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Coexpression cluster:C2244: Difference between revisions

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|full_id=C2244_extraskeletal_maxillary_pineal_cerebellum_small_Neutrophils_occipital
|full_id=C2244_extraskeletal_maxillary_pineal_cerebellum_small_Neutrophils_occipital
|id=C2244
|id=C2244
|ontology_enrichment_celltype=CL:0002057!1.24e-07!42;CL:0000766!4.07e-07!76
|ontology_enrichment_celltype=CL:0000766!5.11e-07!72
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.61e-33!115;UBERON:0001049!6.68e-30!57;UBERON:0005068!6.68e-30!57;UBERON:0006241!6.68e-30!57;UBERON:0007135!6.68e-30!57;UBERON:0000073!1.02e-28!94;UBERON:0001016!1.02e-28!94;UBERON:0005743!1.54e-28!86;UBERON:0001017!4.66e-28!82;UBERON:0002616!7.27e-28!59;UBERON:0002346!6.02e-25!90;UBERON:0000955!9.35e-24!69;UBERON:0006238!9.35e-24!69;UBERON:0002780!2.57e-23!41;UBERON:0001890!2.57e-23!41;UBERON:0006240!2.57e-23!41;UBERON:0003075!2.89e-23!86;UBERON:0007284!2.89e-23!86;UBERON:0003080!3.71e-23!42;UBERON:0002020!2.25e-19!34;UBERON:0003528!2.25e-19!34;UBERON:0003056!2.42e-19!61;UBERON:0001893!5.04e-19!34;UBERON:0001869!5.91e-19!32;UBERON:0002791!2.02e-18!33;UBERON:0000956!3.78e-15!25;UBERON:0000203!3.78e-15!25;UBERON:0000033!6.24e-15!123;UBERON:0000924!7.22e-15!173;UBERON:0006601!7.22e-15!173;UBERON:0002619!1.88e-14!22;UBERON:0000153!3.82e-14!129;UBERON:0007811!3.82e-14!129;UBERON:0004121!1.26e-13!169;UBERON:0001950!2.37e-13!20;UBERON:0000468!3.29e-12!659;UBERON:0000062!1.41e-09!511;UBERON:0000467!7.06e-09!625;UBERON:0000480!1.07e-08!626;UBERON:0000922!3.05e-08!612;UBERON:0003076!6.88e-08!15;UBERON:0003057!6.88e-08!15;UBERON:0002050!3.92e-07!605;UBERON:0005423!3.92e-07!605;UBERON:0000923!5.84e-07!604;UBERON:0005291!5.84e-07!604;UBERON:0006598!5.84e-07!604;UBERON:0002532!5.84e-07!604;UBERON:0004733!6.71e-07!12;UBERON:0002028!6.71e-07!12;UBERON:0007277!6.71e-07!12
|ontology_enrichment_uberon=UBERON:0001049!2.90e-34!56;UBERON:0005068!2.90e-34!56;UBERON:0006241!2.90e-34!56;UBERON:0007135!2.90e-34!56;UBERON:0000073!3.09e-33!53;UBERON:0002616!3.09e-33!53;UBERON:0001016!2.87e-32!89;UBERON:0001017!3.35e-32!81;UBERON:0007023!5.22e-28!114;UBERON:0000955!1.86e-27!68;UBERON:0006238!1.86e-27!68;UBERON:0002780!1.95e-27!41;UBERON:0001890!1.95e-27!41;UBERON:0003080!1.95e-27!41;UBERON:0006240!1.95e-27!41;UBERON:0002346!8.03e-25!86;UBERON:0003075!1.27e-23!82;UBERON:0007284!1.27e-23!82;UBERON:0003528!1.41e-22!34;UBERON:0002020!1.41e-22!34;UBERON:0001893!2.61e-22!34;UBERON:0001869!2.88e-22!32;UBERON:0002791!2.52e-21!32;UBERON:0003056!4.41e-20!61;UBERON:0011216!1.80e-19!223;UBERON:0000956!7.05e-18!25;UBERON:0000203!7.05e-18!25;UBERON:0002619!5.84e-17!22;UBERON:0004121!3.04e-16!171;UBERON:0000924!3.04e-16!171;UBERON:0006601!3.04e-16!171;UBERON:0010371!5.46e-16!104;UBERON:0001950!1.14e-15!20;UBERON:0010314!7.18e-13!132;UBERON:0000468!8.16e-09!656;UBERON:0000923!2.94e-08!560;UBERON:0010316!2.94e-08!560;UBERON:0005291!2.94e-08!560;UBERON:0006598!2.94e-08!560;UBERON:0010317!2.94e-08!560;UBERON:0002532!2.94e-08!560;UBERON:0002050!4.26e-08!564;UBERON:0003076!4.78e-08!15;UBERON:0003057!4.78e-08!15;UBERON:0000467!4.93e-08!624;UBERON:0000480!6.57e-08!625;UBERON:0000062!6.68e-08!503;UBERON:0000922!1.56e-07!592;UBERON:0005423!3.62e-07!581;UBERON:0004733!4.61e-07!12;UBERON:0002028!4.61e-07!12;UBERON:0007277!4.61e-07!12;UBERON:0000477!5.61e-07!373
|tf_chipseq_enrich=HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185677124467442
|tf_chipseq_enrich=HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185677124467442
|tfbs_overrepresentation=0.191353,0.0774498,0.00177175,0.0631091,0.257053,0.363996,0.0569281,0.510252,0.043387,0.0341265,0.181435,0.288577,0.243414,0.164339,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,0.172742,0.107781,0.124486,0.0550418,0.00443949,0.268949,0.119094,0.186914,0.122514,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,0.0725724,0.0568767,0.157159,0.000121319,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.145553,0.158244,0.19996,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.273035,0.103044,0.138225,0.0390464,0.194086,0.142115,0.0999599,0.0720888,0.0667453,0.439574,0.0792005,0.113084,0.216289,0.133576,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.150119,0.368178,0.320801,0.0848546,0.0397921,0.713984,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.327332,0.199405,0.121709,0.347653,0.0759036,0.350158,0.184542,0.0491142,0.00467523,0.0541957,0.0883058,0.423154,0.187509,0.0665478,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.275495,0.182323,0.112709,0.134107,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,0.202388,0.122756,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.258146,0.186826,0.233377,0.0352845,0.0565357,0.153577,0.0984158,0.00532488,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.192028,0.000978216,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.2321,0.017128,0.202544,0.0715212,0.105131,0.118265,0.182591,0.0300065,0.230552,0.0472274,0.205973,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.241581,0.160458,0.292792,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.329956,0.346995,0.197158,0.265132,0.0288641,0.0606832,0.136664,0.158184,0.147626,0.393313,0.218801,0.21271,0.132273,0.0830988,0.134907,0.184613,0.462724,0.202467,0.208718,0.0972471,0.165147,0.180711,0.112956,0.0797807,0.0790532,0.675167,0.476758,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.435782,0.128998,0.109226,0.151958,0.178155,0.107176,0.146021,0.463127,2.76811e-05,0.206234,0.238926,0.239646,0.128521,0.1286,0.207017,0.14037,0.259646,0.0916845,0.324438,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.106603,0.106727,0.12083,0.154253,0.0993998,0.352707,0.0834863,0.324356,0.18736,0.113754,0.0504034,0.169684,0.690367,0.0880794,0.0560372,0.73998,0.005515,0.20358,0.179737,0.018014,0.73391,0.332539,0.00863402,0.464128,0.389374,0.594055,0.414547,0.489273,0.413223,0.639461,0.720642,0.34505,0.369161,0.500422,0.49089,0.687176,0.702495,0.241524,0.45167,0.234628,0.520726,0.143893,0.41477,0.279946,0.524104,0.467825,0.563725,0.404903,0.632838,0.624969,0.460819,0.511459,0.221488,0.0073977,0.00976201,0.380582,0.583749,0.398372,0.0455719,0.606558,0.000294371,0.359128,0.395864,0.00120797,0.368633,0.547291,0.000190643,0.512763,0.369971,0.0569945,0.537928,0.464342,0.683088,0.356005,0.235444,0.48585,0.668093,0.840703,0.349116,0.302142,0.239545,0.432689,0.00401934,0.343881,0.145459,0.239383,0.617741,0.626346,0.316925,0.00110973,0.573659,0.211506,0.0883859,0.0962508,0.238465,0.341199,0.853221,0.112487,0.508325,0.773224,0.284591,0.656755,0.54723,0.280307,0.090261,0.794849,0.0596868,0.0984075,0.293026,0.408321,0.117621,0.605423,0.372182,0.429205,0.578951,0.365653,0.41035,0.784024,0.00989849,0.180014,0.525923,0.291917,0.421082,0.25441,0.202782,0.672876,0.517933,0.0594062,0.517001,0.252778,0.266107,0.419676,0.188259,0.189182,0.138387,0.46699,0.187849,0.560187,0.321282,0.198207,0.0616078,0.178485,0.329745,0.175552,0.129238,0.651295,0.0793782,0.360161,0.429696,0.386216,0.385297,0.706685,0.606408,0.627185,0.074467,0.00825487,0.447838,0.289666,0.500627,0.513045,0.000402693,0.565545,0.845507,0.265037,0.629795,0.000636845,0.53531,0.341771,0.424526,0.657528,0.356381,0.184395,0.55524,0.624689,0.206945,0.304719,0.462531,0.296994,0.244339,0.117049,0.0786167,0.000571771,0.729876,0.111753,0.64428,0.436806,0.576549,0.499072,0.744662,0.734628,0.397546,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.286156,0.261868,0.0445868,0.540322,0.247151,0.146385,0.365815,0.0576261,0.382413,0.164977,0.175633,0.139918,0.34669,0.0828344,0.135364,0.0238089,0.383126,0.354433,0.48311,0.0614918,0.219485,0.149782,0.136923,0.118103,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.249506,0.432751,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.417003,0.251882,0.172263,0.243319,0.0637178,0.257309,0.500692,0.166608,0.227224,0.238082,0.219023,8.45402e-06,0.124916,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.224626,0.183585,0.00419343,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.621787,0.178782,0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}}
}}

Revision as of 13:47, 19 October 2012


Full id: C2244_extraskeletal_maxillary_pineal_cerebellum_small_Neutrophils_occipital



Phase1 CAGE Peaks

Hg19::chr12:81331647..81331658,-p6@LIN7A
Hg19::chr12:81331675..81331696,-p4@LIN7A
Hg19::chr12:81331697..81331733,-p2@LIN7A
Hg19::chr12:81331735..81331748,-p5@LIN7A


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
myeloid leukocyte5.11e-0772
Uber Anatomy
Ontology termp-valuen
neural tube2.90e-3456
neural rod2.90e-3456
future spinal cord2.90e-3456
neural keel2.90e-3456
regional part of nervous system3.09e-3353
regional part of brain3.09e-3353
nervous system2.87e-3289
central nervous system3.35e-3281
adult organism5.22e-28114
brain1.86e-2768
future brain1.86e-2768
regional part of forebrain1.95e-2741
forebrain1.95e-2741
anterior neural tube1.95e-2741
future forebrain1.95e-2741
neurectoderm8.03e-2586
neural plate1.27e-2382
presumptive neural plate1.27e-2382
brain grey matter1.41e-2234
gray matter1.41e-2234
telencephalon2.61e-2234
cerebral hemisphere2.88e-2232
regional part of telencephalon2.52e-2132
pre-chordal neural plate4.41e-2061
organ system subdivision1.80e-19223
cerebral cortex7.05e-1825
pallium7.05e-1825
regional part of cerebral cortex5.84e-1722
ectoderm-derived structure3.04e-16171
ectoderm3.04e-16171
presumptive ectoderm3.04e-16171
ecto-epithelium5.46e-16104
neocortex1.14e-1520
structure with developmental contribution from neural crest7.18e-13132
multi-cellular organism8.16e-09656
germ layer2.94e-08560
germ layer / neural crest2.94e-08560
embryonic tissue2.94e-08560
presumptive structure2.94e-08560
germ layer / neural crest derived structure2.94e-08560
epiblast (generic)2.94e-08560
embryonic structure4.26e-08564
posterior neural tube4.78e-0815
chordal neural plate4.78e-0815
anatomical system4.93e-08624
anatomical group6.57e-08625
organ6.68e-08503
embryo1.56e-07592
developing anatomical structure3.62e-07581
segmental subdivision of hindbrain4.61e-0712
hindbrain4.61e-0712
presumptive hindbrain4.61e-0712
anatomical cluster5.61e-07373


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
HEY1#2346244.040111043105710.00375304636917980.0185677124467442



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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