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MCL coexpression mm9:973: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!4.00e-12!29;UBERON:0005057!4.00e-12!29;UBERON:0000153!4.64e-10!43;UBERON:0002370!5.72e-09!23;UBERON:0000974!5.72e-09!23;UBERON:0004807!5.72e-09!23;UBERON:0005058!5.72e-09!23;UBERON:0003351!5.72e-09!23;UBERON:0009113!5.72e-09!23;UBERON:0003295!5.72e-09!23;UBERON:0009722!5.72e-09!23;UBERON:0005562!5.72e-09!23;UBERON:0007690!5.72e-09!23;UBERON:0000077!5.80e-09!35;UBERON:0001048!7.74e-09!134;UBERON:0003408!2.53e-08!24;UBERON:0006562!4.27e-08!24;UBERON:0001557!4.27e-08!24;UBERON:0001042!4.27e-08!24;UBERON:0008814!4.27e-08!24;UBERON:0009145!4.27e-08!24;UBERON:0002390!4.54e-08!45;UBERON:0003061!4.54e-08!45;UBERON:0007811!4.62e-08!36;UBERON:0000065!1.72e-07!41;UBERON:0002193!2.21e-07!48;UBERON:0002405!2.21e-07!48;UBERON:0001004!4.09e-07!42
|ontology_enrichment_uberon=UBERON:0004177!4.00e-12!29;UBERON:0005057!4.00e-12!29;UBERON:0000153!4.64e-10!43;UBERON:0002370!5.72e-09!23;UBERON:0000974!5.72e-09!23;UBERON:0004807!5.72e-09!23;UBERON:0005058!5.72e-09!23;UBERON:0003351!5.72e-09!23;UBERON:0009113!5.72e-09!23;UBERON:0003295!5.72e-09!23;UBERON:0009722!5.72e-09!23;UBERON:0005562!5.72e-09!23;UBERON:0007690!5.72e-09!23;UBERON:0000077!5.80e-09!35;UBERON:0001048!7.74e-09!134;UBERON:0003408!2.53e-08!24;UBERON:0006562!4.27e-08!24;UBERON:0001557!4.27e-08!24;UBERON:0001042!4.27e-08!24;UBERON:0008814!4.27e-08!24;UBERON:0009145!4.27e-08!24;UBERON:0002390!4.54e-08!45;UBERON:0003061!4.54e-08!45;UBERON:0007811!4.62e-08!36;UBERON:0000065!1.72e-07!41;UBERON:0002193!2.21e-07!48;UBERON:0002405!2.21e-07!48;UBERON:0001004!4.09e-07!42
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.367606,0.434198,0.260188,0.448401,1.33049,0.515265,0.181564,1.50457,0.494602,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.938682,0.29826,0.332107,0.0622758,1.35437,0.258745,0.374936,0.577606,0.153291,0.469052,0.818708,0.376624,1.15331,0.843667,0.250677,0.425071,0.276324,0.0711618,0.678971,1.29755,0.221921,0.195877,0.256422,0.460258,0.0558565,0.27776,0.209497,0.423266,0.662995,0.484612,0.0447507,0.825035,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,1.39465,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.178433,0.872563,1.03623,0.853709,0.131016,0.42492,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,2.03549,0.293679,0.376919,1.60318,1.65055,1.20871,0.925879,0.856465,0.265734,1.16941,0.202284,0.510015,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.903338,1.59446,1.00333,0.96962,0.337254,1.24884,1.21576,0.254749,1.35445,1.11602,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,1.35892,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,1.33415,0.766041,1.66843,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,1.03572,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.558175
}}
}}

Revision as of 19:12, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr18:34784216..34784245,-p1@Brd8
Mm9::chr1:15795720..15795756,+p1@Terf1
Mm9::chr1:180267871..180267892,-p3@Hnrnpu
Mm9::chr3:95021663..95021687,-p3@Gabpb2
Mm9::chr4:32702403..32702443,+p1@Casp8ap2
Mm9::chr5:144670842..144670916,+p1@Pms2
Mm9::chr8:108160409..108160489,+p1@Ctcf
Mm9::chr9:15162136..15162203,-p1@5830418K08Rik


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:0006259DNA metabolic process0.00669822721368301
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00770354454023687
GO:0045449regulation of transcription0.00770354454023687
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00770354454023687
GO:0006350transcription0.00770354454023687
GO:0010468regulation of gene expression0.00770354454023687
GO:0031323regulation of cellular metabolic process0.00800692130460139
GO:0019222regulation of metabolic process0.00833682578190896
GO:0005634nucleus0.01069598650413
GO:0043283biopolymer metabolic process0.0107983267282468
GO:0032389MutLalpha complex0.0107983267282468
GO:0022402cell cycle process0.0107983267282468
GO:0010467gene expression0.0107983267282468
GO:0006260DNA replication0.0107983267282468
GO:0043028caspase regulator activity0.0107983267282468
GO:0010216maintenance of DNA methylation0.0107983267282468
GO:0042162telomeric DNA binding0.0107983267282468
GO:0008656caspase activator activity0.0107983267282468
GO:0007004telomere maintenance via telomerase0.0129558623042775
GO:0032300mismatch repair complex0.0129558623042775
GO:0007049cell cycle0.0138056554840343
GO:0042802identical protein binding0.0138056554840343
GO:0006278RNA-dependent DNA replication0.014765556762504
GO:0008625induction of apoptosis via death domain receptors0.014765556762504
GO:0016505apoptotic protease activator activity0.014765556762504
GO:0050794regulation of cellular process0.014765556762504
GO:0006355regulation of transcription, DNA-dependent0.014765556762504
GO:0006349genetic imprinting0.014765556762504
GO:0009048dosage compensation, by inactivation of X chromosome0.014765556762504
GO:0006351transcription, DNA-dependent0.014765556762504
GO:0032774RNA biosynthetic process0.014765556762504
GO:0003677DNA binding0.0149914116052312
GO:0002566somatic diversification of immune receptors via somatic mutation0.0151983381739104
GO:0016446somatic hypermutation of immunoglobulin genes0.0151983381739104
GO:0000279M phase0.0151983381739104
GO:0043170macromolecule metabolic process0.0151983381739104
GO:0030983mismatched DNA binding0.015329864948429
GO:0007549dosage compensation0.015329864948429
GO:0050789regulation of biological process0.0165727056289125
GO:0006298mismatch repair0.0176438701986368
GO:0022403cell cycle phase0.0176438701986368
GO:0044424intracellular part0.0176438701986368
GO:0016504protease activator activity0.0176438701986368
GO:0045005maintenance of fidelity during DNA-dependent DNA replication0.0176438701986368
GO:0016070RNA metabolic process0.020206969527929
GO:0005622intracellular0.020206969527929
GO:0006305DNA alkylation0.020206969527929
GO:0006306DNA methylation0.020206969527929
GO:0065007biological regulation0.0206084635137446
GO:0032200telomere organization and biogenesis0.0215470177903846
GO:0000723telomere maintenance0.0215470177903846
GO:0000781chromosome, telomeric region0.0219499579438009
GO:0006304DNA modification0.0219499579438009
GO:0044238primary metabolic process0.0220368393534729
GO:0008624induction of apoptosis by extracellular signals0.0220368393534729
GO:0044237cellular metabolic process0.0220368393534729
GO:0006919caspase activation0.0220368393534729
GO:0043231intracellular membrane-bound organelle0.0220368393534729
GO:0043227membrane-bound organelle0.0220368393534729
GO:0003690double-stranded DNA binding0.0222388548665342
GO:0043280positive regulation of caspase activity0.0222388548665342
GO:0051276chromosome organization and biogenesis0.0228546865612764
GO:0051345positive regulation of hydrolase activity0.0245968543146773
GO:0016445somatic diversification of immunoglobulins0.030235839008093
GO:0003676nucleic acid binding0.0302919443924271
GO:0043281regulation of caspase activity0.0302919443924271
GO:0002200somatic diversification of immune receptors0.0307973407813843
GO:0002377immunoglobulin production0.0364478222951602
GO:0002440production of molecular mediator of immune response0.0364478222951602
GO:0043229intracellular organelle0.0364478222951602
GO:0043226organelle0.0364478222951602
GO:0043414biopolymer methylation0.037552721260962
GO:0040029regulation of gene expression, epigenetic0.0379139366498252
GO:0032259methylation0.0391283390029987
GO:0006261DNA-dependent DNA replication0.0394580715189841
GO:0043566structure-specific DNA binding0.0406185367480307
GO:0008632apoptotic program0.0409195318913317



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>


Uber Anatomy
Ontology termp-valuen
hemopoietic organ4.00e-1229
immune organ4.00e-1229
anterior region of body4.64e-1043
thymus5.72e-0923
neck5.72e-0923
respiratory system epithelium5.72e-0923
hemolymphoid system gland5.72e-0923
pharyngeal epithelium5.72e-0923
thymic region5.72e-0923
pharyngeal gland5.72e-0923
entire pharyngeal arch endoderm5.72e-0923
thymus primordium5.72e-0923
early pharyngeal endoderm5.72e-0923
mixed endoderm/mesoderm-derived structure5.80e-0935
primordium7.74e-09134
gland of gut2.53e-0824
pharynx4.27e-0824
upper respiratory tract4.27e-0824
chordate pharynx4.27e-0824
pharyngeal arch system4.27e-0824
pharyngeal region of foregut4.27e-0824
hematopoietic system4.54e-0845
blood island4.54e-0845
craniocervical region4.62e-0836
respiratory tract1.72e-0741
hemolymphoid system2.21e-0748
immune system2.21e-0748
respiratory system4.09e-0742


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}}}