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Coexpression cluster:C279: Difference between revisions

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0.892707,0.460694,0.610541,0.917912,0.865113,0.82923,0.832572,0.681864,0.359154,0.999935,0.90876,0.455315,0.754195,0.580153,0.688346,0.988744,0.17744,0.626727,0.884044,0.982391,0.91879,0.890211,0.703009,0.945149,0.730142,0.954657,0.986087,0.913749,0.677979,0.939593,0.674578,0.760349,0.977207,0.994424,0.524331,0.451688,0.993977,0.887669,0.709417,0.830173,0.353086,0.884787,0.983119,0.980678,0.557888,0.799172,0.544831,0.624171,0.338782,0.778593,0.688375,0.411821,0.693285,0.731481,0.949354,0.933208,0.976627,0.893908,0.85722,0.962296,0.577917,0.999995,0.597147,0.526529,0.642592,0.618236,0.794127,0.973031,0.678434,0.744725,0.967901,0.426246,0.872304,0.947736,0.99982,1,0.971153,0.977046,0.827473,0.28964,0.828863,0.540181,0.786683,0.970748,0.70032,0.511547,0.833134,0.672839,0.980387,0.922282,0.445179,0.887138,0.506413,0.572503,0.55481,0.775968,0.945083,0.506771,0.535092,0.594498,0.0094422,0.702317,0.994394,0.719771,0.964023,0.890544,0.806587,0.405532,0.787354,0.311665,0.919604,0.62933,0.961471,0.705709,0.994156,0.480897,0.317027,0.771943,0.614274,0.908329,0.713385,0.792162,0.924451,0.779353,0.841447,0.193196,0.981139,0.935889,0.966096,0.856758,0.739055,0.997917,0.841363,0.840001,0.957893,0.792567,0.783021,0.84787,0.98762,1.08696e-14,0.800453,0.833846,0.813277,0.548904,0.327634,0.940304,0.767117,0.86496,0.939258,0.959463,0.727933,0.956531,0.73364,0.823104,0.999799,0.239976,0.931313,0.802759,0.521381,0.766112,0.9015,0.980181,0.430806,0.987743,0.884053,0.149333,0.88911,0.965529,0.993119,0.980777,0.95825,0.767188,0.913374,0.993131,0.922609,0.990847,0.949372,0.850109,0.983374,0.991883,0.996946,0.994664,0.997027,0.999893,0.863031,0.974452,0.995652,0.991508,0.905622,0.978442,0.969565,0.998606,0.999591,0.556706,0.966907,0.921625,0.940513,0.96391,0.994178,0.684413,0.443434,0.994654,0.518596,0.83693,0.762687,0.905038,0.970235,0.949603,0.964304,0.671036,0.947389,0.986108,0.995653,0.981297,0.860989,0.9812,0.0569423,0.962449,0.866384,0.979005,0.973601,0.993724,0.993237,0.77515,0.974967,0.930401,0.97961,0.460606,0.666199,0.867132,0.910383,0.831513,0.744985,0.785829,0.978321,0.0172487,0.903299,0.821333,0.78776,0.927905,0.963408,0.935652,0.982032,0.313593,0.963659,0.986729,0.685621,0.953551,0.882394,0.984288,0.606673,0.813228,0.986289,0.936382,0.998935,0.998267,0.989221,0.999453,0.996193,0.999998,0.991376,0.978717,0.717728,0.914054,0.995921,0.995899,0.978062,0.277226,0.99484,0.667413,0.999401,0.768918,0.850873,0.736853,0.979997,0.997333,0.947838,0.866383,0.842075,0.988256,0.903796,0.916928,0.997184,0.981263,0.968518,0.917347,0.140869,0.866411,0.929283,0.994119,0.649643,0.957442,0.994656,0.996297,0.793814,0.972912,0.660208,0.996114,0.0684456,0.940559,0.756962,0.645902,0.937305,0.594296,0.994172,0.893828,0.850818,0.653201,0.632436,0.839217,0.750111,0.976218,0.98449,0.96315,0.995409,0.925788,0.984198,0.866188,0.971207,0.957248,0.99506,0.6634,0.966191,0.878512,0.850817,0.995685,0.941077,0.985442,0.97265,0.79448,0.211941,0.866796,0.797172,0.711648,0.55432,0.970502,0.408953,0.831983,0.98988,0.619724,0.681597,0.693216,0.755011,0.961255,0.756612,0.977596,0.871919,0.178052,0.454401,0.766462,0.988389,0.851812,0.940105,0.691284,0.947951,0.951777,0.841326,0.978237,0.979108,0.998356,0.820429,0.976963,0.966459,0.613942,0.867098,0.967003,0.398349,0.777315,0.868774,0.952206,0.753782,0.959902,0.159653,0.884106,0.872608,0.81028,0.897266,0.656594,0.972256,0.6986,0.549021,0.910597,0.981615,0.509464,0.90745,0.941219,0.452239,0.282104,0.560458,0.510744,0.991763,0.968327,0.989804,0.924328,0.859637,0.472787,0.525272,0.61,0.976006,0.741312,0.977985,0.964213,0.869149,0.944139,0.664431,0.80881,0.746085,0.989548,0.91834,0.976554,0.86847,0.956013,0.821217,0.110106,0.94305,0.496693,0.969626,0.882765,0.691386,0.904243,0.638265,0.93331,0.56343,0.979754,0.148011,0.787485,0.967607,0.900618,0.653709,0.985267,0.734354,0.884026,0.941551,0.979034,0.944785,0.949359,0.790575,0.8601,0.923153,0.961455,0.521106,0.378783,0.859951,0.822851,0.570356,0.571527,0.715227,0.353747,0.471385,0.571262,0.981286,0.946098,0.973755,0.958752,0.983092,0.624817,0.727471,0.794732,0.638148,0.863778,0.636513,0.816245,0.650864,0.703641,0.879136,0.528955,0.499288,0.287248,0.762956,0.436756,0.891738,0.864741,0.970518,0.759367,0.989067,0.679049,0.947405,0.989256,0.855808,0.980893,0.971896,0.938047,0.800745,0.750745,0.333068,0.885414,0.748686,0.971033,0.853947,0.265261,0.781272,0.851455,0.848534,0.890172,0.744595,0.55999,0.844498,0.835194,0.993742,0.962988,0.987847,0.761729,0.745897,0.778315,0.983888,0.902634,0.871489,0.786778,0.747824,0.9971,0.944323,0.929517,0.216565,0.677315,0.711531,0.485643,0.97893,0.948547,0.927468,0.718863,0.652343,0.867877,0.99188
|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
}}
}}

Revision as of 14:01, 26 November 2012


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)

{{{tfbs_overrepresentation_jaspar}}}



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

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