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Coexpression cluster:C1146: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.465735,0.384703,1.31224,0.343148,0.52784,0.604235,0.226729,0.224331,1.18097,0.497563,0.647852,1.03506,0.592674,0.905441,0.365029,1.93347,0.786991,0.19568,0.66776,0.384762,0.498384,1.29221,0.338096,1.09974,0.670692,0.957451,0.517892,0.346214,0.459534,0.475674,0.864517,0.257226,0.546594,0.309012,1.05693,0.825031,0.529001,0.282922,0.207499,0.307642,0.459366,0.0729319,0.340293,0.265117,0.415364,0.60533,0.486696,0.511111,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,1.38261,0.459282,1.38047,0.905643,1.47735,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.656075,0.744055,1.0929,0.531388,0.971313,0.156354,0.782748,0.850825,0.424224,0.580264,0.798651,0.625403,0.649554,1.04131,0.310394,0.322252,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,1.34301,0.910085,0.759662,0.194299,0.924148,0.715799,0.81992,0.28424,0.875714,0.918549,0.831244,0.753567,2.13786,0.815341,1.43846,1.09919,0.327379,0.395884,0.915771,0.988112,0.507004,1.22894,0.304323,1.42509,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,1.36465,0.738579,1.94751,0.456039,0.26104,2.31423,0.518684,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,1.97961,1.84123,0.7715,0.624608,0.695791,0.602897,1.92424
|tfbs_overrepresentation_jaspar=MA0003.1;0.213534,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;1.26877,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.766755,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.158296,MA0056.1;0,MA0057.1;1.78113,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;0.575931,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.672652,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.538456,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;1.50553,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;0.340955,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;1.14351,MA0113.1;0.665691,MA0114.1;0.741402,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.0807715,MA0146.1;0.547931,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.403603,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.944394,MA0065.2;0.282161,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;1.13451,MA0155.1;0.071478,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.780982,MA0163.1;0.19677,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;1.56673,MA0099.2;0.572,MA0079.2;1.35081,MA0102.2;1.51913,MA0258.1;0.687127,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:44, 22 January 2013


Full id: C1146_pineal_putamen_caudate_cerebellum_nucleus_insula_pituitary



Phase1 CAGE Peaks

Hg19::chr11:62474956..62474959,-p13@BSCL2
Hg19::chr11:62475053..62475064,-p9@BSCL2
Hg19::chr1:67149410..67149413,+p@chr1:67149410..67149413
+
Hg19::chr2:210636697..210636762,+p1@UNC80
Hg19::chr3:184056614..184056641,+p3@FAM131A
Hg19::chr4:21609132..21609144,-p@chr4:21609132..21609144
-
Hg19::chr7:64337894..64337922,-p@chr7:64337894..64337922
-


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:0030176integral to endoplasmic reticulum membrane0.0448502667808
GO:0031227intrinsic to endoplasmic reticulum membrane0.0448502667808



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 tube4.76e-10956
neural rod4.76e-10956
future spinal cord4.76e-10956
neural keel4.76e-10956
regional part of nervous system2.91e-10253
regional part of brain2.91e-10253
central nervous system2.56e-9581
nervous system9.90e-9489
regional part of forebrain1.79e-8841
forebrain1.79e-8841
anterior neural tube1.79e-8841
future forebrain1.79e-8841
neural plate5.19e-8582
presumptive neural plate5.19e-8582
neurectoderm2.32e-8386
brain2.47e-8268
future brain2.47e-8268
telencephalon1.88e-7134
brain grey matter2.49e-7134
gray matter2.49e-7134
pre-chordal neural plate2.97e-7161
cerebral hemisphere2.66e-6732
regional part of telencephalon8.54e-6732
ecto-epithelium2.68e-66104
structure with developmental contribution from neural crest4.67e-53132
ectoderm-derived structure9.95e-52171
ectoderm9.95e-52171
presumptive ectoderm9.95e-52171
adult organism5.52e-51114
cerebral cortex1.14e-5025
pallium1.14e-5025
regional part of cerebral cortex4.70e-4522
neocortex1.44e-4020
organ system subdivision1.25e-34223
tube1.88e-25192
basal ganglion6.55e-229
nuclear complex of neuraxis6.55e-229
aggregate regional part of brain6.55e-229
collection of basal ganglia6.55e-229
cerebral subcortex6.55e-229
neural nucleus1.10e-219
nucleus of brain1.10e-219
posterior neural tube4.64e-2115
chordal neural plate4.64e-2115
anatomical cluster1.68e-19373
diencephalon6.77e-187
future diencephalon6.77e-187
anatomical conduit1.79e-17240
telencephalic nucleus2.39e-177
gyrus1.09e-156
epithelium1.19e-15306
cell layer2.39e-15309
segmental subdivision of hindbrain3.74e-1512
hindbrain3.74e-1512
presumptive hindbrain3.74e-1512
segmental subdivision of nervous system7.67e-1413
organ part1.89e-13218
parietal lobe3.66e-135
limbic system5.17e-135
temporal lobe6.59e-136
regional part of metencephalon8.12e-139
metencephalon8.12e-139
future metencephalon8.12e-139
multi-tissue structure1.33e-11342
corpus striatum1.47e-114
striatum1.47e-114
ventral part of telencephalon1.47e-114
future corpus striatum1.47e-114
gland of diencephalon2.16e-114
neuroendocrine gland2.16e-114
regional part of diencephalon3.09e-114
embryo1.13e-10592
germ layer2.09e-10560
germ layer / neural crest2.09e-10560
embryonic tissue2.09e-10560
presumptive structure2.09e-10560
germ layer / neural crest derived structure2.09e-10560
epiblast (generic)2.09e-10560
embryonic structure3.35e-10564
brainstem4.68e-106
developing anatomical structure6.22e-10581
caudate-putamen3.09e-093
dorsal striatum3.09e-093
organ1.08e-08503
occipital lobe1.11e-085
frontal cortex1.27e-083
pons4.17e-083
anatomical system5.45e-08624
anatomical group6.02e-08625
spinal cord6.59e-083
dorsal region element6.59e-083
dorsum6.59e-083
multi-cellular organism9.09e-08656
ciliary epithelium5.77e-073
ciliary body5.77e-073


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)
MA0003.10.213534
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.11.26877
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.11.78113
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.672652
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.11.50553
MA0101.10.347695
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.547931
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.403603
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.944394
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.11.13451
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.780982
MA0163.10.19677
MA0164.10.678332
MA0080.20.344472
MA0018.21.56673
MA0099.20.572
MA0079.21.35081
MA0102.21.51913
MA0258.10.687127
MA0259.10.289405
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
CTBP2#1488217.91914295409380.005060297063777310.023565004906757
JUND#372743.99695082392630.01017659347259770.0380139935507219



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:C1146&oldid=2569657"