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Coexpression cluster:C1572: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.26722,4.86949,0.500341,1.57627,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,2.11893,0.721271,0.453496,1.20439,0.963929,2.70927,0.287891,0.969147,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,1.55072,0.458349,1.90917,0.598009,1.00172,2.53869,1.38854,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,1.06799,0.580638,0.132849,1.14615,0.476793,0.533483,0.734485,0.609718,0.785708,0.458489,0.817229,0.746838,1.06581,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.05625,1.23387,0.741483,2.82451,1.25519,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.99322,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,1.70662,0.549347,1.11542,2.20213,1.05402,1.23742,0.631235,1.37132,0.412056,1.49495,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,1.44357,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,3.51312,0.177807,0.126633,1.15522,1.51895,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,1.29666,0.906429,0.754576,0.35004,0.731946,0.443702
|tfbs_overrepresentation_for_novel_motifs=1.26722,4.86949,0.500341,1.57627,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,0.621241,0.778743,2.11893,0.721271,0.453496,1.20439,0.963929,2.70927,0.287891,0.969147,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.25115,1.55072,0.458349,1.90917,0.598009,1.00172,2.53869,1.38854,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,1.06799,0.580638,0.132849,1.14615,0.476793,0.533483,0.734485,0.609718,0.785708,0.458489,0.817229,0.746838,1.06581,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.86107,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.05625,1.23387,0.741483,2.82451,1.25519,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.99322,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,1.70662,0.549347,1.11542,2.20213,1.05402,1.23742,0.631235,1.37132,0.412056,1.49495,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,1.44357,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,3.51312,0.177807,0.126633,1.15522,1.51895,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,1.29666,0.906429,0.754576,0.35004,0.731946,0.443702
|tfbs_overrepresentation_jaspar=MA0003.1;0.481059,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.161847,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;1.7452,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.569896,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;4.86996,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.00220137,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;1.3271,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;3.01153,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;2.17648,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.868598,MA0146.1;0.6031,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.0575907,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.449243,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.514087,MA0155.1;1.3196,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.21472,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.00732454,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:01, 22 January 2013


Full id: C1572_small_pineal_smallcell_carcinoid_amygdala_peripheral_thalamus



Phase1 CAGE Peaks

Hg19::chr10:1700804..1700825,-p@chr10:1700804..1700825
-
Hg19::chr10:1779648..1779662,-p6@ADARB2
Hg19::chr10:1779663..1779676,-p9@ADARB2
Hg19::chr10:1779683..1779697,-p11@ADARB2
Hg19::chr10:1779710..1779726,-p2@ADARB2


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
neuron3.82e-076
neuroblast3.82e-076
electrically signaling cell3.82e-076
Uber Anatomy
Ontology termp-valuen
nervous system7.60e-5589
central nervous system1.68e-5481
neural tube2.30e-5456
neural rod2.30e-5456
future spinal cord2.30e-5456
neural keel2.30e-5456
regional part of nervous system1.17e-5053
regional part of brain1.17e-5053
regional part of forebrain6.91e-4641
forebrain6.91e-4641
anterior neural tube6.91e-4641
future forebrain6.91e-4641
brain9.83e-4568
future brain9.83e-4568
neurectoderm3.91e-4486
neural plate4.20e-4182
presumptive neural plate4.20e-4182
adult organism3.54e-40114
brain grey matter5.05e-3734
gray matter5.05e-3734
telencephalon6.06e-3734
pre-chordal neural plate2.04e-3661
cerebral hemisphere9.11e-3532
regional part of telencephalon2.32e-3432
organ system subdivision2.12e-33223
regional part of cerebral cortex2.18e-3022
ectoderm-derived structure2.47e-30171
ectoderm2.47e-30171
presumptive ectoderm2.47e-30171
ecto-epithelium7.64e-30104
neocortex1.63e-2720
cerebral cortex5.99e-2625
pallium5.99e-2625
structure with developmental contribution from neural crest1.06e-23132
anatomical cluster4.25e-16373
organ part9.86e-14218
basal ganglion7.11e-139
nuclear complex of neuraxis7.11e-139
aggregate regional part of brain7.11e-139
collection of basal ganglia7.11e-139
cerebral subcortex7.11e-139
neural nucleus1.61e-129
nucleus of brain1.61e-129
larynx7.25e-129
tube4.93e-11192
diencephalon2.90e-107
future diencephalon2.90e-107
posterior neural tube5.26e-1015
chordal neural plate5.26e-1015
gyrus6.44e-106
telencephalic nucleus6.52e-107
upper respiratory tract2.07e-0919
limbic system7.26e-095
anatomical conduit7.77e-09240
multi-tissue structure7.78e-09342
parietal lobe1.50e-085
temporal lobe1.77e-086
occipital lobe3.86e-085
segmental subdivision of nervous system4.81e-0813
respiratory primordium2.89e-0738
endoderm of foregut2.89e-0738
regional part of diencephalon4.05e-074
respiratory tract4.64e-0754
segmental subdivision of hindbrain6.70e-0712
hindbrain6.70e-0712
presumptive hindbrain6.70e-0712
Disease
Ontology termp-valuen
neuroectodermal tumor9.60e-0710


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)
MA0003.10.481059
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.14.86996
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.13.01153
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.12.17648
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.868598
MA0146.10.6031
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0575907
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.11.3196
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.00732454
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
IRF4#3662417.53161014939532.08739444052064e-050.000460607200451162
MAX#414945.16204440720570.002526309009485180.0139933803575509
NFKB1#479044.390450739355070.004707732692524960.0221933237643141
RFX5#599349.638328661756080.000221480125815720.00249554028051224
SP1#666744.558705102512720.00407573565781680.0194741401942871
ZNF263#1012746.577473309608540.0009875103237900160.00708926249012273



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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