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Coexpression cluster:C4126: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;5.30359,MA0004.1;3.20493,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.24048,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;1.70328,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.407479,MA0074.1;2.15449,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;2.626,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;2.29491,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;1.3784,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;1.12079,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;1.98824,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.62945,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;1.2307,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;3.52399,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;1.54885,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;2.40872,MA0442.1;0
}}
}}

Revision as of 21:51, 22 January 2013


Full id: C4126_salivary_astrocytoma_spinal_hippocampus_medulla_thalamus_amygdala



Phase1 CAGE Peaks

Hg19::chr2:131594446..131594472,+p3@ARHGEF4
Hg19::chr2:131594478..131594502,+p2@ARHGEF4
Hg19::chr2:131594505..131594522,+p5@ARHGEF4


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
epithelial cell5.19e-18253
endo-epithelial cell5.10e-1642
endodermal cell1.28e-1158
respiratory epithelial cell1.33e-0813
epithelial cell of alimentary canal6.19e-0820
Uber Anatomy
Ontology termp-valuen
central nervous system6.31e-3481
neural tube1.04e-3356
neural rod1.04e-3356
future spinal cord1.04e-3356
neural keel1.04e-3356
nervous system1.42e-3289
organ system subdivision1.89e-32223
ectoderm-derived structure4.69e-31171
ectoderm4.69e-31171
presumptive ectoderm4.69e-31171
regional part of nervous system6.34e-3153
regional part of brain6.34e-3153
brain4.73e-2968
future brain4.73e-2968
ecto-epithelium6.96e-28104
neurectoderm6.14e-2586
neural plate9.05e-2582
presumptive neural plate9.05e-2582
regional part of forebrain1.16e-2341
forebrain1.16e-2341
anterior neural tube1.16e-2341
future forebrain1.16e-2341
brain grey matter4.07e-2034
gray matter4.07e-2034
telencephalon6.24e-2034
pre-chordal neural plate1.17e-1861
regional part of telencephalon1.54e-1832
adult organism1.84e-18114
cerebral hemisphere2.57e-1832
anatomical cluster1.32e-15373
structure with developmental contribution from neural crest5.01e-15132
organ part4.64e-14218
organ9.72e-14503
cerebral cortex2.54e-1325
pallium2.54e-1325
respiratory system1.82e-1274
regional part of cerebral cortex4.68e-1222
embryo7.29e-12592
posterior neural tube3.92e-1115
chordal neural plate3.92e-1115
multi-tissue structure1.35e-10342
neocortex1.73e-1020
respiratory tract2.39e-1054
multi-cellular organism5.40e-10656
segment of respiratory tract1.13e-0947
anatomical conduit4.25e-09240
respiratory primordium4.60e-0938
endoderm of foregut4.60e-0938
embryonic structure5.32e-09564
developing anatomical structure6.07e-09581
segmental subdivision of nervous system7.88e-0913
neural nucleus1.50e-089
nucleus of brain1.50e-089
anatomical system1.56e-08624
segmental subdivision of hindbrain1.88e-0812
hindbrain1.88e-0812
presumptive hindbrain1.88e-0812
anatomical group2.03e-08625
anatomical space2.86e-0895
organ segment3.22e-0898
basal ganglion3.34e-089
nuclear complex of neuraxis3.34e-089
aggregate regional part of brain3.34e-089
collection of basal ganglia3.34e-089
cerebral subcortex3.34e-089
foregut3.39e-0887
germ layer4.31e-08560
germ layer / neural crest4.31e-08560
embryonic tissue4.31e-08560
presumptive structure4.31e-08560
germ layer / neural crest derived structure4.31e-08560
epiblast (generic)4.31e-08560
endoderm-derived structure6.62e-08160
endoderm6.62e-08160
presumptive endoderm6.62e-08160
digestive system1.62e-07145
digestive tract1.62e-07145
primitive gut1.62e-07145
telencephalic nucleus5.96e-077
subdivision of digestive tract7.15e-07118
Disease
Ontology termp-valuen
carcinoma8.27e-17106
cell type cancer7.74e-13143
squamous cell carcinoma2.64e-0814
cancer1.23e-07235
disease of cellular proliferation1.46e-07239


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)
MA0003.15.30359
MA0004.13.20493
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.11.70328
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
MA0073.10.407479
MA0074.12.15449
MA0076.10.734647
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
MA0093.12.626
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
MA0113.12.29491
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.11.98824
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
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
MA0162.13.52399
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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
BHLHE40#8553344.87181354697741.10603738662898e-050.000284936947760592
E2F1#186934.907389214879320.008460985347239390.0326084670534092
EGR1#195834.988179094810140.008056488137383440.032128434250265
GABPB1#255337.067683836182170.002832212825417420.015442102598474
TCF7L2#6934310.77017656313730.0008003181298398380.00614862624410349
USF1#739136.361499277207960.00388404057290560.0190703452302989



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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