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Coexpression cluster:C1440: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,1.82196,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,4.6479,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,3.26873,0.436569,0.6169,0.576478,0.387783,3.11928,0.730467,4.1132,0.574247,0.396295,0.547818,1.31499,0.92701,0.302275,0.225641,2.52957,0.909936,1.66498,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,0.0393783,0.468392,0.66382,0.542147,0.0909286,2.71594,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,1.50361,0.186533,1.50144,0.968558,1.59978,2.08535,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,2.12614,0.146905,1.15727,0.218784,1.12235,0.192925,0.84426,0.913168,0.477584,4.50493,0.86037,0.684313,0.272514,1.10535,14.2156,15.0275,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,1.02023,2.36544,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,3.40905,0.877269,0.647343,0.483695,1.74379,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,8.17862,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,3.22613,0.683502,0.29379,0.661335,1.90555
|tfbs_overrepresentation_for_novel_motifs=0.44418,1.82196,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,4.6479,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,3.26873,0.436569,0.6169,0.576478,0.387783,3.11928,0.730467,4.1132,0.574247,0.396295,0.547818,1.31499,0.92701,0.302275,0.225641,2.52957,0.909936,1.66498,0.585658,0.329602,0.248856,0.355745,0.513952,0.0979105,0.390088,0.0393783,0.468392,0.66382,0.542147,0.0909286,2.71594,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,1.50361,0.186533,1.50144,0.968558,1.59978,2.08535,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,2.12614,0.146905,1.15727,0.218784,1.12235,0.192925,0.84426,0.913168,0.477584,4.50493,0.86037,0.684313,0.272514,1.10535,14.2156,15.0275,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,1.02023,2.36544,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,3.40905,0.877269,0.647343,0.483695,1.74379,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,8.17862,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,3.22613,0.683502,0.29379,0.661335,1.90555
|tfbs_overrepresentation_jaspar=MA0003.1;1.04263,MA0004.1;0.558729,MA0006.1;1.79433,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.788761,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;2.69832,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;1.22849,MA0056.1;0,MA0057.1;2.04333,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;9.11474,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;3.22865,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;36.4837,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.993014,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;1.19942,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;2.24895,MA0145.1;3.7317,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;4.88217,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;2.35074,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.413181,MA0155.1;4.31015,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;5.32721,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.150673,MA0163.1;0.813808,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;5.47519,MA0099.2;0.629739,MA0079.2;9.5645,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:56, 22 January 2013


Full id: C1440_gastrointestinal_small_occipital_retinoblastoma_parietal_temporal_carcinoid



Phase1 CAGE Peaks

Hg19::chr18:31804736..31804754,-p@chr18:31804736..31804754
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Hg19::chr18:31804765..31804783,-p@chr18:31804765..31804783
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Hg19::chr18:31804789..31804820,-p@chr18:31804789..31804820
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Hg19::chr18:31804823..31804833,-p@chr18:31804823..31804833
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Hg19::chr18:31804835..31804861,-p@chr18:31804835..31804861
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Hg19::chr18:31804864..31804900,-p@chr18:31804864..31804900
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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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
neuronal stem cell1.63e-118
neural cell8.19e-1125
neurectodermal cell1.25e-0859
neuron1.95e-086
neuroblast1.95e-086
electrically signaling cell1.95e-086
Uber Anatomy
Ontology termp-valuen
central nervous system1.53e-7981
nervous system5.30e-7789
neural tube2.76e-7356
neural rod2.76e-7356
future spinal cord2.76e-7356
neural keel2.76e-7356
regional part of nervous system2.60e-6953
regional part of brain2.60e-6953
brain3.97e-6268
future brain3.97e-6268
regional part of forebrain6.36e-6241
forebrain6.36e-6241
anterior neural tube6.36e-6241
future forebrain6.36e-6241
neurectoderm1.58e-5986
neural plate2.73e-5882
presumptive neural plate2.73e-5882
pre-chordal neural plate1.02e-5161
telencephalon3.89e-5134
brain grey matter4.65e-5134
gray matter4.65e-5134
cerebral hemisphere7.95e-4932
regional part of telencephalon2.23e-4832
ecto-epithelium1.33e-45104
ectoderm-derived structure9.48e-44171
ectoderm9.48e-44171
presumptive ectoderm9.48e-44171
cerebral cortex3.00e-3925
pallium3.00e-3925
adult organism1.24e-37114
regional part of cerebral cortex5.63e-3622
structure with developmental contribution from neural crest4.34e-34132
neocortex2.36e-3320
organ system subdivision3.29e-30223
anatomical cluster1.50e-16373
tube6.41e-15192
basal ganglion1.82e-139
nuclear complex of neuraxis1.82e-139
aggregate regional part of brain1.82e-139
collection of basal ganglia1.82e-139
cerebral subcortex1.82e-139
neural nucleus4.81e-139
nucleus of brain4.81e-139
posterior neural tube7.12e-1315
chordal neural plate7.12e-1315
diencephalon6.78e-127
future diencephalon6.78e-127
temporal lobe8.67e-126
organ part1.15e-10218
telencephalic nucleus1.76e-107
gyrus1.91e-106
anatomical conduit3.09e-10240
epithelium1.38e-09306
segmental subdivision of hindbrain1.95e-0912
hindbrain1.95e-0912
presumptive hindbrain1.95e-0912
parietal lobe2.00e-095
cell layer2.55e-09309
occipital lobe3.26e-095
brainstem3.60e-096
embryo4.03e-09592
limbic system1.13e-085
segmental subdivision of nervous system1.48e-0813
gland of diencephalon3.35e-084
neuroendocrine gland3.35e-084
regional part of diencephalon1.76e-074
corpus striatum3.22e-074
striatum3.22e-074
ventral part of telencephalon3.22e-074
future corpus striatum3.22e-074
germ layer3.24e-07560
germ layer / neural crest3.24e-07560
embryonic tissue3.24e-07560
presumptive structure3.24e-07560
germ layer / neural crest derived structure3.24e-07560
epiblast (generic)3.24e-07560
developing anatomical structure3.37e-07581
embryonic structure5.50e-07564
multi-tissue structure6.11e-07342
multi-cellular organism9.57e-07656


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)
MA0003.11.04263
MA0004.10.558729
MA0006.11.79433
MA0007.10.539222
MA0009.11.03681
MA0014.10.788761
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.12.69832
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.22849
MA0056.10
MA0057.12.04333
MA0058.10.458909
MA0059.10.457555
MA0060.19.11474
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.13.22865
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.136.4837
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.12.24895
MA0145.13.7317
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.24.88217
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.22.35074
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.14.31015
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.15.32721
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.10.813808
MA0164.10.738243
MA0080.20.394469
MA0018.25.47519
MA0099.20.629739
MA0079.29.5645
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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#1066465.360256373075034.21437267579784e-050.000755224550253347
EP300#203366.77394172622321.03454107484288e-050.000269576934419949
JUND#372766.994663941871038.53468650061654e-060.000232123469645284
MAX#414966.452555509007121.3848964723355e-050.000334498618580591
MYC#460965.22228187160944.92821127172503e-050.000854127874224512
NRF1#4899612.21027944771093.01474934717981e-071.51958208045421e-05
POLR2A#543062.147453176558070.01019570676818780.0380282639606716
RAD21#5885610.35503389545638.10515055094479e-073.54181513970763e-05
REST#597869.650028716128021.23743801704917e-064.98983741554435e-05
SRF#6722613.79717826216781.44812893459755e-078.17078000002344e-06
TCF12#6938610.63446490218646.9082259011154e-073.11254618156424e-05
USF2#7392510.82683115422471.51592052313491e-050.000358517263396031
ZNF143#7702613.50087655222791.64963374888971e-079.12049227635216e-06



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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