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Coexpression cluster:C1236: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1236_acute_Mesenchymal_iPS_Skeletal_Bronchial_chronic_embryonic
|full_id=C1236_acute_Mesenchymal_iPS_Skeletal_Bronchial_chronic_embryonic
|gostat_on_coexpression_clusters=GO:0033279!ribosomal subunit!8.46541406768146e-08!6201;6164;6202;6139$GO:0005830!cytosolic ribosome (sensu Eukaryota)!9.49265585536572e-07!6201;6164;6202$GO:0003735!structural constituent of ribosome!4.18593866862922e-06!6201;6164;6202;6139$GO:0005840!ribosome!4.45499684263136e-06!6201;6164;6202;6139$GO:0003723!RNA binding!5.25917983946982e-06!6201;6164;6202;6139$GO:0044445!cytosolic part!5.25917983946982e-06!6201;6164;6202$GO:0030529!ribonucleoprotein complex!8.23244723203298e-06!6201;6164;6202;6139$GO:0006412!translation!9.11860074703107e-06!6201;6164;6202;6139$GO:0009059!macromolecule biosynthetic process!2.28763759932242e-05!6201;6164;6202;6139$GO:0005843!cytosolic small ribosomal subunit (sensu Eukaryota)!2.6799510277966e-05!6201;6202$GO:0044249!cellular biosynthetic process!4.41598008983352e-05!6201;6164;6202;6139$GO:0005829!cytosol!7.04056771737254e-05!6201;6164;6202$GO:0009058!biosynthetic process!9.61263843812998e-05!6201;6164;6202;6139$GO:0043232!intracellular non-membrane-bound organelle!0.000162564217958898!6201;6164;6202;6139$GO:0043228!non-membrane-bound organelle!0.000162564217958898!6201;6164;6202;6139$GO:0015934!large ribosomal subunit!0.000162564217958898!6164;6139$GO:0015935!small ribosomal subunit!0.000203313742897541!6201;6202$GO:0032991!macromolecular complex!0.000435587953843731!6201;6164;6202;6139$GO:0044446!intracellular organelle part!0.000501752069462546!6201;6164;6202;6139$GO:0044422!organelle part!0.000501752069462546!6201;6164;6202;6139$GO:0044444!cytoplasmic part!0.000730416704183392!6201;6164;6202;6139$GO:0010467!gene expression!0.00138774622843352!6201;6164;6202;6139$GO:0044267!cellular protein metabolic process!0.00145860309969479!6201;6164;6202;6139$GO:0044260!cellular macromolecule metabolic process!0.00147134878170099!6201;6164;6202;6139$GO:0019538!protein metabolic process!0.00162540887295163!6201;6164;6202;6139$GO:0003676!nucleic acid binding!0.00219499584095007!6201;6164;6202;6139$GO:0005737!cytoplasm!0.00400598022910381!6201;6164;6202;6139$GO:0005842!cytosolic large ribosomal subunit (sensu Eukaryota)!0.00753137890643941!6164$GO:0043229!intracellular organelle!0.0154713065329693!6201;6164;6202;6139$GO:0043226!organelle!0.0154713065329693!6201;6164;6202;6139$GO:0043170!macromolecule metabolic process!0.0171758779144423!6201;6164;6202;6139$GO:0005730!nucleolus!0.0269440353263539!6201$GO:0044237!cellular metabolic process!0.0269440353263539!6201;6164;6202;6139$GO:0044238!primary metabolic process!0.026953438245518!6201;6164;6202;6139$GO:0044424!intracellular part!0.0278120385522976!6201;6164;6202;6139$GO:0005622!intracellular!0.0473496982711292!6201;6164;6202;6139$GO:0043234!protein complex!0.0478253109342925!6201;6202
|gostat_on_coexpression_clusters=GO:0033279!ribosomal subunit!8.46541406768146e-08!6201;6164;6202;6139$GO:0005830!cytosolic ribosome (sensu Eukaryota)!9.49265585536572e-07!6201;6164;6202$GO:0003735!structural constituent of ribosome!4.18593866862922e-06!6201;6164;6202;6139$GO:0005840!ribosome!4.45499684263136e-06!6201;6164;6202;6139$GO:0003723!RNA binding!5.25917983946982e-06!6201;6164;6202;6139$GO:0044445!cytosolic part!5.25917983946982e-06!6201;6164;6202$GO:0030529!ribonucleoprotein complex!8.23244723203298e-06!6201;6164;6202;6139$GO:0006412!translation!9.11860074703107e-06!6201;6164;6202;6139$GO:0009059!macromolecule biosynthetic process!2.28763759932242e-05!6201;6164;6202;6139$GO:0005843!cytosolic small ribosomal subunit (sensu Eukaryota)!2.6799510277966e-05!6201;6202$GO:0044249!cellular biosynthetic process!4.41598008983352e-05!6201;6164;6202;6139$GO:0005829!cytosol!7.04056771737254e-05!6201;6164;6202$GO:0009058!biosynthetic process!9.61263843812998e-05!6201;6164;6202;6139$GO:0043232!intracellular non-membrane-bound organelle!0.000162564217958898!6201;6164;6202;6139$GO:0043228!non-membrane-bound organelle!0.000162564217958898!6201;6164;6202;6139$GO:0015934!large ribosomal subunit!0.000162564217958898!6164;6139$GO:0015935!small ribosomal subunit!0.000203313742897541!6201;6202$GO:0032991!macromolecular complex!0.000435587953843731!6201;6164;6202;6139$GO:0044446!intracellular organelle part!0.000501752069462546!6201;6164;6202;6139$GO:0044422!organelle part!0.000501752069462546!6201;6164;6202;6139$GO:0044444!cytoplasmic part!0.000730416704183392!6201;6164;6202;6139$GO:0010467!gene expression!0.00138774622843352!6201;6164;6202;6139$GO:0044267!cellular protein metabolic process!0.00145860309969479!6201;6164;6202;6139$GO:0044260!cellular macromolecule metabolic process!0.00147134878170099!6201;6164;6202;6139$GO:0019538!protein metabolic process!0.00162540887295163!6201;6164;6202;6139$GO:0003676!nucleic acid binding!0.00219499584095007!6201;6164;6202;6139$GO:0005737!cytoplasm!0.00400598022910381!6201;6164;6202;6139$GO:0005842!cytosolic large ribosomal subunit (sensu Eukaryota)!0.00753137890643941!6164$GO:0043229!intracellular organelle!0.0154713065329693!6201;6164;6202;6139$GO:0043226!organelle!0.0154713065329693!6201;6164;6202;6139$GO:0043170!macromolecule metabolic process!0.0171758779144423!6201;6164;6202;6139$GO:0005730!nucleolus!0.0269440353263539!6201$GO:0044237!cellular metabolic process!0.0269440353263539!6201;6164;6202;6139$GO:0044238!primary metabolic process!0.026953438245518!6201;6164;6202;6139$GO:0044424!intracellular part!0.0278120385522976!6201;6164;6202;6139$GO:0005622!intracellular!0.0473496982711292!6201;6164;6202;6139$GO:0043234!protein complex!0.0478253109342925!6201;6202

Revision as of 13:44, 12 September 2012


Full id: C1236_acute_Mesenchymal_iPS_Skeletal_Bronchial_chronic_embryonic



Phase1 CAGE Peaks

Hg19::chr18:47018869..47018896,-p2@RPL17
Hg19::chr18:47018897..47018922,-p3@RPL17
Hg19::chr1:45241186..45241289,+p1@RPS8
Hg19::chr2:3622817..3622828,+p4@RPS7
Hg19::chr2:3622829..3622838,+p5@RPS7
Hg19::chr2:3622840..3622882,+p1@RPS7
Hg19::chr4:109541684..109541697,+p4@RPL34


Enriched pathways on this co-expression cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

p.valueFDRnGenesnPathwayName
1.01011768964648e-103.34070889167409e-08492Ribosome (KEGG):03010
1.05551623749576e-103.34070889167409e-08493Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.133023502997e-081.19533979566183e-064296Metabolism of proteins (Reactome):REACT_17015
2.41231788802606e-105.08999074373498e-084114Regulation of beta-cell development (Reactome):REACT_13698
4.66478822294209e-083.69101368140293e-064421Gene Expression (Reactome):REACT_71
1.40005596835204e-081.2660506113812e-064312Diabetes pathways (Reactome):REACT_15380
6.03784237646204e-107.64390844860094e-084143Influenza Infection (Reactome):REACT_6167
5.22856572235584e-107.64390844860094e-084138{RPS27A,138} (Static Module):NA



Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0033279ribosomal subunit8.46541406768146e-08
GO:0005830cytosolic ribosome (sensu Eukaryota)9.49265585536572e-07
GO:0003735structural constituent of ribosome4.18593866862922e-06
GO:0005840ribosome4.45499684263136e-06
GO:0003723RNA binding5.25917983946982e-06
GO:0044445cytosolic part5.25917983946982e-06
GO:0030529ribonucleoprotein complex8.23244723203298e-06
GO:0006412translation9.11860074703107e-06
GO:0009059macromolecule biosynthetic process2.28763759932242e-05
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)2.6799510277966e-05
GO:0044249cellular biosynthetic process4.41598008983352e-05
GO:0005829cytosol7.04056771737254e-05
GO:0009058biosynthetic process9.61263843812998e-05
GO:0043232intracellular non-membrane-bound organelle0.000162564217958898
GO:0043228non-membrane-bound organelle0.000162564217958898
GO:0015934large ribosomal subunit0.000162564217958898
GO:0015935small ribosomal subunit0.000203313742897541
GO:0032991macromolecular complex0.000435587953843731
GO:0044446intracellular organelle part0.000501752069462546
GO:0044422organelle part0.000501752069462546
GO:0044444cytoplasmic part0.000730416704183392
GO:0010467gene expression0.00138774622843352
GO:0044267cellular protein metabolic process0.00145860309969479
GO:0044260cellular macromolecule metabolic process0.00147134878170099
GO:0019538protein metabolic process0.00162540887295163
GO:0003676nucleic acid binding0.00219499584095007
GO:0005737cytoplasm0.00400598022910381
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.00753137890643941
GO:0043229intracellular organelle0.0154713065329693
GO:0043226organelle0.0154713065329693
GO:0043170macromolecule metabolic process0.0171758779144423
GO:0005730nucleolus0.0269440353263539
GO:0044237cellular metabolic process0.0269440353263539
GO:0044238primary metabolic process0.026953438245518
GO:0044424intracellular part0.0278120385522976
GO:0005622intracellular0.0473496982711292
GO:0043234protein complex0.0478253109342925



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
multilaminar epithelium1.46e-1482
somite2.66e-1483
paraxial mesoderm2.66e-1483
presomitic mesoderm2.66e-1483
presumptive segmental plate2.66e-1483
trunk paraxial mesoderm2.66e-1483
presumptive paraxial mesoderm2.66e-1483
dermomyotome6.27e-1470
mesenchyme4.76e-13238
entire embryonic mesenchyme4.76e-13238
unilaminar epithelium1.85e-12138
skeletal muscle tissue1.40e-1161
striated muscle tissue1.40e-1161
myotome1.40e-1161
trunk mesenchyme1.61e-11143
trunk5.22e-11216
muscle tissue2.80e-1063
musculature2.80e-1063
musculature of body2.80e-1063
artery2.54e-0742
arterial blood vessel2.54e-0742
arterial system2.54e-0742
vasculature6.11e-0779
vascular system6.11e-0779
Disease
Ontology termp-valuen
disease of cellular proliferation2.03e-18239
cancer1.58e-17235
organ system cancer1.09e-08137
cell type cancer2.48e-08143
hematologic cancer1.13e-0751
immune system cancer1.13e-0751
carcinoma2.46e-07106


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BATF#10538310.43905791098730.00213725079298980.0123505967780148
BCL3#602629.61180240320434.00448178379027e-093.2776181270946e-07
BCLAF1#9774515.46617686437274.07501217827014e-060.000129555615490519
BRCA1#672720.18423064322387.31084756176234e-106.92865343469054e-08
CHD2#1106710.34402283411697.88338195961115e-084.72365191325203e-06
CTBP2#1488326.87871443114060.0001350903031296680.0017700032829707
E2F4#187447.238891608733970.001117741430524870.007666368770118
E2F6#187653.583682665498130.004598101897827240.0217274981498135
ELF1#199774.258097958807543.93848941900192e-050.000735440544307423
ELK4#200549.277532376267440.0004328178589665770.00404284629036851
EP300#203365.806235765334176.3256174139893e-050.00103225180796817
ETS1#211356.949114944430240.0002014062633330390.0023935672207828
FAM48A#555782330.0482142857141.55944547998347e-050.000365500283850974
FOSL2#235537.255800259097870.006020775093849750.0269872845504967
FOXA1#316946.332239856791690.001854681016920170.0109435610579732
GABPB1#255344.038676477818380.00980113494696150.036850051577713
GATA3#2625311.67279272451690.001549108698473610.00984467344285538
GTF2B#2959731.94382993432422.93605109232773e-113.41467973309149e-09
GTF2F1#2962712.73966087675771.83364622006546e-081.31889929461031e-06
HDAC2#306647.666068706643580.0008986373447057820.00668657634965283
HEY1#2346274.040111043105715.68979821988558e-050.000950626837764566
HNF4A#3172413.21845163597350.0001099302546513230.00152855889569025
HNF4G#3174416.43052715796964.70133893497423e-050.000822175380157022
IRF1#365955.455116966831360.00064157947210550.00525949124703503
IRF3#3661213.42341491756850.00885816023056540.0336169112034891
IRF4#3662412.52257867813950.0001356731131035550.00177674786952003
JUNB#3726313.11884256849480.00110478999316960.00767890071187542
JUND#372765.995426235889455.24232039014691e-050.000891407846347368
KAT2A#26486528.0771428571431.21570198874926e-162.44166730774968e-14
MAX#414976.452555509007122.14589603858566e-067.77098600464106e-05
MEF2A#4205410.71041766265370.0002487360970091120.00268282032794946
MEF2C#4208317.70486621112460.0004611347670711750.00424807744007642
MYC#460975.22228187160949.4355989882785e-060.000251004717966586
NANOG#79923520.88912748643769.25196150281741e-073.96986691615755e-05
NFKB1#479075.488063424193846.66568321176054e-060.000194892858049569
NR2C2#7182523.29615064660065.39462754436063e-072.51185691531645e-05
NR3C1#290836.417009999074160.008497228015651550.0324333746336756
PAX5#507965.716770455295286.92762487228137e-050.00109906458155278
POLR2A#543072.147453176558070.004747636447610280.022346135605569
POU2F2#545279.106124057742521.92426562613847e-071.0483483449571e-05
REST#597879.650028716128021.28195528172884e-077.32018193922787e-06
RFX5#599346.884520472682910.001352207031528580.0089032373071374
RXRA#6256514.3390122422385.91222266390468e-060.000177483938716741
SETDB1#9869317.28001121914730.000495101030461790.00437831130570694
SIN3A#2594264.636186908698690.0002351678146357830.00256615728688188
SIX5#147912717.0867153554592.34744782955753e-092.00134778670334e-07
SMC3#912636.447828362114080.008384311283437850.0329463874682431
SP1#666754.070272412957780.002549206128991580.0141119759835552
SP2#6668311.20865592593340.001741515330916110.0107178620887182
SPI1#668867.032277293019482.05436318006376e-050.000455242173058941
SRF#6722611.82615279614389.50741412579311e-074.0661131199169e-05
STAT1#6772514.79041964085665.07663030596835e-060.000156539177007685
STAT2#6773327.97018765133170.000120105768178720.00162799822489517
TAF1#687273.343046285745290.0002142336319622450.00246657990172031
TAF7#6879711.43306940492393.91151708659369e-082.59045613828001e-06
TBP#690873.706770687096390.0001039672097505110.00145144117352408
TCF12#693869.11525563044554.4461156654571e-060.000139151295770055
TCF7L2#693446.154386607507050.002064676148138040.0119729434889166
THAP1#55145313.44391911550770.001029040833692380.00728969650885158
TRIM28#1015537.967367876541080.004622341263156460.0218331463607615
WRNIP1#56897578.44283167812581.2872343948194e-091.16699195278249e-07
YY1#752874.911170749853861.45048003565243e-050.000345465642972642
ZBTB33#10009522.61766073570086.24429259373417e-072.86155188326899e-05
ZEB1#693549.650532581453630.0003718916645689250.00369869474868241
ZNF143#7702611.57217990190961.08146108094101e-064.50166256805092e-05
ZZZ3#260094136.807549962991.04657769083544e-087.8976537177141e-07



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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