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Coexpression cluster:C1740: Difference between revisions

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|full_id=C1740_Keratinocyte_Mammary_Mallassezderived_Gingival_Small_Sebocyte_Tracheal
|full_id=C1740_Keratinocyte_Mammary_Mallassezderived_Gingival_Small_Sebocyte_Tracheal
|id=C1740
|id=C1740
|ontology_enrichment_celltype=CL:0000548!1.43e-09!679;CL:0000004!1.43e-09!679;CL:0000255!1.43e-09!679;CL:0000012!3.40e-09!682;CL:0002371!3.55e-09!591;CL:0002076!2.95e-08!43;CL:0002368!6.39e-08!13;CL:0002159!9.32e-08!13;CL:0000066!2.41e-07!254;CL:0000144!4.95e-07!625;CL:0000220!6.70e-07!246
|ontology_enrichment_celltype=CL:0002076!5.30e-32!42;CL:0002368!3.24e-31!13;CL:0002159!6.43e-29!14;CL:0000066!1.60e-24!253;CL:0000223!7.09e-22!58;CL:0002327!2.30e-17!4;CL:0002202!1.79e-16!9;CL:0002632!1.79e-16!9;CL:0002077!1.42e-15!34;CL:0002621!3.87e-14!3;CL:0002166!1.08e-13!3;CL:0000068!1.66e-13!3;CL:0000069!1.66e-13!3;CL:0000307!1.66e-13!3;CL:0000377!1.66e-13!3;CL:0002328!2.86e-13!3;CL:0000362!4.12e-12!9;CL:0000240!7.37e-12!6;CL:0000311!7.37e-12!6;CL:0000079!7.37e-12!6;CL:0000237!7.37e-12!6;CL:0000036!7.37e-12!6;CL:0000357!7.37e-12!6;CL:0000114!7.37e-12!6;CL:0000317!8.75e-10!2;CL:1000448!8.75e-10!2;CL:0002308!8.75e-10!2;CL:0002140!8.75e-10!2;CL:0000076!1.27e-09!63;CL:0002251!1.59e-09!20;CL:0000575!4.92e-09!2;CL:0002321!5.43e-09!250;CL:0000312!1.44e-08!5;CL:0000622!2.04e-08!5;CL:0000154!4.48e-07!6;CL:0000221!6.50e-07!72
|ontology_enrichment_disease=DOID:2394!3.65e-07!14
|ontology_enrichment_disease=DOID:1749!1.81e-09!14
|ontology_enrichment_uberon=UBERON:0000486!5.86e-09!82;UBERON:0003102!7.13e-09!95;UBERON:0000161!3.77e-08!35;UBERON:0000926!7.96e-08!448;UBERON:0004120!7.96e-08!448;UBERON:0006603!7.96e-08!448;UBERON:0000923!4.64e-07!604;UBERON:0005291!4.64e-07!604;UBERON:0006598!4.64e-07!604;UBERON:0002532!4.64e-07!604;UBERON:0002050!5.91e-07!605;UBERON:0005423!5.91e-07!605;UBERON:0000467!6.79e-07!625;UBERON:0003100!8.33e-07!41;UBERON:0000480!8.64e-07!626
|ontology_enrichment_uberon=UBERON:0001911!2.30e-17!4;UBERON:0005333!2.30e-17!4;UBERON:0008425!2.30e-17!4;UBERON:0005311!2.30e-17!4;UBERON:0001949!3.87e-14!3;UBERON:0001004!4.00e-14!74;UBERON:0005157!5.95e-14!47;UBERON:0003102!1.27e-13!99;UBERON:0005153!1.74e-13!37;UBERON:0004815!2.86e-13!3;UBERON:0002031!2.86e-13!3;UBERON:0007196!8.92e-13!15;UBERON:0001558!8.92e-13!15;UBERON:0004119!3.33e-11!160;UBERON:0000925!3.33e-11!160;UBERON:0006595!3.33e-11!160;UBERON:0001708!2.22e-10!4;UBERON:0008895!2.22e-10!4;UBERON:0000065!3.16e-10!54;UBERON:0002419!8.75e-10!2;UBERON:0007771!8.75e-10!2;UBERON:0003297!8.75e-10!2;UBERON:0001821!8.75e-10!2;UBERON:0003487!8.75e-10!2;UBERON:0001820!8.75e-10!2;UBERON:0005089!8.75e-10!2;UBERON:0005088!8.75e-10!2;UBERON:0003126!9.80e-10!7;UBERON:0001005!9.80e-10!7;UBERON:0000161!1.44e-09!36;UBERON:0000076!1.02e-08!8;UBERON:0011159!2.20e-08!5;UBERON:0005178!2.85e-08!34;UBERON:0002224!2.85e-08!34;UBERON:0000033!2.88e-08!56;UBERON:0002185!3.89e-08!5;UBERON:0003729!4.89e-08!13;UBERON:0005181!5.44e-08!35;UBERON:0005085!1.83e-07!31;UBERON:0000153!3.10e-07!62;UBERON:0007811!3.10e-07!62;UBERON:0001003!4.01e-07!15;UBERON:0007376!4.01e-07!15;UBERON:0007383!4.01e-07!15;UBERON:0010188!4.77e-07!6;UBERON:0002539!4.77e-07!6;UBERON:0008816!4.77e-07!6;UBERON:0000344!5.59e-07!20
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097,0.254847,0.300809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.0547349,0.080156,0.0415903,0.53753,0.0545112,0.510703,0.33844,0.0649137,0.0974216,0.595767,0.195675,0.174786,0.0165942,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.385962,0.0636691,0.296227,0.208788,0.566117,0.36304,0.430936,0.123626,0.0404561,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.0108776,0.460679,0.11021,0.0775891,0.153079,0.62577,0.211515,0.125701,0.175283,0.204954,0.209341,0.855975,0.629422,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.228398,0.056055,0.120552,0.41771,0.893893,0.529713,0.335207,0.434016,0.190688,0.299739,0.278645,0.733648,0.0940982,0.0780533,0.564811,0.0993772,0.0417776,0.448923,0.11602,0.067657,0.113233,0.0585992,0.00157918,0.274438,0.911136,0.989834,0.319826,0.336512,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.347759,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.0151089,0.0663381,0.0934526,0.359135,0.123404,0.430769,0.240825,0.00601426,0.336623,0.163542,0.483244,0.00417724,0.033523,0.239667,0.10226,0.29809,0.235147,0.689826,0.245965,0.00711862,0.0116046,0.0983658,0.228743,0.0309424,0.156976,0.244789,0.267391,0.0508431,0.21807,0.350528,0.382904,0.432408,0.190404,0.135865,0.488841,0.0175433,0.180609,0.291283,0.273972,0.153023,0.0935746,0.37958,0.22307,0.160699,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.769574,0.262486,0.294204,0.131936,0.0464308,0.246621,0.463617,0.697373,0.0965376,0.377203,0.279263,0.336564,0.35463,0.581771,0.800557,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.53612,0.261842,0.581874,0.355154,0.377285,0.251388,0.537088,0.603804,0.261576,0.306963,0.569605,0.526495,0.580285,0.0473662,0.424482,0.00844668,0.610475,0.167927,0.561689,0.672416,0.321844,0.623136,0.0367384,0.96913,0.967174,0.349068,0.344004,0.00609778,0.557035,0.427789,0.689998,0.386595,0.0700328,0.111685,0.258394,0.277222,0.432123,0.759415,0.661773,0.149969,0.651196,0.392155,0.00344962,0.371758,0.71344,0.0513067,0.890566,0.570752,0.254547,0.0309722,0.821811,0.680843,0.28054,0.541378,0.725301,0.660884,0.922144,0.401389,0.705225,0.00684942,0.311289,0.318577,0.120474,0.088424,0.236714,0.0361061,0.553178,0.246387,0.224252,0.587237,0.155054,0.0260973,0.518234,0.0365373,0.353942,0.192234,0.427276,0.400353,0.466967,0.283682,0.424668,0.7175,0.797471,0.218352,0.122953,0.0281446,0.530902,0.152704,0.465544,0.55798,0.00171287,0.932831,0.723248,0.34194,0.592696,0.592314,0.0869207,0.647996,0.177129,0.317485,0.265627,0.220564,0.845182,0.037907,0.307462,0.135076,0.469588,0.298027,0.274593,0.490712,0.541363,0.709432,0.583627,0.531474,0.364391,0.562305,0.528646,0.361524,0.31558,0.412744,0.185983,0.62698,0.513592,0.415367,0.503942,0.45585,0.36864,0.181824,0.125335,0.122994,0.00116776,0.557093,0.693441,0.0846803,0.048225,0.639572,0.326875,0.0655077,0.332211,0.0525779,0.0497423,0.278436,0.784543,0.457741,0.0851712,0.426239,0.401917,0.289012,0.572661,0.412586,0.534679,0.101367,0.55475,0.294859,0.523749,0.499347,0.307426,0.462582,0.196912,0.146949,0.714189,0.44799,0.00751053,0.318338,0.276338,0.126433,0.102654,0.318174,0.0555558,0.295666,0.0899804,0.293641,0.116969,0.401231,0.255983,0.0494979,0.256708,0.338258,0.322052,0.145568,0.153833,0.261242,0.38389,0.188453,0.388459,0.0582761,0.0780866,0.0437263,0.301366,0.340343,0.00906953,0.501812,0.462092,0.336254,0.053444,0.0473553,0.19697,0.309816,0.0537285,0.15063,0.198077,0.281455,0.348739,0.419895,0.138495,0.208834,0.32256,0.082459,0.0667472,0.109684,0.00738257,0.403482,0.181288,0.230841,0.0709982,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.0968383,0.312881,0.162482,0.0327199,0.192188,0.158985,0.174153,0.0972854,0.333309,0.034215,0.339517,0.303699,0.198326,0.394084,0.126349,0.282501,0.252005,0.390891,0.238377,0.063694,0.0210139,0.287909,0.289389,0.117618,0.0017322,0.396962,0.316002,0.330317,0.321404,0.225079,0.050521,0.379651,0.0184244,0.0680703,0.0122731,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.0140126,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.109896,0.0354176,0.224871,0.092937,0.088016,0.310732,0.349611,0.11881,0.385709,0.278202,0.426488,0.0938069,0.209809,0.0351523,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.0676318,0.184651,0.303359,0.0494743,0.018596,0.425912,0.380826,0.259046,0.345068,0.151046,0.142558,0.347171,0.321735,0.15463,0.13907,0.0267252,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.0420678,0.248127,0.33299,0.384731,0.319112,0.172492
}}
}}

Revision as of 11:38, 19 October 2012


Full id: C1740_Keratinocyte_Mammary_Mallassezderived_Gingival_Small_Sebocyte_Tracheal



Phase1 CAGE Peaks

Hg19::chr15:45940864..45940902,+p@chr15:45940864..45940902
+
Hg19::chr2:69026957..69026966,+p@chr2:69026957..69026966
+
Hg19::chr2:69027041..69027079,+p@chr2:69027041..69027079
+
Hg19::chr6:106975163..106975184,+p@chr6:106975163..106975184
+
Hg19::chr6:106975193..106975220,+p@chr6:106975193..106975220
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
endo-epithelial cell5.30e-3242
respiratory epithelial cell3.24e-3113
general ecto-epithelial cell6.43e-2914
epithelial cell1.60e-24253
endodermal cell7.09e-2258
mammary gland epithelial cell2.30e-174
epithelial cell of tracheobronchial tree1.79e-169
epithelial cell of lower respiratory tract1.79e-169
ecto-epithelial cell1.42e-1534
gingival epithelial cell3.87e-143
epithelial cell of Malassez1.08e-133
duct epithelial cell1.66e-133
branched duct epithelial cell1.66e-133
tracheal epithelial cell1.66e-133
tracheoblast1.66e-133
bronchial epithelial cell2.86e-133
epidermal cell4.12e-129
stratified squamous epithelial cell7.37e-126
keratin accumulating cell7.37e-126
stratified epithelial cell7.37e-126
keratinizing barrier epithelial cell7.37e-126
epithelial fate stem cell7.37e-126
stratified epithelial stem cell7.37e-126
surface ectodermal cell7.37e-126
sebum secreting cell8.75e-102
epithelial cell of sweat gland8.75e-102
epithelial cell of skin gland8.75e-102
acinar cell of sebaceous gland8.75e-102
squamous epithelial cell1.27e-0963
epithelial cell of alimentary canal1.59e-0920
corneal epithelial cell4.92e-092
embryonic cell5.43e-09250
keratinocyte1.44e-085
acinar cell2.04e-085
protein secreting cell4.48e-076
ectodermal cell6.50e-0772
Uber Anatomy
Ontology termp-valuen
mammary gland2.30e-174
mammary bud2.30e-174
mammary ridge2.30e-174
mammary placode2.30e-174
gingival epithelium3.87e-143
respiratory system4.00e-1474
epithelial fold5.95e-1447
surface structure1.27e-1399
epithelial bud1.74e-1337
lower respiratory tract epithelium2.86e-133
epithelium of bronchus2.86e-133
tracheobronchial tree8.92e-1315
lower respiratory tract8.92e-1315
endoderm-derived structure3.33e-11160
endoderm3.33e-11160
presumptive endoderm3.33e-11160
jaw skeleton2.22e-104
splanchnocranium2.22e-104
respiratory tract3.16e-1054
skin gland8.75e-102
epidermis gland8.75e-102
gland of integumental system8.75e-102
sebaceous gland8.75e-102
skin sebaceous gland8.75e-102
sweat gland8.75e-102
sweat gland placode8.75e-102
sebaceous gland placode8.75e-102
trachea9.80e-107
respiratory airway9.80e-107
orifice1.44e-0936
external ectoderm1.02e-088
primary subdivision of cranial skeletal system2.20e-085
thoracic cavity element2.85e-0834
thoracic cavity2.85e-0834
head2.88e-0856
bronchus3.89e-085
mouth mucosa4.89e-0813
thoracic segment organ5.44e-0835
ectodermal placode1.83e-0731
anterior region of body3.10e-0762
craniocervical region3.10e-0762
skin epidermis4.01e-0715
outer epithelium4.01e-0715
enveloping layer of ectoderm4.01e-0715
protuberance4.77e-076
pharyngeal arch4.77e-076
embryonic head4.77e-076
mucosa5.59e-0720
Disease
Ontology termp-valuen
squamous cell carcinoma1.81e-0914


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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