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MCL coexpression mm9:260: Difference between revisions

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{{MCL_coexpression_mm9
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regulation of cell fate specification;0.0327773654156251;14581!GO:0042659;regulation of cell fate specification;0.0327773654156251;14581!GO:0010453;regulation of cell fate commitment;0.0327773654156251;14581!GO:0009996;negative regulation of cell fate specification;0.0327773654156251;14581!GO:0010454;negative regulation of cell fate commitment;0.0327773654156251;14581!GO:0043154;negative regulation of caspase activity;0.0382809443418322;12633!GO:0007638;mechanosensory behavior;0.0382809443418322;14581!GO:0043066;negative regulation of apoptosis;0.0382809443418322;11800,12633!GO:0043069;negative regulation of programmed cell death;0.0382809443418322;11800,12633!GO:0005522;profilin 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|gostat_on_MCL_coexpression=GO:0042660;positive regulation of cell fate specification;0.0327773654156251;14581!GO:0042659;regulation of cell fate specification;0.0327773654156251;14581!GO:0010453;regulation of cell fate commitment;0.0327773654156251;14581!GO:0009996;negative regulation of cell fate specification;0.0327773654156251;14581!GO:0010454;negative regulation of cell fate commitment;0.0327773654156251;14581!GO:0043154;negative regulation of caspase activity;0.0382809443418322;12633!GO:0007638;mechanosensory behavior;0.0382809443418322;14581!GO:0043066;negative regulation of apoptosis;0.0382809443418322;11800,12633!GO:0043069;negative regulation of programmed cell death;0.0382809443418322;11800,12633!GO:0005522;profilin binding;0.0491283492655764;215280!
|ontology_enrichment_celltype=CL:0000838!5.43e-23!12;CL:0000791!1.30e-21!9;CL:0000789!1.30e-21!9;CL:0002420!1.30e-21!9;CL:0002419!1.30e-21!9;CL:0000790!1.30e-21!9;CL:0000542!4.99e-21!13;CL:0000051!4.99e-21!13;CL:0000084!5.39e-21!11;CL:0000827!5.39e-21!11;CL:0000988!5.26e-20!32;CL:0002032!5.26e-20!32;CL:0000037!5.26e-20!32;CL:0000566!5.26e-20!32;CL:0000837!5.26e-20!32;CL:0000624!2.13e-19!8;CL:0002242!1.30e-16!16;CL:0000738!1.73e-15!17;CL:0002087!1.73e-15!17;CL:0000893!5.39e-15!6;CL:0002489!5.39e-15!6;CL:0000898!5.39e-15!6;CL:0000809!5.39e-15!6;CL:0000810!5.39e-15!6;CL:0000895!5.39e-15!6;CL:0000808!5.39e-15!6;CL:0000894!5.39e-15!6;CL:0000806!5.39e-15!6;CL:0000807!5.39e-15!6;CL:0000805!5.39e-15!6;CL:0002425!5.39e-15!6;CL:0002436!5.39e-15!6;CL:0002427!5.39e-15!6;CL:0002428!5.39e-15!6;CL:0002429!5.39e-15!6;CL:0002433!5.39e-15!6;CL:0002431!5.39e-15!6;CL:0002432!5.39e-15!6;CL:0002320!3.79e-14!46;CL:0000134!3.79e-14!46;CL:0002031!1.37e-13!25;CL:0000219!1.05e-12!54;CL:0000034!1.15e-09!97;CL:0000723!1.32e-07!91;CL:0000048!1.32e-07!91
|ontology_enrichment_disease=DOID:0060100!1.69e-08!3;DOID:4045!1.69e-08!3
|ontology_enrichment_uberon=UBERON:0002384!3.79e-14!46;UBERON:0002193!5.12e-14!48;UBERON:0002405!5.12e-14!48;UBERON:0002370!5.90e-14!23;UBERON:0000974!5.90e-14!23;UBERON:0004807!5.90e-14!23;UBERON:0005058!5.90e-14!23;UBERON:0003351!5.90e-14!23;UBERON:0009113!5.90e-14!23;UBERON:0003295!5.90e-14!23;UBERON:0009722!5.90e-14!23;UBERON:0005562!5.90e-14!23;UBERON:0007690!5.90e-14!23;UBERON:0002390!1.49e-13!45;UBERON:0003061!1.49e-13!45;UBERON:0006562!2.97e-13!24;UBERON:0003408!2.97e-13!24;UBERON:0001557!2.97e-13!24;UBERON:0001042!2.97e-13!24;UBERON:0008814!2.97e-13!24;UBERON:0009145!2.97e-13!24;UBERON:0004177!3.76e-12!29;UBERON:0005057!3.76e-12!29;UBERON:0000072!1.85e-11!27;UBERON:0000077!4.59e-11!35;UBERON:0000063!3.37e-08!35;UBERON:0007811!6.79e-08!36;UBERON:0000065!8.84e-08!41;UBERON:0001004!1.59e-07!42
|tfbs_overrepresentation_for_novel_motifs=0.464314,0.275767,0.183547,0.0755031,0.403653,0.586776,0.401081,0.0859655,0.580724,0.148944,0.340369,0.384124,0.188374,0.418601,0.447409,0,0.259755,0.633675,0.160901,0.17599,0.339522,0.38226,0.417302,0.399688,0.74741,0.458764,0.273327,0.306197,0.0285758,0.291087,0.288134,0.892346,0.193804,0.372412,0.448703,0.105131,0.0147176,0.379077,0.51446,0.418456,0.203128,1.02935,0.830337,0.239128,0.139102,0.248078,0.590335,1.11271,0.345469,0.289613,0.247239,0.166621,0.614824,1.14457,0.465864,0.428923,0.0317166,0.366398,0.249356,0.137352,0.85762,0.172475,0.230012,0.239273,0.44515,0.268299,0.584509,0.907487,0.849558,0.768874,0.0425289,0.357014,0.0513316,0.494514,0.0157647,0.105383,0.11583,0.572368,0.307225,0.62578,0.829399,0.272401,0.171576,0.176026,0.397678,0.150777,0.000101229,0.168746,0.207637,1.06309,0.64713,0.40175,0.34595,0.218578,0.0529479,0.441628,1.06751,0.348163,0.59074,0.125187,0.354785,0.335693,0.436484,0.247661,0.246912,0.0872264,0.290513,0.661283,0.15524,0.342885,0.449672,0.437975,0.629125,0.106977,0.653522,0.64149,0.166513,0.0771455,0.722152,0.345519,0.499163,0.638433,0.461462,1.08366,0.702969,0.310043,0.132139,0.340627,0.58316,0.223308,0.422342,0.252711,0.556974,0.880148,0.673182,0.249312,0.832351,0.296517,0.628575,1.42304,1.03234,0.588705,0.158669,0.910596,0.242322,0.295293,0.206447,1.38398,0.0625146,0.408198,0.0872909,0.00084391,0.452434,0.0465279,0.145874,0.522448,0.500553,0.479846,0.209338,0.481369,0.637161,0.396979,0.835186,0.445014,0.674221,0.859524,0.587533,0.381906,0.26753
|tfbs_overrepresentation_jaspar=MA0003.1;0.0149142,MA0004.1;0.26216,MA0006.1;0.0915448,MA0007.1;0.894156,MA0009.1;0.356735,MA0014.1;0.0464179,MA0017.1;0.272987,MA0019.1;0.221321,MA0024.1;0.322453,MA0025.1;0.553002,MA0027.1;1.91746,MA0028.1;1.50081,MA0029.1;1.49459,MA0030.1;0.836147,MA0031.1;0.775496,MA0038.1;0.458648,MA0040.1;0.366712,MA0041.1;0.0464556,MA0042.1;0.371303,MA0043.1;0.435645,MA0046.1;0.385571,MA0048.1;0.0610475,MA0050.1;0.0934518,MA0051.1;0.155655,MA0052.1;0.373177,MA0055.1;0.263203,MA0056.1;0,MA0057.1;0.472501,MA0058.1;0.156036,MA0059.1;0.168372,MA0060.1;0.424937,MA0061.1;1.91638,MA0063.1;0,MA0066.1;0.442501,MA0067.1;0.652366,MA0068.1;0.926827,MA0069.1;0.975461,MA0070.1;0.365675,MA0071.1;0.641034,MA0072.1;0.358914,MA0073.1;0.0386207,MA0074.1;0.781809,MA0076.1;1.72718,MA0077.1;0.341791,MA0078.1;0.175945,MA0081.1;0.750335,MA0083.1;1.10972,MA0084.1;0.958921,MA0087.1;0.399335,MA0088.1;0.0473616,MA0089.1;0,MA0090.1;0.221633,MA0091.1;0.0815192,MA0092.1;0.0617042,MA0093.1;0.106412,MA0095.1;0,MA0098.1;0,MA0100.1;0.374893,MA0101.1;1.0896,MA0103.1;0.122326,MA0105.1;2.0607,MA0106.1;0.533809,MA0107.1;0.830301,MA0108.2;0.237143,MA0109.1;0,MA0111.1;0.512045,MA0113.1;0.490789,MA0114.1;0.517641,MA0115.1;1.11622,MA0116.1;0.435156,MA0117.1;0.411186,MA0119.1;0.400754,MA0122.1;0.427622,MA0124.1;0.604388,MA0125.1;0.538769,MA0130.1;0,MA0131.1;0.218222,MA0132.1;0,MA0133.1;0,MA0135.1;0.466327,MA0136.1;0.830118,MA0139.1;0.524161,MA0140.1;0.374733,MA0141.1;1.33852,MA0142.1;0.27329,MA0143.1;0.173388,MA0144.1;0.801834,MA0145.1;1.06607,MA0146.1;0.0442898,MA0147.1;0.172105,MA0148.1;0.0829136,MA0149.1;0.183385,MA0062.2;2.54234,MA0035.2;0.381271,MA0039.2;0.119095,MA0138.2;0.212837,MA0002.2;0.784408,MA0137.2;0.585976,MA0104.2;0.0342485,MA0047.2;0.149878,MA0112.2;0.0245567,MA0065.2;0.310259,MA0150.1;0.522782,MA0151.1;0,MA0152.1;0.149941,MA0153.1;0.480495,MA0154.1;0.354879,MA0155.1;0.972646,MA0156.1;2.22073,MA0157.1;0.250083,MA0158.1;0,MA0159.1;0.365833,MA0160.1;1.00658,MA0161.1;0,MA0162.1;0.350434,MA0163.1;0.0905096,MA0164.1;0.134941,MA0080.2;0.833803,MA0018.2;0.433858,MA0099.2;1.77332,MA0079.2;0.164037,MA0102.2;1.0092,MA0258.1;0.0481808,MA0259.1;0.15721,MA0442.1;0
}}

Latest revision as of 14:59, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:59837508..59837512,+p@chr10:59837508..59837512
+
Mm9::chr10:61969030..61969043,-p@chr10:61969030..61969043
-
Mm9::chr11:70464139..70464152,+p@chr11:70464139..70464152
+
Mm9::chr11:82877968..82877973,+p@chr11:82877968..82877973
+
Mm9::chr11:82877992..82878000,+p@chr11:82877992..82878000
+
Mm9::chr15:78402228..78402241,+p@chr15:78402228..78402241
+
Mm9::chr17:21587400..21587411,+p@chr17:21587400..21587411
+
Mm9::chr17:35399747..35399768,+p3@H2-D1
Mm9::chr1:163001536..163001548,-p@chr1:163001536..163001548
-
Mm9::chr1:58770164..58770176,+p4@Cflar
Mm9::chr1:92949614..92949625,-p@chr1:92949614..92949625
-
Mm9::chr1:92950423..92950427,-p@chr1:92950423..92950427
-
Mm9::chr1:92950550..92950569,+p@chr1:92950550..92950569
+
Mm9::chr1:92953199..92953213,+p@chr1:92953199..92953213
+
Mm9::chr1:92953250..92953273,+p@chr1:92953250..92953273
+
Mm9::chr1:92954465..92954475,+p@chr1:92954465..92954475
+
Mm9::chr2:73301971..73301982,-p@chr2:73301971..73301982
-
Mm9::chr2:73323739..73323761,-p12@Wipf1
Mm9::chr2:94278218..94278232,-p2@Api5
Mm9::chr4:8840833..8840836,-p@chr4:8840833..8840836
-
Mm9::chr5:108155037..108155060,-p2@Gfi1
Mm9::chr5:32000704..32000714,-p@chr5:32000704..32000714
-
Mm9::chr5:32436063..32436081,+p@chr5:32436063..32436081
+
Mm9::chr5:32436178..32436190,+p@chr5:32436178..32436190
+
Mm9::chr7:109398056..109398073,-p@chr7:109398056..109398073
-
Mm9::chr7:31203177..31203188,+p@chr7:31203177..31203188
+
Mm9::chr7:31204934..31204968,+p@chr7:31204934..31204968
+
Mm9::chr7:31205383..31205392,-p@chr7:31205383..31205392
-
Mm9::chr7:31206627..31206655,-p@chr7:31206627..31206655
-
Mm9::chr8:129376078..129376081,-p@chr8:129376078..129376081
-
Mm9::chr8:85856266..85856269,-p3@Elmod2
Mm9::chr9:66767453..66767517,-p1@Rab8b


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:0042660positive regulation of cell fate specification0.0327773654156251
GO:0042659regulation of cell fate specification0.0327773654156251
GO:0010453regulation of cell fate commitment0.0327773654156251
GO:0009996negative regulation of cell fate specification0.0327773654156251
GO:0010454negative regulation of cell fate commitment0.0327773654156251
GO:0043154negative regulation of caspase activity0.0382809443418322
GO:0007638mechanosensory behavior0.0382809443418322
GO:0043066negative regulation of apoptosis0.0382809443418322
GO:0043069negative regulation of programmed cell death0.0382809443418322
GO:0005522profilin binding0.0491283492655764



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>disease_data<br>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell5.43e-2312
mature alpha-beta T cell1.30e-219
alpha-beta T cell1.30e-219
immature T cell1.30e-219
mature T cell1.30e-219
immature alpha-beta T cell1.30e-219
lymphocyte4.99e-2113
common lymphoid progenitor4.99e-2113
T cell5.39e-2111
pro-T cell5.39e-2111
hematopoietic cell5.26e-2032
hematopoietic oligopotent progenitor cell5.26e-2032
hematopoietic stem cell5.26e-2032
angioblastic mesenchymal cell5.26e-2032
hematopoietic multipotent progenitor cell5.26e-2032
CD4-positive, alpha-beta T cell2.13e-198
nucleate cell1.30e-1616
leukocyte1.73e-1517
nongranular leukocyte1.73e-1517
thymocyte5.39e-156
double negative thymocyte5.39e-156
naive T cell5.39e-156
double-positive, alpha-beta thymocyte5.39e-156
CD4-positive, alpha-beta thymocyte5.39e-156
naive thymus-derived CD4-positive, alpha-beta T cell5.39e-156
DN4 thymocyte5.39e-156
DN1 thymic pro-T cell5.39e-156
DN2 thymocyte5.39e-156
DN3 thymocyte5.39e-156
immature single positive thymocyte5.39e-156
early T lineage precursor5.39e-156
mature CD4 single-positive thymocyte5.39e-156
resting double-positive thymocyte5.39e-156
double-positive blast5.39e-156
CD69-positive double-positive thymocyte5.39e-156
CD69-positive, CD4-positive single-positive thymocyte5.39e-156
CD4-positive, CD8-intermediate double-positive thymocyte5.39e-156
CD24-positive, CD4 single-positive thymocyte5.39e-156
connective tissue cell3.79e-1446
mesenchymal cell3.79e-1446
hematopoietic lineage restricted progenitor cell1.37e-1325
motile cell1.05e-1254
stem cell1.15e-0997
somatic stem cell1.32e-0791
multi fate stem cell1.32e-0791

Uber Anatomy
Ontology termp-valuen
connective tissue3.79e-1446
hemolymphoid system5.12e-1448
immune system5.12e-1448
thymus5.90e-1423
neck5.90e-1423
respiratory system epithelium5.90e-1423
hemolymphoid system gland5.90e-1423
pharyngeal epithelium5.90e-1423
thymic region5.90e-1423
pharyngeal gland5.90e-1423
entire pharyngeal arch endoderm5.90e-1423
thymus primordium5.90e-1423
early pharyngeal endoderm5.90e-1423
hematopoietic system1.49e-1345
blood island1.49e-1345
pharynx2.97e-1324
gland of gut2.97e-1324
upper respiratory tract2.97e-1324
chordate pharynx2.97e-1324
pharyngeal arch system2.97e-1324
pharyngeal region of foregut2.97e-1324
hemopoietic organ3.76e-1229
immune organ3.76e-1229
segment of respiratory tract1.85e-1127
mixed endoderm/mesoderm-derived structure4.59e-1135
organ segment3.37e-0835
craniocervical region6.79e-0836
respiratory tract8.84e-0841
respiratory system1.59e-0742

Disease
Ontology termp-valuen
musculoskeletal system cancer1.69e-083
muscle cancer1.69e-083


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)
MA0003.10.0149142
MA0004.10.26216
MA0006.10.0915448
MA0007.10.894156
MA0009.10.356735
MA0014.10.0464179
MA0017.10.272987
MA0019.10.221321
MA0024.10.322453
MA0025.10.553002
MA0027.11.91746
MA0028.11.50081
MA0029.11.49459
MA0030.10.836147
MA0031.10.775496
MA0038.10.458648
MA0040.10.366712
MA0041.10.0464556
MA0042.10.371303
MA0043.10.435645
MA0046.10.385571
MA0048.10.0610475
MA0050.10.0934518
MA0051.10.155655
MA0052.10.373177
MA0055.10.263203
MA0056.10
MA0057.10.472501
MA0058.10.156036
MA0059.10.168372
MA0060.10.424937
MA0061.11.91638
MA0063.10
MA0066.10.442501
MA0067.10.652366
MA0068.10.926827
MA0069.10.975461
MA0070.10.365675
MA0071.10.641034
MA0072.10.358914
MA0073.10.0386207
MA0074.10.781809
MA0076.11.72718
MA0077.10.341791
MA0078.10.175945
MA0081.10.750335
MA0083.11.10972
MA0084.10.958921
MA0087.10.399335
MA0088.10.0473616
MA0089.10
MA0090.10.221633
MA0091.10.0815192
MA0092.10.0617042
MA0093.10.106412
MA0095.10
MA0098.10
MA0100.10.374893
MA0101.11.0896
MA0103.10.122326
MA0105.12.0607
MA0106.10.533809
MA0107.10.830301
MA0108.20.237143
MA0109.10
MA0111.10.512045
MA0113.10.490789
MA0114.10.517641
MA0115.11.11622
MA0116.10.435156
MA0117.10.411186
MA0119.10.400754
MA0122.10.427622
MA0124.10.604388
MA0125.10.538769
MA0130.10
MA0131.10.218222
MA0132.10
MA0133.10
MA0135.10.466327
MA0136.10.830118
MA0139.10.524161
MA0140.10.374733
MA0141.11.33852
MA0142.10.27329
MA0143.10.173388
MA0144.10.801834
MA0145.11.06607
MA0146.10.0442898
MA0147.10.172105
MA0148.10.0829136
MA0149.10.183385
MA0062.22.54234
MA0035.20.381271
MA0039.20.119095
MA0138.20.212837
MA0002.20.784408
MA0137.20.585976
MA0104.20.0342485
MA0047.20.149878
MA0112.20.0245567
MA0065.20.310259
MA0150.10.522782
MA0151.10
MA0152.10.149941
MA0153.10.480495
MA0154.10.354879
MA0155.10.972646
MA0156.12.22073
MA0157.10.250083
MA0158.10
MA0159.10.365833
MA0160.11.00658
MA0161.10
MA0162.10.350434
MA0163.10.0905096
MA0164.10.134941
MA0080.20.833803
MA0018.20.433858
MA0099.21.77332
MA0079.20.164037
MA0102.21.0092
MA0258.10.0481808
MA0259.10.15721
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:260&oldid=3072259"