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Coexpression cluster:C693: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.649083,0.128687,0.635061,0.345441,0.556358,0.910346,0.411652,0.340819,1.13732,0.782861,0.851693,0.451026,1.41978,0.401301,1.05539,0.207465,0.617549,0.148925,0.285173,0.533397,1.18892,0.356848,0.337221,1.64894,0.722285,0.471832,0.499542,0.335332,0.562141,0.454328,0.809412,0.65246,0.790946,0.268295,0.163884,0.117596,0.161511,0.912597,0.14439,0.306232,0.162847,0.777985,0.658594,0.187953,1.55214,0.693545,0.412635,0.308385,0.188988,0.192687,0.484909,0.423285,0.347648,0.725869,0.873575,1.83807,1.70369,0.374657,0.789982,0.373762,0.691524,0.414771,0.103208,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.273995,1.17358,0.341688,0.871629,0.546891,0.510252,0.216432,0.575479,0.639503,0.710503,0.611084,0.590372,0.4307,0.703506,0.821696,0.00480132,0.0287315,1.17597,0.508983,1.42111,1.05129,0.795567,0.66846,0.130784,0.190761,0.853171,0.282722,0.709167,0.51326,0.701432,0.145361,0.663075,0.703825,0.621018,0.54826,0.313822,0.606045,1.02975,0.260543,0.177931,0.656353,0.701175,0.21882,0.325885,1.00416,0.483536,0.889895,0.297931,0.556847,0.414358,0.863578,0.506732,0.341589,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.856092,0.796235,0.301402,0.919079,0.437919,1.06395,0.740677,0.293853,0.892152,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,0.282284,0.128495,0.133101,0.0750447,0.796604,0.0978005,0.414334,1.19239,0.494,0.179455,0.260802,0.237047,0.984474,1.8329,0.638755,0.239672,0.564971,0.429983,1.25158,0.410452,0.51183
|tfbs_overrepresentation_for_novel_motifs=0.649083,0.128687,0.635061,0.345441,0.556358,0.910346,0.411652,0.340819,1.13732,0.782861,0.851693,0.451026,1.41978,0.401301,1.05539,0.207465,0.617549,0.148925,0.285173,0.533397,1.18892,0.356848,0.337221,1.64894,0.722285,0.471832,0.499542,0.335332,0.562141,0.454328,0.809412,0.65246,0.790946,0.268295,0.163884,0.117596,0.161511,0.912597,0.14439,0.306232,0.162847,0.777985,0.658594,0.187953,1.55214,0.693545,0.412635,0.308385,0.188988,0.192687,0.484909,0.423285,0.347648,0.725869,0.873575,1.83807,1.70369,0.374657,0.789982,0.373762,0.691524,0.414771,0.103208,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.273995,1.17358,0.341688,0.871629,0.546891,0.510252,0.216432,0.575479,0.639503,0.710503,0.611084,0.590372,0.4307,0.703506,0.821696,0.00480132,0.0287315,1.17597,0.508983,1.42111,1.05129,0.795567,0.66846,0.130784,0.190761,0.853171,0.282722,0.709167,0.51326,0.701432,0.145361,0.663075,0.703825,0.621018,0.54826,0.313822,0.606045,1.02975,0.260543,0.177931,0.656353,0.701175,0.21882,0.325885,1.00416,0.483536,0.889895,0.297931,0.556847,0.414358,0.863578,0.506732,0.341589,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.856092,0.796235,0.301402,0.919079,0.437919,1.06395,0.740677,0.293853,0.892152,1.02226,1.87395,1.47317,0.985665,0.407489,0.70579,0.549903,0.367151,0.534339,1.71519,0.282284,0.128495,0.133101,0.0750447,0.796604,0.0978005,0.414334,1.19239,0.494,0.179455,0.260802,0.237047,0.984474,1.8329,0.638755,0.239672,0.564971,0.429983,1.25158,0.410452,0.51183
|tfbs_overrepresentation_jaspar=MA0003.1;0.162801,MA0004.1;0.32225,MA0006.1;0.188769,MA0007.1;0.825205,MA0009.1;0.756202,MA0014.1;0.169227,MA0017.1;0.627635,MA0019.1;0.45566,MA0024.1;0.654931,MA0025.1;0.886436,MA0027.1;2.35633,MA0028.1;0.201461,MA0029.1;0.673506,MA0030.1;0.662482,MA0031.1;0.600685,MA0038.1;0.414169,MA0040.1;0.67914,MA0041.1;0.338572,MA0042.1;0.310552,MA0043.1;0.756508,MA0046.1;0.745626,MA0048.1;0.0399193,MA0050.1;0.837296,MA0051.1;0.410316,MA0052.1;0.682867,MA0055.1;0.400018,MA0056.1;0,MA0057.1;0.0373953,MA0058.1;0.676094,MA0059.1;0.673606,MA0060.1;0.103131,MA0061.1;1.01669,MA0063.1;0,MA0066.1;1.87432,MA0067.1;1.06751,MA0068.1;0.0633085,MA0069.1;0.741884,MA0070.1;0.731026,MA0071.1;0.379038,MA0072.1;0.726666,MA0073.1;0.00203399,MA0074.1;0.40963,MA0076.1;0.254045,MA0077.1;0.719193,MA0078.1;0.502027,MA0081.1;0.239862,MA0083.1;0.763502,MA0084.1;1.25286,MA0087.1;0.724294,MA0088.1;0.0806254,MA0089.1;0,MA0090.1;0.734839,MA0091.1;0.324543,MA0092.1;0.793019,MA0093.1;0.191154,MA0095.1;0,MA0098.1;0,MA0100.1;0.426863,MA0101.1;0.19375,MA0103.1;0.181541,MA0105.1;0.890241,MA0106.1;0.452066,MA0107.1;0.137948,MA0108.2;0.597764,MA0109.1;0,MA0111.1;0.277713,MA0113.1;0.467266,MA0114.1;0.828144,MA0115.1;0.992167,MA0116.1;0.854781,MA0117.1;0.792789,MA0119.1;0.226505,MA0122.1;0.818044,MA0124.1;0.951337,MA0125.1;0.868909,MA0130.1;0,MA0131.1;0.519055,MA0132.1;0,MA0133.1;0,MA0135.1;0.785738,MA0136.1;0.420617,MA0139.1;0.268952,MA0140.1;0.376643,MA0141.1;0.670251,MA0142.1;0.570448,MA0143.1;1.17969,MA0144.1;0.783809,MA0145.1;1.05522,MA0146.1;0.139505,MA0147.1;0.143012,MA0148.1;0.344198,MA0149.1;0.367947,MA0062.2;0.0823902,MA0035.2;0.376007,MA0039.2;0.0035182,MA0138.2;0.503176,MA0002.2;1.08633,MA0137.2;1.1244,MA0104.2;0.102626,MA0047.2;0.440861,MA0112.2;0.216805,MA0065.2;0.733267,MA0150.1;0.261236,MA0151.1;0,MA0152.1;0.382565,MA0153.1;0.852412,MA0154.1;0.5526,MA0155.1;0.64751,MA0156.1;0.208455,MA0157.1;0.544523,MA0158.1;0,MA0159.1;0.867657,MA0160.1;0.357736,MA0161.1;0,MA0162.1;0.00310762,MA0163.1;0.00158421,MA0164.1;0.478818,MA0080.2;0.191221,MA0018.2;1.14938,MA0099.2;0.382887,MA0079.2;0.0178219,MA0102.2;1.28978,MA0258.1;0.754226,MA0259.1;0.149181,MA0442.1;0
}}
}}

Revision as of 19:22, 22 January 2013


Full id: C693_cerebellum_medulla_spinal_locus_Hepatocyte_pons_thalamus



Phase1 CAGE Peaks

Hg19::chr11:7369947..7369952,+p@chr11:7369947..7369952
+
Hg19::chr12:109273861..109273889,+p1@DAO
Hg19::chr19:29493456..29493477,+p1@LOC100505835
Hg19::chr19:29493486..29493497,+p2@LOC100505835
Hg19::chr1:90885631..90885647,-p@chr1:90885631..90885647
-
Hg19::chr1:90885681..90885693,-p@chr1:90885681..90885693
-
Hg19::chr3:125997081..125997085,+p@chr3:125997081..125997085
+
Hg19::chr3:147111505..147111529,+p6@ZIC1
Hg19::chr6:138959791..138959803,-p@chr6:138959791..138959803
-
Hg19::chr9:73736331..73736347,-p3@TRPM3
Hg19::chrX:106692537..106692551,+p@chrX:106692537..106692551
+
Hg19::chrX:106692569..106692585,+p@chrX:106692569..106692585
+


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:0003884D-amino-acid oxidase activity0.0358467233571613
GO:0008589regulation of smoothened signaling pathway0.0358467233571613
GO:0007224smoothened signaling pathway0.0453250397872941
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.0453250397872941
GO:0042472inner ear morphogenesis0.0453250397872941
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.0453250397872941
GO:0042471ear morphogenesis0.0453250397872941
GO:0048839inner ear development0.0477464012889728
GO:0043583ear development0.0477464012889728



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
neural tube1.47e-11456
neural rod1.47e-11456
future spinal cord1.47e-11456
neural keel1.47e-11456
regional part of nervous system1.48e-10253
regional part of brain1.48e-10253
central nervous system4.46e-9381
brain1.69e-8668
future brain1.69e-8668
nervous system3.88e-8389
neural plate4.62e-8082
presumptive neural plate4.62e-8082
neurectoderm5.39e-7686
regional part of forebrain5.50e-7341
forebrain5.50e-7341
anterior neural tube5.50e-7341
future forebrain5.50e-7341
adult organism2.68e-65114
brain grey matter2.48e-6434
gray matter2.48e-6434
telencephalon4.87e-6434
ecto-epithelium1.60e-61104
regional part of telencephalon9.66e-5732
cerebral hemisphere1.65e-5632
structure with developmental contribution from neural crest4.65e-52132
pre-chordal neural plate6.92e-5161
ectoderm-derived structure5.51e-42171
ectoderm5.51e-42171
presumptive ectoderm5.51e-42171
posterior neural tube7.28e-4215
chordal neural plate7.28e-4215
neural nucleus7.39e-389
nucleus of brain7.39e-389
regional part of cerebral cortex1.24e-3722
cerebral cortex6.80e-3325
pallium6.80e-3325
neocortex1.12e-3020
organ system subdivision3.19e-30223
segmental subdivision of hindbrain7.55e-3012
hindbrain7.55e-3012
presumptive hindbrain7.55e-3012
basal ganglion1.66e-299
nuclear complex of neuraxis1.66e-299
aggregate regional part of brain1.66e-299
collection of basal ganglia1.66e-299
cerebral subcortex1.66e-299
telencephalic nucleus2.16e-297
tube6.60e-28192
segmental subdivision of nervous system2.03e-2713
brainstem2.43e-276
anatomical conduit1.20e-20240
regional part of metencephalon5.64e-189
metencephalon5.64e-189
future metencephalon5.64e-189
gyrus3.62e-176
corpus striatum7.83e-174
striatum7.83e-174
ventral part of telencephalon7.83e-174
future corpus striatum7.83e-174
anatomical cluster1.26e-15373
epithelium2.21e-15306
cell layer3.78e-15309
medulla oblongata7.87e-153
myelencephalon7.87e-153
future myelencephalon7.87e-153
spinal cord2.53e-143
dorsal region element2.53e-143
dorsum2.53e-143
pons2.77e-143
limbic system3.10e-145
organ part4.88e-14218
caudate-putamen6.21e-133
dorsal striatum6.21e-133
multi-tissue structure6.88e-11342
regional part of diencephalon1.85e-104
diencephalon2.88e-107
future diencephalon2.88e-107
locus ceruleus3.32e-102
brainstem nucleus3.32e-102
hindbrain nucleus3.32e-102
globus pallidus3.63e-102
pallidum3.63e-102
dorsal plus ventral thalamus4.54e-102
thalamic complex4.54e-102
Ammon's horn6.77e-102
lobe parts of cerebral cortex6.77e-102
hippocampal formation6.77e-102
limbic lobe6.77e-102
temporal lobe9.50e-106
caudate nucleus3.98e-092
future caudate nucleus3.98e-092
middle temporal gyrus4.51e-092
meninx5.57e-092
membrane organ5.57e-092
meningeal cluster5.57e-092
organ1.74e-08503
parietal lobe4.54e-085
occipital lobe4.66e-085
cerebellum1.39e-076
rhombic lip1.39e-076


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)
MA0003.10.162801
MA0004.10.32225
MA0006.10.188769
MA0007.10.825205
MA0009.10.756202
MA0014.10.169227
MA0017.10.627635
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.0399193
MA0050.10.837296
MA0051.10.410316
MA0052.10.682867
MA0055.10.400018
MA0056.10
MA0057.10.0373953
MA0058.10.676094
MA0059.10.673606
MA0060.10.103131
MA0061.11.01669
MA0063.10
MA0066.11.87432
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.00203399
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.0806254
MA0089.10
MA0090.10.734839
MA0091.10.324543
MA0092.10.793019
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.10.181541
MA0105.10.890241
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.828144
MA0115.10.992167
MA0116.10.854781
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.268952
MA0140.10.376643
MA0141.10.670251
MA0142.10.570448
MA0143.11.17969
MA0144.10.783809
MA0145.11.05522
MA0146.10.139505
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.20.0035182
MA0138.20.503176
MA0002.21.08633
MA0137.21.1244
MA0104.20.102626
MA0047.20.440861
MA0112.20.216805
MA0065.20.733267
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.5526
MA0155.10.64751
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.867657
MA0160.10.357736
MA0161.10
MA0162.10.00310762
MA0163.10.00158421
MA0164.10.478818
MA0080.20.191221
MA0018.21.14938
MA0099.20.382887
MA0079.20.0178219
MA0102.21.28978
MA0258.10.754226
MA0259.10.149181
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:C693&oldid=2569204"