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MCL coexpression mm9:973: Difference between revisions

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{{MCL_coexpression_mm9
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metabolic process;0.00669822721368301;18861,13018,78656,21749!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00770354454023687;18861,13018,26885,78656,213054,21749!GO:0045449;regulation of transcription;0.00770354454023687;13018,26885,78656,213054,21749!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00770354454023687;13018,26885,78656,213054,21749!GO:0006350;transcription;0.00770354454023687;13018,26885,78656,213054,21749!GO:0010468;regulation of gene expression;0.00770354454023687;13018,26885,78656,213054,21749!GO:0031323;regulation of cellular metabolic process;0.00800692130460139;13018,26885,78656,213054,21749!GO:0019222;regulation of metabolic process;0.00833682578190896;13018,26885,78656,213054,21749!GO:0005634;nucleus;0.01069598650413;18861,13018,26885,78656,213054,21749!GO:0043283;biopolymer metabolic process;0.0107983267282468;18861,13018,26885,78656,213054,21749!GO:0032389;MutLalpha complex;0.0107983267282468;18861!GO:0022402;cell cycle process;0.0107983267282468;18861,13018,21749!GO:0010467;gene expression;0.0107983267282468;13018,26885,78656,213054,21749!GO:0006260;DNA replication;0.0107983267282468;18861,21749!GO:0043028;caspase regulator activity;0.0107983267282468;26885!GO:0010216;maintenance of DNA methylation;0.0107983267282468;13018!GO:0042162;telomeric DNA binding;0.0107983267282468;21749!GO:0008656;caspase activator activity;0.0107983267282468;26885!GO:0007004;telomere maintenance via telomerase;0.0129558623042775;21749!GO:0032300;mismatch repair complex;0.0129558623042775;18861!GO:0007049;cell cycle;0.0138056554840343;18861,13018,21749!GO:0042802;identical protein binding;0.0138056554840343;26885,213054!GO:0006278;RNA-dependent DNA replication;0.014765556762504;21749!GO:0008625;induction of apoptosis via death domain receptors;0.014765556762504;26885!GO:0016505;apoptotic protease activator activity;0.014765556762504;26885!GO:0050794;regulation of cellular process;0.014765556762504;13018,26885,78656,213054,21749!GO:0006355;regulation of transcription, DNA-dependent;0.014765556762504;13018,26885,78656,213054!GO:0006349;genetic imprinting;0.014765556762504;13018!GO:0009048;dosage compensation, by inactivation of X chromosome;0.014765556762504;13018!GO:0006351;transcription, DNA-dependent;0.014765556762504;13018,26885,78656,213054!GO:0032774;RNA biosynthetic process;0.014765556762504;13018,26885,78656,213054!GO:0003677;DNA binding;0.0149914116052312;18861,13018,213054,21749!GO:0002566;somatic diversification of immune receptors via somatic mutation;0.0151983381739104;18861!GO:0016446;somatic hypermutation of immunoglobulin genes;0.0151983381739104;18861!GO:0000279;M phase;0.0151983381739104;18861,21749!GO:0043170;macromolecule metabolic process;0.0151983381739104;18861,13018,26885,78656,213054,21749!GO:0030983;mismatched DNA binding;0.015329864948429;18861!GO:0007549;dosage compensation;0.015329864948429;13018!GO:0050789;regulation of biological process;0.0165727056289125;13018,26885,78656,213054,21749!GO:0006298;mismatch repair;0.0176438701986368;18861!GO:0022403;cell cycle phase;0.0176438701986368;18861,21749!GO:0044424;intracellular part;0.0176438701986368;18861,13018,51810,26885,78656,213054,21749!GO:0016504;protease activator activity;0.0176438701986368;26885!GO:0045005;maintenance of fidelity during DNA-dependent DNA replication;0.0176438701986368;18861!GO:0016070;RNA metabolic process;0.020206969527929;13018,26885,78656,213054!GO:0005622;intracellular;0.020206969527929;18861,13018,51810,26885,78656,213054,21749!GO:0006305;DNA alkylation;0.020206969527929;13018!GO:0006306;DNA methylation;0.020206969527929;13018!GO:0065007;biological regulation;0.0206084635137446;13018,26885,78656,213054,21749!GO:0032200;telomere organization and biogenesis;0.0215470177903846;21749!GO:0000723;telomere maintenance;0.0215470177903846;21749!GO:0000781;chromosome, telomeric region;0.0219499579438009;21749!GO:0006304;DNA modification;0.0219499579438009;13018!GO:0044238;primary metabolic process;0.0220368393534729;18861,13018,26885,78656,213054,21749!GO:0008624;induction of apoptosis by extracellular signals;0.0220368393534729;26885!GO:0044237;cellular metabolic process;0.0220368393534729;18861,13018,26885,78656,213054,21749!GO:0006919;caspase activation;0.0220368393534729;26885!GO:0043231;intracellular membrane-bound organelle;0.0220368393534729;18861,13018,26885,78656,213054,21749!GO:0043227;membrane-bound organelle;0.0220368393534729;18861,13018,26885,78656,213054,21749!GO:0003690;double-stranded DNA binding;0.0222388548665342;18861!GO:0043280;positive regulation of caspase activity;0.0222388548665342;26885!GO:0051276;chromosome organization and biogenesis;0.0228546865612764;78656,21749!GO:0051345;positive regulation of hydrolase activity;0.0245968543146773;26885!GO:0016445;somatic diversification of immunoglobulins;0.030235839008093;18861!GO:0003676;nucleic acid binding;0.0302919443924271;18861,13018,213054,21749!GO:0043281;regulation of caspase activity;0.0302919443924271;26885!GO:0002200;somatic diversification of immune receptors;0.0307973407813843;18861!GO:0002377;immunoglobulin production;0.0364478222951602;18861!GO:0002440;production of molecular mediator of immune response;0.0364478222951602;18861!GO:0043229;intracellular organelle;0.0364478222951602;18861,13018,26885,78656,213054,21749!GO:0043226;organelle;0.0364478222951602;18861,13018,26885,78656,213054,21749!GO:0043414;biopolymer methylation;0.037552721260962;13018!GO:0040029;regulation of gene expression, epigenetic;0.0379139366498252;13018!GO:0032259;methylation;0.0391283390029987;13018!GO:0006261;DNA-dependent DNA replication;0.0394580715189841;18861!GO:0043566;structure-specific DNA binding;0.0406185367480307;18861!GO:0008632;apoptotic 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|gostat_on_MCL_coexpression=GO:0006259;DNA metabolic process;0.00669822721368301;18861,13018,78656,21749!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00770354454023687;18861,13018,26885,78656,213054,21749!GO:0045449;regulation of transcription;0.00770354454023687;13018,26885,78656,213054,21749!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00770354454023687;13018,26885,78656,213054,21749!GO:0006350;transcription;0.00770354454023687;13018,26885,78656,213054,21749!GO:0010468;regulation of gene expression;0.00770354454023687;13018,26885,78656,213054,21749!GO:0031323;regulation of cellular metabolic process;0.00800692130460139;13018,26885,78656,213054,21749!GO:0019222;regulation of metabolic process;0.00833682578190896;13018,26885,78656,213054,21749!GO:0005634;nucleus;0.01069598650413;18861,13018,26885,78656,213054,21749!GO:0043283;biopolymer metabolic process;0.0107983267282468;18861,13018,26885,78656,213054,21749!GO:0032389;MutLalpha complex;0.0107983267282468;18861!GO:0022402;cell cycle process;0.0107983267282468;18861,13018,21749!GO:0010467;gene expression;0.0107983267282468;13018,26885,78656,213054,21749!GO:0006260;DNA replication;0.0107983267282468;18861,21749!GO:0043028;caspase regulator activity;0.0107983267282468;26885!GO:0010216;maintenance of DNA methylation;0.0107983267282468;13018!GO:0042162;telomeric DNA binding;0.0107983267282468;21749!GO:0008656;caspase activator activity;0.0107983267282468;26885!GO:0007004;telomere maintenance via telomerase;0.0129558623042775;21749!GO:0032300;mismatch repair complex;0.0129558623042775;18861!GO:0007049;cell cycle;0.0138056554840343;18861,13018,21749!GO:0042802;identical protein binding;0.0138056554840343;26885,213054!GO:0006278;RNA-dependent DNA replication;0.014765556762504;21749!GO:0008625;induction of apoptosis via death domain receptors;0.014765556762504;26885!GO:0016505;apoptotic protease activator activity;0.014765556762504;26885!GO:0050794;regulation of cellular process;0.014765556762504;13018,26885,78656,213054,21749!GO:0006355;regulation of transcription, DNA-dependent;0.014765556762504;13018,26885,78656,213054!GO:0006349;genetic imprinting;0.014765556762504;13018!GO:0009048;dosage compensation, by inactivation of X chromosome;0.014765556762504;13018!GO:0006351;transcription, DNA-dependent;0.014765556762504;13018,26885,78656,213054!GO:0032774;RNA biosynthetic process;0.014765556762504;13018,26885,78656,213054!GO:0003677;DNA binding;0.0149914116052312;18861,13018,213054,21749!GO:0002566;somatic diversification of immune receptors via somatic mutation;0.0151983381739104;18861!GO:0016446;somatic hypermutation of immunoglobulin genes;0.0151983381739104;18861!GO:0000279;M phase;0.0151983381739104;18861,21749!GO:0043170;macromolecule metabolic process;0.0151983381739104;18861,13018,26885,78656,213054,21749!GO:0030983;mismatched DNA binding;0.015329864948429;18861!GO:0007549;dosage compensation;0.015329864948429;13018!GO:0050789;regulation of biological process;0.0165727056289125;13018,26885,78656,213054,21749!GO:0006298;mismatch repair;0.0176438701986368;18861!GO:0022403;cell cycle phase;0.0176438701986368;18861,21749!GO:0044424;intracellular part;0.0176438701986368;18861,13018,51810,26885,78656,213054,21749!GO:0016504;protease activator activity;0.0176438701986368;26885!GO:0045005;maintenance of fidelity during DNA-dependent DNA replication;0.0176438701986368;18861!GO:0016070;RNA metabolic process;0.020206969527929;13018,26885,78656,213054!GO:0005622;intracellular;0.020206969527929;18861,13018,51810,26885,78656,213054,21749!GO:0006305;DNA alkylation;0.020206969527929;13018!GO:0006306;DNA methylation;0.020206969527929;13018!GO:0065007;biological regulation;0.0206084635137446;13018,26885,78656,213054,21749!GO:0032200;telomere organization and biogenesis;0.0215470177903846;21749!GO:0000723;telomere maintenance;0.0215470177903846;21749!GO:0000781;chromosome, telomeric region;0.0219499579438009;21749!GO:0006304;DNA modification;0.0219499579438009;13018!GO:0044238;primary metabolic process;0.0220368393534729;18861,13018,26885,78656,213054,21749!GO:0008624;induction of apoptosis by extracellular signals;0.0220368393534729;26885!GO:0044237;cellular metabolic process;0.0220368393534729;18861,13018,26885,78656,213054,21749!GO:0006919;caspase activation;0.0220368393534729;26885!GO:0043231;intracellular membrane-bound organelle;0.0220368393534729;18861,13018,26885,78656,213054,21749!GO:0043227;membrane-bound organelle;0.0220368393534729;18861,13018,26885,78656,213054,21749!GO:0003690;double-stranded DNA binding;0.0222388548665342;18861!GO:0043280;positive regulation of caspase activity;0.0222388548665342;26885!GO:0051276;chromosome organization and biogenesis;0.0228546865612764;78656,21749!GO:0051345;positive regulation of hydrolase activity;0.0245968543146773;26885!GO:0016445;somatic diversification of immunoglobulins;0.030235839008093;18861!GO:0003676;nucleic acid binding;0.0302919443924271;18861,13018,213054,21749!GO:0043281;regulation of caspase activity;0.0302919443924271;26885!GO:0002200;somatic diversification of immune receptors;0.0307973407813843;18861!GO:0002377;immunoglobulin production;0.0364478222951602;18861!GO:0002440;production of molecular mediator of immune response;0.0364478222951602;18861!GO:0043229;intracellular organelle;0.0364478222951602;18861,13018,26885,78656,213054,21749!GO:0043226;organelle;0.0364478222951602;18861,13018,26885,78656,213054,21749!GO:0043414;biopolymer methylation;0.037552721260962;13018!GO:0040029;regulation of gene expression, epigenetic;0.0379139366498252;13018!GO:0032259;methylation;0.0391283390029987;13018!GO:0006261;DNA-dependent DNA replication;0.0394580715189841;18861!GO:0043566;structure-specific DNA binding;0.0406185367480307;18861!GO:0008632;apoptotic program;0.0409195318913317;26885!
}}

Latest revision as of 16:11, 17 September 2013


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)
MA0003.10.848341
MA0004.10.434673
MA0006.11.37063
MA0007.11.07722
MA0009.10.870101
MA0014.10.829081
MA0017.10.296816
MA0019.10.688051
MA0024.13.20576
MA0025.11.10341
MA0027.12.51754
MA0028.12.15675
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.11.64072
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.353484
MA0060.14.97066
MA0061.10.224905
MA0063.10
MA0066.13.48842
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.00296875
MA0074.10.531046
MA0076.10.845594
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.11.79592
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.787675
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.506952
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.10.385068
MA0147.11.24068
MA0148.10.450593
MA0149.10.367458
MA0062.21.96779
MA0035.20.524137
MA0039.22.04793
MA0138.20.675599
MA0002.20.513194
MA0137.20.32312
MA0104.21.64215
MA0047.20.576767
MA0112.20.527225
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.0804339
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.11.14982
MA0161.10
MA0162.10.71453
MA0163.10.0186439
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.118858
MA0102.21.59466
MA0258.11.13923
MA0259.12.63282
MA0442.10
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