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MCL coexpression mm9:1160: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!3.86e-20!48;UBERON:0002405!3.86e-20!48;UBERON:0002390!6.46e-18!45;UBERON:0003061!6.46e-18!45;UBERON:0000077!6.15e-17!35;UBERON:0004177!2.39e-16!29;UBERON:0005057!2.39e-16!29;UBERON:0003408!1.80e-14!24;UBERON:0006562!4.81e-14!24;UBERON:0001557!4.81e-14!24;UBERON:0001042!4.81e-14!24;UBERON:0008814!4.81e-14!24;UBERON:0009145!4.81e-14!24;UBERON:0002370!9.20e-14!23;UBERON:0000974!9.20e-14!23;UBERON:0004807!9.20e-14!23;UBERON:0005058!9.20e-14!23;UBERON:0003351!9.20e-14!23;UBERON:0009113!9.20e-14!23;UBERON:0003295!9.20e-14!23;UBERON:0009722!9.20e-14!23;UBERON:0005562!9.20e-14!23;UBERON:0007690!9.20e-14!23;UBERON:0004119!1.24e-12!118;UBERON:0000925!1.24e-12!118;UBERON:0006595!1.24e-12!118;UBERON:0001041!1.41e-12!80;UBERON:0001007!4.24e-12!116;UBERON:0001555!4.24e-12!116;UBERON:0007026!4.24e-12!116;UBERON:0000072!1.65e-11!27;UBERON:0001004!3.59e-11!42;UBERON:0004921!3.87e-11!114;UBERON:0000065!1.45e-10!41;UBERON:0002530!5.04e-09!65;UBERON:0007811!8.43e-09!36;UBERON:0005911!1.54e-08!69;UBERON:0003081!3.90e-08!87;UBERON:0003929!4.35e-08!55;UBERON:0000063!5.54e-08!35;UBERON:0002368!4.26e-07!60
|ontology_enrichment_uberon=UBERON:0002193!3.86e-20!48;UBERON:0002405!3.86e-20!48;UBERON:0002390!6.46e-18!45;UBERON:0003061!6.46e-18!45;UBERON:0000077!6.15e-17!35;UBERON:0004177!2.39e-16!29;UBERON:0005057!2.39e-16!29;UBERON:0003408!1.80e-14!24;UBERON:0006562!4.81e-14!24;UBERON:0001557!4.81e-14!24;UBERON:0001042!4.81e-14!24;UBERON:0008814!4.81e-14!24;UBERON:0009145!4.81e-14!24;UBERON:0002370!9.20e-14!23;UBERON:0000974!9.20e-14!23;UBERON:0004807!9.20e-14!23;UBERON:0005058!9.20e-14!23;UBERON:0003351!9.20e-14!23;UBERON:0009113!9.20e-14!23;UBERON:0003295!9.20e-14!23;UBERON:0009722!9.20e-14!23;UBERON:0005562!9.20e-14!23;UBERON:0007690!9.20e-14!23;UBERON:0004119!1.24e-12!118;UBERON:0000925!1.24e-12!118;UBERON:0006595!1.24e-12!118;UBERON:0001041!1.41e-12!80;UBERON:0001007!4.24e-12!116;UBERON:0001555!4.24e-12!116;UBERON:0007026!4.24e-12!116;UBERON:0000072!1.65e-11!27;UBERON:0001004!3.59e-11!42;UBERON:0004921!3.87e-11!114;UBERON:0000065!1.45e-10!41;UBERON:0002530!5.04e-09!65;UBERON:0007811!8.43e-09!36;UBERON:0005911!1.54e-08!69;UBERON:0003081!3.90e-08!87;UBERON:0003929!4.35e-08!55;UBERON:0000063!5.54e-08!35;UBERON:0002368!4.26e-07!60
|tfbs_overrepresentation_for_novel_motifs=0.438063,1.02534,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.215218,0.0609112,0.542749,0.575086,0.206435,1.46059,0.847296,0,0.795315,0.291368,0.19222,0.112498,0.374752,0.08187,0.598814,0.29769,0.419327,0.62766,1.0368,0.516511,0.344372,0.145661,1.25421,0.897561,0.289148,0.166577,0.316253,0.101236,0.279977,0.57142,0.258564,0.230656,0.295233,1.26538,0.54842,0.317766,0.0275764,0.469348,0.714592,0.532496,0.478447,0.917701,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,1.59144,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.0869413,1.09164,0.17012,0.936963,0.166511,0.703064,2.00003,0.378988,1.14907,0.812889,0.663039,0.200155,0.975495,0.0369809,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.203879,0.913319,0.71485,0.127063,0.7665,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.92994,1.02459,0.380122,1.35148,1.27206,0.796976,0.187586,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,1.26843,1.24438,2.07659,1.67603,1.19971,1.54859,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.227149
}}
}}

Revision as of 19:29, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr17:35576137..35576140,+p1@H2-Q7
p1@H2-Q8
p1@H2-Q9
p1@LOC100044019
p1@LOC100044020
Mm9::chr18:80895129..80895141,-p@chr18:80895129..80895141
-
Mm9::chr1:61034742..61034781,+p1@Icos
Mm9::chr3:87650762..87650776,+p3@Sh2d2a
Mm9::chr5:122682269..122682291,+p@chr5:122682269..122682291
+
Mm9::chr7:132746957..132746988,+p1@Il21r
Mm9::chr7:132746995..132747010,+p3@Il21r


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


GO IDGO nameFDR corrected p-value
GO:0005070SH3/SH2 adaptor activity0.0403155565721875
GO:0042612MHC class I protein complex0.0403155565721875
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0403155565721875
GO:0030674protein binding, bridging0.0403155565721875
GO:0042611MHC protein complex0.0403155565721875
GO:0004907interleukin receptor activity0.0403155565721875
GO:0048002antigen processing and presentation of peptide antigen0.0403155565721875
GO:0019965interleukin binding0.0403155565721875
GO:0060090molecular adaptor activity0.0437708186230869
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0463438870390452
GO:0019882antigen processing and presentation0.0463438870390452
GO:0019955cytokine binding0.049893815526705



Relative expression of the co-expression cluster over median <br>Analyst:





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
hematopoietic lineage restricted progenitor cell5.22e-1325
lymphoid lineage restricted progenitor cell1.08e-1112
T cell6.31e-1111
pro-T cell6.31e-1111
leukocyte1.73e-1017
nongranular leukocyte1.73e-1017
lymphocyte2.13e-1013
common lymphoid progenitor2.13e-1013
hematopoietic cell4.05e-1032
hematopoietic oligopotent progenitor cell4.05e-1032
hematopoietic stem cell4.05e-1032
angioblastic mesenchymal cell4.05e-1032
hematopoietic multipotent progenitor cell4.05e-1032
mature alpha-beta T cell6.93e-109
alpha-beta T cell6.93e-109
immature T cell6.93e-109
mature T cell6.93e-109
immature alpha-beta T cell6.93e-109
CD4-positive, alpha-beta T cell6.39e-098
nucleate cell1.54e-0716
thymocyte4.60e-076
double negative thymocyte4.60e-076
naive T cell4.60e-076
double-positive, alpha-beta thymocyte4.60e-076
CD4-positive, alpha-beta thymocyte4.60e-076
naive thymus-derived CD4-positive, alpha-beta T cell4.60e-076
DN4 thymocyte4.60e-076
DN1 thymic pro-T cell4.60e-076
DN2 thymocyte4.60e-076
DN3 thymocyte4.60e-076
immature single positive thymocyte4.60e-076
early T lineage precursor4.60e-076
mature CD4 single-positive thymocyte4.60e-076
resting double-positive thymocyte4.60e-076
double-positive blast4.60e-076
CD69-positive double-positive thymocyte4.60e-076
CD69-positive, CD4-positive single-positive thymocyte4.60e-076
CD4-positive, CD8-intermediate double-positive thymocyte4.60e-076
CD24-positive, CD4 single-positive thymocyte4.60e-076

Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.86e-2048
immune system3.86e-2048
hematopoietic system6.46e-1845
blood island6.46e-1845
mixed endoderm/mesoderm-derived structure6.15e-1735
hemopoietic organ2.39e-1629
immune organ2.39e-1629
gland of gut1.80e-1424
pharynx4.81e-1424
upper respiratory tract4.81e-1424
chordate pharynx4.81e-1424
pharyngeal arch system4.81e-1424
pharyngeal region of foregut4.81e-1424
thymus9.20e-1423
neck9.20e-1423
respiratory system epithelium9.20e-1423
hemolymphoid system gland9.20e-1423
pharyngeal epithelium9.20e-1423
thymic region9.20e-1423
pharyngeal gland9.20e-1423
entire pharyngeal arch endoderm9.20e-1423
thymus primordium9.20e-1423
early pharyngeal endoderm9.20e-1423
endoderm-derived structure1.24e-12118
endoderm1.24e-12118
presumptive endoderm1.24e-12118
foregut1.41e-1280
digestive system4.24e-12116
digestive tract4.24e-12116
primitive gut4.24e-12116
segment of respiratory tract1.65e-1127
respiratory system3.59e-1142
subdivision of digestive tract3.87e-11114
respiratory tract1.45e-1041
gland5.04e-0965
craniocervical region8.43e-0936
endo-epithelium1.54e-0869
lateral plate mesoderm3.90e-0887
gut epithelium4.35e-0855
organ segment5.54e-0835
endocrine gland4.26e-0760


TFBS overrepresentation<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}}}