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Coexpression cluster:C1961: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,0.654974,2.01096,1.57264,0.733342,0.324142,0.321368,0.345702,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,1.02276,0.287891,0.167776,0.500405,0.384437,0.645033,0.44943,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.815792,0.415749,0.580638,0.132849,0.451846,0.0606304,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.659455,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,3.2897,1.18161,0.0719601,0.49825,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,1.97764,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,1.05995,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.953361,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
|tfbs_overrepresentation_jaspar=MA0003.1;0.00991994,MA0004.1;2.5741,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.0418333,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;1.48918,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.288856,MA0056.1;0,MA0057.1;0.189508,MA0058.1;3.29768,MA0059.1;1.29682,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;1.28241,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;0.818263,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;1.43794,MA0093.1;2.99362,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;2.16859,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;2.64838,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;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;0.0359558,MA0147.1;1.77656,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.0118463,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.858845,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.514087,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.81299,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;1.02361,MA0442.1;0
}}
}}

Revision as of 20:19, 22 January 2013


Full id: C1961_Neural_cerebellum_medulla_mesothelioma_hippocampus_spinal_Astrocyte



Phase1 CAGE Peaks

Hg19::chr5:36607366..36607379,+p@chr5:36607366..36607379
+
Hg19::chr5:36608318..36608354,+p2@SLC1A3
Hg19::chr5:36608367..36608383,+p3@SLC1A3
Hg19::chr5:36608422..36608435,+p4@SLC1A3
Hg19::chr5:36687555..36687567,+p@chr5:36687555..36687567
+


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>

Uber Anatomy
Ontology termp-valuen
neural tube5.05e-7656
neural rod5.05e-7656
future spinal cord5.05e-7656
neural keel5.05e-7656
central nervous system9.33e-7481
regional part of nervous system4.94e-7053
regional part of brain4.94e-7053
nervous system3.28e-6789
brain1.04e-6168
future brain1.04e-6168
neural plate1.02e-5682
presumptive neural plate1.02e-5682
telencephalon5.67e-5434
brain grey matter8.44e-5434
gray matter8.44e-5434
neurectoderm2.18e-5386
regional part of forebrain7.41e-5341
forebrain7.41e-5341
anterior neural tube7.41e-5341
future forebrain7.41e-5341
cerebral hemisphere3.38e-5032
regional part of telencephalon6.77e-5032
ecto-epithelium1.43e-41104
pre-chordal neural plate5.40e-4161
cerebral cortex9.48e-3725
pallium9.48e-3725
structure with developmental contribution from neural crest1.50e-35132
ectoderm-derived structure8.24e-34171
ectoderm8.24e-34171
presumptive ectoderm8.24e-34171
regional part of cerebral cortex2.76e-3122
adult organism9.64e-31114
neocortex2.59e-2720
organ system subdivision4.24e-24223
posterior neural tube2.31e-2315
chordal neural plate2.31e-2315
neural nucleus1.81e-189
nucleus of brain1.81e-189
basal ganglion2.28e-189
nuclear complex of neuraxis2.28e-189
aggregate regional part of brain2.28e-189
collection of basal ganglia2.28e-189
cerebral subcortex2.28e-189
segmental subdivision of hindbrain1.07e-1712
hindbrain1.07e-1712
presumptive hindbrain1.07e-1712
tube9.34e-17192
segmental subdivision of nervous system3.87e-1613
telencephalic nucleus1.17e-147
gyrus9.47e-146
brainstem9.68e-146
anatomical cluster8.04e-13373
anatomical conduit1.19e-12240
regional part of metencephalon1.32e-119
metencephalon1.32e-119
future metencephalon1.32e-119
limbic system1.50e-115
cell layer4.19e-11309
epithelium8.59e-11306
organ part1.31e-10218
multi-tissue structure1.64e-09342
corpus striatum2.67e-094
striatum2.67e-094
ventral part of telencephalon2.67e-094
future corpus striatum2.67e-094
medulla oblongata3.80e-083
myelencephalon3.80e-083
future myelencephalon3.80e-083
temporal lobe4.91e-086
parietal lobe8.07e-085
frontal cortex1.16e-073
spinal cord1.92e-073
dorsal region element1.92e-073
dorsum1.92e-073
pons2.82e-073
caudate-putamen3.01e-073
dorsal striatum3.01e-073
occipital lobe4.17e-075
germ layer4.89e-07560
germ layer / neural crest4.89e-07560
embryonic tissue4.89e-07560
presumptive structure4.89e-07560
germ layer / neural crest derived structure4.89e-07560
epiblast (generic)4.89e-07560
embryonic structure7.54e-07564


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)
MA0003.10.00991994
MA0004.12.5741
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
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
MA0050.11.48918
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.189508
MA0058.13.29768
MA0059.11.29682
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.28241
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
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.11.43794
MA0093.12.99362
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.22.16859
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.12.64838
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
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.11.77656
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.81299
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.00732454
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
CEBPB#105157.971147625824823.10621793420244e-050.000629067858891154
GTF2F1#2962410.19172870140610.000177833889427640.00215987830886537
TFAP2A#702039.911180623826970.002021546977511280.0117469729474378
TFAP2C#702236.485537165916130.006858951517940.0290652453778356



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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