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Coexpression cluster:C279: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0144922,0.00649508,0.0637571,0.393245,0.676075,0.1727,0.251493,0.267525,0.0727929,3.9173e-05,0.036615,0.626805,0.774639,0.0674845,0.432473,0.0531482,0.185123,0.289891,0.0168764,0.00944618,0.849263,0.011396,0.165427,0.655856,0.0925656,0.329864,0.00841165,0.163422,0.123591,0.0180036,0.126765,0.208225,0.361339,0.0861283,0.0288913,1.11646,0.0277885,0.173798,0.274776,0.716255,0.78673,0.113825,0.167297,4.688,0.00444949,0.0183191,0.0723718,0.0337541,0.20497,0.0440825,0.107144,0.953557,0.079172,0.259727,0.373267,0.0686071,0.70602,0.454954,0.017958,0.453026,0.235165,0.255378,0.0732848,0.168459,0.275941,0.148683,0.444327,0.768402,0.201596,0.621219,0.0242888,0.642019,0.00617833,1.72705,0.000356064,0.00211713,0.00148624,0.158618,0.199539,0.693384,0.01844,0.167826,0.27553,0.431697,0.332069,0.000737147,5.68025,0.016118,0.120022,0.860953,0.522821,0.311831,1.17285,2.57709,0.00831842,0.260649,0.852295,0.247685,0.122374,0.00323163,0.673887,0.215435,0.243872,1.04841,0.142306,0.141289,0.52619,0.234986,0.0210449,0.00670162,0.0702726,0.241987,0.323546,0.0392115,5.39441,0.0824728,4.12703e-05,0.125788,0.147378,0.0532585,0.957347,0.378328,0.170099,0.288769,0.577125,0.159055,0.0694627,0.222406,0.398874,0.0611188,0.312344,0.305407,0.410414,0.596352,0.533887,0.0721801,0.536632,0.373503,0.497634,1.29861,0.910351,1.17719,0.527118,0.245272,0.440934,0.19843,0.827938,1.14349,0.111271,0.00235125,0.00439759,0.000130822,0.312627,0.134884,0.0731181,0.648552,0.360413,1.21648,2.37558,0.0159977,0.465252,0.298975,0.199042,0.0757571,0.152239,0.976302,0.0418631,0.250005,5.66196e-08
|tfbs_overrepresentation_for_novel_motifs=0.0144922,0.00649508,0.0637571,0.393245,0.676075,0.1727,0.251493,0.267525,0.0727929,3.9173e-05,0.036615,0.626805,0.774639,0.0674845,0.432473,0.0531482,0.185123,0.289891,0.0168764,0.00944618,0.849263,0.011396,0.165427,0.655856,0.0925656,0.329864,0.00841165,0.163422,0.123591,0.0180036,0.126765,0.208225,0.361339,0.0861283,0.0288913,1.11646,0.0277885,0.173798,0.274776,0.716255,0.78673,0.113825,0.167297,4.688,0.00444949,0.0183191,0.0723718,0.0337541,0.20497,0.0440825,0.107144,0.953557,0.079172,0.259727,0.373267,0.0686071,0.70602,0.454954,0.017958,0.453026,0.235165,0.255378,0.0732848,0.168459,0.275941,0.148683,0.444327,0.768402,0.201596,0.621219,0.0242888,0.642019,0.00617833,1.72705,0.000356064,0.00211713,0.00148624,0.158618,0.199539,0.693384,0.01844,0.167826,0.27553,0.431697,0.332069,0.000737147,5.68025,0.016118,0.120022,0.860953,0.522821,0.311831,1.17285,2.57709,0.00831842,0.260649,0.852295,0.247685,0.122374,0.00323163,0.673887,0.215435,0.243872,1.04841,0.142306,0.141289,0.52619,0.234986,0.0210449,0.00670162,0.0702726,0.241987,0.323546,0.0392115,5.39441,0.0824728,4.12703e-05,0.125788,0.147378,0.0532585,0.957347,0.378328,0.170099,0.288769,0.577125,0.159055,0.0694627,0.222406,0.398874,0.0611188,0.312344,0.305407,0.410414,0.596352,0.533887,0.0721801,0.536632,0.373503,0.497634,1.29861,0.910351,1.17719,0.527118,0.245272,0.440934,0.19843,0.827938,1.14349,0.111271,0.00235125,0.00439759,0.000130822,0.312627,0.134884,0.0731181,0.648552,0.360413,1.21648,2.37558,0.0159977,0.465252,0.298975,0.199042,0.0757571,0.152239,0.976302,0.0418631,0.250005,5.66196e-08
|tfbs_overrepresentation_jaspar=MA0003.1;9.31629e-10,MA0004.1;0.149807,MA0006.1;0.0418213,MA0007.1;0.0330293,MA0009.1;0.282049,MA0014.1;3.30608e-08,MA0017.1;0.326942,MA0019.1;0.308124,MA0024.1;0.209896,MA0025.1;0.383675,MA0027.1;1.77546,MA0028.1;0.00983297,MA0029.1;0.633517,MA0030.1;0.215031,MA0031.1;0.51788,MA0038.1;0.254626,MA0040.1;0.226506,MA0041.1;0.675054,MA0042.1;2.29739,MA0043.1;0.282278,MA0046.1;0.753137,MA0048.1;3.87469e-05,MA0050.1;0.324596,MA0051.1;0.249836,MA0052.1;0.2291,MA0055.1;8.00362e-06,MA0056.1;0,MA0057.1;0.440606,MA0058.1;0.0766141,MA0059.1;0.0757992,MA0060.1;0.00788673,MA0061.1;0.190797,MA0063.1;0,MA0066.1;0.0732172,MA0067.1;0.537012,MA0068.1;0.443922,MA0069.1;0.271442,MA0070.1;2.06451,MA0071.1;0.0583578,MA0072.1;0.260306,MA0073.1;0.981738,MA0074.1;0.0710606,MA0076.1;0.0870507,MA0077.1;0.254892,MA0078.1;1.22624,MA0081.1;0.629296,MA0083.1;0.783458,MA0084.1;0.703837,MA0087.1;0.258584,MA0088.1;0.0345497,MA0089.1;0,MA0090.1;0.240463,MA0091.1;0.350729,MA0092.1;0.287028,MA0093.1;0.0431902,MA0095.1;0,MA0098.1;0,MA0100.1;0.0787315,MA0101.1;0.449727,MA0103.1;0.108723,MA0105.1;0.0279116,MA0106.1;0.0905927,MA0107.1;0.253705,MA0108.2;0.172469,MA0109.1;0,MA0111.1;0.0252311,MA0113.1;0.66502,MA0114.1;0.0546908,MA0115.1;0.471806,MA0116.1;0.0190182,MA0117.1;0.309701,MA0119.1;0.0660527,MA0122.1;1.57815,MA0124.1;0.437263,MA0125.1;0.966786,MA0130.1;0,MA0131.1;0.12559,MA0132.1;0,MA0133.1;0,MA0135.1;0.821509,MA0136.1;0.0759094,MA0139.1;0.0139421,MA0140.1;0.0574137,MA0141.1;0.192805,MA0142.1;0.155551,MA0143.1;0.323899,MA0144.1;0.54022,MA0145.1;0.0012993,MA0146.1;4.85067e-07,MA0147.1;0.003339,MA0148.1;0.390676,MA0149.1;0.769503,MA0062.2;0.00402933,MA0035.2;0.208625,MA0039.2;1.00116e-06,MA0138.2;0.11686,MA0002.2;0.128802,MA0137.2;0.291852,MA0104.2;0.00777397,MA0047.2;1.50548,MA0112.2;0.00324659,MA0065.2;0.00468678,MA0150.1;0.716372,MA0151.1;0,MA0152.1;2.89109,MA0153.1;0.93763,MA0154.1;0.0531342,MA0155.1;0.00251611,MA0156.1;0.0537852,MA0157.1;0.140121,MA0158.1;0,MA0159.1;0.145708,MA0160.1;0.187803,MA0161.1;0,MA0162.1;1.71584e-05,MA0163.1;3.73016e-07,MA0164.1;0.339401,MA0080.2;0.121711,MA0018.2;0.30505,MA0099.2;0.0598901,MA0079.2;3.96917e-07,MA0102.2;0.737926,MA0258.1;0.190277,MA0259.1;0.0224311,MA0442.1;0
}}
}}

Revision as of 18:57, 22 January 2013


Full id: C279_parietal_cerebellum_occipital_temporal_middle_duodenum_medial



Phase1 CAGE Peaks

Hg19::chr10:13141974..13141997,-p3@CCDC3
Hg19::chr11:33424626..33424658,+p1@ENST00000532231
Hg19::chr11:70463500..70463520,-p@chr11:70463500..70463520
-
Hg19::chr12:78063535..78063545,+p@chr12:78063535..78063545
+
Hg19::chr12:99361526..99361530,-p@chr12:99361526..99361530
-
Hg19::chr12:99384339..99384342,-p@chr12:99384339..99384342
-
Hg19::chr13:26511516..26511519,+p@chr13:26511516..26511519
+
Hg19::chr14:23982540..23982582,+p1@ENST00000554403
p1@uc001wkc.1
Hg19::chr16:6536107..6536111,+p@chr16:6536107..6536111
+
Hg19::chr16:6706532..6706568,+p@chr16:6706532..6706568
+
Hg19::chr16:6742581..6742607,+p@chr16:6742581..6742607
+
Hg19::chr16:6742644..6742656,+p@chr16:6742644..6742656
+
Hg19::chr16:6742665..6742685,+p@chr16:6742665..6742685
+
Hg19::chr16:6742720..6742775,+p@chr16:6742720..6742775
+
Hg19::chr16:6742782..6742813,+p@chr16:6742782..6742813
+
Hg19::chr16:6742892..6742925,+p@chr16:6742892..6742925
+
Hg19::chr16:6742966..6743000,+p@chr16:6742966..6743000
+
Hg19::chr16:6743276..6743304,+p@chr16:6743276..6743304
+
Hg19::chr16:6743318..6743394,+p@chr16:6743318..6743394
+
Hg19::chr16:6913753..6913756,+p@chr16:6913753..6913756
+
Hg19::chr16:7117462..7117465,+p@chr16:7117462..7117465
+
Hg19::chr16:7150584..7150589,+p@chr16:7150584..7150589
+
Hg19::chr16:7182015..7182018,+p@chr16:7182015..7182018
+
Hg19::chr16:7199503..7199506,+p@chr16:7199503..7199506
+
Hg19::chr16:7438669..7438673,+p@chr16:7438669..7438673
+
Hg19::chr17:44047160..44047193,+p@chr17:44047160..44047193
+
Hg19::chr19:36288768..36288814,-p1@ENST00000433059
p1@uc002obw.1
Hg19::chr1:16796987..16797016,-p@chr1:16796987..16797016
-
Hg19::chr1:241436474..241436478,-p@chr1:241436474..241436478
-
Hg19::chr21:15421332..15421334,+p@chr21:15421332..15421334
+
Hg19::chr2:1946780..1946825,+p@chr2:1946780..1946825
+
Hg19::chr2:203726992..203726997,-p@chr2:203726992..203726997
-
Hg19::chr2:51057134..51057137,-p1@ENST00000426912
Hg19::chr3:134514187..134514201,+p3@EPHB1
Hg19::chr3:49706223..49706234,+p@chr3:49706223..49706234
+
Hg19::chr3:96772914..96772943,+p@chr3:96772914..96772943
+
Hg19::chr4:6437090..6437101,-p@chr4:6437090..6437101
-
Hg19::chr7:158037602..158037617,-p@chr7:158037602..158037617
-
Hg19::chr7:45675228..45675230,+p@chr7:45675228..45675230
+
Hg19::chr7:82582997..82583024,-p@chr7:82582997..82583024
-
Hg19::chr8:10221208..10221236,+p@chr8:10221208..10221236
+
Hg19::chr8:10316929..10316947,+p@chr8:10316929..10316947
+
Hg19::chr8:133358414..133358435,-p@chr8:133358414..133358435
-
Hg19::chr8:85285149..85285159,+p@chr8:85285149..85285159
+
Hg19::chr8:85398264..85398268,+p@chr8:85398264..85398268
+
Hg19::chr9:68418929..68418958,+p@chr9:68418929..68418958
+


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 tube2.86e-10756
neural rod2.86e-10756
future spinal cord2.86e-10756
neural keel2.86e-10756
regional part of nervous system7.77e-9953
regional part of brain7.77e-9953
central nervous system7.66e-8881
nervous system1.09e-8489
brain grey matter1.91e-8434
gray matter1.91e-8434
telencephalon2.88e-8434
regional part of forebrain2.78e-8341
forebrain2.78e-8341
anterior neural tube2.78e-8341
future forebrain2.78e-8341
cerebral hemisphere6.79e-7932
regional part of telencephalon1.29e-7832
brain1.71e-7768
future brain1.71e-7768
neural plate2.37e-7382
presumptive neural plate2.37e-7382
neurectoderm1.17e-7286
regional part of cerebral cortex2.86e-6622
neocortex4.80e-6020
ecto-epithelium2.60e-58104
cerebral cortex6.67e-5825
pallium6.67e-5825
pre-chordal neural plate1.21e-5661
adult organism8.64e-45114
ectoderm-derived structure1.55e-44171
ectoderm1.55e-44171
presumptive ectoderm1.55e-44171
structure with developmental contribution from neural crest1.02e-43132
organ system subdivision6.50e-33223
basal ganglion3.23e-289
nuclear complex of neuraxis3.23e-289
aggregate regional part of brain3.23e-289
collection of basal ganglia3.23e-289
cerebral subcortex3.23e-289
neural nucleus1.24e-279
nucleus of brain1.24e-279
tube2.12e-26192
posterior neural tube8.18e-2415
chordal neural plate8.18e-2415
telencephalic nucleus5.08e-227
gyrus4.61e-206
anatomical conduit7.29e-19240
temporal lobe3.55e-176
occipital lobe5.55e-175
parietal lobe6.76e-175
limbic system7.22e-175
segmental subdivision of hindbrain2.20e-1612
hindbrain2.20e-1612
presumptive hindbrain2.20e-1612
anatomical cluster1.33e-15373
organ part3.67e-15218
segmental subdivision of nervous system5.16e-1513
epithelium4.76e-14306
corpus striatum7.17e-144
striatum7.17e-144
ventral part of telencephalon7.17e-144
future corpus striatum7.17e-144
cell layer8.42e-14309
brainstem4.92e-136
regional part of metencephalon5.60e-139
metencephalon5.60e-139
future metencephalon5.60e-139
frontal cortex4.40e-113
caudate-putamen5.20e-113
dorsal striatum5.20e-113
pons3.21e-103
multi-tissue structure5.81e-10342
spinal cord8.78e-103
dorsal region element8.78e-103
dorsum8.78e-103
middle frontal gyrus4.88e-082
middle temporal gyrus5.23e-082
caudate nucleus6.40e-082
future caudate nucleus6.40e-082
amygdala6.62e-082
Ammon's horn8.64e-082
lobe parts of cerebral cortex8.64e-082
hippocampal formation8.64e-082
limbic lobe8.64e-082
locus ceruleus2.62e-072
brainstem nucleus2.62e-072
hindbrain nucleus2.62e-072
germ layer2.94e-07560
germ layer / neural crest2.94e-07560
embryonic tissue2.94e-07560
presumptive structure2.94e-07560
germ layer / neural crest derived structure2.94e-07560
epiblast (generic)2.94e-07560
globus pallidus2.98e-072
pallidum2.98e-072
embryonic structure4.10e-07564


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)
MA0003.19.31629e-10
MA0004.10.149807
MA0006.10.0418213
MA0007.10.0330293
MA0009.10.282049
MA0014.13.30608e-08
MA0017.10.326942
MA0019.10.308124
MA0024.10.209896
MA0025.10.383675
MA0027.11.77546
MA0028.10.00983297
MA0029.10.633517
MA0030.10.215031
MA0031.10.51788
MA0038.10.254626
MA0040.10.226506
MA0041.10.675054
MA0042.12.29739
MA0043.10.282278
MA0046.10.753137
MA0048.13.87469e-05
MA0050.10.324596
MA0051.10.249836
MA0052.10.2291
MA0055.18.00362e-06
MA0056.10
MA0057.10.440606
MA0058.10.0766141
MA0059.10.0757992
MA0060.10.00788673
MA0061.10.190797
MA0063.10
MA0066.10.0732172
MA0067.10.537012
MA0068.10.443922
MA0069.10.271442
MA0070.12.06451
MA0071.10.0583578
MA0072.10.260306
MA0073.10.981738
MA0074.10.0710606
MA0076.10.0870507
MA0077.10.254892
MA0078.11.22624
MA0081.10.629296
MA0083.10.783458
MA0084.10.703837
MA0087.10.258584
MA0088.10.0345497
MA0089.10
MA0090.10.240463
MA0091.10.350729
MA0092.10.287028
MA0093.10.0431902
MA0095.10
MA0098.10
MA0100.10.0787315
MA0101.10.449727
MA0103.10.108723
MA0105.10.0279116
MA0106.10.0905927
MA0107.10.253705
MA0108.20.172469
MA0109.10
MA0111.10.0252311
MA0113.10.66502
MA0114.10.0546908
MA0115.10.471806
MA0116.10.0190182
MA0117.10.309701
MA0119.10.0660527
MA0122.11.57815
MA0124.10.437263
MA0125.10.966786
MA0130.10
MA0131.10.12559
MA0132.10
MA0133.10
MA0135.10.821509
MA0136.10.0759094
MA0139.10.0139421
MA0140.10.0574137
MA0141.10.192805
MA0142.10.155551
MA0143.10.323899
MA0144.10.54022
MA0145.10.0012993
MA0146.14.85067e-07
MA0147.10.003339
MA0148.10.390676
MA0149.10.769503
MA0062.20.00402933
MA0035.20.208625
MA0039.21.00116e-06
MA0138.20.11686
MA0002.20.128802
MA0137.20.291852
MA0104.20.00777397
MA0047.21.50548
MA0112.20.00324659
MA0065.20.00468678
MA0150.10.716372
MA0151.10
MA0152.12.89109
MA0153.10.93763
MA0154.10.0531342
MA0155.10.00251611
MA0156.10.0537852
MA0157.10.140121
MA0158.10
MA0159.10.145708
MA0160.10.187803
MA0161.10
MA0162.11.71584e-05
MA0163.13.73016e-07
MA0164.10.339401
MA0080.20.121711
MA0018.20.30505
MA0099.20.0598901
MA0079.23.96917e-07
MA0102.20.737926
MA0258.10.190277
MA0259.10.0224311
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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C279&oldid=2568790"