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MCL coexpression mm9:540: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000153!5.56e-10!43;UBERON:0007811!2.46e-09!36;UBERON:0001004!5.52e-09!42;UBERON:0000065!6.58e-09!41;UBERON:0004177!1.17e-08!29;UBERON:0005057!1.17e-08!29;UBERON:0003408!1.98e-08!24;UBERON:0002370!2.08e-08!23;UBERON:0000974!2.08e-08!23;UBERON:0004807!2.08e-08!23;UBERON:0005058!2.08e-08!23;UBERON:0003351!2.08e-08!23;UBERON:0009113!2.08e-08!23;UBERON:0003295!2.08e-08!23;UBERON:0009722!2.08e-08!23;UBERON:0005562!2.08e-08!23;UBERON:0007690!2.08e-08!23;UBERON:0006562!5.41e-08!24;UBERON:0001557!5.41e-08!24;UBERON:0001042!5.41e-08!24;UBERON:0008814!5.41e-08!24;UBERON:0009145!5.41e-08!24;UBERON:0000077!3.82e-07!35
|ontology_enrichment_uberon=UBERON:0000153!5.56e-10!43;UBERON:0007811!2.46e-09!36;UBERON:0001004!5.52e-09!42;UBERON:0000065!6.58e-09!41;UBERON:0004177!1.17e-08!29;UBERON:0005057!1.17e-08!29;UBERON:0003408!1.98e-08!24;UBERON:0002370!2.08e-08!23;UBERON:0000974!2.08e-08!23;UBERON:0004807!2.08e-08!23;UBERON:0005058!2.08e-08!23;UBERON:0003351!2.08e-08!23;UBERON:0009113!2.08e-08!23;UBERON:0003295!2.08e-08!23;UBERON:0009722!2.08e-08!23;UBERON:0005562!2.08e-08!23;UBERON:0007690!2.08e-08!23;UBERON:0006562!5.41e-08!24;UBERON:0001557!5.41e-08!24;UBERON:0001042!5.41e-08!24;UBERON:0008814!5.41e-08!24;UBERON:0009145!5.41e-08!24;UBERON:0000077!3.82e-07!35
|tfbs_overrepresentation_for_novel_motifs=0.6379,0.462564,1.11498,0.25808,0.123731,0.269875,0.346405,0.237242,0.251553,1.25777,0.308886,0.336042,0.511203,0.357027,0.419678,0,0.530547,0.118546,0.215337,0.751449,0.176628,0.165365,1.67324,0.388504,0.603782,0.381085,0.0554034,0.782755,0.154744,0.338204,0.75617,0.624931,0.373899,0.176308,0.420513,0.850523,1.19268,0.885722,0.322338,2.01331,0.121091,0.76591,0.0536251,0.136236,0.314995,0.695306,1.15859,0.812613,0.112678,0.156829,0.514446,1.04423,0.137142,0.759566,0.776306,0.363247,0.490599,0.868243,0.190698,0.949048,0.606104,0.413233,0.0784106,0.504093,0.974413,1.33757,0.908031,1.25063,0.60172,1.10561,1.05857,0.526777,0.88203,0.808562,0.181606,0.674012,0.0464428,1.13643,0.590017,0.531085,0.247973,0.546623,0.411949,0.493111,2.80181,0.620777,0.0223411,0.611818,1.16814,1.41118,0.975915,0.702809,0.636995,0.401201,1.08418,0.0848579,0.503836,0.639644,0.457849,0.119684,0.111186,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.804983,0.183341,1.60173,0.62491,0.744577,0.533113,1.5213,0.982794,0.119923,1.42983,0.723174,0.53175,0.714691,0.813766,0.484912,0.382687,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.406303,0.726634,0.702495,0.877862,0.375176,1.0039,1.15925,0.231086,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,0.232952,0.394117,0.148959,0.500318,0.761071,0.0882878,0.977476,0.839715,1.04618,0.143092,0.222538,0.652913,0.96517,0.697256,0.593895,1.16538,0.50503,0.367885,0.356446,0.33468,0.559027
}}
}}

Revision as of 18:31, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr13:14156043..14156089,+p1@Arid4b
Mm9::chr14:55305442..55305484,-p1@Acin1
Mm9::chr16:91648104..91648150,+p1@Son
Mm9::chr17:21145885..21145977,+p1@Zfp160
Mm9::chr1:13364108..13364150,-p1@Ncoa2
Mm9::chr2:90585696..90585760,+p1@Fnbp4
Mm9::chr3:103718483..103718528,+p1@Rsbn1
Mm9::chr4:33397281..33397362,+p1@Rngtt
Mm9::chr4:97439116..97439202,+p5@Nfia
Mm9::chr5:28643693..28643760,+p1@Rbm33
Mm9::chr5:87233239..87233301,+p1@Ythdc1
Mm9::chr5:87233329..87233344,+p3@Ythdc1
Mm9::chr7:97591284..97591375,+p1@Crebzf
Mm9::chr9:3404058..3404098,+p1@Cwf19l2


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:0005634nucleus0.0048379566785366
GO:0003676nucleic acid binding0.0163873355820728
GO:0008192RNA guanylyltransferase activity0.0163873355820728
GO:0004651polynucleotide 5'-phosphatase activity0.0163873355820728
GO:0004484mRNA guanylyltransferase activity0.0163873355820728
GO:0016070RNA metabolic process0.0163873355820728
GO:0019204nucleotide phosphatase activity0.0163873355820728
GO:0006370mRNA capping0.0163873355820728
GO:0009452RNA capping0.0163873355820728
GO:0030375thyroid hormone receptor coactivator activity0.0163873355820728
GO:0043231intracellular membrane-bound organelle0.0183524153970818
GO:0043227membrane-bound organelle0.0183524153970818
GO:0010467gene expression0.0220637460588127
GO:0006355regulation of transcription, DNA-dependent0.0220637460588127
GO:0006351transcription, DNA-dependent0.0220637460588127
GO:0032774RNA biosynthetic process0.0220637460588127
GO:0003677DNA binding0.0220637460588127
GO:0030374ligand-dependent nuclear receptor transcription coactivator activity0.0220637460588127
GO:0045449regulation of transcription0.0220637460588127
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0228643097388343
GO:0006350transcription0.0230680736278133
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0232827137626862
GO:0010468regulation of gene expression0.0238818840034528
GO:0043229intracellular organelle0.0238818840034528
GO:0043226organelle0.0238818840034528
GO:0031323regulation of cellular metabolic process0.0257273200703863
GO:0019222regulation of metabolic process0.0290358876100918
GO:0035257nuclear hormone receptor binding0.0321101553567733
GO:0051427hormone receptor binding0.0338120948335617
GO:0030518steroid hormone receptor signaling pathway0.0353990829736296
GO:0030522intracellular receptor-mediated signaling pathway0.0473681302617389



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><br>uberon_data<br><br>



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}}}