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Coexpression cluster:C1798: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,0.654974,1.15291,0.653236,1.73914,0.324142,0.859849,1.16078,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.501863,0.500405,0.121147,0.645033,0.44943,1.35492,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,0.359091,0.27659,0.417272,0.195238,1.06371,1.57519,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,2.44935,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,1.78554,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,1.66643,1.23387,0.269111,0.255232,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.873042,1.18161,1.89992,4.57343,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.99322,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,2.40164,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,1.05995,0.597842,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,1.55197,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,1.00998,1.29319,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.233587
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,0.654974,1.15291,0.653236,1.73914,0.324142,0.859849,1.16078,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.501863,0.500405,0.121147,0.645033,0.44943,1.35492,0.802434,0.25115,0.642741,0.458349,0.659743,0.598009,1.00172,0.359091,0.27659,0.417272,0.195238,1.06371,1.57519,0.388123,0.301779,0.415749,0.580638,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,2.44935,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,1.78554,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,1.66643,1.23387,0.269111,0.255232,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.873042,1.18161,1.89992,4.57343,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.99322,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,2.40164,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,1.05995,0.597842,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,1.55197,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,1.00998,1.29319,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,1.2893,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.233587
|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;0.369468,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;0.736268,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;1.73592,MA0052.1;1.03442,MA0055.1;0.288856,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;1.74614,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;4.40502,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;0.412364,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;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;1.40074,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,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;0.759606,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.777733,MA0035.2;0.691506,MA0039.2;0.801354,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.425004,MA0065.2;0.880827,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.409315,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;1.72541,MA0163.1;0.680296,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.475695,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:11, 22 January 2013


Full id: C1798_brain_temporal_medial_postcentral_insula_parietal_occipital



Phase1 CAGE Peaks

Hg19::chr18:3874426..3874429,-p21@DLGAP1
Hg19::chr2:56410925..56410946,+p5@CCDC85A
Hg19::chr4:6565771..6565783,-p22@PPP2R2C
Hg19::chr5:149630260..149630271,+p@chr5:149630260..149630271
+
Hg19::chr6:40555176..40555188,-p6@LRFN2


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

GO IDGO nameFDR corrected p-value
GO:0000159protein phosphatase type 2A complex0.0404544285717854
GO:0008601protein phosphatase type 2A regulator activity0.0404544285717854
GO:0008287protein serine/threonine phosphatase complex0.0404544285717854
GO:0019888protein phosphatase regulator activity0.0404544285717854
GO:0019208phosphatase regulator activity0.0404544285717854



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
telencephalon5.23e-7834
cerebral hemisphere1.30e-7532
regional part of nervous system2.17e-7453
regional part of brain2.17e-7453
regional part of cerebral cortex2.69e-7222
brain8.17e-7168
future brain8.17e-7168
brain grey matter9.18e-7134
gray matter9.18e-7134
neocortex1.64e-7020
neural tube3.34e-7056
neural rod3.34e-7056
future spinal cord3.34e-7056
neural keel3.34e-7056
regional part of telencephalon2.65e-6832
regional part of forebrain2.95e-6441
forebrain2.95e-6441
anterior neural tube2.95e-6441
future forebrain2.95e-6441
cerebral cortex1.52e-6325
pallium1.52e-6325
central nervous system3.36e-6381
nervous system1.76e-5689
neural plate1.39e-4682
presumptive neural plate1.39e-4682
neurectoderm3.35e-4486
pre-chordal neural plate4.62e-4261
adult organism3.03e-38114
gyrus4.48e-366
ecto-epithelium1.01e-35104
structure with developmental contribution from neural crest2.09e-29132
ectoderm-derived structure3.21e-27171
ectoderm3.21e-27171
presumptive ectoderm3.21e-27171
organ system subdivision8.74e-23223
parietal lobe7.57e-205
occipital lobe1.28e-195
frontal cortex7.15e-193
tube5.34e-17192
brainstem3.11e-156
temporal lobe4.30e-146
corpus striatum1.98e-134
striatum1.98e-134
ventral part of telencephalon1.98e-134
future corpus striatum1.98e-134
middle frontal gyrus3.25e-132
organ part4.69e-13218
middle temporal gyrus5.28e-132
anatomical conduit1.55e-12240
segmental subdivision of hindbrain1.49e-1112
hindbrain1.49e-1112
presumptive hindbrain1.49e-1112
anatomical cluster2.36e-11373
limbic system4.32e-115
segmental subdivision of nervous system1.19e-1013
basal ganglion1.86e-109
nuclear complex of neuraxis1.86e-109
aggregate regional part of brain1.86e-109
collection of basal ganglia1.86e-109
cerebral subcortex1.86e-109
neural nucleus2.52e-109
nucleus of brain2.52e-109
posterior neural tube3.30e-0915
chordal neural plate3.30e-0915
multi-tissue structure7.51e-09342
epithelium1.12e-08306
cell layer1.54e-08309
medulla oblongata1.69e-083
caudate-putamen1.69e-083
myelencephalon1.69e-083
dorsal striatum1.69e-083
future myelencephalon1.69e-083
pons2.04e-083
telencephalic nucleus6.89e-087
postcentral gyrus1.20e-071
occipital pole1.27e-071
pole of cerebral hemisphere1.27e-071
insula1.54e-071
paracentral gyrus1.85e-071
olfactory region3.85e-071
primary subdivision of skull3.85e-071
cranium3.85e-071
neurocranium3.85e-071
chondrocranium3.85e-071
cartilaginous neurocranium3.85e-071
head paraxial mesoderm3.85e-071
nucleus accumbens4.08e-071
ventral striatum4.08e-071
putamen4.89e-071
corpus callosum5.19e-071
central nervous system cell part cluster5.19e-071
axon tract5.19e-071
intercerebral commissure5.19e-071
dorsal telencephalic commissure5.19e-071
brain white matter5.19e-071
brain commissure5.19e-071
white matter5.19e-071
nervous system commissure5.19e-071
cerebral hemisphere white matter5.19e-071


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
MA0014.10.369468
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
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.11.73592
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.11.74614
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.14.40502
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
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
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.475695
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

No analysis results for this cluster

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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