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Coexpression cluster:C3081: Difference between revisions

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{{Coexpression_clusters
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cell cycle spindle assembly checkpoint!0.0123605750498787!472$GO:0031577!spindle checkpoint!0.0123605750498787!472$GO:0010212!response to ionizing radiation!0.0123605750498787!472$GO:0035004!phosphoinositide 3-kinase activity!0.0123605750498787!472$GO:0016303!1-phosphatidylinositol-3-kinase activity!0.0123605750498787!472$GO:0007131!meiotic recombination!0.0151058126866206!472$GO:0007093!mitotic cell cycle checkpoint!0.0158893604484329!472$GO:0007127!meiosis I!0.0160630702308775!472$GO:0001727!lipid kinase activity!0.0160630702308775!472$GO:0047485!protein N-terminus binding!0.0160630702308775!472$GO:0000075!cell cycle checkpoint!0.0182682777581781!472$GO:0004428!inositol or phosphatidylinositol kinase activity!0.0182682777581781!472$GO:0007088!regulation of mitosis!0.0182682777581781!472$GO:0051327!M phase of meiotic cell cycle!0.0182682777581781!472$GO:0007126!meiosis!0.0182682777581781!472$GO:0051321!meiotic cell cycle!0.0182682777581781!472$GO:0009314!response to radiation!0.0244477946042987!472$GO:0009628!response to abiotic stimulus!0.0376850227570919!472$GO:0006310!DNA recombination!0.042605422489093!472$GO:0045786!negative regulation of progression through cell cycle!0.0457285926147825!472$GO:0007067!mitosis!0.0457285926147825!472$GO:0000087!M phase of mitotic cell 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|full_id=C3081_Mast_CD19_pituitary_CD4_CD8_Peripheral_spinal
|id=C3081
}}

Latest revision as of 12:18, 17 September 2013


Full id: C3081_Mast_CD19_pituitary_CD4_CD8_Peripheral_spinal



Phase1 CAGE Peaks

Hg19::chr11:108093755..108093832,+p1@ATM
Hg19::chr11:108094037..108094072,+p2@ATM
Hg19::chr15:62352570..62352658,-p1@VPS13C


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

No results for this coexpression

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:0007094mitotic cell cycle spindle assembly checkpoint0.0123605750498787
GO:0031577spindle checkpoint0.0123605750498787
GO:0010212response to ionizing radiation0.0123605750498787
GO:0035004phosphoinositide 3-kinase activity0.0123605750498787
GO:00163031-phosphatidylinositol-3-kinase activity0.0123605750498787
GO:0007131meiotic recombination0.0151058126866206
GO:0007093mitotic cell cycle checkpoint0.0158893604484329
GO:0007127meiosis I0.0160630702308775
GO:0001727lipid kinase activity0.0160630702308775
GO:0047485protein N-terminus binding0.0160630702308775
GO:0000075cell cycle checkpoint0.0182682777581781
GO:0004428inositol or phosphatidylinositol kinase activity0.0182682777581781
GO:0007088regulation of mitosis0.0182682777581781
GO:0051327M phase of meiotic cell cycle0.0182682777581781
GO:0007126meiosis0.0182682777581781
GO:0051321meiotic cell cycle0.0182682777581781
GO:0009314response to radiation0.0244477946042987
GO:0009628response to abiotic stimulus0.0376850227570919
GO:0006310DNA recombination0.042605422489093
GO:0045786negative regulation of progression through cell cycle0.0457285926147825
GO:0007067mitosis0.0457285926147825
GO:0000087M phase of mitotic cell cycle0.0457285926147825



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><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.17e-21114
neural tube2.45e-1256
neural rod2.45e-1256
future spinal cord2.45e-1256
neural keel2.45e-1256
regional part of nervous system2.77e-1153
regional part of brain2.77e-1153
regional part of forebrain1.97e-1041
forebrain1.97e-1041
anterior neural tube1.97e-1041
future forebrain1.97e-1041
brain2.03e-0968
future brain2.03e-0968
nervous system6.28e-0989
central nervous system8.44e-0981
brain grey matter1.01e-0734
gray matter1.01e-0734
neurectoderm2.77e-0786
telencephalon2.88e-0734
regional part of telencephalon4.87e-0732


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)
MA0003.10.401049
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.12.91768
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.22.96208
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



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
CCNT2#90536.336201576962630.003930750035764890.0189129090106537
CTCF#1066435.360256373075030.0064925092527670.0278240120578471
CTCFL#140690319.74647435897440.0001298372005551160.00171061781112348
E2F1#186934.907389214879320.008460985347239390.0323577153568543
E2F6#187635.017155731697390.00791769806886330.0320410906933514
EGR1#195834.988179094810140.008056488137383440.0319066991991274
ELF1#199734.258097958807540.01295179875054610.0460061529728686
ELK4#2005210.8237877723120.01091284719516480.0401736640188867
ETS1#211339.728760922202340.001085840092584840.00759826153631275
IRF1#365937.63716375356390.002244692747297240.0127603671802186
IRF4#3662214.60967512449610.006056122473217890.0268074669399171
MAX#414936.452555509007120.003721913834265510.0185738225791693
MEF2A#4205318.74323090964410.0001518243905622470.00194795915551971
NFKB1#479035.488063424193840.006049381815655430.0268595947387653
NRF1#4899312.21027944771090.0005492172401020010.00469430389876528
PAX5#507936.669565531177830.003370290999677260.0172273796845778
RAD21#5885310.35503389545630.0009004912073565420.00661692824914584
RFX5#5993312.04791082719510.0005717246050312580.00482937124109184
RXRA#6256213.38307809275550.007196434429465730.0298166547141259
SIN3A#2594235.408884726815140.006318961977991520.0275402107423718
SMC3#9126315.04493284493280.0002935825420371870.0030800067411172
TRIM28#10155212.39368336350830.008368344129438470.032891069265935
USF1#739136.361499277207960.00388404057290560.0189500753710963
USF2#7392312.99219738506960.0004558979393427810.00420391355174119
YY1#752834.911170749853860.008441455341808260.0327921575020685
ZEB1#6935211.25895467836260.01010222676646330.0377929742186717
ZNF143#7702313.50087655222790.0004062804962997170.00387644150859182



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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