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Coexpression cluster:C372: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!4.32e-104!56;UBERON:0005068!4.32e-104!56;UBERON:0006241!4.32e-104!56;UBERON:0007135!4.32e-104!56;UBERON:0000073!3.40e-89!53;UBERON:0002616!3.40e-89!53;UBERON:0001017!1.55e-74!81;UBERON:0000955!1.25e-72!68;UBERON:0006238!1.25e-72!68;UBERON:0003075!7.67e-70!82;UBERON:0007284!7.67e-70!82;UBERON:0001016!1.00e-66!89;UBERON:0002346!2.18e-66!86;UBERON:0002780!1.14e-64!41;UBERON:0001890!1.14e-64!41;UBERON:0003080!1.14e-64!41;UBERON:0006240!1.14e-64!41;UBERON:0003528!5.82e-58!34;UBERON:0002020!5.82e-58!34;UBERON:0001893!1.12e-57!34;UBERON:0010371!4.30e-54!104;UBERON:0002791!1.03e-48!32;UBERON:0001869!1.80e-48!32;UBERON:0007023!5.49e-46!114;UBERON:0003056!2.18e-42!61;UBERON:0010314!1.43e-41!132;UBERON:0003076!2.59e-40!15;UBERON:0003057!2.59e-40!15;UBERON:0002298!9.59e-38!6;UBERON:0002619!9.11e-35!22;UBERON:0000125!8.16e-33!9;UBERON:0002308!8.16e-33!9;UBERON:0004121!9.87e-33!171;UBERON:0000924!9.87e-33!171;UBERON:0006601!9.87e-33!171;UBERON:0001950!5.67e-32!20;UBERON:0000956!1.70e-30!25;UBERON:0000203!1.70e-30!25;UBERON:0000025!6.07e-27!192;UBERON:0004733!7.34e-25!12;UBERON:0002028!7.34e-25!12;UBERON:0007277!7.34e-25!12;UBERON:0002420!5.81e-24!9;UBERON:0007245!5.81e-24!9;UBERON:0010009!5.81e-24!9;UBERON:0010011!5.81e-24!9;UBERON:0000454!5.81e-24!9;UBERON:0011216!8.52e-24!223;UBERON:0004732!6.95e-23!13;UBERON:0009663!1.01e-21!7;UBERON:0004111!1.82e-20!240;UBERON:0001896!4.48e-20!3;UBERON:0005290!4.48e-20!3;UBERON:0010096!4.48e-20!3;UBERON:0002240!7.42e-20!3;UBERON:0005174!7.42e-20!3;UBERON:0001137!7.42e-20!3;UBERON:0000988!1.78e-19!3;UBERON:0000200!3.71e-16!6;UBERON:0000483!7.60e-15!306;UBERON:0000119!1.20e-14!309;UBERON:0000369!5.18e-14!4;UBERON:0002435!5.18e-14!4;UBERON:0000204!5.18e-14!4;UBERON:0010082!5.18e-14!4;UBERON:0002148!9.74e-14!2;UBERON:0006331!9.74e-14!2;UBERON:0009662!9.74e-14!2;UBERON:0001897!1.33e-13!2;UBERON:0010225!1.33e-13!2;UBERON:0000064!2.56e-12!218;UBERON:0000477!4.66e-12!373;UBERON:0000349!1.67e-11!5;UBERON:0002680!3.58e-11!9;UBERON:0001895!3.58e-11!9;UBERON:0010092!3.58e-11!9;UBERON:0001872!3.67e-11!5;UBERON:0000481!1.99e-09!342;UBERON:0005383!5.97e-09!3;UBERON:0005382!5.97e-09!3;UBERON:0001870!7.01e-09!3;UBERON:0001894!1.57e-08!7;UBERON:0006222!1.57e-08!7;UBERON:0001871!2.96e-08!6;UBERON:0002038!9.71e-08!1;UBERON:0009661!9.71e-08!1;UBERON:0002950!9.71e-08!1;UBERON:0001891!9.71e-08!1;UBERON:0009616!9.71e-08!1;UBERON:0010286!9.71e-08!1;UBERON:0002336!1.25e-07!1;UBERON:0011215!1.25e-07!1;UBERON:0001018!1.25e-07!1;UBERON:0002473!1.25e-07!1;UBERON:0005340!1.25e-07!1;UBERON:0003544!1.25e-07!1;UBERON:0005970!1.25e-07!1;UBERON:0002316!1.25e-07!1;UBERON:0001020!1.25e-07!1;UBERON:0002437!1.25e-07!1;UBERON:0000062!1.92e-07!503;UBERON:0001874!2.83e-07!1;UBERON:0007190!3.01e-07!1;UBERON:0001882!3.20e-07!1;UBERON:0005403!3.20e-07!1;UBERON:0002784!3.21e-07!4;UBERON:0002902!3.84e-07!1;UBERON:0009899!3.84e-07!1;UBERON:0002581!4.34e-07!1;UBERON:0002022!4.90e-07!1
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8535,0.429323,0.322452,0.120093,0.967297,0.717185,0.67184,0.675904,0.946577,0.244611,0.996078,0.778964,0.3182,0.587136,0.421393,0.192102,0.156813,0.42126,0.0561036,0.742902,0.953933,0.4856,0.634477,0.534843,0.839625,0.562107,0.857762,0.98064,0.457081,0.771088,0.829567,0.768911,0.593683,0.972157,0.232226,0.374018,0.618506,0.977596,0.747999,0.541196,0.672984,0.735591,0.743942,0.68486,0.978655,0.402234,0.0825296,0.391164,0.460416,0.176545,0.613467,0.443466,0.284366,0.525299,0.956568,0.989344,0.943302,0.684531,0.963165,0.706861,0.873379,0.849595,0.999535,0.436271,0.375843,0.991977,0.45506,0.844846,0.968448,0.510936,0.702271,0.96406,0.295481,0.726786,0.118654,0.999999,0.999998,0.893047,0.907395,0.669716,0.146817,0.305692,0.38725,0.622432,0.892102,0.532193,0.363464,0.311514,0.505588,0.916138,0.800223,0.310229,0.747249,0.359254,0.414769,0.690465,0.610585,0.277284,0.290623,0.911274,0.433937,0.924274,0.53416,0.961922,0.797705,0.877067,0.907485,0.645042,0.735766,0.547781,0.982232,0.471571,0.465098,0.87164,0.788772,0.998875,0.0840577,0.513825,0.0682081,0.122089,0.778305,0.793651,0.628576,0.803756,0.835464,0.615389,0.759911,0.918182,0.93918,0.839548,0.346415,0.571281,0.9796,0.686738,0.685045,0.593163,0.843854,0.618359,0.795427,0.937255,0.768678,0.637987,0.943829,0.652833,0.686477,0.221396,0.530247,0.600956,0.745245,0.526948,0.867462,0.55985,0.861497,0.806501,0.87557,0.992261,0.445019,0.935848,0.85034,0.907438,0.720814,0.993629,0.999913,0.299017,0.886372,0.742915,0.349178,0.750042,0.893784,0.936619,0.0685241,0.993638,0.921504,0.999503,0.114084,0.822706,0.783119,0.128805,0.357573,0.539943,0.269345,0.96075,0.841331,0.462553,0.300688,0.0105444,0.984,0.855937,0.773278,0.799041,0.666872,0.0312759,0.999775,0.99998,0.710692,0.560161,0.982834,0.991109,0.833671,0.906775,0.950233,0.998592,0.116893,0.251734,0.849215,0.234124,0.964562,0.439759,0.98098,0.0472803,0.0281499,0.977937,0.932526,0.998773,0.952016,0.999963,0.998897,0.243787,0.999979,0.997241,0.492906,0.999975,0.0883486,0.99905,0.98627,0.999009,0.999826,0.946265,0.0723301,0.0685567,0.651416,0.859258,0.162722,0.621158,0.0262511,0.0487906,0.0259941,0.433022,0.963801,0.623636,0.162736,0.417112,0.0315321,0.249678,0.351134,0.404738,9.22544e-05,0.973988,0.855584,0.398879,0.996412,0.899311,0.881483,0.405015,0.518211,0.0188183,0.909017,0.994294,0.200201,0.71775,0.999482,0.999419,0.0373257,0.891923,0.594559,0.997534,0.999963,0.919812,0.183691,0.832177,0.764318,0.95824,0.26008,0.881266,0.569004,0.5012,0.986976,0.844628,0.901875,0.939945,0.42635,0.39839,0.933559,0.129038,0.991705,0.273768,0.925896,0.180503,0.813519,0.666988,0.675648,0.0272223,0.204116,0.925275,0.280132,0.278712,0.167423,0.686536,0.463198,0.989849,0.198604,0.680736,0.528962,0.844888,0.541173,0.518848,0.909703,0.531845,0.625648,0.871919,0.397529,0.97727,0.869269,0.708412,0.223342,0.958055,0.282684,0.869418,0.595744,0.935681,0.377358,0.99084,0.439095,0.430044,0.909346,0.628183,0.551883,0.695303,0.549031,0.849764,0.451736,0.851601,0.383362,0.559363,0.185465,0.819937,0.891531,0.282169,0.332231,0.553046,0.866848,0.513974,0.797041,0.0954478,0.336688,0.513144,0.690404,0.0275873,0.598458,0.252775,0.52399,0.0659082,0.181376,0.319715,0.894439,0.219724,0.56949,0.344977,0.433686,0.699902,0.767887,0.292872,0.907186,0.630645,0.593697,0.719816,0.883588,0.274076,0.612063,0.722048,0.852961,0.916866,0.611339,0.578792,0.393804,0.659516,0.76025,0.438322,0.146762,0.192561,0.184157,0.322919,0.78178,0.919488,0.0302636,0.245296,0.533168,0.315775,0.483695,0.404427,0.362804,0.804636,0.370961,0.785893,0.803555,0.71,0.265804,0.30456,0.447678,0.417566,0.496728,0.692808,0.620243,0.722549,0.786346,0.689745,0.30317,0.0908227,0.781452,0.211321,0.684097,0.365665,0.860458,0.0509956,0.0373499,0.551963,0.790695,0.378049,0.205859,0.390348,0.772127,0.874218,0.937297,0.69626,0.445517,0.292722,0.547934,0.884937,0.766726,0.165576,0.131047,0.489426,0.0491243,0.780752,0.228948,0.838955,0.121997,0.258949,0.177297,0.483215,0.61763,0.0344245,0.563758,0.887189,0.664165,0.412918,0.413927,0.212482,0.543971,0.330952,0.413698,0.886241,0.790655,0.199628,0.596675,0.92363,0.868889,0.55938,0.631478,0.473155,0.715424,0.471656,0.656322,0.484904,0.535468,0.736095,0.672902,0.353439,0.488234,0.596475,0.303646,0.753794,0.647929,0.966278,0.113045,0.589663,0.771772,0.176743,0.161467,0.172516,0.71169,0.132683,0.773355,0.563646,0.62522,0.00102008,0.744821,0.816032,0.653339,0.363279,0.0489077,0.483582,0.0160216,0.118325,0.686669,0.102164,0.693951,0.877128,0.60705,0.397201,0.83124,0.765553,0.25309,0.703278,0.245763,0.189946,0.915698,0.894776,0.622539,0.580421,0.167578,0.112075,0.235446,0.0899939,0.509864,0.364014,0.642801,0.438997,0.0417285,0.492364,0.680223,0.154986,0.385125,0.436473
|tfbs_overrepresentation_for_novel_motifs=0.197853,0.0361238,0.422512,0.747299,0.339547,0.368696,0.158494,0.497522,0.488724,0.108034,0.0995348,0.185675,0.00534452,0.15157,0.60928,0.168654,0.312612,1.08189,0.386787,0.310458,0.422633,0.361839,0.111006,0.141474,0.242214,0.200538,0.153882,0.354996,0.149458,0.601895,0.088911,0.341173,0.368873,0.19749,0.0273355,0.309479,0.0265279,0.115713,0.438438,0.0413545,0.813033,0.584031,0.799484,0.334058,0.285955,0.0625393,0.159157,0.0941929,0.381848,0.623045,0.210045,0.16639,0.597553,0.402924,0.532737,0.153325,1.41325,0.134204,0.846293,0.133632,0.976157,0.1606,1.06217,0.291591,0.171703,0.266103,0.611096,0.954146,0.33304,0.800453,0.0754767,1.48079,0.0270998,0.530988,0.0278383,0.478508,0.424496,0.764065,0.330507,0.234869,0.905304,0.290785,0.171482,0.147002,0.486416,0.00230791,0.101368,0.0506093,0.227861,1.04966,0.695939,0.463366,0.354445,0.639633,0.0372148,1.0186,0.868554,0.388689,0.231068,1.25395,0.232609,0.349965,0.384158,0.315425,1.31893,0.0972887,0.303327,0.456614,0.0685845,0.0323327,0.445751,0.381914,1.57097,0.104282,0.652077,0.110297,0.258846,0.0883435,0.264397,0.394953,0.523757,0.641925,0.113636,1.01317,0.753832,0.765351,0.469437,0.358416,0.561176,0.222109,3.02839,0.30248,0.573914,0.523168,0.707783,0.769646,0.607425,0.11017,0.668879,1.49486,1.10037,0.634967,0.919194,0.385822,0.259011,0.129436,1.97909,1.33792,0.273743,0.19455,0.51993,0.000149682,0.464277,0.71028,0.160304,0.829202,0.216727,0.0328973,0.242284,0.0571684,0.633868,0.448609,0.329893,0.212291,0.270734,0.170987,0.0671382,0.157687,0.0496019
}}
}}

Revision as of 14:10, 26 November 2012


Full id: C372_spinal_medulla_substantia_locus_thalamus_corpus_globus



Phase1 CAGE Peaks

Hg19::chr10:130489605..130489614,-p@chr10:130489605..130489614
-
Hg19::chr10:130489635..130489656,-p@chr10:130489635..130489656
-
Hg19::chr10:14066483..14066492,-p@chr10:14066483..14066492
-
Hg19::chr10:6425090..6425094,-p@chr10:6425090..6425094
-
Hg19::chr10:66295438..66295453,+p@chr10:66295438..66295453
+
Hg19::chr11:114146042..114146050,-p@chr11:114146042..114146050
-
Hg19::chr11:65207271..65207286,+p9@AK129631
Hg19::chr11:81982984..81982991,+p@chr11:81982984..81982991
+
Hg19::chr13:34922094..34922105,+p@chr13:34922094..34922105
+
Hg19::chr17:42984508..42984535,-p8@GFAP
Hg19::chr17:42993715..42993719,-p@chr17:42993715..42993719
-
Hg19::chr17:42993904..42993912,-p@chr17:42993904..42993912
-
Hg19::chr17:42994283..42994286,-p@chr17:42994283..42994286
-
Hg19::chr18:24445821..24445829,+p@chr18:24445821..24445829
+
Hg19::chr18:74690849..74690860,-p@chr18:74690849..74690860
-
Hg19::chr1:95332264..95332266,+p@chr1:95332264..95332266
+
Hg19::chr2:20665905..20665909,-p@chr2:20665905..20665909
-
Hg19::chr3:16215714..16215728,+p9@GALNTL2
Hg19::chr3:16215730..16215743,+p3@GALNTL2
Hg19::chr3:16215758..16215779,+p8@GALNTL2
Hg19::chr4:67195068..67195099,-p@chr4:67195068..67195099
-
Hg19::chr5:132113658..132113680,-p10@SEPT8
Hg19::chr5:132115740..132115752,-p@chr5:132115740..132115752
-
Hg19::chr5:72570629..72570651,-p@chr5:72570629..72570651
-
Hg19::chr5:72570665..72570692,-p@chr5:72570665..72570692
-
Hg19::chr7:44145241..44145259,+p@chr7:44145241..44145259
+
Hg19::chr7:73779766..73779773,-p@chr7:73779766..73779773
-
Hg19::chr8:27522642..27522647,+p@chr8:27522642..27522647
+
Hg19::chr9:132312044..132312058,-p@chr9:132312044..132312058
-


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 tube4.32e-10456
neural rod4.32e-10456
future spinal cord4.32e-10456
neural keel4.32e-10456
regional part of nervous system3.40e-8953
regional part of brain3.40e-8953
central nervous system1.55e-7481
brain1.25e-7268
future brain1.25e-7268
neural plate7.67e-7082
presumptive neural plate7.67e-7082
nervous system1.00e-6689
neurectoderm2.18e-6686
regional part of forebrain1.14e-6441
forebrain1.14e-6441
anterior neural tube1.14e-6441
future forebrain1.14e-6441
brain grey matter5.82e-5834
gray matter5.82e-5834
telencephalon1.12e-5734
ecto-epithelium4.30e-54104
regional part of telencephalon1.03e-4832
cerebral hemisphere1.80e-4832
adult organism5.49e-46114
pre-chordal neural plate2.18e-4261
structure with developmental contribution from neural crest1.43e-41132
posterior neural tube2.59e-4015
chordal neural plate2.59e-4015
brainstem9.59e-386
regional part of cerebral cortex9.11e-3522
neural nucleus8.16e-339
nucleus of brain8.16e-339
ectoderm-derived structure9.87e-33171
ectoderm9.87e-33171
presumptive ectoderm9.87e-33171
neocortex5.67e-3220
cerebral cortex1.70e-3025
pallium1.70e-3025
tube6.07e-27192
segmental subdivision of hindbrain7.34e-2512
hindbrain7.34e-2512
presumptive hindbrain7.34e-2512
basal ganglion5.81e-249
nuclear complex of neuraxis5.81e-249
aggregate regional part of brain5.81e-249
collection of basal ganglia5.81e-249
cerebral subcortex5.81e-249
organ system subdivision8.52e-24223
segmental subdivision of nervous system6.95e-2313
telencephalic nucleus1.01e-217
anatomical conduit1.82e-20240
medulla oblongata4.48e-203
myelencephalon4.48e-203
future myelencephalon4.48e-203
spinal cord7.42e-203
dorsal region element7.42e-203
dorsum7.42e-203
pons1.78e-193
gyrus3.71e-166
epithelium7.60e-15306
cell layer1.20e-14309
corpus striatum5.18e-144
striatum5.18e-144
ventral part of telencephalon5.18e-144
future corpus striatum5.18e-144
locus ceruleus9.74e-142
brainstem nucleus9.74e-142
hindbrain nucleus9.74e-142
dorsal plus ventral thalamus1.33e-132
thalamic complex1.33e-132
organ part2.56e-12218
anatomical cluster4.66e-12373
limbic system1.67e-115
regional part of metencephalon3.58e-119
metencephalon3.58e-119
future metencephalon3.58e-119
parietal lobe3.67e-115
multi-tissue structure1.99e-09342
caudate-putamen5.97e-093
dorsal striatum5.97e-093
frontal cortex7.01e-093
diencephalon1.57e-087
future diencephalon1.57e-087
temporal lobe2.96e-086
substantia nigra9.71e-081
midbrain nucleus9.71e-081
regional part of midbrain9.71e-081
midbrain9.71e-081
presumptive midbrain9.71e-081
midbrain neural tube9.71e-081
corpus callosum1.25e-071
central nervous system cell part cluster1.25e-071
axon tract1.25e-071
intercerebral commissure1.25e-071
dorsal telencephalic commissure1.25e-071
brain white matter1.25e-071
brain commissure1.25e-071
white matter1.25e-071
nervous system commissure1.25e-071
cerebral hemisphere white matter1.25e-071


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

This analysis result is provided for C0 - C305 clusters.

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