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Coexpression cluster:C3243: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3243_occipital_temporal_pons_paracentral_insula_parietal_postcentral
|id=C3243
}}

Latest revision as of 12:22, 17 September 2013


Full id: C3243_occipital_temporal_pons_paracentral_insula_parietal_postcentral



Phase1 CAGE Peaks

Hg19::chr12:117176090..117176112,+p2@RNFT2
Hg19::chr12:117176113..117176135,+p1@RNFT2
Hg19::chr12:117176138..117176147,+p3@RNFT2


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

No GOStat results

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>

Cell Type
Ontology termp-valuen
neural cell7.27e-1025
neurectodermal cell3.04e-0959
migratory neural crest cell1.01e-0841
Uber Anatomy
Ontology termp-valuen
nervous system2.68e-3889
central nervous system2.59e-3581
brain4.89e-2968
future brain4.89e-2968
neural tube1.47e-2856
neural rod1.47e-2856
future spinal cord1.47e-2856
neural keel1.47e-2856
neurectoderm5.30e-2886
regional part of nervous system3.94e-2753
regional part of brain3.94e-2753
neural plate7.91e-2782
presumptive neural plate7.91e-2782
pre-chordal neural plate9.98e-2461
organ system subdivision1.47e-23223
regional part of forebrain9.13e-2341
forebrain9.13e-2341
anterior neural tube9.13e-2341
future forebrain9.13e-2341
ectoderm-derived structure7.11e-21171
ectoderm7.11e-21171
presumptive ectoderm7.11e-21171
telencephalon6.35e-1934
brain grey matter1.56e-1834
gray matter1.56e-1834
ecto-epithelium2.08e-18104
cerebral hemisphere4.70e-1832
regional part of telencephalon1.23e-1732
anatomical cluster5.44e-15373
cerebral cortex2.61e-1425
pallium2.61e-1425
structure with developmental contribution from neural crest3.03e-13132
regional part of cerebral cortex3.49e-1322
neocortex3.86e-1220
organ part1.84e-10218
multi-tissue structure4.10e-09342
tube2.24e-07192
posterior neural tube4.73e-0715
chordal neural plate4.73e-0715
cell layer9.23e-07309
Disease
Ontology termp-valuen
cell type cancer1.36e-19143
carcinoma3.62e-15106
disease of cellular proliferation2.63e-14239
cancer2.70e-14235


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)
MA0003.11.54338
MA0004.11.93041
MA0006.11.5435
MA0007.11.88666
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.13.56214
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.12.8588
MA0059.10.714521
MA0060.16.72372
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
MA0074.12.15449
MA0076.14.21544
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.13.82193
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
MA0131.12.4174
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.12.26598
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.22.70092
MA0104.21.2307
MA0047.20.973066
MA0112.22.07067
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
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
ATF3#467322.46317452600878.81932387510763e-050.00129310875500823
BHLHE40#8553344.87181354697741.10603738662898e-050.000283886553507358
BRCA1#672320.18423064322380.0001215704860271640.00163955320121267
CCNT2#90536.336201576962630.003930750035764890.0189338438790356
CHD2#1106310.34402283411690.0009033701102746880.0065884826080292
E2F1#186934.907389214879320.008460985347239390.0323944881838967
E2F6#187635.017155731697390.00791769806886330.0320758909470137
EGR1#195834.988179094810140.008056488137383440.0319345515629342
ELF1#199734.258097958807540.01295179875054610.0460421699073584
ELK4#2005316.2356816584680.0002336043955745990.0025512296841384
EP300#203336.77394172622320.003216880500103790.0167006900904876
FOS#235338.99795530889440.001372499272417130.0089533074023718
FOSL1#8061339.7135797163731.59554825631833e-050.000370305476314734
GABPB1#255337.067683836182170.002832212825417420.0153690883962262
GATA1#2623313.56030814380040.0004009615963782630.00387060062521022
GTF2F1#2962312.73966087675770.0004835525047438590.00432896794470632
HMGN3#932438.178547723350590.001827766942164210.0108411035706888
IRF1#365937.63716375356390.002244692747297240.0127721855535264
IRF3#3661346.98195221148969.63568551583244e-060.000253295081698471
JUND#372736.994663941871030.002921845042734990.0156273147138936
MAX#414936.452555509007120.003721913834265510.0185924790231432
NANOG#79923329.24477848101273.99627955670032e-050.000734672488333436
NFE2#4778377.2042606516292.17039522930409e-067.82173593351588e-05
NFKB1#479035.488063424193840.006049381815655430.0268767340556106
NFYA#4800318.42558069983050.0001598135507814160.00199126311501555
NFYB#4801316.75979325353650.0002123649923296180.00245100977278296
NRF1#4899312.21027944771090.0005492172401020010.00469814885240502
PAX5#507936.669565531177830.003370290999677260.0172442593432929
PBX3#5090321.91451268674419.49854535978121e-050.00136228862789095
REST#597839.650028716128020.001112636247114590.00765699901241438
RFX5#5993312.04791082719510.0005717246050312580.00483367166071882
SIRT6#515483153.6384039900252.75057764221434e-071.39721584812852e-05
SP1#666735.69838137814090.005403962701712170.0245640868995524
SP2#6668326.15353049384465.58768218891694e-050.000938218553260926
SREBF1#6720347.00584944048839.62099323994382e-060.000254252761383222
STAT1#6772320.70658749719920.0001125992441046670.00154530255651081
TAF7#6879311.43306940492390.0006690181981945830.00541011162224112
TFAP2A#7020316.5186343730450.0002218033880766340.00247541398240389
TFAP2C#7022310.80922860986020.0007916746575753130.00613547859620868
THAP1#55145331.36914460285133.23800758564397e-050.000645370752360822
USF1#739136.361499277207960.00388404057290560.0189660236297778
USF2#7392312.99219738506960.0004558979393427810.00420651337459323
YY1#752834.911170749853860.008441455341808260.032821456924281
ZEB1#6935316.88843201754390.0002075486917327580.00242191930903659
ZNF143#7702313.50087655222790.0004062804962997170.00387963141200019



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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