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MCL coexpression mm9:298: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0005634;nucleus;3.76419046431649e-05;20843,12747,216578,71713,16588,170791,72567,19664,12750,67418,23857,231386,80732,73274!GO:0043283;biopolymer metabolic process;0.000311836934344768;12747,216578,71713,16588,170791,72567,19664,12750,231386,19255,30052,80732,73274!GO:0043170;macromolecule metabolic process;0.000497536975592701;12747,216578,71713,16588,170791,72567,19664,12750,67418,231386,19255,30052,80732,73274!GO:0043231;intracellular membrane-bound organelle;0.000586687245999991;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,73274!GO:0043227;membrane-bound organelle;0.000586687245999991;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,73274!GO:0003676;nucleic acid binding;0.000746427899461023;216578,16588,170791,72567,19664,23857,67418,231386,80732,73274!GO:0016070;RNA metabolic process;0.000774831726398036;216578,71713,16588,170791,72567,19664,231386,80732,73274!GO:0016485;protein processing;0.00127511598646046;12747,12750,30052!GO:0006397;mRNA processing;0.0019505498710537;216578,71713,16588,170791!GO:0044238;primary metabolic process;0.0019505498710537;12747,216578,71713,16588,170791,72567,19664,12750,67418,231386,19255,30052,80732,73274!GO:0044237;cellular metabolic process;0.0019505498710537;12747,216578,71713,16588,170791,72567,19664,12750,67418,231386,19255,30052,80732,73274!GO:0010467;gene expression;0.0019505498710537;216578,71713,16588,170791,72567,19664,231386,80732,73274!GO:0043229;intracellular organelle;0.0019505498710537;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,73274!GO:0043226;organelle;0.0019505498710537;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,73274!GO:0016071;mRNA metabolic process;0.0019505498710537;216578,71713,16588,170791!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00383249314735907;216578,71713,16588,170791,72567,19664,231386,80732,73274!GO:0003677;DNA binding;0.00418382364513257;16588,72567,19664,23857,80732,231386,73274!GO:0044424;intracellular part;0.00494269684193766;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,19255,73274!GO:0006396;RNA processing;0.00494269684193766;216578,71713,16588,170791!GO:0006350;transcription;0.00494269684193766;216578,170791,72567,19664,80732,231386,73274!GO:0046777;protein amino acid autophosphorylation;0.00615239353534538;12747,12750!GO:0016540;protein autoprocessing;0.00660974729994499;12747,12750!GO:0005622;intracellular;0.00668764818428192;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,19255,73274!GO:0018212;peptidyl-tyrosine modification;0.0143628569552499;12747,12750!GO:0018108;peptidyl-tyrosine phosphorylation;0.0143628569552499;12747,12750!GO:0006355;regulation of transcription, DNA-dependent;0.0143628569552499;19664,231386,170791,80732,72567,73274!GO:0006351;transcription, DNA-dependent;0.0145152041548976;19664,231386,170791,80732,72567,73274!GO:0032774;RNA biosynthetic process;0.0145152041548976;19664,231386,170791,80732,72567,73274!GO:0045449;regulation of transcription;0.0160271656701653;19664,231386,170791,80732,72567,73274!GO:0003723;RNA binding;0.0160271656701653;216578,67418,16588,170791!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0172785291018028;19664,231386,170791,80732,72567,73274!GO:0010468;regulation of gene expression;0.0218552790271866;19664,231386,170791,80732,72567,73274!GO:0031323;regulation of cellular metabolic process;0.026685242233463;19664,231386,170791,80732,72567,73274!GO:0018193;peptidyl-amino acid modification;0.0288652314441864;12747,12750!GO:0004652;polynucleotide adenylyltransferase activity;0.0288652314441864;216578!GO:0019222;regulation of metabolic process;0.0300666077364779;19664,231386,170791,80732,72567,73274!GO:0048505;regulation of timing of cell differentiation;0.0332166159399697;19664!GO:0040034;regulation of development, heterochronic;0.0332166159399697;19664!GO:0016486;peptide hormone processing;0.0430581140249115;30052!GO:0018210;peptidyl-threonine modification;0.0430581140249115;12747!GO:0018107;peptidyl-threonine phosphorylation;0.0430581140249115;12747!GO:0001837;epithelial to mesenchymal transition;0.0480139548102052;19664!
|gostat_on_MCL_coexpression=GO:0005634;nucleus;3.76419046431649e-05;20843,12747,216578,71713,16588,170791,72567,19664,12750,67418,23857,231386,80732,73274!GO:0043283;biopolymer metabolic process;0.000311836934344768;12747,216578,71713,16588,170791,72567,19664,12750,231386,19255,30052,80732,73274!GO:0043170;macromolecule metabolic process;0.000497536975592701;12747,216578,71713,16588,170791,72567,19664,12750,67418,231386,19255,30052,80732,73274!GO:0043231;intracellular membrane-bound organelle;0.000586687245999991;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,73274!GO:0043227;membrane-bound organelle;0.000586687245999991;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,73274!GO:0003676;nucleic acid binding;0.000746427899461023;216578,16588,170791,72567,19664,23857,67418,231386,80732,73274!GO:0016070;RNA metabolic process;0.000774831726398036;216578,71713,16588,170791,72567,19664,231386,80732,73274!GO:0016485;protein processing;0.00127511598646046;12747,12750,30052!GO:0006397;mRNA processing;0.0019505498710537;216578,71713,16588,170791!GO:0044238;primary metabolic process;0.0019505498710537;12747,216578,71713,16588,170791,72567,19664,12750,67418,231386,19255,30052,80732,73274!GO:0044237;cellular metabolic process;0.0019505498710537;12747,216578,71713,16588,170791,72567,19664,12750,67418,231386,19255,30052,80732,73274!GO:0010467;gene expression;0.0019505498710537;216578,71713,16588,170791,72567,19664,231386,80732,73274!GO:0043229;intracellular organelle;0.0019505498710537;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,73274!GO:0043226;organelle;0.0019505498710537;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,73274!GO:0016071;mRNA metabolic process;0.0019505498710537;216578,71713,16588,170791!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00383249314735907;216578,71713,16588,170791,72567,19664,231386,80732,73274!GO:0003677;DNA binding;0.00418382364513257;16588,72567,19664,23857,80732,231386,73274!GO:0044424;intracellular part;0.00494269684193766;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,19255,73274!GO:0006396;RNA processing;0.00494269684193766;216578,71713,16588,170791!GO:0006350;transcription;0.00494269684193766;216578,170791,72567,19664,80732,231386,73274!GO:0046777;protein amino acid autophosphorylation;0.00615239353534538;12747,12750!GO:0016540;protein autoprocessing;0.00660974729994499;12747,12750!GO:0005622;intracellular;0.00668764818428192;20843,12747,170791,67418,23857,231386,30052,80732,216578,71713,16588,72567,19664,12750,19255,73274!GO:0018212;peptidyl-tyrosine modification;0.0143628569552499;12747,12750!GO:0018108;peptidyl-tyrosine phosphorylation;0.0143628569552499;12747,12750!GO:0006355;regulation of transcription, DNA-dependent;0.0143628569552499;19664,231386,170791,80732,72567,73274!GO:0006351;transcription, DNA-dependent;0.0145152041548976;19664,231386,170791,80732,72567,73274!GO:0032774;RNA biosynthetic process;0.0145152041548976;19664,231386,170791,80732,72567,73274!GO:0045449;regulation of transcription;0.0160271656701653;19664,231386,170791,80732,72567,73274!GO:0003723;RNA binding;0.0160271656701653;216578,67418,16588,170791!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0172785291018028;19664,231386,170791,80732,72567,73274!GO:0010468;regulation of gene expression;0.0218552790271866;19664,231386,170791,80732,72567,73274!GO:0031323;regulation of cellular metabolic process;0.026685242233463;19664,231386,170791,80732,72567,73274!GO:0018193;peptidyl-amino acid modification;0.0288652314441864;12747,12750!GO:0004652;polynucleotide adenylyltransferase activity;0.0288652314441864;216578!GO:0019222;regulation of metabolic process;0.0300666077364779;19664,231386,170791,80732,72567,73274!GO:0048505;regulation of timing of cell differentiation;0.0332166159399697;19664!GO:0040034;regulation of development, heterochronic;0.0332166159399697;19664!GO:0016486;peptide hormone processing;0.0430581140249115;30052!GO:0018210;peptidyl-threonine modification;0.0430581140249115;12747!GO:0018107;peptidyl-threonine phosphorylation;0.0430581140249115;12747!GO:0001837;epithelial to mesenchymal transition;0.0480139548102052;19664!
}}
}}

Revision as of 12:39, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:20032330..20032345,+p3@Bclaf1
Mm9::chr10:40602879..40602936,-p1@Cdc40
Mm9::chr10:7512695..7512734,+p1@Ppil4
Mm9::chr11:104303623..104303641,-p4@1700081L11Rik
Mm9::chr11:23795208..23795280,-p1@Papolg
Mm9::chr11:51076623..51076699,+p1@Clk4
Mm9::chr12:82046510..82046528,+p1@Gm12966
p1@Srsf5
Mm9::chr13:112280043..112280098,-p1@Gpbp1
Mm9::chr18:67884180..67884213,-p2@Ptpn2
Mm9::chr1:55084221..55084250,-p1@Sf3b1
Mm9::chr1:58480851..58480872,-p1@Clk1
Mm9::chr1:58480886..58480908,-p2@Clk1
Mm9::chr2:10002227..10002245,+p1@Kin
Mm9::chr2:156005871..156005937,-p1@Rbm39
Mm9::chr2:34657856..34657911,+p1@uc008jiw.1
Mm9::chr3:30501539..30501575,+p@chr3:30501539..30501575
+
Mm9::chr5:148241729..148241793,+p1@Pan3
Mm9::chr5:20457587..20457642,-p1@Rsbn1l
Mm9::chr5:22939123..22939162,-p1@uc008wpw.1
p1@uc008wpx.1
Mm9::chr5:53981912..53981942,+p1@Rbpj
Mm9::chr5:87233306..87233322,+p2@Ythdc1
Mm9::chr5:9161692..9161762,-p1@Dmtf1
Mm9::chr6:120314411..120314466,+p2@Kdm5a
Mm9::chr7:80686605..80686623,-p2@Chd2
Mm9::chr7:80686624..80686644,-p1@Chd2
Mm9::chr8:72240749..72240811,-p1@Zfp869
Mm9::chrX:39503903..39503928,+p3@Stag2


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:0005634nucleus3.76419046431649e-05
GO:0043283biopolymer metabolic process0.000311836934344768
GO:0043170macromolecule metabolic process0.000497536975592701
GO:0043231intracellular membrane-bound organelle0.000586687245999991
GO:0043227membrane-bound organelle0.000586687245999991
GO:0003676nucleic acid binding0.000746427899461023
GO:0016070RNA metabolic process0.000774831726398036
GO:0016485protein processing0.00127511598646046
GO:0006397mRNA processing0.0019505498710537
GO:0044238primary metabolic process0.0019505498710537
GO:0044237cellular metabolic process0.0019505498710537
GO:0010467gene expression0.0019505498710537
GO:0043229intracellular organelle0.0019505498710537
GO:0043226organelle0.0019505498710537
GO:0016071mRNA metabolic process0.0019505498710537
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00383249314735907
GO:0003677DNA binding0.00418382364513257
GO:0044424intracellular part0.00494269684193766
GO:0006396RNA processing0.00494269684193766
GO:0006350transcription0.00494269684193766
GO:0046777protein amino acid autophosphorylation0.00615239353534538
GO:0016540protein autoprocessing0.00660974729994499
GO:0005622intracellular0.00668764818428192
GO:0018212peptidyl-tyrosine modification0.0143628569552499
GO:0018108peptidyl-tyrosine phosphorylation0.0143628569552499
GO:0006355regulation of transcription, DNA-dependent0.0143628569552499
GO:0006351transcription, DNA-dependent0.0145152041548976
GO:0032774RNA biosynthetic process0.0145152041548976
GO:0045449regulation of transcription0.0160271656701653
GO:0003723RNA binding0.0160271656701653
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0172785291018028
GO:0010468regulation of gene expression0.0218552790271866
GO:0031323regulation of cellular metabolic process0.026685242233463
GO:0018193peptidyl-amino acid modification0.0288652314441864
GO:0004652polynucleotide adenylyltransferase activity0.0288652314441864
GO:0019222regulation of metabolic process0.0300666077364779
GO:0048505regulation of timing of cell differentiation0.0332166159399697
GO:0040034regulation of development, heterochronic0.0332166159399697
GO:0016486peptide hormone processing0.0430581140249115
GO:0018210peptidyl-threonine modification0.0430581140249115
GO:0018107peptidyl-threonine phosphorylation0.0430581140249115
GO:0001837epithelial to mesenchymal transition0.0480139548102052



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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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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