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Coexpression cluster:C335: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.143948,0.00503553,0.137153,0.294916,0.470143,1.52028,0.393141,0.0305595,0.0883366,0.459075,0.256108,0.454646,0.384441,0.118408,0.753506,0.286634,0.73324,1.18292,0.0190937,0.184634,0.321453,0.0740958,0.283248,0.456729,0.407145,0.945871,0.182286,0.280584,0.478343,0.0730581,0.230716,0.292383,1.33681,0.124205,0.38192,2.29686,0.191651,0.613203,0.538548,0.708576,0.378503,0.0584668,0.257038,0.747806,0.029893,0.166385,0.394651,0.243373,0.1394,0.104212,0.509118,0.131509,0.769427,0.350976,0.475837,0.119953,0.107617,0.337373,0.148813,0.336051,0.32323,0.397937,0.552329,0.245859,0.136236,0.222166,0.551996,0.889382,0.284717,0.737624,0.766256,0.032916,0.0790282,0.474142,0.048133,0.190552,0.439809,0.66053,0.282332,0.175286,0.0649382,0.245107,0.422637,0.572385,0.431067,0.395006,3.32352,0.139545,0.186966,0.984017,0.634935,1.05302,0.304922,0.275832,0.472107,0.304987,1.18671,1.60713,0.1899,0.913956,0.543149,0.300686,0.886085,0.739294,0.614234,0.250761,0.256823,0.750137,0.0481039,0.224443,0.616751,0.330971,0.311498,0.267371,0.592003,0.370269,0.130507,0.229352,0.220587,0.483881,0.467142,0.185428,0.289431,0.14239,0.691757,0.234645,0.384386,0.30868,0.503421,0.152384,0.409436,0.233981,0.515797,0.140501,0.646547,1.26969,0.838745,0.281279,0.608436,1.42699,1.03434,0.575287,0.386763,0.889616,1.15926,0.099088,0.204563,1.27059,0.796431,0.463809,0.669201,0.229728,0.409747,0.323402,0.397263,0.765951,0.523955,1.43032,0.0482085,0.153009,0.574213,0.394694,0.281754,1.00132,0.226459,0.135598,0.946231,0.782249,0.174493
|tfbs_overrepresentation_for_novel_motifs=0.143948,0.00503553,0.137153,0.294916,0.470143,1.52028,0.393141,0.0305595,0.0883366,0.459075,0.256108,0.454646,0.384441,0.118408,0.753506,0.286634,0.73324,1.18292,0.0190937,0.184634,0.321453,0.0740958,0.283248,0.456729,0.407145,0.945871,0.182286,0.280584,0.478343,0.0730581,0.230716,0.292383,1.33681,0.124205,0.38192,2.29686,0.191651,0.613203,0.538548,0.708576,0.378503,0.0584668,0.257038,0.747806,0.029893,0.166385,0.394651,0.243373,0.1394,0.104212,0.509118,0.131509,0.769427,0.350976,0.475837,0.119953,0.107617,0.337373,0.148813,0.336051,0.32323,0.397937,0.552329,0.245859,0.136236,0.222166,0.551996,0.889382,0.284717,0.737624,0.766256,0.032916,0.0790282,0.474142,0.048133,0.190552,0.439809,0.66053,0.282332,0.175286,0.0649382,0.245107,0.422637,0.572385,0.431067,0.395006,3.32352,0.139545,0.186966,0.984017,0.634935,1.05302,0.304922,0.275832,0.472107,0.304987,1.18671,1.60713,0.1899,0.913956,0.543149,0.300686,0.886085,0.739294,0.614234,0.250761,0.256823,0.750137,0.0481039,0.224443,0.616751,0.330971,0.311498,0.267371,0.592003,0.370269,0.130507,0.229352,0.220587,0.483881,0.467142,0.185428,0.289431,0.14239,0.691757,0.234645,0.384386,0.30868,0.503421,0.152384,0.409436,0.233981,0.515797,0.140501,0.646547,1.26969,0.838745,0.281279,0.608436,1.42699,1.03434,0.575287,0.386763,0.889616,1.15926,0.099088,0.204563,1.27059,0.796431,0.463809,0.669201,0.229728,0.409747,0.323402,0.397263,0.765951,0.523955,1.43032,0.0482085,0.153009,0.574213,0.394694,0.281754,1.00132,0.226459,0.135598,0.946231,0.782249,0.174493
|tfbs_overrepresentation_jaspar=MA0003.1;0.00687678,MA0004.1;0.262334,MA0006.1;1.10032,MA0007.1;0.515741,MA0009.1;0.375925,MA0014.1;0.0850783,MA0017.1;0.0330569,MA0019.1;0.151679,MA0024.1;0.294311,MA0025.1;0.487069,MA0027.1;1.90579,MA0028.1;0.027018,MA0029.1;0.308904,MA0030.1;0.300221,MA0031.1;0.252799,MA0038.1;0.126016,MA0040.1;0.313366,MA0041.1;1.00423,MA0042.1;1.87562,MA0043.1;0.376179,MA0046.1;1.71137,MA0048.1;0.272397,MA0050.1;0.0704881,MA0051.1;0.78189,MA0052.1;0.316327,MA0055.1;0.538038,MA0056.1;0,MA0057.1;0.753099,MA0058.1;0.360926,MA0059.1;0.156159,MA0060.1;0.193055,MA0061.1;0.269952,MA0063.1;0,MA0066.1;0.126249,MA0067.1;0.649823,MA0068.1;1.20404,MA0069.1;0.364099,MA0070.1;0.935158,MA0071.1;0.105665,MA0072.1;0.351626,MA0073.1;4.05474,MA0074.1;0.123313,MA0076.1;0.0455123,MA0077.1;0.345539,MA0078.1;0.182227,MA0081.1;0.358793,MA0083.1;0.381987,MA0084.1;0.823032,MA0087.1;0.349692,MA0088.1;0.253263,MA0089.1;0,MA0090.1;0.0504181,MA0091.1;0.265508,MA0092.1;0.221134,MA0093.1;0.251813,MA0095.1;0,MA0098.1;0,MA0100.1;0.133688,MA0101.1;0.25728,MA0103.1;0.231834,MA0105.1;0.472984,MA0106.1;0.14939,MA0107.1;0.298233,MA0108.2;0.250614,MA0109.1;0,MA0111.1;0.055257,MA0113.1;0.480586,MA0114.1;0.0513379,MA0115.1;0.581155,MA0116.1;0.151824,MA0117.1;0.406527,MA0119.1;0.596156,MA0122.1;0.42795,MA0124.1;0.544476,MA0125.1;0.471774,MA0130.1;0,MA0131.1;0.193896,MA0132.1;0,MA0133.1;0,MA0135.1;0.400588,MA0136.1;0.129893,MA0139.1;0.394126,MA0140.1;0.104326,MA0141.1;0.0395007,MA0142.1;0.230443,MA0143.1;0.159255,MA0144.1;0.25542,MA0145.1;0.201269,MA0146.1;0.0348478,MA0147.1;0.156503,MA0148.1;0.611137,MA0149.1;0.0995233,MA0062.2;0.00301306,MA0035.2;0.103973,MA0039.2;0.101267,MA0138.2;1.63061,MA0002.2;0.171397,MA0137.2;0.118838,MA0104.2;0.191608,MA0047.2;0.438572,MA0112.2;0.0567379,MA0065.2;0.211429,MA0150.1;0.72007,MA0151.1;0,MA0152.1;0.349115,MA0153.1;0.457467,MA0154.1;0.00191347,MA0155.1;0.00832059,MA0156.1;0.0292146,MA0157.1;0.211768,MA0158.1;0,MA0159.1;0.0586669,MA0160.1;0.0939956,MA0161.1;0,MA0162.1;1.77495,MA0163.1;0.0364486,MA0164.1;0.166704,MA0080.2;0.102716,MA0018.2;0.150204,MA0099.2;0.107829,MA0079.2;1.26374,MA0102.2;0.858102,MA0258.1;0.41289,MA0259.1;0.0634142,MA0442.1;0
}}
}}

Revision as of 19:04, 22 January 2013


Full id: C335_cerebellum_parietal_occipital_temporal_duodenum_brain_medial



Phase1 CAGE Peaks

Hg19::chr10:13141961..13141973,-p6@CCDC3
Hg19::chr12:100378565..100378574,-p27@ANKS1B
Hg19::chr14:23982515..23982529,+p2@ENST00000554403
p2@uc001wkc.1
Hg19::chr17:48207157..48207212,-p2@SAMD14
Hg19::chr18:40695590..40695602,-p3@RIT2
Hg19::chr19:42547060..42547064,-p4@GRIK5
Hg19::chr1:151032142..151032195,+p5@MLLT11
Hg19::chr20:62795834..62795878,+p2@MYT1
Hg19::chr2:122247922..122247956,-p6@CLASP1
Hg19::chr2:131513104..131513119,+p1@FAM123C
Hg19::chr2:2336983..2336994,-p@chr2:2336983..2336994
-
Hg19::chr2:50809613..50809617,-p@chr2:50809613..50809617
-
Hg19::chr3:115371232..115371236,+p@chr3:115371232..115371236
+
Hg19::chr4:176733522..176733548,-p10@GPM6A
Hg19::chr5:87438363..87438394,+p@chr5:87438363..87438394
+
Hg19::chr8:10192316..10192321,-p@chr8:10192316..10192321
-
Hg19::chr8:10306862..10306874,+p@chr8:10306862..10306874
+
Hg19::chr8:85095305..85095312,+p17@RALYL
Hg19::chr8:85095736..85095748,+p7@RALYL
Hg19::chr8:85101923..85101927,+p@chr8:85101923..85101927
+
Hg19::chr8:85155756..85155760,+p@chr8:85155756..85155760
+
Hg19::chr8:85208884..85208887,+p@chr8:85208884..85208887
+
Hg19::chr8:85247963..85247966,+p@chr8:85247963..85247966
+
Hg19::chr8:85289710..85289715,+p@chr8:85289710..85289715
+
Hg19::chr8:9953136..9953190,+p3@MSRA
Hg19::chr8:9953214..9953226,+p5@MSRA
Hg19::chr9:73736417..73736430,-p8@TRPM3
Hg19::chr9:73736712..73736721,-p10@TRPM3
Hg19::chrX:10645578..10645591,-p15@MID1
Hg19::chrX:124338153..124338169,-p1@ENST00000422498
Hg19::chrX:124338174..124338186,-p2@ENST00000422498
Hg19::chrX:124338245..124338250,-p4@ENST00000422498
Hg19::chrX:23351515..23351543,-p@chrX:23351515..23351543
-
Hg19::chrX:32173579..32173593,-p5@DMD


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube6.80e-11756
neural rod6.80e-11756
future spinal cord6.80e-11756
neural keel6.80e-11756
regional part of nervous system6.44e-10853
regional part of brain6.44e-10853
central nervous system2.79e-10081
brain1.19e-9368
future brain1.19e-9368
nervous system5.37e-9389
regional part of forebrain2.81e-8641
forebrain2.81e-8641
anterior neural tube2.81e-8641
future forebrain2.81e-8641
brain grey matter3.62e-8234
gray matter3.62e-8234
telencephalon7.12e-8234
neural plate2.66e-8082
presumptive neural plate2.66e-8082
cerebral hemisphere2.93e-7632
neurectoderm4.26e-7686
regional part of telencephalon5.41e-7632
ecto-epithelium6.20e-64104
regional part of cerebral cortex1.71e-6222
pre-chordal neural plate6.44e-5961
neocortex4.65e-5620
adult organism9.13e-55114
cerebral cortex1.30e-5425
pallium1.30e-5425
structure with developmental contribution from neural crest2.44e-48132
ectoderm-derived structure1.79e-47171
ectoderm1.79e-47171
presumptive ectoderm1.79e-47171
organ system subdivision5.07e-37223
posterior neural tube7.89e-3015
chordal neural plate7.89e-3015
neural nucleus5.61e-299
nucleus of brain5.61e-299
tube3.71e-28192
basal ganglion3.26e-239
nuclear complex of neuraxis3.26e-239
aggregate regional part of brain3.26e-239
collection of basal ganglia3.26e-239
cerebral subcortex3.26e-239
telencephalic nucleus5.95e-237
segmental subdivision of hindbrain1.25e-2112
hindbrain1.25e-2112
presumptive hindbrain1.25e-2112
gyrus1.60e-206
anatomical conduit2.49e-20240
segmental subdivision of nervous system7.89e-2013
brainstem3.92e-196
anatomical cluster2.35e-18373
occipital lobe8.33e-185
parietal lobe2.40e-175
epithelium2.46e-15306
organ part2.46e-15218
cell layer4.45e-15309
corpus striatum1.29e-144
striatum1.29e-144
ventral part of telencephalon1.29e-144
future corpus striatum1.29e-144
regional part of metencephalon1.17e-139
metencephalon1.17e-139
future metencephalon1.17e-139
temporal lobe1.39e-126
multi-tissue structure8.49e-12342
limbic system1.17e-115
caudate-putamen1.83e-113
dorsal striatum1.83e-113
frontal cortex2.59e-113
pons1.55e-103
medulla oblongata2.55e-103
myelencephalon2.55e-103
future myelencephalon2.55e-103
spinal cord3.00e-103
dorsal region element3.00e-103
dorsum3.00e-103
germ layer1.07e-08560
germ layer / neural crest1.07e-08560
embryonic tissue1.07e-08560
presumptive structure1.07e-08560
germ layer / neural crest derived structure1.07e-08560
epiblast (generic)1.07e-08560
embryonic structure1.51e-08564
organ2.48e-08503
caudate nucleus3.20e-082
future caudate nucleus3.20e-082
middle frontal gyrus3.56e-082
middle temporal gyrus4.39e-082
Ammon's horn4.70e-082
lobe parts of cerebral cortex4.70e-082
hippocampal formation4.70e-082
limbic lobe4.70e-082
developing anatomical structure6.32e-08581
locus ceruleus9.99e-082
brainstem nucleus9.99e-082
hindbrain nucleus9.99e-082
embryo1.53e-07592
dorsal plus ventral thalamus1.89e-072


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)
MA0003.10.00687678
MA0004.10.262334
MA0006.11.10032
MA0007.10.515741
MA0009.10.375925
MA0014.10.0850783
MA0017.10.0330569
MA0019.10.151679
MA0024.10.294311
MA0025.10.487069
MA0027.11.90579
MA0028.10.027018
MA0029.10.308904
MA0030.10.300221
MA0031.10.252799
MA0038.10.126016
MA0040.10.313366
MA0041.11.00423
MA0042.11.87562
MA0043.10.376179
MA0046.11.71137
MA0048.10.272397
MA0050.10.0704881
MA0051.10.78189
MA0052.10.316327
MA0055.10.538038
MA0056.10
MA0057.10.753099
MA0058.10.360926
MA0059.10.156159
MA0060.10.193055
MA0061.10.269952
MA0063.10
MA0066.10.126249
MA0067.10.649823
MA0068.11.20404
MA0069.10.364099
MA0070.10.935158
MA0071.10.105665
MA0072.10.351626
MA0073.14.05474
MA0074.10.123313
MA0076.10.0455123
MA0077.10.345539
MA0078.10.182227
MA0081.10.358793
MA0083.10.381987
MA0084.10.823032
MA0087.10.349692
MA0088.10.253263
MA0089.10
MA0090.10.0504181
MA0091.10.265508
MA0092.10.221134
MA0093.10.251813
MA0095.10
MA0098.10
MA0100.10.133688
MA0101.10.25728
MA0103.10.231834
MA0105.10.472984
MA0106.10.14939
MA0107.10.298233
MA0108.20.250614
MA0109.10
MA0111.10.055257
MA0113.10.480586
MA0114.10.0513379
MA0115.10.581155
MA0116.10.151824
MA0117.10.406527
MA0119.10.596156
MA0122.10.42795
MA0124.10.544476
MA0125.10.471774
MA0130.10
MA0131.10.193896
MA0132.10
MA0133.10
MA0135.10.400588
MA0136.10.129893
MA0139.10.394126
MA0140.10.104326
MA0141.10.0395007
MA0142.10.230443
MA0143.10.159255
MA0144.10.25542
MA0145.10.201269
MA0146.10.0348478
MA0147.10.156503
MA0148.10.611137
MA0149.10.0995233
MA0062.20.00301306
MA0035.20.103973
MA0039.20.101267
MA0138.21.63061
MA0002.20.171397
MA0137.20.118838
MA0104.20.191608
MA0047.20.438572
MA0112.20.0567379
MA0065.20.211429
MA0150.10.72007
MA0151.10
MA0152.10.349115
MA0153.10.457467
MA0154.10.00191347
MA0155.10.00832059
MA0156.10.0292146
MA0157.10.211768
MA0158.10
MA0159.10.0586669
MA0160.10.0939956
MA0161.10
MA0162.11.77495
MA0163.10.0364486
MA0164.10.166704
MA0080.20.102716
MA0018.20.150204
MA0099.20.107829
MA0079.21.26374
MA0102.20.858102
MA0258.10.41289
MA0259.10.0634142
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.

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