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Coexpression cluster:C3846: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3846_astrocytoma_alveolar_mesothelioma_small_mucinous_Pericytes_Mesenchymal
|id=C3846
}}

Latest revision as of 12:34, 17 September 2013


Full id: C3846_astrocytoma_alveolar_mesothelioma_small_mucinous_Pericytes_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:110198761..110198791,+p4@GSTM4
Hg19::chr1:110198920..110198942,+p3@GSTM4
Hg19::chr1:110198944..110198996,+p2@GSTM4


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
organ system subdivision2.20e-22223
adult organism2.50e-22114
central nervous system1.02e-1881
multi-tissue structure5.16e-18342
brain5.20e-1768
future brain5.20e-1768
neural tube1.08e-1656
neural rod1.08e-1656
future spinal cord1.08e-1656
neural keel1.08e-1656
regional part of nervous system9.83e-1653
regional part of brain9.83e-1653
nervous system1.29e-1589
anatomical cluster2.86e-15373
neurectoderm7.74e-1486
neural plate1.74e-1382
presumptive neural plate1.74e-1382
organ3.48e-13503
multi-cellular organism1.58e-12656
structure with developmental contribution from neural crest2.89e-11132
ectoderm-derived structure3.87e-11171
ectoderm3.87e-11171
presumptive ectoderm3.87e-11171
regional part of forebrain4.64e-1141
forebrain4.64e-1141
anterior neural tube4.64e-1141
future forebrain4.64e-1141
telencephalon2.81e-1034
brain grey matter1.04e-0934
gray matter1.04e-0934
pre-chordal neural plate1.98e-0961
ecto-epithelium2.14e-09104
anatomical group2.14e-09625
cerebral hemisphere2.17e-0932
regional part of telencephalon2.31e-0932
anatomical system2.58e-09624
embryo5.97e-09592
germ layer2.37e-08560
germ layer / neural crest2.37e-08560
embryonic tissue2.37e-08560
presumptive structure2.37e-08560
germ layer / neural crest derived structure2.37e-08560
epiblast (generic)2.37e-08560
developing anatomical structure5.19e-08581
embryonic structure6.13e-08564
organ part7.63e-08218
posterior neural tube3.72e-0715
chordal neural plate3.72e-0715
cerebral cortex4.83e-0725
pallium4.83e-0725


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.16.45108
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
MA0060.10.492218
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
MA0073.10.0834661
MA0074.10.935474
MA0076.11.74184
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
MA0092.11.84783
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
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
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
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.22.74132
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
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.84145
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
CTCF#1066435.360256373075030.0064925092527670.0279478680178771
CTCFL#140690319.74647435897440.0001298372005551160.0017177688610053
E2F6#187635.017155731697390.00791769806886330.0322258951135625
EBF1#187938.9064668465690.00141523283560980.00915204347481439
ELF1#199734.258097958807540.01295179875054610.0462373238662889
GABPB1#255337.067683836182170.002832212825417420.0154147415328454
HNF4A#3172323.13229036295378.07584663437677e-050.00122788374821324
HNF4G#3174328.75342252644684.20470658818262e-050.000756738499678106
IRF1#365937.63716375356390.002244692747297240.0128105719035506
MYC#460935.22228187160940.007020843755740150.0294548847515765
NFKB1#479035.488063424193840.006049381815655430.026965061350629
PAX5#507936.669565531177830.003370290999677260.017293397942188
REST#597839.650028716128020.001112636247114590.00767621991097904
SIN3A#2594235.408884726815140.006318961977991520.0276811404731117
SP1#666735.69838137814090.005403962701712170.0246552994890619
ZBTB7A#5134137.35190930787590.002516255860282270.0140217290466343



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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