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MCL coexpression mm9:458: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.495526165035161,0.150873434206496,0.129051050740229,0.0260164338684039,0.0166660626832929,0.404971603638282,0.37131961272948,0,0,0,0.338766773960858,0.241055669205254,0.356631716265397,0,0.0205563265474198,0,0,0.0896964873768703,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.940416858636806,0.628253809143442,0.622164492143509,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.100004302423367,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.13336176105449,0.0380499309585096,0.0519509775191307,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0497277316172017,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0447367441903353,0.123568095281294,0.230386905221361,0.193248801984092,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.031895734489288,0,0.0403878614760544,0.0581625411619175,0.0240026547541851,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.495526165035161,0.150873434206496,0.129051050740229,0.0260164338684039,0.0166660626832929,0.404971603638282,0.37131961272948,0,0,0,0.338766773960858,0.241055669205254,0.356631716265397,0,0.0205563265474198,0,0,0.0896964873768703,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.940416858636806,0.628253809143442,0.622164492143509,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.100004302423367,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.13336176105449,0.0380499309585096,0.0519509775191307,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0497277316172017,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0447367441903353,0.123568095281294,0.230386905221361,0.193248801984092,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.031895734489288,0,0.0403878614760544,0.0581625411619175,0.0240026547541851,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0045028;purinergic nucleotide receptor activity, G-protein coupled;0.0295558126620671;78826!GO:0001608;nucleotide receptor activity, G-protein coupled;0.0295558126620671;78826!GO:0016502;nucleotide receptor activity;0.0295558126620671;78826!GO:0001614;purinergic nucleotide receptor activity;0.0295558126620671;78826!
|gostat_on_MCL_coexpression=GO:0045028;purinergic nucleotide receptor activity, G-protein coupled;0.0295558126620671;78826!GO:0001608;nucleotide receptor activity, G-protein coupled;0.0295558126620671;78826!GO:0016502;nucleotide receptor activity;0.0295558126620671;78826!GO:0001614;purinergic nucleotide receptor activity;0.0295558126620671;78826!
|ontology_enrichment_celltype=CL:0000838!1.01e-31!12;CL:0000988!5.95e-30!32;CL:0002032!5.95e-30!32;CL:0000037!5.95e-30!32;CL:0000566!5.95e-30!32;CL:0000837!5.95e-30!32;CL:0000542!4.00e-29!13;CL:0000051!4.00e-29!13;CL:0000791!7.65e-29!9;CL:0000789!7.65e-29!9;CL:0002420!7.65e-29!9;CL:0002419!7.65e-29!9;CL:0000790!7.65e-29!9;CL:0000084!2.24e-28!11;CL:0000827!2.24e-28!11;CL:0000624!1.57e-25!8;CL:0002031!1.26e-23!25;CL:0002242!2.84e-23!16;CL:0000738!8.80e-22!17;CL:0002087!8.80e-22!17;CL:0002320!1.01e-19!46;CL:0000134!1.01e-19!46;CL:0000893!5.95e-19!6;CL:0002489!5.95e-19!6;CL:0000898!5.95e-19!6;CL:0000809!5.95e-19!6;CL:0000810!5.95e-19!6;CL:0000895!5.95e-19!6;CL:0000808!5.95e-19!6;CL:0000894!5.95e-19!6;CL:0000806!5.95e-19!6;CL:0000807!5.95e-19!6;CL:0000805!5.95e-19!6;CL:0002425!5.95e-19!6;CL:0002436!5.95e-19!6;CL:0002427!5.95e-19!6;CL:0002428!5.95e-19!6;CL:0002429!5.95e-19!6;CL:0002433!5.95e-19!6;CL:0002431!5.95e-19!6;CL:0002432!5.95e-19!6;CL:0000219!2.98e-16!54;CL:0000034!5.98e-11!97;CL:0000723!3.80e-08!91;CL:0000048!3.80e-08!91;CL:0000049!1.49e-07!19
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.01e-19!46;UBERON:0002193!8.36e-16!48;UBERON:0002405!8.36e-16!48;UBERON:0002390!5.82e-13!45;UBERON:0003061!5.82e-13!45;UBERON:0002370!6.28e-12!23;UBERON:0000974!6.28e-12!23;UBERON:0004807!6.28e-12!23;UBERON:0005058!6.28e-12!23;UBERON:0003351!6.28e-12!23;UBERON:0009113!6.28e-12!23;UBERON:0003295!6.28e-12!23;UBERON:0009722!6.28e-12!23;UBERON:0005562!6.28e-12!23;UBERON:0007690!6.28e-12!23;UBERON:0006562!2.33e-11!24;UBERON:0003408!2.33e-11!24;UBERON:0001557!2.33e-11!24;UBERON:0001042!2.33e-11!24;UBERON:0008814!2.33e-11!24;UBERON:0009145!2.33e-11!24;UBERON:0004177!4.56e-11!29;UBERON:0005057!4.56e-11!29;UBERON:0000072!6.62e-10!27;UBERON:0000077!7.86e-09!35;UBERON:0000063!2.98e-07!35;UBERON:0007811!5.28e-07!36
}}
}}

Revision as of 20:43, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:95861417..95861427,+p@chr10:95861417..95861427
+
Mm9::chr13:51862932..51862937,-p@chr13:51862932..51862937
-
Mm9::chr14:70174964..70175000,+p@chr14:70174964..70175000
+
Mm9::chr15:81997354..81997363,-p@chr15:81997354..81997363
-
Mm9::chr17:31204294..31204303,+p@chr17:31204294..31204303
+
Mm9::chr18:49915420..49915439,+p1@ENSMUST00000149935
p1@uc008ewm.1
Mm9::chr19:57191894..57191911,+p@chr19:57191894..57191911
+
Mm9::chr1:179188927..179188939,+p@chr1:179188927..179188939
+
Mm9::chr1:55188467..55188498,-p@chr1:55188467..55188498
-
Mm9::chr1:66109380..66109430,+p2@ENSMUST00000118496
Mm9::chr3:87945548..87945561,-p@chr3:87945548..87945561
-
Mm9::chr5:66252597..66252607,+p7@Rhoh
Mm9::chr6:22280831..22280835,+p@chr6:22280831..22280835
+
Mm9::chr8:26213486..26213502,-p@chr8:26213486..26213502
-
Mm9::chrX:104284681..104284722,+p1@P2ry10
Mm9::chrX:104284725..104284748,+p2@P2ry10


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:0045028purinergic nucleotide receptor activity, G-protein coupled0.0295558126620671
GO:0001608nucleotide receptor activity, G-protein coupled0.0295558126620671
GO:0016502nucleotide receptor activity0.0295558126620671
GO:0001614purinergic nucleotide receptor activity0.0295558126620671



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
lymphoid lineage restricted progenitor cell1.01e-3112
hematopoietic cell5.95e-3032
hematopoietic oligopotent progenitor cell5.95e-3032
hematopoietic stem cell5.95e-3032
angioblastic mesenchymal cell5.95e-3032
hematopoietic multipotent progenitor cell5.95e-3032
lymphocyte4.00e-2913
common lymphoid progenitor4.00e-2913
mature alpha-beta T cell7.65e-299
alpha-beta T cell7.65e-299
immature T cell7.65e-299
mature T cell7.65e-299
immature alpha-beta T cell7.65e-299
T cell2.24e-2811
pro-T cell2.24e-2811
CD4-positive, alpha-beta T cell1.57e-258
hematopoietic lineage restricted progenitor cell1.26e-2325
nucleate cell2.84e-2316
leukocyte8.80e-2217
nongranular leukocyte8.80e-2217
connective tissue cell1.01e-1946
mesenchymal cell1.01e-1946
thymocyte5.95e-196
double negative thymocyte5.95e-196
naive T cell5.95e-196
double-positive, alpha-beta thymocyte5.95e-196
CD4-positive, alpha-beta thymocyte5.95e-196
naive thymus-derived CD4-positive, alpha-beta T cell5.95e-196
DN4 thymocyte5.95e-196
DN1 thymic pro-T cell5.95e-196
DN2 thymocyte5.95e-196
DN3 thymocyte5.95e-196
immature single positive thymocyte5.95e-196
early T lineage precursor5.95e-196
mature CD4 single-positive thymocyte5.95e-196
resting double-positive thymocyte5.95e-196
double-positive blast5.95e-196
CD69-positive double-positive thymocyte5.95e-196
CD69-positive, CD4-positive single-positive thymocyte5.95e-196
CD4-positive, CD8-intermediate double-positive thymocyte5.95e-196
CD24-positive, CD4 single-positive thymocyte5.95e-196
motile cell2.98e-1654
stem cell5.98e-1197
somatic stem cell3.80e-0891
multi fate stem cell3.80e-0891
common myeloid progenitor1.49e-0719

Uber Anatomy
Ontology termp-valuen
connective tissue1.01e-1946
hemolymphoid system8.36e-1648
immune system8.36e-1648
hematopoietic system5.82e-1345
blood island5.82e-1345
thymus6.28e-1223
neck6.28e-1223
respiratory system epithelium6.28e-1223
hemolymphoid system gland6.28e-1223
pharyngeal epithelium6.28e-1223
thymic region6.28e-1223
pharyngeal gland6.28e-1223
entire pharyngeal arch endoderm6.28e-1223
thymus primordium6.28e-1223
early pharyngeal endoderm6.28e-1223
pharynx2.33e-1124
gland of gut2.33e-1124
upper respiratory tract2.33e-1124
chordate pharynx2.33e-1124
pharyngeal arch system2.33e-1124
pharyngeal region of foregut2.33e-1124
hemopoietic organ4.56e-1129
immune organ4.56e-1129
segment of respiratory tract6.62e-1027
mixed endoderm/mesoderm-derived structure7.86e-0935
organ segment2.98e-0735
craniocervical region5.28e-0736


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}}}

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