0043234protein complex0.0361460514474408
GO:0019842vitamin binding0.0376539411407996
GO:0009055electron carrier activity0.0382786005924434
GO:0009165nucleotide biosynthetic process0.0382786005924434
GO:0016020membrane0.0398697691353846
GO:0022890inorganic cation transmembrane transporter activity0.0398697691353846
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0398697691353846
GO:0043492ATPase activity, coupled to movement of substances0.0398697691353846
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0402804128244258
GO:0006732coenzyme metabolic process0.0404037484717721
GO:0015399primary active transmembrane transporter activity0.0415947791500103
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0415947791500103
GO:0009117nucleotide metabolic process0.0460605578777584
GO:0051186cofactor metabolic process0.0460605578777584
GO:0043229intracellular organelle0.0477710713261117
GO:0043226organelle0.0477710713261117
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0477710713261117



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 cell5.66e-17253
embryonic cell8.94e-11250
Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.90e-20342
anatomical cluster1.36e-17373
cell layer5.95e-16309
epithelium1.48e-15306
anatomical conduit9.27e-14240
tube2.48e-13192
compound organ8.49e-1168
organism subdivision1.41e-10264
mesenchyme1.55e-10160
entire embryonic mesenchyme1.55e-10160
trunk1.72e-10199
epithelial tube2.67e-10117
organ part8.87e-09218
trunk mesenchyme3.53e-08122
subdivision of trunk1.21e-07112
organ system subdivision1.37e-07223
unilaminar epithelium1.85e-07148
primordium4.80e-07160
embryo5.39e-07592
Disease
Ontology termp-valuen
carcinoma6.93e-12106
cell type cancer8.40e-11143
disease of cellular proliferation1.43e-10239
cancer2.00e-10235


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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0055.11.28887
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.10.604454
MA0060.11.80156
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
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
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.12.00595
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
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
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.13.58384
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
ATF3#467211.23158726300440.01119559039922220.041120318822028
CCNT2#90534.752151182721970.01386206996689490.0487012051425483
E2F4#1874412.66806031528443.88145892637771e-050.000725569516398715
E2F6#187645.017155731697390.00157802193473060.00995091370856955
EGR1#195844.988179094810140.001615011500076050.0101279083737506
ELF1#199744.258097958807540.003041525565781240.0160561003115966
ETS1#211349.728760922202340.0001115955317418140.00154328995492363
GABPB1#255335.300762877136630.01012678824234270.0378374226260029
GTF2F1#296239.554745657568240.001820362319304780.0108961955677368
HEY1#2346244.040111043105710.00375304636917980.0185580422210487
IRF1#365935.727872815172930.008097114790333330.0319863292074901
IRF3#3661223.49097610574480.002641101425375540.0145913029922131
IRF4#3662210.95725634337210.01174530180688030.0428156221783168
JUND#372735.245997956403270.01043432751748420.038666952829668
MAX#414934.839416631755340.01315737137836840.0465937443844233
MXI1#460149.96157162875930.0001015224754950450.0014213010480197
MYC#460945.22228187160940.001344309395272740.0088568211539799
NFKB1#479045.488063424193840.001102199566301980.00766497672826024
PAX5#507935.002174148383370.01196533174786410.0434750654889777
POU2F2#545249.106124057742520.000145395665174930.00188095848819577
RAD21#588537.766275421592250.0033411193858720.0172624501603387
RFX5#599339.035933120396320.002144561191324070.0123805110972691
SIN3A#2594245.408884726815140.001168172384885160.00794495674036343
SP2#6668319.61514787038350.0002171004269245340.00248479468356946
SPI1#668836.153242631392040.006580387113059030.0280899636107567
STAT1#6772210.35329374859960.01310777476171260.0464843086023261
TAF1#687243.343046285745290.008005664898701650.0321294099971372
TAF7#687938.574802053692940.00250055433515240.0140270380389398
TBP#690843.706770687096390.005296377814784350.0243516796213191
USF1#739134.771124457905970.01370465887188020.0482748446126443
YY1#752844.911170749853860.00171871838055440.0106623836618189
ZNF143#7702310.12565741417090.001534861610688180.0097606656371347



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.