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Coexpression cluster:C1913: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.508327,1.20042,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.703495,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.969147,0.500405,0.770467,0.645033,0.44943,0.549618,0.802434,1.29435,0.642741,0.458349,1.22891,0.598009,1.00172,1.68319,0.27659,0.417272,1.1597,0.413782,0.654459,0.388123,0.815792,0.415749,1.42042,0.414516,0.451846,1.74542,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,1.22844,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,0.189341,1.23387,0.269111,0.709554,0.240727,0.917983,0.987729,0.543014,1.44891,0.934302,0.755403,0.327263,1.18161,0.914416,0.166306,1.20877,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,1.45429,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,1.44357,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,2.0258,2.09294,0.577088,0.363423,0.526389,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.720819
|tfbs_overrepresentation_for_novel_motifs=0.508327,1.20042,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.703495,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.784337,0.969147,0.500405,0.770467,0.645033,0.44943,0.549618,0.802434,1.29435,0.642741,0.458349,1.22891,0.598009,1.00172,1.68319,0.27659,0.417272,1.1597,0.413782,0.654459,0.388123,0.815792,0.415749,1.42042,0.414516,0.451846,1.74542,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,1.22844,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.880217,0.189341,1.23387,0.269111,0.709554,0.240727,0.917983,0.987729,0.543014,1.44891,0.934302,0.755403,0.327263,1.18161,0.914416,0.166306,1.20877,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.606298,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,1.45429,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,1.44357,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,2.0258,2.09294,0.577088,0.363423,0.526389,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.720819
|tfbs_overrepresentation_jaspar=MA0003.1;1.40197,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.660087,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;0.731787,MA0052.1;1.03442,MA0055.1;1.01397,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;2.23433,MA0060.1;0.321781,MA0061.1;0.791444,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.692739,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.362215,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;1.15584,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;1.12656,MA0105.1;1.58771,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;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;1.29278,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;1.82062,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.527987,MA0138.2;1.95446,MA0002.2;1.50443,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;1.41695,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.98952,MA0155.1;0.813062,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.469165,MA0163.1;0.168633,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.230892,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:17, 22 January 2013


Full id: C1913_brain_parietal_insula_temporal_frontal_postcentral_paracentral



Phase1 CAGE Peaks

Hg19::chr2:73286210..73286217,-p10@SFXN5
Hg19::chr3:196731256..196731267,-p9@MFI2
Hg19::chr4:2060590..2060605,+p@chr4:2060590..2060605
+
Hg19::chr4:3392202..3392212,+p@chr4:3392202..3392212
+
Hg19::chr6:34497272..34497283,-p@chr6:34497272..34497283
-


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:0006826iron ion transport0.000179782242216466
GO:0000041transition metal ion transport0.00029011852432864
GO:0015674di-, tri-valent inorganic cation transport0.00114076113215925
GO:0005506iron ion binding0.00355545855679128
GO:0030001metal ion transport0.00523173083580828
GO:0006812cation transport0.00675828032833279
GO:0006811ion transport0.0149587772796448
GO:0008199ferric iron binding0.0176890209421288
GO:0055072iron ion homeostasis0.0214120650479812
GO:0006879cellular iron ion homeostasis0.0214120650479812
GO:0048503GPI anchor binding0.0437522451688784
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0481393143616867
GO:0055066di-, tri-valent inorganic cation homeostasis0.0481393143616867
GO:0030003cellular cation homeostasis0.0481393143616867
GO:0055080cation homeostasis0.0481393143616867
GO:0055082cellular chemical homeostasis0.0481393143616867
GO:0006873cellular ion homeostasis0.0481393143616867
GO:0006810transport0.0481393143616867
GO:0035091phosphoinositide binding0.0481393143616867
GO:0051234establishment of localization0.0481393143616867
GO:0050801ion homeostasis0.0484630294109158



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
regional part of nervous system4.43e-8353
regional part of brain4.43e-8353
neural tube1.93e-7856
neural rod1.93e-7856
future spinal cord1.93e-7856
neural keel1.93e-7856
telencephalon2.52e-7334
brain4.19e-7368
future brain4.19e-7368
brain grey matter4.73e-7334
gray matter4.73e-7334
cerebral hemisphere7.41e-7132
regional part of forebrain2.73e-6641
forebrain2.73e-6641
anterior neural tube2.73e-6641
future forebrain2.73e-6641
central nervous system3.12e-6581
regional part of telencephalon1.22e-6332
nervous system2.47e-5889
regional part of cerebral cortex1.17e-5722
neocortex2.21e-5520
neural plate2.89e-5282
presumptive neural plate2.89e-5282
cerebral cortex1.18e-5025
pallium1.18e-5025
neurectoderm1.26e-4986
adult organism4.48e-46114
pre-chordal neural plate1.80e-4361
ecto-epithelium3.15e-40104
structure with developmental contribution from neural crest3.33e-33132
ectoderm-derived structure2.70e-28171
ectoderm2.70e-28171
presumptive ectoderm2.70e-28171
gyrus9.24e-266
brainstem1.65e-246
neural nucleus1.59e-239
nucleus of brain1.59e-239
organ system subdivision4.49e-22223
parietal lobe2.00e-205
tube1.80e-19192
pons1.73e-183
segmental subdivision of hindbrain3.49e-1712
hindbrain3.49e-1712
presumptive hindbrain3.49e-1712
basal ganglion8.60e-179
nuclear complex of neuraxis8.60e-179
aggregate regional part of brain8.60e-179
collection of basal ganglia8.60e-179
cerebral subcortex8.60e-179
segmental subdivision of nervous system7.95e-1613
anatomical conduit1.62e-14240
corpus striatum1.66e-144
striatum1.66e-144
ventral part of telencephalon1.66e-144
future corpus striatum1.66e-144
temporal lobe2.13e-146
telencephalic nucleus3.57e-147
organ part8.48e-14218
posterior neural tube1.19e-1315
chordal neural plate1.19e-1315
middle temporal gyrus2.99e-132
locus ceruleus1.22e-122
brainstem nucleus1.22e-122
hindbrain nucleus1.22e-122
occipital lobe7.48e-125
limbic system1.86e-115
anatomical cluster5.14e-11373
regional part of metencephalon1.02e-109
metencephalon1.02e-109
future metencephalon1.02e-109
epithelium3.18e-10306
cell layer4.51e-10309
multi-tissue structure1.83e-09342
frontal cortex2.75e-093
caudate-putamen3.38e-093
dorsal striatum3.38e-093
medulla oblongata8.92e-093
myelencephalon8.92e-093
future myelencephalon8.92e-093
insula8.00e-081
postcentral gyrus9.10e-081
paracentral gyrus9.71e-081
occipital pole1.25e-071
pole of cerebral hemisphere1.25e-071
nucleus accumbens1.61e-071
ventral striatum1.61e-071
olfactory region1.72e-071
primary subdivision of skull1.72e-071
cranium1.72e-071
neurocranium1.72e-071
chondrocranium1.72e-071
cartilaginous neurocranium1.72e-071
head paraxial mesoderm1.72e-071
putamen1.95e-071
corpus callosum4.90e-071
central nervous system cell part cluster4.90e-071
axon tract4.90e-071
intercerebral commissure4.90e-071
dorsal telencephalic commissure4.90e-071
brain white matter4.90e-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)
MA0003.11.40197
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
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
MA0051.10.731787
MA0052.11.03442
MA0055.11.01397
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.12.23433
MA0060.10.321781
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.362215
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
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.12656
MA0105.11.58771
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
MA0119.10.504689
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
MA0141.11.29278
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.11.82062
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.527987
MA0138.21.95446
MA0002.21.50443
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.230892
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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1913&oldid=2570424"