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MCL coexpression mm9:318: Difference between revisions

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{{MCL_coexpression_mm9
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dendritic cell activation;0.018015548174587;18034!GO:0002268;follicular dendritic cell differentiation;0.018015548174587;18034!GO:0016149;translation release factor activity, codon specific;0.018015548174587;225363!GO:0010467;gene expression;0.018015548174587;80859,16477,225363,18034,56706!GO:0008023;transcription elongation factor complex;0.018015548174587;56706!GO:0008079;translation termination factor activity;0.018015548174587;225363!GO:0006415;translational termination;0.018015548174587;225363!GO:0003747;translation release factor activity;0.018015548174587;225363!GO:0006355;regulation of transcription, DNA-dependent;0.0187493882502284;80859,16477,18034,56706!GO:0003700;transcription factor activity;0.0187493882502284;80859,16477,18034!GO:0002467;germinal center formation;0.0187493882502284;18034!GO:0006351;transcription, DNA-dependent;0.0187493882502284;80859,16477,18034,56706!GO:0032774;RNA biosynthetic process;0.0187493882502284;80859,16477,18034,56706!GO:0045449;regulation of transcription;0.0187493882502284;80859,16477,18034,56706!GO:0048536;spleen development;0.0187493882502284;18034!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0187493882502284;80859,16477,18034,56706!GO:0006350;transcription;0.0187493882502284;80859,16477,18034,56706!GO:0010468;regulation of gene expression;0.0200238177225507;80859,16477,18034,56706!GO:0031323;regulation of cellular metabolic process;0.0215902506335981;80859,16477,18034,56706!GO:0043624;cellular protein complex disassembly;0.0215902506335981;225363!GO:0043241;protein complex disassembly;0.0217480607147832;225363!GO:0019222;regulation of metabolic process;0.0217480607147832;80859,16477,18034,56706!GO:0032984;macromolecular complex disassembly;0.0218959546766158;225363!GO:0016070;RNA metabolic process;0.0219455121922195;80859,16477,18034,56706!GO:0048535;lymph node development;0.0244488528490187;18034!GO:0051726;regulation of cell cycle;0.0261174403194484;16477,56706!GO:0022411;cellular component disassembly;0.0292719506150735;225363!GO:0003676;nucleic acid binding;0.0394693602620986;80859,16477,225363,18034!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic 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|gostat_on_MCL_coexpression=GO:0002266;follicular dendritic cell activation;0.018015548174587;18034!GO:0002268;follicular dendritic cell differentiation;0.018015548174587;18034!GO:0016149;translation release factor activity, codon specific;0.018015548174587;225363!GO:0010467;gene expression;0.018015548174587;80859,16477,225363,18034,56706!GO:0008023;transcription elongation factor complex;0.018015548174587;56706!GO:0008079;translation termination factor activity;0.018015548174587;225363!GO:0006415;translational termination;0.018015548174587;225363!GO:0003747;translation release factor activity;0.018015548174587;225363!GO:0006355;regulation of transcription, DNA-dependent;0.0187493882502284;80859,16477,18034,56706!GO:0003700;transcription factor activity;0.0187493882502284;80859,16477,18034!GO:0002467;germinal center formation;0.0187493882502284;18034!GO:0006351;transcription, DNA-dependent;0.0187493882502284;80859,16477,18034,56706!GO:0032774;RNA biosynthetic process;0.0187493882502284;80859,16477,18034,56706!GO:0045449;regulation of transcription;0.0187493882502284;80859,16477,18034,56706!GO:0048536;spleen development;0.0187493882502284;18034!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0187493882502284;80859,16477,18034,56706!GO:0006350;transcription;0.0187493882502284;80859,16477,18034,56706!GO:0010468;regulation of gene expression;0.0200238177225507;80859,16477,18034,56706!GO:0031323;regulation of cellular metabolic process;0.0215902506335981;80859,16477,18034,56706!GO:0043624;cellular protein complex disassembly;0.0215902506335981;225363!GO:0043241;protein complex disassembly;0.0217480607147832;225363!GO:0019222;regulation of metabolic process;0.0217480607147832;80859,16477,18034,56706!GO:0032984;macromolecular complex disassembly;0.0218959546766158;225363!GO:0016070;RNA metabolic process;0.0219455121922195;80859,16477,18034,56706!GO:0048535;lymph node development;0.0244488528490187;18034!GO:0051726;regulation of cell cycle;0.0261174403194484;16477,56706!GO:0022411;cellular component disassembly;0.0292719506150735;225363!GO:0003676;nucleic acid binding;0.0394693602620986;80859,16477,225363,18034!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0498253690261291;80859,16477,18034,56706!
|ontology_enrichment_celltype=CL:0000988!3.06e-13!32;CL:0002032!3.06e-13!32;CL:0000037!3.06e-13!32;CL:0000566!3.06e-13!32;CL:0000837!3.06e-13!32;CL:0002320!8.13e-11!46;CL:0000134!8.13e-11!46;CL:0002031!8.11e-10!25;CL:0000066!2.13e-09!25;CL:0000838!3.34e-09!12;CL:0000738!9.22e-09!17;CL:0002087!9.22e-09!17;CL:0002242!1.08e-08!16;CL:0000542!1.75e-08!13;CL:0000051!1.75e-08!13;CL:0000084!1.94e-08!11;CL:0000827!1.94e-08!11;CL:0000791!6.19e-08!9;CL:0000789!6.19e-08!9;CL:0002420!6.19e-08!9;CL:0002419!6.19e-08!9;CL:0000790!6.19e-08!9;CL:0000219!6.52e-08!54;CL:0000624!3.18e-07!8;CL:0000223!8.82e-07!20
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!8.13e-11!46;UBERON:0000490!5.69e-09!66;UBERON:0000344!3.48e-08!15;UBERON:0000485!1.13e-07!11;UBERON:0002193!1.36e-07!48;UBERON:0002405!1.36e-07!48;UBERON:0001242!2.72e-07!13;UBERON:0000060!2.72e-07!13;UBERON:0001262!2.72e-07!13;UBERON:0004786!2.72e-07!13;UBERON:0004119!4.66e-07!118;UBERON:0000925!4.66e-07!118;UBERON:0006595!4.66e-07!118;UBERON:0000065!4.72e-07!41;UBERON:0001007!6.26e-07!116;UBERON:0001555!6.26e-07!116;UBERON:0007026!6.26e-07!116;UBERON:0001004!7.38e-07!42
|tfbs_overrepresentation_for_novel_motifs=0.653885,0.62037,0.282026,0.118279,0.0375683,0.126473,0.538273,0.339268,0.364548,0.514602,0.154519,0.51908,0.569961,0.558008,0.165983,0,0.88698,0.0350587,0.779971,0.553915,0.234822,1.25327,1.05992,0.614199,0.609268,0.209658,0.13702,0.847446,0.438605,1.06928,0.408389,0.416414,0.587062,0.2343,1.04451,0.219075,0.304603,0.513348,0.108255,0.408915,0.335087,0.824637,0.103389,0.168167,0.689276,0.729854,0.271716,0.148281,0.0106876,0.0548502,0.319672,1.20905,0.499975,0.538915,0.554419,1.08144,0.0584059,0.498914,0.258637,0.566281,1.0329,1.23477,0.0804985,0.310832,0.20328,2.46068,0.678037,1.00855,0.395762,0.867464,0.547195,0.0689862,0.244404,0.584436,0.946234,1.55136,0.234136,1.33919,0.38541,0.0679477,0.358206,0.347414,0.234292,0.161313,0.48244,1.14698,0.130721,0.18408,0.275409,1.16606,0.74267,0.486763,0.427209,0.0395006,0.480156,0.0202823,0.559504,0.429584,0.747888,0.266292,0.128784,0.416179,0.523506,0.8571,0.855238,0.823515,0.961759,0.145827,0.526859,0.874904,0.636848,0.525078,0.241499,0.157745,0.749248,0.142314,1.49915,0.767099,0.334542,0.546827,0.589296,0.294572,0.210922,0.262524,0.800032,1.00844,0.551377,0.421488,0.67664,1.0077,0.508573,0.366432,0.649498,0.205008,0.769462,0.216471,0.100083,0.418217,0.723554,1.52843,1.13499,0.682379,0.219341,0.425235,0.31422,0.416785,0.274066,1.4892,0.332285,0.976125,0.340986,0.305475,0.540306,0.724307,0.590347,0.613593,0.229288,0.711495,0.0944954,2.2419,0.732404,0.481698,1.78626,0.631413,0.311631,0.199302,0.302433,0.516562,4.10385
|tfbs_overrepresentation_jaspar=MA0003.1;1.68721,MA0004.1;0.118549,MA0006.1;0.658229,MA0007.1;0.356106,MA0009.1;0.438777,MA0014.1;1.23141,MA0017.1;0.0511807,MA0019.1;0.790934,MA0024.1;0.401898,MA0025.1;1.55622,MA0027.1;2.02409,MA0028.1;2.01624,MA0029.1;0.383872,MA0030.1;0.389298,MA0031.1;0.360121,MA0038.1;0.209603,MA0040.1;0.449452,MA0041.1;0.0795363,MA0042.1;0.0734808,MA0043.1;0.522621,MA0046.1;0.469568,MA0048.1;1.22054,MA0050.1;0.435264,MA0051.1;0.617538,MA0052.1;0.456356,MA0055.1;0.439076,MA0056.1;0,MA0057.1;0.590066,MA0058.1;0.24722,MA0059.1;0.945113,MA0060.1;2.29103,MA0061.1;2.06337,MA0063.1;0,MA0066.1;0.20204,MA0067.1;0.748059,MA0068.1;0.40797,MA0069.1;0.456647,MA0070.1;0.448343,MA0071.1;0.140522,MA0072.1;0.44111,MA0073.1;1.72831,MA0074.1;0.526923,MA0076.1;2.26621,MA0077.1;0.422739,MA0078.1;0.239324,MA0081.1;0.0869359,MA0083.1;0.521922,MA0084.1;1.0607,MA0087.1;0.484199,MA0088.1;0.130249,MA0089.1;0,MA0090.1;0.100075,MA0091.1;0.125983,MA0092.1;0.100239,MA0093.1;0.181765,MA0095.1;0,MA0098.1;0,MA0100.1;0.508591,MA0101.1;2.61573,MA0103.1;0.203213,MA0105.1;1.21313,MA0106.1;0.685785,MA0107.1;2.74682,MA0108.2;2.29183,MA0109.1;0,MA0111.1;0.348856,MA0113.1;0.224694,MA0114.1;0.265028,MA0115.1;0.525089,MA0116.1;1.02179,MA0117.1;0.496768,MA0119.1;0.275337,MA0122.1;1.27963,MA0124.1;0.698593,MA0125.1;0.630583,MA0130.1;0,MA0131.1;0.78304,MA0132.1;0,MA0133.1;0,MA0135.1;0.554905,MA0136.1;0.191208,MA0139.1;0.329061,MA0140.1;0.50841,MA0141.1;0.0633664,MA0142.1;0.34839,MA0143.1;0.665806,MA0144.1;0.111883,MA0145.1;0.414538,MA0146.1;1.49808,MA0147.1;0.541171,MA0148.1;0.401483,MA0149.1;0.0827548,MA0062.2;2.97286,MA0035.2;0.173482,MA0039.2;2.46861,MA0138.2;0.281269,MA0002.2;0.0134937,MA0137.2;0.223304,MA0104.2;0.375225,MA0047.2;0.209072,MA0112.2;1.3933,MA0065.2;0.264546,MA0150.1;0.110236,MA0151.1;0,MA0152.1;0.209147,MA0153.1;0.569763,MA0154.1;0.64506,MA0155.1;0.491393,MA0156.1;0.464199,MA0157.1;0.863107,MA0158.1;0,MA0159.1;0.133167,MA0160.1;0.129493,MA0161.1;0,MA0162.1;2.03781,MA0163.1;1.6014,MA0164.1;1.06464,MA0080.2;0.197063,MA0018.2;0.575122,MA0099.2;0.758369,MA0079.2;4.82848,MA0102.2;1.11159,MA0258.1;0.240529,MA0259.1;0.50878,MA0442.1;0
}}

Latest revision as of 15:05, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:12912536..12912606,-p@chr10:12912536..12912606
-
Mm9::chr10:62486081..62486100,+p@chr10:62486081..62486100
+
Mm9::chr11:69223942..69223955,-p@chr11:69223942..69223955
-
Mm9::chr11:69224857..69224885,+p@chr11:69224857..69224885
+
Mm9::chr11:98064472..98064487,-p@chr11:98064472..98064487
-
Mm9::chr11:98820837..98820841,-p@chr11:98820837..98820841
-
Mm9::chr12:56590796..56590811,-p@chr12:56590796..56590811
-
Mm9::chr15:101077003..101077018,+p@chr15:101077003..101077018
+
Mm9::chr16:55822241..55822258,-p1@Nfkbiz
Mm9::chr16:94792724..94792748,-p@chr16:94792724..94792748
-
Mm9::chr18:35091545..35091574,-p2@Etf1
Mm9::chr19:46378880..46378896,+p8@Nfkb2
Mm9::chr19:46379032..46379054,-p@chr19:46379032..46379054
-
Mm9::chr1:182781262..182781303,+p1@BC031781
Mm9::chr3:65762096..65762111,-p1@Ccnl1
Mm9::chr4:33335475..33335493,-p1@Pnrc1
Mm9::chr5:22938641..22938646,+p@chr5:22938641..22938646
+
Mm9::chr6:56664952..56664965,+p4@Avl9
Mm9::chr8:72240726..72240742,-p3@Zfp869
Mm9::chr8:87186740..87186758,-p1@Ier2
Mm9::chr8:87502000..87502015,-p@chr8:87502000..87502015
-
Mm9::chr8:87502350..87502362,-p2@Junb
Mm9::chr8:87502423..87502439,-p4@Junb
Mm9::chr8:87502608..87502623,-p1@Junb
Mm9::chrX:48371786..48371860,-p@chrX:48371786..48371860
-


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:0002266follicular dendritic cell activation0.018015548174587
GO:0002268follicular dendritic cell differentiation0.018015548174587
GO:0016149translation release factor activity, codon specific0.018015548174587
GO:0010467gene expression0.018015548174587
GO:0008023transcription elongation factor complex0.018015548174587
GO:0008079translation termination factor activity0.018015548174587
GO:0006415translational termination0.018015548174587
GO:0003747translation release factor activity0.018015548174587
GO:0006355regulation of transcription, DNA-dependent0.0187493882502284
GO:0003700transcription factor activity0.0187493882502284
GO:0002467germinal center formation0.0187493882502284
GO:0006351transcription, DNA-dependent0.0187493882502284
GO:0032774RNA biosynthetic process0.0187493882502284
GO:0045449regulation of transcription0.0187493882502284
GO:0048536spleen development0.0187493882502284
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0187493882502284
GO:0006350transcription0.0187493882502284
GO:0010468regulation of gene expression0.0200238177225507
GO:0031323regulation of cellular metabolic process0.0215902506335981
GO:0043624cellular protein complex disassembly0.0215902506335981
GO:0043241protein complex disassembly0.0217480607147832
GO:0019222regulation of metabolic process0.0217480607147832
GO:0032984macromolecular complex disassembly0.0218959546766158
GO:0016070RNA metabolic process0.0219455121922195
GO:0048535lymph node development0.0244488528490187
GO:0051726regulation of cell cycle0.0261174403194484
GO:0022411cellular component disassembly0.0292719506150735
GO:0003676nucleic acid binding0.0394693602620986
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0498253690261291



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 cell3.06e-1332
hematopoietic oligopotent progenitor cell3.06e-1332
hematopoietic stem cell3.06e-1332
angioblastic mesenchymal cell3.06e-1332
hematopoietic multipotent progenitor cell3.06e-1332
connective tissue cell8.13e-1146
mesenchymal cell8.13e-1146
hematopoietic lineage restricted progenitor cell8.11e-1025
epithelial cell2.13e-0925
lymphoid lineage restricted progenitor cell3.34e-0912
leukocyte9.22e-0917
nongranular leukocyte9.22e-0917
nucleate cell1.08e-0816
lymphocyte1.75e-0813
common lymphoid progenitor1.75e-0813
T cell1.94e-0811
pro-T cell1.94e-0811
mature alpha-beta T cell6.19e-089
alpha-beta T cell6.19e-089
immature T cell6.19e-089
mature T cell6.19e-089
immature alpha-beta T cell6.19e-089
motile cell6.52e-0854
CD4-positive, alpha-beta T cell3.18e-078
endodermal cell8.82e-0720

Uber Anatomy
Ontology termp-valuen
connective tissue8.13e-1146
unilaminar epithelium5.69e-0966
mucosa3.48e-0815
simple columnar epithelium1.13e-0711
hemolymphoid system1.36e-0748
immune system1.36e-0748
intestinal mucosa2.72e-0713
anatomical wall2.72e-0713
wall of intestine2.72e-0713
gastrointestinal system mucosa2.72e-0713
endoderm-derived structure4.66e-07118
endoderm4.66e-07118
presumptive endoderm4.66e-07118
respiratory tract4.72e-0741
digestive system6.26e-07116
digestive tract6.26e-07116
primitive gut6.26e-07116
respiratory system7.38e-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)
MA0003.11.68721
MA0004.10.118549
MA0006.10.658229
MA0007.10.356106
MA0009.10.438777
MA0014.11.23141
MA0017.10.0511807
MA0019.10.790934
MA0024.10.401898
MA0025.11.55622
MA0027.12.02409
MA0028.12.01624
MA0029.10.383872
MA0030.10.389298
MA0031.10.360121
MA0038.10.209603
MA0040.10.449452
MA0041.10.0795363
MA0042.10.0734808
MA0043.10.522621
MA0046.10.469568
MA0048.11.22054
MA0050.10.435264
MA0051.10.617538
MA0052.10.456356
MA0055.10.439076
MA0056.10
MA0057.10.590066
MA0058.10.24722
MA0059.10.945113
MA0060.12.29103
MA0061.12.06337
MA0063.10
MA0066.10.20204
MA0067.10.748059
MA0068.10.40797
MA0069.10.456647
MA0070.10.448343
MA0071.10.140522
MA0072.10.44111
MA0073.11.72831
MA0074.10.526923
MA0076.12.26621
MA0077.10.422739
MA0078.10.239324
MA0081.10.0869359
MA0083.10.521922
MA0084.11.0607
MA0087.10.484199
MA0088.10.130249
MA0089.10
MA0090.10.100075
MA0091.10.125983
MA0092.10.100239
MA0093.10.181765
MA0095.10
MA0098.10
MA0100.10.508591
MA0101.12.61573
MA0103.10.203213
MA0105.11.21313
MA0106.10.685785
MA0107.12.74682
MA0108.22.29183
MA0109.10
MA0111.10.348856
MA0113.10.224694
MA0114.10.265028
MA0115.10.525089
MA0116.11.02179
MA0117.10.496768
MA0119.10.275337
MA0122.11.27963
MA0124.10.698593
MA0125.10.630583
MA0130.10
MA0131.10.78304
MA0132.10
MA0133.10
MA0135.10.554905
MA0136.10.191208
MA0139.10.329061
MA0140.10.50841
MA0141.10.0633664
MA0142.10.34839
MA0143.10.665806
MA0144.10.111883
MA0145.10.414538
MA0146.11.49808
MA0147.10.541171
MA0148.10.401483
MA0149.10.0827548
MA0062.22.97286
MA0035.20.173482
MA0039.22.46861
MA0138.20.281269
MA0002.20.0134937
MA0137.20.223304
MA0104.20.375225
MA0047.20.209072
MA0112.21.3933
MA0065.20.264546
MA0150.10.110236
MA0151.10
MA0152.10.209147
MA0153.10.569763
MA0154.10.64506
MA0155.10.491393
MA0156.10.464199
MA0157.10.863107
MA0158.10
MA0159.10.133167
MA0160.10.129493
MA0161.10
MA0162.12.03781
MA0163.11.6014
MA0164.11.06464
MA0080.20.197063
MA0018.20.575122
MA0099.20.758369
MA0079.24.82848
MA0102.21.11159
MA0258.10.240529
MA0259.10.50878
MA0442.10
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