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Coexpression cluster:C376: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.765264,1.59687,0.741916,0.115973,0.339547,0.115097,0.930842,0.497522,0.747901,1.43201,0.327522,0.185675,2.24236,0.461744,0.145089,0.168654,0.312612,0.240825,0.386787,0.656547,0.0508801,0.51164,1.74297,0.0354608,0.242214,1.10054,0.0680967,1.1843,0.622658,0.601895,1.54095,0.341173,0.368873,0.561639,0.818635,0.866515,0.503302,0.746129,0.438438,3.55227,0.11321,0.985113,0.292915,0.334058,1.73228,1.27185,0.480607,1.07732,0.0895191,0.973887,1.1377,0.498457,1.085,0.402924,0.532737,0.466119,0.153794,0.82781,1.45544,0.825331,1.73422,0.939578,1.06217,0.792735,0.511492,0.266103,0.611096,0.954146,0.33304,0.800453,1.40858,0.150977,2.83074,0.530988,2.63419,2.46694,0.424496,0.764065,0.330507,0.234869,0.0374788,0.290785,0.171482,0.147002,1.22041,2.69448,0.101368,0.380635,0.227861,1.04966,0.695939,0.463366,0.354445,0.0778659,0.147147,0.0876739,0.10074,1.00892,0.231068,1.25395,0.0934024,0.349965,0.384158,0.846519,0.25774,0.66118,0.819287,0.456614,0.24191,1.73757,1.18654,0.381914,1.11419,1.14677,0.652077,0.0261337,2.42823,2.1058,0.730665,0.394953,0.523757,0.641925,0.113636,0.178598,0.753832,0.27955,0.154657,0.942299,0.561176,0.424823,0.463953,0.30248,0.573914,0.176484,0.707783,0.354931,0.086099,0.11017,0.668879,1.49486,1.10037,0.634967,0.155698,0.385822,0.259011,0.129436,1.27895,1.33792,0.273743,1.29735,0.350692,1.47636,0.464277,0.129488,0.938352,0.829202,0.216727,0.133083,0.889231,1.21172,1.53216,0.448609,0.329893,0.212291,0.270734,0.170987,0.874352,0.476964,0.760364
|tfbs_overrepresentation_for_novel_motifs=0.765264,1.59687,0.741916,0.115973,0.339547,0.115097,0.930842,0.497522,0.747901,1.43201,0.327522,0.185675,2.24236,0.461744,0.145089,0.168654,0.312612,0.240825,0.386787,0.656547,0.0508801,0.51164,1.74297,0.0354608,0.242214,1.10054,0.0680967,1.1843,0.622658,0.601895,1.54095,0.341173,0.368873,0.561639,0.818635,0.866515,0.503302,0.746129,0.438438,3.55227,0.11321,0.985113,0.292915,0.334058,1.73228,1.27185,0.480607,1.07732,0.0895191,0.973887,1.1377,0.498457,1.085,0.402924,0.532737,0.466119,0.153794,0.82781,1.45544,0.825331,1.73422,0.939578,1.06217,0.792735,0.511492,0.266103,0.611096,0.954146,0.33304,0.800453,1.40858,0.150977,2.83074,0.530988,2.63419,2.46694,0.424496,0.764065,0.330507,0.234869,0.0374788,0.290785,0.171482,0.147002,1.22041,2.69448,0.101368,0.380635,0.227861,1.04966,0.695939,0.463366,0.354445,0.0778659,0.147147,0.0876739,0.10074,1.00892,0.231068,1.25395,0.0934024,0.349965,0.384158,0.846519,0.25774,0.66118,0.819287,0.456614,0.24191,1.73757,1.18654,0.381914,1.11419,1.14677,0.652077,0.0261337,2.42823,2.1058,0.730665,0.394953,0.523757,0.641925,0.113636,0.178598,0.753832,0.27955,0.154657,0.942299,0.561176,0.424823,0.463953,0.30248,0.573914,0.176484,0.707783,0.354931,0.086099,0.11017,0.668879,1.49486,1.10037,0.634967,0.155698,0.385822,0.259011,0.129436,1.27895,1.33792,0.273743,1.29735,0.350692,1.47636,0.464277,0.129488,0.938352,0.829202,0.216727,0.133083,0.889231,1.21172,1.53216,0.448609,0.329893,0.212291,0.270734,0.170987,0.874352,0.476964,0.760364
|tfbs_overrepresentation_jaspar=MA0003.1;2.66983,MA0004.1;0.102156,MA0006.1;0.336062,MA0007.1;0.639929,MA0009.1;0.429031,MA0014.1;2.08264,MA0017.1;0.414482,MA0019.1;0.188957,MA0024.1;0.343215,MA0025.1;0.544326,MA0027.1;1.97447,MA0028.1;0.160829,MA0029.1;0.358654,MA0030.1;0.349473,MA0031.1;0.299024,MA0038.1;0.160193,MA0040.1;0.363365,MA0041.1;0.111817,MA0042.1;0.0954223,MA0043.1;0.429296,MA0046.1;0.419892,MA0048.1;1.75721,MA0050.1;0.0958601,MA0051.1;0.157595,MA0052.1;0.366488,MA0055.1;0.265943,MA0056.1;0,MA0057.1;1.35806,MA0058.1;0.0589349,MA0059.1;0.464811,MA0060.1;0.0102756,MA0061.1;0.620016,MA0063.1;0,MA0066.1;0.483822,MA0067.1;0.711124,MA0068.1;0.935489,MA0069.1;0.416668,MA0070.1;0.407339,MA0071.1;0.42511,MA0072.1;0.403605,MA0073.1;1.69128,MA0074.1;0.475593,MA0076.1;0.065346,MA0077.1;0.397221,MA0078.1;0.222673,MA0081.1;0.212556,MA0083.1;0.435361,MA0084.1;0.887042,MA0087.1;0.401577,MA0088.1;1.55672,MA0089.1;0,MA0090.1;0.91056,MA0091.1;0.103495,MA0092.1;0.601706,MA0093.1;0.037369,MA0095.1;0,MA0098.1;0,MA0100.1;0.168841,MA0101.1;0.150934,MA0103.1;0.318372,MA0105.1;0.946202,MA0106.1;1.04455,MA0107.1;0.414244,MA0108.2;0.296685,MA0109.1;0,MA0111.1;0.266972,MA0113.1;1.08759,MA0114.1;0.207446,MA0115.1;0.640975,MA0116.1;1.40605,MA0117.1;1.16571,MA0119.1;0.0523174,MA0122.1;0.483183,MA0124.1;0.60338,MA0125.1;0.528543,MA0130.1;0,MA0131.1;0.663587,MA0132.1;0,MA0133.1;0,MA0135.1;0.454747,MA0136.1;0.164568,MA0139.1;1.12225,MA0140.1;0.135474,MA0141.1;0.80074,MA0142.1;0.275028,MA0143.1;0.197366,MA0144.1;0.0711193,MA0145.1;0.221306,MA0146.1;0.151317,MA0147.1;0.0908362,MA0148.1;0.369009,MA0149.1;1.3141,MA0062.2;0.0340128,MA0035.2;0.135068,MA0039.2;1.82716,MA0138.2;0.223528,MA0002.2;0.448749,MA0137.2;0.0436553,MA0104.2;0.28434,MA0047.2;0.178535,MA0112.2;0.83854,MA0065.2;0.357886,MA0150.1;0.52088,MA0151.1;0,MA0152.1;0.139287,MA0153.1;0.513757,MA0154.1;1.18887,MA0155.1;0.780312,MA0156.1;0.0444235,MA0157.1;0.708688,MA0158.1;0,MA0159.1;0.228288,MA0160.1;0.390619,MA0161.1;0,MA0162.1;1.21507,MA0163.1;3.07374,MA0164.1;0.205602,MA0080.2;0.0373957,MA0018.2;0.549438,MA0099.2;0.139496,MA0079.2;9.51475,MA0102.2;0.922526,MA0258.1;0.338434,MA0259.1;0.739179,MA0442.1;0
}}
}}

Revision as of 19:07, 22 January 2013


Full id: C376_brain_temporal_insula_frontal_occipital_postcentral_paracentral



Phase1 CAGE Peaks

Hg19::chr11:20690677..20690691,+p4@NELL1
Hg19::chr11:70672700..70672711,-p21@SHANK2
Hg19::chr15:52043722..52043735,-p7@LYSMD2
Hg19::chr15:75249573..75249587,-p12@RPP25
Hg19::chr15:77988485..77988494,-p27@LINGO1
Hg19::chr16:2230120..2230121,-p@chr16:2230120..2230121
-
Hg19::chr16:57406456..57406465,+p3@CX3CL1
Hg19::chr19:12945382..12945400,-p2@RTBDN
Hg19::chr19:12945478..12945499,-p6@RTBDN
Hg19::chr19:18311186..18311201,+p@chr19:18311186..18311201
+
Hg19::chr19:40724239..40724242,-p3@TTC9B
Hg19::chr19:42482880..42482902,+p@chr19:42482880..42482902
+
Hg19::chr19:46296190..46296207,-p4@DMWD
Hg19::chr19:822429..822477,-p4@MIR3187
Hg19::chr1:155291286..155291312,+p10@RUSC1
Hg19::chr20:36560066..36560087,-p@chr20:36560066..36560087
-
Hg19::chr2:73511460..73511470,-p8@FBXO41
Hg19::chr2:74757308..74757330,+p6@HTRA2
Hg19::chr3:68053515..68053522,+p5@FAM19A1
Hg19::chr4:150999349..150999359,+p13@DCLK2
Hg19::chr4:6564686..6564690,-p@chr4:6564686..6564690
-
Hg19::chr5:112043148..112043155,+p14@APC
Hg19::chr5:63257007..63257019,-p7@HTR1A
Hg19::chr6:33395473..33395504,+p1@AK124666
Hg19::chr7:45613934..45613945,+p4@ADCY1
Hg19::chr8:10158713..10158718,+p22@MSRA
Hg19::chr8:4852171..4852180,-p14@CSMD1
Hg19::chr9:139872612..139872634,+p@chr9:139872612..139872634
+
Hg19::chr9:34957921..34957934,+p7@KIAA1045


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:0051983regulation of chromosome segregation0.0315259625574002
GO:0051041positive regulation of calcium-independent cell-cell adhesion0.0315259625574002
GO:0051988regulation of attachment of spindle microtubules to kinetochore0.0315259625574002
GO:0050902leukocyte adhesive activation0.0315259625574002
GO:0051040regulation of calcium-independent cell-cell adhesion0.0315259625574002
GO:0008608attachment of spindle microtubules to kinetochore0.0315259625574002



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 system8.80e-9553
regional part of brain8.80e-9553
neural tube1.65e-9456
neural rod1.65e-9456
future spinal cord1.65e-9456
neural keel1.65e-9456
brain3.88e-8568
future brain3.88e-8568
telencephalon4.76e-8434
brain grey matter9.26e-8434
gray matter9.26e-8434
cerebral hemisphere4.40e-8332
central nervous system2.13e-8281
regional part of forebrain1.48e-7941
forebrain1.48e-7941
anterior neural tube1.48e-7941
future forebrain1.48e-7941
regional part of cerebral cortex3.32e-7922
nervous system3.45e-7789
regional part of telencephalon2.41e-7632
neocortex3.05e-7120
cerebral cortex1.85e-6925
pallium1.85e-6925
neural plate6.91e-6682
presumptive neural plate6.91e-6682
neurectoderm1.78e-6286
pre-chordal neural plate2.52e-5561
ecto-epithelium2.45e-50104
adult organism1.06e-45114
structure with developmental contribution from neural crest2.33e-40132
ectoderm-derived structure1.21e-38171
ectoderm1.21e-38171
presumptive ectoderm1.21e-38171
organ system subdivision2.68e-29223
gyrus4.01e-266
temporal lobe2.12e-226
tube4.22e-22192
parietal lobe6.77e-225
limbic system8.04e-225
brainstem4.12e-176
basal ganglion2.08e-169
nuclear complex of neuraxis2.08e-169
aggregate regional part of brain2.08e-169
collection of basal ganglia2.08e-169
cerebral subcortex2.08e-169
posterior neural tube2.51e-1615
chordal neural plate2.51e-1615
anatomical conduit4.72e-16240
segmental subdivision of hindbrain4.99e-1612
hindbrain4.99e-1612
presumptive hindbrain4.99e-1612
neural nucleus5.56e-169
nucleus of brain5.56e-169
anatomical cluster6.02e-15373
organ part6.76e-15218
segmental subdivision of nervous system1.01e-1413
frontal cortex4.67e-143
occipital lobe4.68e-145
pons3.49e-133
epithelium1.08e-11306
cell layer1.68e-11309
regional part of metencephalon2.04e-119
metencephalon2.04e-119
future metencephalon2.04e-119
multi-tissue structure2.01e-10342
corpus striatum4.78e-104
striatum4.78e-104
ventral part of telencephalon4.78e-104
future corpus striatum4.78e-104
amygdala6.93e-102
middle frontal gyrus9.40e-102
middle temporal gyrus1.22e-092
telencephalic nucleus1.23e-097
Ammon's horn1.51e-092
lobe parts of cerebral cortex1.51e-092
hippocampal formation1.51e-092
limbic lobe1.51e-092
locus ceruleus3.24e-092
brainstem nucleus3.24e-092
hindbrain nucleus3.24e-092
organ2.62e-07503
germ layer8.08e-07560
germ layer / neural crest8.08e-07560
embryonic tissue8.08e-07560
presumptive structure8.08e-07560
germ layer / neural crest derived structure8.08e-07560
epiblast (generic)8.08e-07560


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)
MA0003.12.66983
MA0004.10.102156
MA0006.10.336062
MA0007.10.639929
MA0009.10.429031
MA0014.12.08264
MA0017.10.414482
MA0019.10.188957
MA0024.10.343215
MA0025.10.544326
MA0027.11.97447
MA0028.10.160829
MA0029.10.358654
MA0030.10.349473
MA0031.10.299024
MA0038.10.160193
MA0040.10.363365
MA0041.10.111817
MA0042.10.0954223
MA0043.10.429296
MA0046.10.419892
MA0048.11.75721
MA0050.10.0958601
MA0051.10.157595
MA0052.10.366488
MA0055.10.265943
MA0056.10
MA0057.11.35806
MA0058.10.0589349
MA0059.10.464811
MA0060.10.0102756
MA0061.10.620016
MA0063.10
MA0066.10.483822
MA0067.10.711124
MA0068.10.935489
MA0069.10.416668
MA0070.10.407339
MA0071.10.42511
MA0072.10.403605
MA0073.11.69128
MA0074.10.475593
MA0076.10.065346
MA0077.10.397221
MA0078.10.222673
MA0081.10.212556
MA0083.10.435361
MA0084.10.887042
MA0087.10.401577
MA0088.11.55672
MA0089.10
MA0090.10.91056
MA0091.10.103495
MA0092.10.601706
MA0093.10.037369
MA0095.10
MA0098.10
MA0100.10.168841
MA0101.10.150934
MA0103.10.318372
MA0105.10.946202
MA0106.11.04455
MA0107.10.414244
MA0108.20.296685
MA0109.10
MA0111.10.266972
MA0113.11.08759
MA0114.10.207446
MA0115.10.640975
MA0116.11.40605
MA0117.11.16571
MA0119.10.0523174
MA0122.10.483183
MA0124.10.60338
MA0125.10.528543
MA0130.10
MA0131.10.663587
MA0132.10
MA0133.10
MA0135.10.454747
MA0136.10.164568
MA0139.11.12225
MA0140.10.135474
MA0141.10.80074
MA0142.10.275028
MA0143.10.197366
MA0144.10.0711193
MA0145.10.221306
MA0146.10.151317
MA0147.10.0908362
MA0148.10.369009
MA0149.11.3141
MA0062.20.0340128
MA0035.20.135068
MA0039.21.82716
MA0138.20.223528
MA0002.20.448749
MA0137.20.0436553
MA0104.20.28434
MA0047.20.178535
MA0112.20.83854
MA0065.20.357886
MA0150.10.52088
MA0151.10
MA0152.10.139287
MA0153.10.513757
MA0154.11.18887
MA0155.10.780312
MA0156.10.0444235
MA0157.10.708688
MA0158.10
MA0159.10.228288
MA0160.10.390619
MA0161.10
MA0162.11.21507
MA0163.13.07374
MA0164.10.205602
MA0080.20.0373957
MA0018.20.549438
MA0099.20.139496
MA0079.29.51475
MA0102.20.922526
MA0258.10.338434
MA0259.10.739179
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:C376&oldid=2568887"