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MCL coexpression mm9:776: Difference between revisions

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{{MCL_coexpression_mm9
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constituent of ribosome;1.12158341245474e-09;67671,67115,67427,67186,26961!GO:0005840;ribosome;1.12158341245474e-09;67671,67115,67427,67186,26961!GO:0006412;translation;8.64843970314163e-08;67671,67115,67427,67186,26961!GO:0030529;ribonucleoprotein complex;8.64843970314163e-08;67671,67115,67427,67186,26961!GO:0009059;macromolecule biosynthetic process;4.38474181368054e-07;67671,67115,67427,67186,26961!GO:0044249;cellular biosynthetic process;1.43704854847439e-06;67671,67115,67427,67186,26961!GO:0009058;biosynthetic process;5.6054167329473e-06;67671,67115,67427,67186,26961!GO:0043232;intracellular non-membrane-bound organelle;1.53399351754213e-05;67671,67115,67427,67186,26961!GO:0043228;non-membrane-bound organelle;1.53399351754213e-05;67671,67115,67427,67186,26961!GO:0032991;macromolecular complex;6.01455326125107e-05;67671,67115,67427,67186,26961!GO:0044267;cellular protein metabolic process;0.000202127295949223;67671,67115,67427,67186,26961!GO:0044260;cellular macromolecule metabolic process;0.000202127295949223;67671,67115,67427,67186,26961!GO:0010467;gene expression;0.000202127295949223;67671,67115,67427,67186,26961!GO:0005830;cytosolic ribosome (sensu Eukaryota);0.000202127295949223;67427,26961!GO:0019538;protein metabolic process;0.000202848986937148;67671,67115,67427,67186,26961!GO:0033279;ribosomal subunit;0.000296038486067175;67427,26961!GO:0044444;cytoplasmic part;0.000325187293197688;67671,67115,67427,67186,26961!GO:0044445;cytosolic part;0.000606120219334295;67427,26961!GO:0005737;cytoplasm;0.00444001011736896;67671,67115,67427,67186,26961!GO:0043170;macromolecule metabolic process;0.00444001011736896;67671,67115,67427,67186,26961!GO:0005842;cytosolic large ribosomal subunit (sensu Eukaryota);0.00492637565283138;26961!GO:0005829;cytosol;0.00625365607878693;67427,26961!GO:0005843;cytosolic small ribosomal subunit (sensu Eukaryota);0.00699304871529693;67427!GO:0044238;primary metabolic process;0.00740623914031388;67671,67115,67427,67186,26961!GO:0044237;cellular metabolic process;0.00740623914031388;67671,67115,67427,67186,26961!GO:0019843;rRNA binding;0.0101529563835987;26961!GO:0003723;RNA binding;0.0118358102948665;67427,26961!GO:0015935;small ribosomal subunit;0.0118358102948665;67427!GO:0043229;intracellular organelle;0.0118358102948665;67671,67115,67427,67186,26961!GO:0043226;organelle;0.0118358102948665;67671,67115,67427,67186,26961!GO:0015934;large ribosomal subunit;0.0118358102948665;26961!GO:0006414;translational elongation;0.0164570234412212;67186!GO:0043284;biopolymer biosynthetic process;0.0225029067506786;67186!GO:0044424;intracellular part;0.0257399456334986;67671,67115,67427,67186,26961!GO:0005622;intracellular;0.0296374758110184;67671,67115,67427,67186,26961!|ontology_enrichment_celltype=CL:0000548!7.11e-29!115;CL:0000255!7.11e-29!115;CL:0002371!3.08e-27!118;CL:0000034!8.20e-27!97;CL:0000723!4.56e-24!91;CL:0000048!4.56e-24!91;CL:0000219!7.45e-23!54;CL:0002320!4.51e-20!46;CL:0000134!4.51e-20!46;CL:0000988!4.14e-18!32;CL:0002032!4.14e-18!32;CL:0000037!4.14e-18!32;CL:0000566!4.14e-18!32;CL:0000837!4.14e-18!32;CL:0002031!7.00e-15!25;CL:0000049!6.29e-11!19;CL:0000738!4.37e-10!17;CL:0002087!4.37e-10!17;CL:0002242!7.88e-10!16;CL:0000763!2.63e-09!16;CL:0000838!1.55e-08!12;CL:0000055!2.19e-08!49;CL:0000542!2.89e-08!13;CL:0000051!2.89e-08!13;CL:0000084!6.70e-08!11;CL:0000827!6.70e-08!11;CL:0000839!1.14e-07!13;CL:0002321!1.65e-07!70;CL:0000791!5.59e-07!9;CL:0000789!5.59e-07!9;CL:0002420!5.59e-07!9;CL:0002419!5.59e-07!9;CL:0000790!5.59e-07!9|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002384!4.51e-20!46;UBERON:0002371!2.59e-09!16;UBERON:0002193!9.40e-08!48;UBERON:0002405!9.40e-08!48;UBERON:0002390!9.65e-08!45;UBERON:0003061!9.65e-08!45|tfbs_overrepresentation_for_novel_motifs=0.93395,0.227469,0.330161,0.394491,0.227651,0.40827,1.24018,0.448965,0.154135,0.573183,0.453212,0.484001,0.449446,0.507558,0.24249,0,0.696644,0.22065,0.829774,0.0703872,0.802917,0.179861,1.26371,0.226287,0.337218,0.534339,0.128175,0.428336,0.268347,0.319094,0.414842,0.796599,0.624261,0.113369,0.681042,0.137663,1.1396,0.480503,0.559915,0.167387,0.224094,0.419787,0.371854,0.244285,0.059071,0.998423,0.618203,0.443479,0.573356,0.271021,0.679429,1.37808,0.30602,0.937018,0.954342,0.514504,0.764433,0.471658,0.384731,2.20234,0.776777,0.569793,0.163832,0.668331,1.30341,0.708248,1.08987,1.43807,0.772155,1.29123,0.840217,0.151245,0.424998,0.987652,0.371787,0.107966,0.113315,0.607043,0.759798,0.299972,0.463363,0.713779,0.568383,0.436063,0.873141,1.33784,0.231102,0.657454,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.551605,0.515495,0.14449,0.812053,0.618454,0.585565,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.821842,0.297733,0.919252,0.921485,0.301014,0.458194,1.16629,0.222515,0.795864,0.398075,0.697928,0.597328,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.663857,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.362565,1.0797,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,1.613,0.420221,0.621266,1.92834,0.364791,1.2115,0.665499,0.659481,0.938577,0.178329,0.526881,1.01974,0.561556,0.705025,0.352329,0.950885,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.442118|tfbs_overrepresentation_jaspar=MA0003.1;0.170768,MA0004.1;1.02263,MA0006.1;0.670874,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.119217,MA0017.1;0.26239,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;3.64201,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.589612,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.0198867,MA0056.1;0,MA0057.1;0.549903,MA0058.1;0.823526,MA0059.1;0.316585,MA0060.1;0.169058,MA0061.1;0.56663,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.266547,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;2.9934e-06,MA0074.1;0.488775,MA0076.1;5.91592,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;1.60954,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;1.5772,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.709711,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.720048,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.441109,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.77191,MA0146.1;0.77944,MA0147.1;1.12076,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;6.35383,MA0035.2;0.482026,MA0039.2;0.618828,MA0138.2;0.630612,MA0002.2;0.145685,MA0137.2;0.287486,MA0104.2;0.476119,MA0047.2;0.533516,MA0112.2;0.442124,MA0065.2;0.200864,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.581988,MA0155.1;0.490492,MA0156.1;0.763978,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.0672805,MA0163.1;0.160428,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.13055,MA0102.2;1.5442,MA0258.1;0.533988,MA0259.1;0.571417,MA0442.1;0}}
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|gostat_on_MCL_coexpression=GO:0003735;structural constituent of ribosome;1.12158341245474e-09;67671,67115,67427,67186,26961!GO:0005840;ribosome;1.12158341245474e-09;67671,67115,67427,67186,26961!GO:0006412;translation;8.64843970314163e-08;67671,67115,67427,67186,26961!GO:0030529;ribonucleoprotein complex;8.64843970314163e-08;67671,67115,67427,67186,26961!GO:0009059;macromolecule biosynthetic process;4.38474181368054e-07;67671,67115,67427,67186,26961!GO:0044249;cellular biosynthetic process;1.43704854847439e-06;67671,67115,67427,67186,26961!GO:0009058;biosynthetic process;5.6054167329473e-06;67671,67115,67427,67186,26961!GO:0043232;intracellular non-membrane-bound organelle;1.53399351754213e-05;67671,67115,67427,67186,26961!GO:0043228;non-membrane-bound organelle;1.53399351754213e-05;67671,67115,67427,67186,26961!GO:0032991;macromolecular complex;6.01455326125107e-05;67671,67115,67427,67186,26961!GO:0044267;cellular protein metabolic process;0.000202127295949223;67671,67115,67427,67186,26961!GO:0044260;cellular macromolecule metabolic process;0.000202127295949223;67671,67115,67427,67186,26961!GO:0010467;gene expression;0.000202127295949223;67671,67115,67427,67186,26961!GO:0005830;cytosolic ribosome (sensu Eukaryota);0.000202127295949223;67427,26961!GO:0019538;protein metabolic process;0.000202848986937148;67671,67115,67427,67186,26961!GO:0033279;ribosomal subunit;0.000296038486067175;67427,26961!GO:0044444;cytoplasmic part;0.000325187293197688;67671,67115,67427,67186,26961!GO:0044445;cytosolic part;0.000606120219334295;67427,26961!GO:0005737;cytoplasm;0.00444001011736896;67671,67115,67427,67186,26961!GO:0043170;macromolecule metabolic process;0.00444001011736896;67671,67115,67427,67186,26961!GO:0005842;cytosolic large ribosomal subunit (sensu Eukaryota);0.00492637565283138;26961!GO:0005829;cytosol;0.00625365607878693;67427,26961!GO:0005843;cytosolic small ribosomal subunit (sensu Eukaryota);0.00699304871529693;67427!GO:0044238;primary metabolic process;0.00740623914031388;67671,67115,67427,67186,26961!GO:0044237;cellular metabolic process;0.00740623914031388;67671,67115,67427,67186,26961!GO:0019843;rRNA binding;0.0101529563835987;26961!GO:0003723;RNA binding;0.0118358102948665;67427,26961!GO:0015935;small ribosomal subunit;0.0118358102948665;67427!GO:0043229;intracellular organelle;0.0118358102948665;67671,67115,67427,67186,26961!GO:0043226;organelle;0.0118358102948665;67671,67115,67427,67186,26961!GO:0015934;large ribosomal subunit;0.0118358102948665;26961!GO:0006414;translational elongation;0.0164570234412212;67186!GO:0043284;biopolymer biosynthetic process;0.0225029067506786;67186!GO:0044424;intracellular part;0.0257399456334986;67671,67115,67427,67186,26961!GO:0005622;intracellular;0.0296374758110184;67671,67115,67427,67186,26961!
}}

Latest revision as of 15:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:114529884..114529921,+p1@Rpl38
Mm9::chr15:76734500..76734522,+p1@Rpl8
Mm9::chr17:34092603..34092631,-p1@Gm10260
p1@Rps18
Mm9::chr1:72757833..72757870,+p1@Gm14173
p1@Rpl37a
Mm9::chr2:179992110..179992133,+p1@Gm5963
p1@Rps21
Mm9::chr4:3762742..3762749,-p1@Rps20
Mm9::chr7:148633544..148633554,+p1@Rplp2
Mm9::chr8:105389768..105389776,-p1@Gm8730
Mm9::chr9:120480615..120480639,+p1@Rpl14


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:0003735structural constituent of ribosome1.12158341245474e-09
GO:0005840ribosome1.12158341245474e-09
GO:0006412translation8.64843970314163e-08
GO:0030529ribonucleoprotein complex8.64843970314163e-08
GO:0009059macromolecule biosynthetic process4.38474181368054e-07
GO:0044249cellular biosynthetic process1.43704854847439e-06
GO:0009058biosynthetic process5.6054167329473e-06
GO:0043232intracellular non-membrane-bound organelle1.53399351754213e-05
GO:0043228non-membrane-bound organelle1.53399351754213e-05
GO:0032991macromolecular complex6.01455326125107e-05
GO:0044267cellular protein metabolic process0.000202127295949223
GO:0044260cellular macromolecule metabolic process0.000202127295949223
GO:0010467gene expression0.000202127295949223
GO:0005830cytosolic ribosome (sensu Eukaryota)0.000202127295949223
GO:0019538protein metabolic process0.000202848986937148
GO:0033279ribosomal subunit0.000296038486067175
GO:0044444cytoplasmic part0.000325187293197688
GO:0044445cytosolic part0.000606120219334295
GO:0005737cytoplasm0.00444001011736896
GO:0043170macromolecule metabolic process0.00444001011736896
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)0.00492637565283138
GO:0005829cytosol0.00625365607878693
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.00699304871529693
GO:0044238primary metabolic process0.00740623914031388
GO:0044237cellular metabolic process0.00740623914031388
GO:0019843rRNA binding0.0101529563835987
GO:0003723RNA binding0.0118358102948665
GO:0015935small ribosomal subunit0.0118358102948665
GO:0043229intracellular organelle0.0118358102948665
GO:0043226organelle0.0118358102948665
GO:0015934large ribosomal subunit0.0118358102948665
GO:0006414translational elongation0.0164570234412212
GO:0043284biopolymer biosynthetic process0.0225029067506786
GO:0044424intracellular part0.0257399456334986
GO:0005622intracellular0.0296374758110184



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
animal cell7.11e-29115
eukaryotic cell7.11e-29115
somatic cell3.08e-27118
stem cell8.20e-2797
somatic stem cell4.56e-2491
multi fate stem cell4.56e-2491
motile cell7.45e-2354
connective tissue cell4.51e-2046
mesenchymal cell4.51e-2046
hematopoietic cell4.14e-1832
hematopoietic oligopotent progenitor cell4.14e-1832
hematopoietic stem cell4.14e-1832
angioblastic mesenchymal cell4.14e-1832
hematopoietic multipotent progenitor cell4.14e-1832
hematopoietic lineage restricted progenitor cell7.00e-1525
common myeloid progenitor6.29e-1119
leukocyte4.37e-1017
nongranular leukocyte4.37e-1017
nucleate cell7.88e-1016
myeloid cell2.63e-0916
lymphoid lineage restricted progenitor cell1.55e-0812
non-terminally differentiated cell2.19e-0849
lymphocyte2.89e-0813
common lymphoid progenitor2.89e-0813
T cell6.70e-0811
pro-T cell6.70e-0811
myeloid lineage restricted progenitor cell1.14e-0713
embryonic cell1.65e-0770
mature alpha-beta T cell5.59e-079
alpha-beta T cell5.59e-079
immature T cell5.59e-079
mature T cell5.59e-079
immature alpha-beta T cell5.59e-079

Uber Anatomy
Ontology termp-valuen
connective tissue4.51e-2046
bone marrow2.59e-0916
hemolymphoid system9.40e-0848
immune system9.40e-0848
hematopoietic system9.65e-0845
blood island9.65e-0845


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)
MA0003.10.170768
MA0004.11.02263
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.10.119217
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.13.64201
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.589612
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.0198867
MA0056.10
MA0057.10.549903
MA0058.10.823526
MA0059.10.316585
MA0060.10.169058
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.266547
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.12.9934e-06
MA0074.10.488775
MA0076.15.91592
MA0077.10.804033
MA0078.10.575205
MA0081.11.60954
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.11.5772
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.709711
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.720048
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.77191
MA0146.10.77944
MA0147.11.12076
MA0148.10.410398
MA0149.10.330018
MA0062.26.35383
MA0035.20.482026
MA0039.20.618828
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.476119
MA0047.20.533516
MA0112.20.442124
MA0065.20.200864
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.490492
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0672805
MA0163.10.160428
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.13055
MA0102.21.5442
MA0258.10.533988
MA0259.10.571417
MA0442.10
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