Personal tools

Coexpression cluster:C2383

From FANTOM5_SSTAR

Jump to: navigation, search


Full id: C2383_Eosinophils_CD14_Monocytederived_Neutrophils_Alveolar_Mesenchymal_Melanocyte



Phase1 CAGE Peaks

  Short description
Hg19::chr16:67514983..67515130,- p1@ATP6V0D1
Hg19::chr19:48018203..48018358,- p1@NAPA
Hg19::chr19:7587491..7587547,+ p1@MCOLN1
Hg19::chr1:44440575..44440646,+ p1@ATP6V0B


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
0.00012655531054290.01144421593909362132Oxidative phosphorylation (KEGG):00190
2.96233908517502e-070.0001875160640915793121Lysosome (KEGG):04142
0.0001767677946094820.01398675174847522156Phagosome (KEGG):04145
2.10227775867002e-050.00443580607079374254Vibrio cholerae infection (KEGG):05110
3.34441238781418e-050.00529253260371594268Epithelial cell signaling in Helicobacter pylori infection (KEGG):05120
0.0002405290563859760.0169172102991472182Tuberculosis (KEGG):05152
6.13871776917587e-050.00777161669577665292Rheumatoid arthritis (KEGG):05323
8.46702301374934e-050.008932709279505562108Signaling by Insulin receptor (Reactome):REACT_498
1.08913416837795e-050.003447109642916213401Transmembrane transport of small molecules (Reactome):REACT_15518



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:0005774vacuolar membrane2.12690639495335e-06
GO:0044437vacuolar part2.12690639495335e-06
GO:0005773vacuole7.05626795813025e-05
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.000654494485802874
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.000654494485802874
GO:0015985energy coupled proton transport, down electrochemical gradient0.000654494485802874
GO:0015986ATP synthesis coupled proton transport0.000654494485802874
GO:0006754ATP biosynthetic process0.000654494485802874
GO:0006753nucleoside phosphate metabolic process0.000654494485802874
GO:0046034ATP metabolic process0.000679327575874629
GO:0019829cation-transporting ATPase activity0.000679327575874629
GO:0016469proton-transporting two-sector ATPase complex0.000679327575874629
GO:0006812cation transport0.000679327575874629
GO:0008324cation transmembrane transporter activity0.000679327575874629
GO:0009145purine nucleoside triphosphate biosynthetic process0.000679327575874629
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.000679327575874629
GO:0009201ribonucleoside triphosphate biosynthetic process0.000679327575874629
GO:0009142nucleoside triphosphate biosynthetic process0.000679327575874629
GO:0009205purine ribonucleoside triphosphate metabolic process0.000679327575874629
GO:0009144purine nucleoside triphosphate metabolic process0.000679327575874629
GO:0009199ribonucleoside triphosphate metabolic process0.000679327575874629
GO:0015992proton transport0.000679327575874629
GO:0006818hydrogen transport0.000679327575874629
GO:0006752group transfer coenzyme metabolic process0.000680308140524998
GO:0009141nucleoside triphosphate metabolic process0.00071262377934093
GO:0009152purine ribonucleotide biosynthetic process0.00071262377934093
GO:0009150purine ribonucleotide metabolic process0.000722588983265508
GO:0009260ribonucleotide biosynthetic process0.000722588983265508
GO:0006119oxidative phosphorylation0.000722588983265508
GO:0006164purine nucleotide biosynthetic process0.000722588983265508
GO:0006163purine nucleotide metabolic process0.000765303057262317
GO:0009259ribonucleotide metabolic process0.000765303057262317
GO:0009108coenzyme biosynthetic process0.000976243098870716
GO:0006810transport0.000976243098870716
GO:0015078hydrogen ion transmembrane transporter activity0.000992598112457579
GO:0051234establishment of localization0.000992598112457579
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.000992598112457579
GO:0015075ion transmembrane transporter activity0.00100129924810985
GO:0015077monovalent inorganic cation transmembrane transporter activity0.00102071509263668
GO:0051188cofactor biosynthetic process0.00102071509263668
GO:0006811ion transport0.00102071509263668
GO:0051179localization0.0012022022451786
GO:0009165nucleotide biosynthetic process0.00125724219440041
GO:0044444cytoplasmic part0.00125724219440041
GO:0031090organelle membrane0.00125724219440041
GO:0022891substrate-specific transmembrane transporter activity0.00125724219440041
GO:0022890inorganic cation transmembrane transporter activity0.00134974205414562
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.00134974205414562
GO:0043492ATPase activity, coupled to movement of substances0.00134974205414562
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.00137805436761323
GO:0006732coenzyme metabolic process0.00137805436761323
GO:0022857transmembrane transporter activity0.00137805436761323
GO:0015399primary active transmembrane transporter activity0.0014539511882513
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0014539511882513
GO:0022892substrate-specific transporter activity0.0016371179135362
GO:0009117nucleotide metabolic process0.00176300585492439
GO:0051186cofactor metabolic process0.00176300585492439
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.00198205606435121
GO:0033176proton-transporting V-type ATPase complex0.00229343837091778
GO:0016471vacuolar proton-transporting V-type ATPase complex0.00229343837091778
GO:0045176apical protein localization0.00257799018318488
GO:0008105asymmetric protein localization0.00317023212644919
GO:0042623ATPase activity, coupled0.00369739411654434
GO:0015672monovalent inorganic cation transport0.00369739411654434
GO:0006891intra-Golgi vesicle-mediated transport0.00506942459940437
GO:0016887ATPase activity0.00506942459940437
GO:0008553hydrogen-exporting ATPase activity, phosphorylative mechanism0.00527870060479556
GO:0019905syntaxin binding0.00547717104572753
GO:0022804active transmembrane transporter activity0.00547717104572753
GO:0005737cytoplasm0.00560961641398419
GO:0000149SNARE binding0.00581075732840653
GO:0031902late endosome membrane0.00791013438453246
GO:0006944membrane fusion0.00993720419036831
GO:0006091generation of precursor metabolites and energy0.00993720419036831
GO:0043231intracellular membrane-bound organelle0.0100104220092021
GO:0043227membrane-bound organelle0.0100104220092021
GO:0017111nucleoside-triphosphatase activity0.0108493781914646
GO:0016462pyrophosphatase activity0.0115653026832529
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.0116131230087479
GO:0016817hydrolase activity, acting on acid anhydrides0.0116181970340841
GO:0005765lysosomal membrane0.0122026095197474
GO:0005770late endosome0.0122026095197474
GO:0044446intracellular organelle part0.012978169055937
GO:0044422organelle part0.012978169055937
GO:0016020membrane0.0133078004997655
GO:0016310phosphorylation0.0185497400184379
GO:0043229intracellular organelle0.0187225231232309
GO:0044440endosomal part0.0187225231232309
GO:0010008endosome membrane0.0187225231232309
GO:0043226organelle0.0187225231232309
GO:0048193Golgi vesicle transport0.0191564945824311
GO:0006793phosphorus metabolic process0.0251155195204847
GO:0006796phosphate metabolic process0.0251155195204847
GO:0007420brain development0.0288998111940217
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0298220377738366
GO:0044249cellular biosynthetic process0.0314260659506957
GO:0044424intracellular part0.0364240838290581
GO:0006816calcium ion transport0.0364240838290581
GO:0005768endosome0.0380096433782001
GO:0005764lysosome0.0389788408700863
GO:0000323lytic vacuole0.0389788408700863
GO:0030182neuron differentiation0.040111091519398
GO:0007417central nervous system development0.0442719283451152
GO:0046872metal ion binding0.0442719283451152
GO:0045045secretory pathway0.0442719283451152
GO:0048699generation of neurons0.0442719283451152
GO:0009058biosynthetic process0.0442719283451152
GO:0015674di-, tri-valent inorganic cation transport0.0444844505046673
GO:0043167ion binding0.0445540920969773
GO:0022008neurogenesis0.0462972966958267
GO:0016044membrane organization and biogenesis0.0496843878099752



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


Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm7.02e-35203
bone marrow1.46e-2676
mesoderm2.42e-26315
mesoderm-derived structure2.42e-26315
presumptive mesoderm2.42e-26315
hemolymphoid system3.60e-26108
hematopoietic system4.59e-2598
blood island4.59e-2598
immune system1.41e-2493
bone element1.53e-2382
skeletal element1.90e-2290
musculoskeletal system2.76e-22167
skeletal system5.85e-20100
multi-cellular organism4.38e-19656
developing anatomical structure1.15e-18581
embryonic structure1.19e-18564
germ layer1.20e-18560
germ layer / neural crest1.20e-18560
embryonic tissue1.20e-18560
presumptive structure1.20e-18560
germ layer / neural crest derived structure1.20e-18560
epiblast (generic)1.20e-18560
anatomical system2.42e-18624
anatomical group4.66e-18625
embryo5.49e-16592
circulatory system8.11e-11112
cardiovascular system1.83e-10109
tissue1.23e-09773
artery2.25e-0942
arterial blood vessel2.25e-0942
arterial system2.25e-0942
organ2.34e-09503
splanchnic layer of lateral plate mesoderm2.40e-0883
vasculature5.47e-0878
vascular system5.47e-0878
vessel7.39e-0868
tube1.60e-07192
systemic artery1.74e-0733
systemic arterial system1.74e-0733
epithelial tube open at both ends5.74e-0759
blood vessel5.74e-0759
blood vasculature5.74e-0759
vascular cord5.74e-0759


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
MA0004.15.48953
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.110.5809
MA0059.12.50216
MA0060.11.01899
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
MA0073.10.380957
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.19.86257
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
MA0119.11.43218
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
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
MA0102.21.75932
MA0258.11.07498
MA0259.10.471671
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#467422.46317452600873.92475754624726e-060.00012733698458295
CCNT2#90546.336201576962630.0006203100587215640.00511807254090863
E2F1#186944.907389214879320.001724022357361790.0106440748983511
E2F4#1874412.66806031528443.88145892637771e-050.000726219435349269
E2F6#187645.017155731697390.00157802193473060.0099641495067309
ELF1#199744.258097958807540.003041525565781240.0160780426463849
EP300#203335.08045629466740.01144298405398240.0418860862054488
ETS1#211349.728760922202340.0001115955317418140.00154451706063918
FOS#235348.99795530889440.0001525147711168630.0019477244045823
FOSL2#2355312.69765045342130.000787568572975710.00616588262316418
GABPB1#255335.300762877136630.01012678824234270.0378536734875459
HEY1#2346244.040111043105710.00375304636917980.0185862017995528
HMGN3#932448.178547723350590.0002234570284440470.00248008805458745
IRF1#365947.63716375356390.0002938853996185490.00307268968372826
MAX#414946.452555509007120.0005767613195645490.00485190297656077
MXI1#460137.471178721569470.003741314738550960.018631469100683
MYC#460945.22228187160940.001344309395272740.00887025075391012
NANOG#79923321.93358386075950.0001557535816382770.00196482042670854
NFE2#4778477.2042606516292.80776035215453e-081.9165992380305e-06
NFKB1#479045.488063424193840.001102199566301980.00767570984230261
NR3C1#2908311.22976749837980.001131672068063850.00775427759588773
NRF1#4899412.21027944771094.49717228915276e-050.000793244682835375
PAX5#507946.669565531177830.0005052774169483260.00443600102123959
POU2F2#545236.829593043306890.004860473775203740.0227552008520936
RXRA#6256210.03730856956660.01391703805920110.048876237065872
SIN3A#2594245.408884726815140.001168172384885160.00795635553052177
SIX5#147912312.81503651659420.0007664471136930380.006014951165238
SMARCB1#6598313.68953683586810.0006305783409379340.0051815083673656
SMARCC2#6601247.07768721344880.0006669282967095870.00545018187637344
SRF#6722310.34788369662590.001439893778401260.00923659887736929
STAT1#6772210.35329374859960.01310777476171260.0464890443284037
TAF1#687243.343046285745290.008005664898701650.0321887829203273
TBP#690843.706770687096390.005296377814784350.0243935615892689
THAP1#55145431.36914460285131.03171810326891e-064.31697143378613e-05
USF1#739146.361499277207960.0006105011399140830.00507644335601011
USF2#7392412.99219738506963.50833029870167e-050.000681179602279426
YY1#752844.911170749853860.00171871838055440.0106737960960172
ZNF143#7702310.12565741417090.001534861610688180.00976423291458021



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.