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Coexpression cluster:C3715: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3715_occipital_paracentral_medial_amygdala_postcentral_parietal_brain
|id=C3715
}}

Latest revision as of 12:31, 17 September 2013


Full id: C3715_occipital_paracentral_medial_amygdala_postcentral_parietal_brain



Phase1 CAGE Peaks

Hg19::chr18:29265234..29265252,-p@chr18:29265234..29265252
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Hg19::chr18:29265256..29265304,-p@chr18:29265256..29265304
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Hg19::chr18:29265316..29265333,-p@chr18:29265316..29265333
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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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube4.20e-2456
neural rod4.20e-2456
future spinal cord4.20e-2456
neural keel4.20e-2456
regional part of nervous system1.43e-2353
regional part of brain1.43e-2353
brain3.35e-2368
future brain3.35e-2368
central nervous system6.00e-2381
regional part of forebrain1.38e-2041
forebrain1.38e-2041
anterior neural tube1.38e-2041
future forebrain1.38e-2041
nervous system3.02e-2089
neural plate2.65e-1982
presumptive neural plate2.65e-1982
ecto-epithelium1.36e-17104
cerebral hemisphere2.35e-1732
telencephalon3.13e-1734
brain grey matter3.40e-1734
gray matter3.40e-1734
pre-chordal neural plate2.10e-1661
neurectoderm2.31e-1686
regional part of telencephalon3.47e-1632
tube1.52e-15192
structure with developmental contribution from neural crest1.83e-15132
regional part of cerebral cortex3.34e-1422
adult organism3.57e-14114
cerebral cortex5.16e-1425
pallium5.16e-1425
anatomical conduit8.19e-14240
cell layer3.98e-13309
epithelium5.11e-13306
neocortex5.25e-1320
anatomical cluster1.87e-12373
ectoderm-derived structure1.21e-11171
ectoderm1.21e-11171
presumptive ectoderm1.21e-11171
organ system subdivision1.87e-09223
multi-tissue structure3.38e-08342
organ part4.27e-08218


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)
MA0003.13.22681
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
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
MA0038.10.94098
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
MA0057.10.886807
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
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
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
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.13.943
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
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.21.62945
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
MA0162.11.43223
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.26.30148
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
CTCF#1066435.360256373075030.0064925092527670.0279271488405986
E2F1#186934.907389214879320.008460985347239390.0325112895025877
E2F6#187635.017155731697390.00791769806886330.0321957821450714
EBF1#187938.9064668465690.00141523283560980.00914694610546769
EGR1#195834.988179094810140.008056488137383440.0320464489861437
ELF1#199734.258097958807540.01295179875054610.0461962675355447
GABPB1#255337.067683836182170.002832212825417420.0154018992592434
NFKB1#479035.488063424193840.006049381815655430.0269455106173599
PAX5#507936.669565531177830.003370290999677260.0172823597837332
SRF#6722313.79717826216780.0003806615025800190.00374878893615791
TAF7#6879311.43306940492390.0006690181981945830.0054252342263564
YY1#752834.911170749853860.008441455341808260.0329145848214715



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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