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MCL coexpression mm9:280: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.581046210684355,0.417990231331606,0.419633443965236,0.0686377264886741,0.0439077673628208,0.452099411850348,0.432062034963759,0,0,0,0.168259719722084,0.165997395643572,0.210256940296116,0,0.145247326194276,0.0429407640179822,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.625072654011601,0.822831777690839,0.927547164909492,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.213137781329907,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.553339617248072,0.447112768205563,0.434119738637111,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.231013950740173,0.319281253633829,0.232119884700318,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.63576452329045,0.672470230361646,0.600289657055601,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00370950506799522,0.0182547339686388,0.0696144684973538,0.0612005723069621,0.0598244186619439,0.0362783024520805,0.031895734489288,0.0213197855509547,0.0403878614760544,0.0764305931706906,0.091228504856109,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0031323;regulation of cellular metabolic process;0.0330644935547988;21888,12702,17131,214855!GO:0046627;negative regulation of insulin receptor signaling pathway;0.0330644935547988;12702!GO:0019222;regulation of metabolic process;0.0330644935547988;21888,12702,17131,214855!GO:0046626;regulation of insulin receptor signaling pathway;0.0383330540041912;12702!GO:0007167;enzyme linked receptor protein signaling pathway;0.0459795060930929;12702,17131!GO:0007182;common-partner SMAD protein phosphorylation;0.0459795060930929;17131!
|ontology_enrichment_celltype=CL:0000988!5.16e-32!32;CL:0002032!5.16e-32!32;CL:0000037!5.16e-32!32;CL:0000566!5.16e-32!32;CL:0000837!5.16e-32!32;CL:0000838!1.10e-29!12;CL:0000542!3.39e-27!13;CL:0000051!3.39e-27!13;CL:0000084!4.51e-27!11;CL:0000827!4.51e-27!11;CL:0002320!4.97e-23!46;CL:0000134!4.97e-23!46;CL:0000791!5.98e-23!9;CL:0000789!5.98e-23!9;CL:0002420!5.98e-23!9;CL:0002419!5.98e-23!9;CL:0000790!5.98e-23!9;CL:0002242!1.35e-21!16;CL:0002031!1.84e-20!25;CL:0000624!2.89e-20!8;CL:0000738!3.62e-20!17;CL:0002087!3.62e-20!17;CL:0000219!7.44e-19!54;CL:0000893!4.16e-15!6;CL:0002489!4.16e-15!6;CL:0000898!4.16e-15!6;CL:0000809!4.16e-15!6;CL:0000810!4.16e-15!6;CL:0000895!4.16e-15!6;CL:0000808!4.16e-15!6;CL:0000894!4.16e-15!6;CL:0000806!4.16e-15!6;CL:0000807!4.16e-15!6;CL:0000805!4.16e-15!6;CL:0002425!4.16e-15!6;CL:0002436!4.16e-15!6;CL:0002427!4.16e-15!6;CL:0002428!4.16e-15!6;CL:0002429!4.16e-15!6;CL:0002433!4.16e-15!6;CL:0002431!4.16e-15!6;CL:0002432!4.16e-15!6;CL:0000034!9.19e-12!97;CL:0000049!1.10e-09!19;CL:0000723!4.00e-09!91;CL:0000048!4.00e-09!91
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!2.41e-26!23;UBERON:0000974!2.41e-26!23;UBERON:0004807!2.41e-26!23;UBERON:0005058!2.41e-26!23;UBERON:0003351!2.41e-26!23;UBERON:0009113!2.41e-26!23;UBERON:0003295!2.41e-26!23;UBERON:0009722!2.41e-26!23;UBERON:0005562!2.41e-26!23;UBERON:0007690!2.41e-26!23;UBERON:0006562!4.34e-25!24;UBERON:0003408!4.34e-25!24;UBERON:0001557!4.34e-25!24;UBERON:0001042!4.34e-25!24;UBERON:0008814!4.34e-25!24;UBERON:0009145!4.34e-25!24;UBERON:0002390!1.21e-23!45;UBERON:0003061!1.21e-23!45;UBERON:0002384!4.97e-23!46;UBERON:0000072!7.04e-22!27;UBERON:0002193!7.63e-22!48;UBERON:0002405!7.63e-22!48;UBERON:0004177!4.15e-20!29;UBERON:0005057!4.15e-20!29;UBERON:0000077!2.95e-18!35;UBERON:0000063!5.15e-16!35;UBERON:0007811!1.82e-15!36;UBERON:0000065!4.00e-13!41;UBERON:0001004!1.01e-12!42;UBERON:0000153!2.43e-12!43;UBERON:0003081!6.25e-11!87;UBERON:0003929!3.54e-10!55;UBERON:0002368!5.23e-09!60;UBERON:0002530!5.06e-08!65;UBERON:0000490!7.64e-08!66;UBERON:0005911!2.44e-07!69;UBERON:0000949!7.05e-07!72
}}

Latest revision as of 15:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:18890493..18890502,-p@chr10:18890493..18890502
-
Mm9::chr11:106020967..106020992,+p@chr11:106020967..106020992
+
Mm9::chr11:109224378..109224390,+p5@Gna13
Mm9::chr11:109287686..109287703,+p6@Amz2
Mm9::chr11:117830598..117830611,-p5@Socs3
Mm9::chr13:81023987..81024006,-p@chr13:81023987..81024006
-
Mm9::chr14:54842161..54842174,-p@chr14:54842161..54842174
-
Mm9::chr14:79935342..79935383,+p@chr14:79935342..79935383
+
Mm9::chr14:79935384..79935398,+p@chr14:79935384..79935398
+
Mm9::chr14:79935447..79935461,+p@chr14:79935447..79935461
+
Mm9::chr18:68387268..68387287,-p@chr18:68387268..68387287
-
Mm9::chr18:75438577..75438615,+p@chr18:75438577..75438615
+
Mm9::chr18:75439125..75439129,+p@chr18:75439125..75439129
+
Mm9::chr18:75527210..75527215,+p4@Smad7
Mm9::chr19:14672223..14672239,-p3@Tle4
Mm9::chr19:44355454..44355460,+p@chr19:44355454..44355460
+
Mm9::chr19:53387914..53387925,+p@chr19:53387914..53387925
+
Mm9::chr1:36364590..36364608,+p1@Arid5a
Mm9::chr1:53830847..53830858,-p@chr1:53830847..53830858
-
Mm9::chr1:74634691..74634719,-p2@Zfp142
Mm9::chr2:127161597..127161615,-p@chr2:127161597..127161615
-
Mm9::chr2:30567865..30567869,+p@chr2:30567865..30567869
+
Mm9::chr3:30995296..30995300,+p6@Skil
Mm9::chr4:40728877..40728888,-p@chr4:40728877..40728888
-
Mm9::chr4:40728906..40728928,-p@chr4:40728906..40728928
-
Mm9::chr7:97502403..97502441,-p@chr7:97502403..97502441
-
Mm9::chr8:86727420..86727426,-p@chr8:86727420..86727426
-
Mm9::chr9:116084258..116084271,-p3@Tgfbr2
Mm9::chr9:44411777..44411802,+p@chr9:44411777..44411802
+
Mm9::chr9:71958988..71959003,+p@chr9:71958988..71959003
+


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:0031323regulation of cellular metabolic process0.0330644935547988
GO:0046627negative regulation of insulin receptor signaling pathway0.0330644935547988
GO:0019222regulation of metabolic process0.0330644935547988
GO:0046626regulation of insulin receptor signaling pathway0.0383330540041912
GO:0007167enzyme linked receptor protein signaling pathway0.0459795060930929
GO:0007182common-partner SMAD protein phosphorylation0.0459795060930929



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
hematopoietic cell5.16e-3232
hematopoietic oligopotent progenitor cell5.16e-3232
hematopoietic stem cell5.16e-3232
angioblastic mesenchymal cell5.16e-3232
hematopoietic multipotent progenitor cell5.16e-3232
lymphoid lineage restricted progenitor cell1.10e-2912
lymphocyte3.39e-2713
common lymphoid progenitor3.39e-2713
T cell4.51e-2711
pro-T cell4.51e-2711
connective tissue cell4.97e-2346
mesenchymal cell4.97e-2346
mature alpha-beta T cell5.98e-239
alpha-beta T cell5.98e-239
immature T cell5.98e-239
mature T cell5.98e-239
immature alpha-beta T cell5.98e-239
nucleate cell1.35e-2116
hematopoietic lineage restricted progenitor cell1.84e-2025
CD4-positive, alpha-beta T cell2.89e-208
leukocyte3.62e-2017
nongranular leukocyte3.62e-2017
motile cell7.44e-1954
thymocyte4.16e-156
double negative thymocyte4.16e-156
naive T cell4.16e-156
double-positive, alpha-beta thymocyte4.16e-156
CD4-positive, alpha-beta thymocyte4.16e-156
naive thymus-derived CD4-positive, alpha-beta T cell4.16e-156
DN4 thymocyte4.16e-156
DN1 thymic pro-T cell4.16e-156
DN2 thymocyte4.16e-156
DN3 thymocyte4.16e-156
immature single positive thymocyte4.16e-156
early T lineage precursor4.16e-156
mature CD4 single-positive thymocyte4.16e-156
resting double-positive thymocyte4.16e-156
double-positive blast4.16e-156
CD69-positive double-positive thymocyte4.16e-156
CD69-positive, CD4-positive single-positive thymocyte4.16e-156
CD4-positive, CD8-intermediate double-positive thymocyte4.16e-156
CD24-positive, CD4 single-positive thymocyte4.16e-156
stem cell9.19e-1297
common myeloid progenitor1.10e-0919
somatic stem cell4.00e-0991
multi fate stem cell4.00e-0991

Uber Anatomy
Ontology termp-valuen
thymus2.41e-2623
neck2.41e-2623
respiratory system epithelium2.41e-2623
hemolymphoid system gland2.41e-2623
pharyngeal epithelium2.41e-2623
thymic region2.41e-2623
pharyngeal gland2.41e-2623
entire pharyngeal arch endoderm2.41e-2623
thymus primordium2.41e-2623
early pharyngeal endoderm2.41e-2623
pharynx4.34e-2524
gland of gut4.34e-2524
upper respiratory tract4.34e-2524
chordate pharynx4.34e-2524
pharyngeal arch system4.34e-2524
pharyngeal region of foregut4.34e-2524
hematopoietic system1.21e-2345
blood island1.21e-2345
connective tissue4.97e-2346
segment of respiratory tract7.04e-2227
hemolymphoid system7.63e-2248
immune system7.63e-2248
hemopoietic organ4.15e-2029
immune organ4.15e-2029
mixed endoderm/mesoderm-derived structure2.95e-1835
organ segment5.15e-1635
craniocervical region1.82e-1536
respiratory tract4.00e-1341
respiratory system1.01e-1242
anterior region of body2.43e-1243
lateral plate mesoderm6.25e-1187
gut epithelium3.54e-1055
endocrine gland5.23e-0960
gland5.06e-0865
unilaminar epithelium7.64e-0866
endo-epithelium2.44e-0769
endocrine system7.05e-0772


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)
MA0003.10.447378
MA0004.10.6063
MA0006.10.489667
MA0007.10.572315
MA0009.10.377631
MA0014.10.580843
MA0017.10.131062
MA0019.10.238713
MA0024.10.342622
MA0025.10.57681
MA0027.11.94532
MA0028.10.280078
MA0029.10.325591
MA0030.10.330711
MA0031.10.303242
MA0038.10.164914
MA0040.11.00699
MA0041.10.199368
MA0042.10.0492946
MA0043.10.457929
MA0046.10.407017
MA0048.10.861524
MA0050.10.341753
MA0051.10.170484
MA0052.11.02141
MA0055.10.0244735
MA0056.10
MA0057.10.37814
MA0058.10.399772
MA0059.10.745425
MA0060.10.283235
MA0061.12.08374
MA0063.10
MA0066.11.4865
MA0067.11.62241
MA0068.11.35086
MA0069.10.39467
MA0070.10.386747
MA0071.10.104441
MA0072.10.379853
MA0073.10.427976
MA0074.10.136938
MA0076.10.149319
MA0077.10.36238
MA0078.10.191654
MA0081.10.216864
MA0083.10.457256
MA0084.10.985399
MA0087.10.421024
MA0088.10.663871
MA0089.10
MA0090.10.903858
MA0091.10.092107
MA0092.10.248035
MA0093.11.24443
MA0095.10
MA0098.10
MA0100.10.130363
MA0101.11.18144
MA0103.10.0353886
MA0105.12.70107
MA0106.10.572177
MA0107.10.579242
MA0108.20.709125
MA0109.10
MA0111.10.0767317
MA0113.11.01256
MA0114.10.0675827
MA0115.10.460306
MA0116.10.261463
MA0117.10.433078
MA0119.10.444528
MA0122.10.449781
MA0124.10.628716
MA0125.10.562419
MA0130.10
MA0131.10.663769
MA0132.10
MA0133.10
MA0135.10.489063
MA0136.10.454208
MA0139.10.0343801
MA0140.10.130298
MA0141.10.160688
MA0142.10.292245
MA0143.10.188991
MA0144.10.8929
MA0145.10.243966
MA0146.10.600938
MA0147.10.200453
MA0148.10.0936023
MA0149.11.20539
MA0062.20.143392
MA0035.20.132954
MA0039.20.390442
MA0138.20.229939
MA0002.20.612056
MA0137.20.64781
MA0104.20.251331
MA0047.20.16444
MA0112.20.73643
MA0065.20.145939
MA0150.10.572061
MA0151.10
MA0152.10.164506
MA0153.10.503426
MA0154.11.11018
MA0155.10.184058
MA0156.10.969141
MA0157.10.26838
MA0158.10
MA0159.10.216399
MA0160.10.095069
MA0161.10
MA0162.10.746666
MA0163.10.831362
MA0164.10.454747
MA0080.20.581847
MA0018.20.469233
MA0099.21.86521
MA0079.21.01001
MA0102.21.03585
MA0258.10.0588775
MA0259.10.361459
MA0442.10
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