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{{Coexpression_clusters
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Latest revision as of 03:36, 17 September 2013


Full id: C3962_occipital_brain_duodenum_merkel_Neurons_retinoblastoma_parietal



Phase1 CAGE Peaks

  Short description
Hg19::chr1:26232902..26232918,- p1@STMN1
Hg19::chr1:26232930..26232945,- p1@MIR3917
Hg19::chr1:26232951..26232959,- p2@STMN1


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


No results for this coexpression

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:0007052mitotic spindle organization and biogenesis0.0115094783939715
GO:0007051spindle organization and biogenesis0.0115094783939715
GO:0007019microtubule depolymerization0.0115094783939715
GO:0031109microtubule polymerization or depolymerization0.0120098904980572
GO:0051261protein depolymerization0.0138113740727658
GO:0015631tubulin binding0.0167638054868715
GO:0000226microtubule cytoskeleton organization and biogenesis0.0218751576928899
GO:0005874microtubule0.0489403037795832
GO:0007017microtubule-based process0.0489403037795832
GO:0000278mitotic cell cycle0.0489403037795832



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
neural cell1.20e-0825
neurectodermal cell2.35e-0759
Uber Anatomy
Ontology termp-valuen
nervous system2.39e-1089
central nervous system1.55e-0981
ectoderm-derived structure6.18e-08171
ectoderm6.18e-08171
presumptive ectoderm6.18e-08171
cerebral cortex1.04e-0725
pallium1.04e-0725
cerebral hemisphere1.27e-0732
pre-chordal neural plate2.44e-0761
brain4.23e-0768
future brain4.23e-0768
neocortex5.51e-0720
regional part of telencephalon6.43e-0732
telencephalon6.78e-0734
Disease
Ontology termp-valuen
cancer3.77e-20235
disease of cellular proliferation1.17e-19239
hematologic cancer1.67e-1951
immune system cancer1.67e-1951
leukemia3.42e-1839
organ system cancer4.33e-16137
myeloid leukemia3.29e-1431


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)
MA0003.10.401049
MA0004.16.09481
MA0006.11.5435
MA0007.11.88666
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.12.26702
MA0024.14.40988
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.14.13609
MA0059.11.70014
MA0060.12.13518
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
MA0073.17.32221
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.12.37746
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
MA0093.15.11284
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
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
MA0139.10.440097
MA0140.10.894983
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.348055
MA0147.13.48176
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.25.45805
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.12.02335
MA0161.10
MA0162.10.8915
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.10519
MA0102.21.88331
MA0258.11.29138
MA0259.13.52796
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#467322.46317452600878.81932387510763e-050.00129674977642174
BHLHE40#8553344.87181354697741.10603738662898e-050.000284726247528085
CCNT2#90536.336201576962630.003930750035764890.0190206923497776
CHD2#1106310.34402283411690.0009033701102746880.00660786321242318
E2F1#186934.907389214879320.008460985347239390.0325640053316751
E2F4#1874312.66806031528440.0004917987006298980.00437541225786574
E2F6#187635.017155731697390.00791769806886330.0322548062805326
EGR1#195834.988179094810140.008056488137383440.0320916726259655
ELF1#199734.258097958807540.01295179875054610.0462705380621291
ETS1#211339.728760922202340.001085840092584840.00762944385289745
FOS#235338.99795530889440.001372499272417130.00898135661102585
GTF2F1#2962312.73966087675770.0004835525047438590.00434348843579117
HMGN3#932438.178547723350590.001827766942164210.0108794113571577
IRF1#365937.63716375356390.002244692747297240.0128182768787236
JUND#372736.994663941871030.002921845042734990.0156899878872024
MAX#414936.452555509007120.003721913834265510.0186719645949109
MYC#460935.22228187160940.007020843755740150.0294773829550049
NFE2#4778377.2042606516292.17039522930409e-067.83254690232516e-05
NFKB1#479035.488063424193840.006049381815655430.0269800310648349
NFYA#4800318.42558069983050.0001598135507814160.0019981763953143
NFYB#4801316.75979325353650.0002123649923296180.00246025373642962
PAX5#507936.669565531177830.003370290999677260.0173053009692868
POU2F2#545239.106124057742520.001324165192682130.00882937422961942
RDBP#79363153.6384039900252.75057764221434e-071.39925756636738e-05
REST#597839.650028716128020.001112636247114590.00768230973240782
SIN3A#2594235.408884726815140.006318961977991520.0277067076711641
SIRT6#515483153.6384039900252.75057764221434e-071.3999394657662e-05
SIX5#147912317.0867153554590.0002004060546325010.00239887770083252
SMARCB1#6598318.25271578115740.000164397760679890.00203261959602782
SP1#666735.69838137814090.005403962701712170.0246757808938491
TAF7#6879311.43306940492390.0006690181981945830.0054353630183776
TAL1#6886329.86861667744023.75103522793067e-050.000720269108604249
TCF12#6938310.63446490218640.0008313523990202070.00629718691625119
TCF7L2#6934310.77017656313730.0008003181298398380.00614230049693878
USF1#739136.361499277207960.00388404057290560.0190443809105018
USF2#7392312.99219738506960.0004558979393427810.00421881312130256
YY1#752834.911170749853860.008441455341808260.032972442009242
ZBTB7A#5134137.35190930787590.002516255860282270.0140337095905169
ZNF143#7702313.50087655222790.0004062804962997170.00389351520949221



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.