Personal tools

MCL coexpression mm9:553: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0002193!1.10e-23!48;UBERON:0002405!1.10e-23!48;UBERON:0004177!2.53e-23!29;UBERON:0005057!2.53e-23!29;UBERON:0002390!1.65e-20!45;UBERON:0003061!1.65e-20!45;UBERON:0002370!2.79e-18!23;UBERON:0000974!2.79e-18!23;UBERON:0004807!2.79e-18!23;UBERON:0005058!2.79e-18!23;UBERON:0003351!2.79e-18!23;UBERON:0009113!2.79e-18!23;UBERON:0003295!2.79e-18!23;UBERON:0009722!2.79e-18!23;UBERON:0005562!2.79e-18!23;UBERON:0007690!2.79e-18!23;UBERON:0000077!5.30e-18!35;UBERON:0006562!2.86e-17!24;UBERON:0003408!2.86e-17!24;UBERON:0001557!2.86e-17!24;UBERON:0001042!2.86e-17!24;UBERON:0008814!2.86e-17!24;UBERON:0009145!2.86e-17!24;UBERON:0000065!1.36e-16!41;UBERON:0001004!5.23e-16!42;UBERON:0000072!1.07e-14!27;UBERON:0001041!6.80e-13!80;UBERON:0000063!2.79e-11!35;UBERON:0003081!4.69e-10!87;UBERON:0001007!9.41e-10!116;UBERON:0001555!9.41e-10!116;UBERON:0007026!9.41e-10!116;UBERON:0007811!1.28e-09!36;UBERON:0004119!2.12e-09!118;UBERON:0000925!2.12e-09!118;UBERON:0006595!2.12e-09!118;UBERON:0005911!4.19e-09!69;UBERON:0004921!1.14e-08!114;UBERON:0000153!3.33e-07!43
|ontology_enrichment_uberon=UBERON:0002193!1.10e-23!48;UBERON:0002405!1.10e-23!48;UBERON:0004177!2.53e-23!29;UBERON:0005057!2.53e-23!29;UBERON:0002390!1.65e-20!45;UBERON:0003061!1.65e-20!45;UBERON:0002370!2.79e-18!23;UBERON:0000974!2.79e-18!23;UBERON:0004807!2.79e-18!23;UBERON:0005058!2.79e-18!23;UBERON:0003351!2.79e-18!23;UBERON:0009113!2.79e-18!23;UBERON:0003295!2.79e-18!23;UBERON:0009722!2.79e-18!23;UBERON:0005562!2.79e-18!23;UBERON:0007690!2.79e-18!23;UBERON:0000077!5.30e-18!35;UBERON:0006562!2.86e-17!24;UBERON:0003408!2.86e-17!24;UBERON:0001557!2.86e-17!24;UBERON:0001042!2.86e-17!24;UBERON:0008814!2.86e-17!24;UBERON:0009145!2.86e-17!24;UBERON:0000065!1.36e-16!41;UBERON:0001004!5.23e-16!42;UBERON:0000072!1.07e-14!27;UBERON:0001041!6.80e-13!80;UBERON:0000063!2.79e-11!35;UBERON:0003081!4.69e-10!87;UBERON:0001007!9.41e-10!116;UBERON:0001555!9.41e-10!116;UBERON:0007026!9.41e-10!116;UBERON:0007811!1.28e-09!36;UBERON:0004119!2.12e-09!118;UBERON:0000925!2.12e-09!118;UBERON:0006595!2.12e-09!118;UBERON:0005911!4.19e-09!69;UBERON:0004921!1.14e-08!114;UBERON:0000153!3.33e-07!43
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.0867717,0.223558,0.279403,0.848472,0.792702,0.370193,0.566731,0.59395,0.282547,0.331725,0.35958,0.567414,0.381063,0.15081,0,0.557619,0.133477,0.244912,0.286444,0.194751,0.197405,0.38026,0.427399,0.229596,0.405649,0.0651848,0.309422,0.171781,0.384773,0.805906,0.653099,0.131928,0.202991,0.151158,0.0412484,0.125578,0.356403,0.725176,0.309817,0.836384,0.301802,1.2184,0.463442,0.119688,0.270091,0.48361,0.322976,0.282668,0.173974,0.541299,0.429887,0.160439,0.788877,0.805733,0.387424,0.18067,0.348382,0.218496,0.385607,0.634076,0.438439,0.628157,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.277751,0.0186364,0.838198,0.0571922,0.0517462,0.0552358,0.473159,0.617814,1.09058,0.587166,0.573903,0.437131,0.258127,0.72691,0.0240533,0.0297453,0.0444451,0.488122,1.44275,1.0064,0.731688,1.59777,0.440626,0.108477,0.0973538,0.559699,0.667958,0.483845,0.329451,0.396021,1.5718,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,0.201775,0.196131,0.671624,0.773781,0.19888,0.336214,1.01331,0.41985,0.404932,0.282562,0.558838,0.389429,0.843435,0.511336,1.04956,0.472327,1.06644,0.621313,1.74685,0.658832,0.936732,0.875241,0.755703,0.273302,0.907893,0.399614,1.03449,0.0751544,0.700863,0.818556,0.986296,1.80931,1.41113,0.942814,1.07314,0.66306,0.53483,0.302189,0.486482,1.76978,0.253405,0.140226,0.0455135,0.0139939,0.790393,0.101059,0.398786,0.869538,0.430798,0.481451,0.242603,0.251242,0.995609,0.726089,0.621734,0.667363,0.531751,1.01654,0.39393,0.358185,0.171655
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.0867717,0.223558,0.279403,0.848472,0.792702,0.370193,0.566731,0.59395,0.282547,0.331725,0.35958,0.567414,0.381063,0.15081,0,0.557619,0.133477,0.244912,0.286444,0.194751,0.197405,0.38026,0.427399,0.229596,0.405649,0.0651848,0.309422,0.171781,0.384773,0.805906,0.653099,0.131928,0.202991,0.151158,0.0412484,0.125578,0.356403,0.725176,0.309817,0.836384,0.301802,1.2184,0.463442,0.119688,0.270091,0.48361,0.322976,0.282668,0.173974,0.541299,0.429887,0.160439,0.788877,0.805733,0.387424,0.18067,0.348382,0.218496,0.385607,0.634076,0.438439,0.628157,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.277751,0.0186364,0.838198,0.0571922,0.0517462,0.0552358,0.473159,0.617814,1.09058,0.587166,0.573903,0.437131,0.258127,0.72691,0.0240533,0.0297453,0.0444451,0.488122,1.44275,1.0064,0.731688,1.59777,0.440626,0.108477,0.0973538,0.559699,0.667958,0.483845,0.329451,0.396021,1.5718,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,0.201775,0.196131,0.671624,0.773781,0.19888,0.336214,1.01331,0.41985,0.404932,0.282562,0.558838,0.389429,0.843435,0.511336,1.04956,0.472327,1.06644,0.621313,1.74685,0.658832,0.936732,0.875241,0.755703,0.273302,0.907893,0.399614,1.03449,0.0751544,0.700863,0.818556,0.986296,1.80931,1.41113,0.942814,1.07314,0.66306,0.53483,0.302189,0.486482,1.76978,0.253405,0.140226,0.0455135,0.0139939,0.790393,0.101059,0.398786,0.869538,0.430798,0.481451,0.242603,0.251242,0.995609,0.726089,0.621734,0.667363,0.531751,1.01654,0.39393,0.358185,0.171655
|tfbs_overrepresentation_jaspar=MA0003.1;0.0390462,MA0004.1;0.279808,MA0006.1;0.451962,MA0007.1;0.267314,MA0009.1;0.678286,MA0014.1;0.00137258,MA0017.1;0.499735,MA0019.1;0.506787,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;0.155127,MA0029.1;0.616052,MA0030.1;0.622264,MA0031.1;0.588678,MA0038.1;0.405578,MA0040.1;0.690239,MA0041.1;0.218039,MA0042.1;0.598261,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;0.142843,MA0050.1;2.31269,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;1.06788,MA0056.1;0,MA0057.1;0.302463,MA0058.1;0.202403,MA0059.1;0.212009,MA0060.1;0.0941959,MA0061.1;1.76228,MA0063.1;0,MA0066.1;0.395746,MA0067.1;1.01206,MA0068.1;1.749,MA0069.1;0.698271,MA0070.1;0.688999,MA0071.1;0.838726,MA0072.1;0.680902,MA0073.1;1.16238,MA0074.1;0.954464,MA0076.1;0.534535,MA0077.1;1.58726,MA0078.1;0.443468,MA0081.1;0.651709,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;1.72985,MA0088.1;0.204026,MA0089.1;0,MA0090.1;0.251458,MA0091.1;0.290854,MA0092.1;0.70143,MA0093.1;0.161141,MA0095.1;0,MA0098.1;0,MA0100.1;0.353762,MA0101.1;1.83027,MA0103.1;0.174916,MA0105.1;0.0530438,MA0106.1;0.450539,MA0107.1;2.22374,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.263095,MA0113.1;1.088,MA0114.1;0.727901,MA0115.1;0.773793,MA0116.1;0.147513,MA0117.1;0.742722,MA0119.1;0.626271,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;0.502588,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;0.38151,MA0139.1;0.262087,MA0140.1;1.66422,MA0141.1;1.05803,MA0142.1;0.575041,MA0143.1;1.12007,MA0144.1;0.365041,MA0145.1;0.698105,MA0146.1;0.0462894,MA0147.1;0.121834,MA0148.1;0.796977,MA0149.1;0.223436,MA0062.2;0.783196,MA0035.2;0.940904,MA0039.2;0.0682581,MA0138.2;0.495254,MA0002.2;0.0773396,MA0137.2;0.55008,MA0104.2;0.0856657,MA0047.2;0.404891,MA0112.2;0.223965,MA0065.2;0.0897174,MA0150.1;0.737147,MA0151.1;0,MA0152.1;0.404987,MA0153.1;0.822355,MA0154.1;0.139881,MA0155.1;0.258579,MA0156.1;1.02086,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.128669,MA0160.1;0.80274,MA0161.1;0,MA0162.1;0.137604,MA0163.1;0.386747,MA0164.1;0.381832,MA0080.2;2.22871,MA0018.2;0.390455,MA0099.2;0.489441,MA0079.2;0.12524,MA0102.2;1.38728,MA0258.1;0.103004,MA0259.1;0.114734,MA0442.1;0
}}
}}

Revision as of 11:56, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:7552113..7552123,+p4@Zc3h12d
Mm9::chr10:7552124..7552165,+p2@Zc3h12d
Mm9::chr10:77761001..77761011,-p23@Agpat3
Mm9::chr12:102245868..102245883,+p@chr12:102245868..102245883
+
Mm9::chr14:59879040..59879065,-p1@Gm6904
Mm9::chr15:97191565..97191586,+p6@Fam113b
Mm9::chr17:27479398..27479415,+p1@ENSMUST00000151398
p1@uc012anv.1
Mm9::chr1:165993128..165993139,-p@chr1:165993128..165993139
-
Mm9::chr3:142159736..142159753,+p2@Gbp5
Mm9::chr3:142159755..142159768,+p5@Gbp5
Mm9::chr6:129130657..129130674,+p2@Clec2d
Mm9::chr6:99255980..99255988,+p@chr6:99255980..99255988
+
Mm9::chr7:25677212..25677252,-p@chr7:25677212..25677252
-


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:0042270protection from natural killer cell mediated cytotoxicity0.0183938166882631
GO:0045953negative regulation of natural killer cell mediated cytotoxicity0.0183938166882631
GO:0001911negative regulation of leukocyte mediated cytotoxicity0.0183938166882631
GO:0045671negative regulation of osteoclast differentiation0.0183938166882631
GO:0046703natural killer cell lectin-like receptor binding0.0183938166882631
GO:0002762negative regulation of myeloid leukocyte differentiation0.0183938166882631
GO:00038411-acylglycerol-3-phosphate O-acyltransferase activity0.0183938166882631
GO:0042269regulation of natural killer cell mediated cytotoxicity0.0183938166882631
GO:0006955immune response0.0183938166882631
GO:0016411acylglycerol O-acyltransferase activity0.0183938166882631
GO:0042267natural killer cell mediated cytotoxicity0.0183938166882631
GO:0001910regulation of leukocyte mediated cytotoxicity0.0183938166882631
GO:0045670regulation of osteoclast differentiation0.0183938166882631
GO:0031341regulation of cell killing0.0183938166882631
GO:0002228natural killer cell mediated immunity0.0183938166882631
GO:0002761regulation of myeloid leukocyte differentiation0.0202254373957362
GO:0045638negative regulation of myeloid cell differentiation0.0202254373957362
GO:0030316osteoclast differentiation0.0202254373957362
GO:0001909leukocyte mediated cytotoxicity0.0202254373957362
GO:0001906cell killing0.0202254373957362
GO:0002376immune system process0.0240773804173256
GO:0008374O-acyltransferase activity0.0250618638310431
GO:0045637regulation of myeloid cell differentiation0.027959922163863
GO:0002573myeloid leukocyte differentiation0.0306143784178908
GO:0008654phospholipid biosynthetic process0.0425731710633747



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
lymphoid lineage restricted progenitor cell1.69e-1312
mature alpha-beta T cell4.66e-139
alpha-beta T cell4.66e-139
immature T cell4.66e-139
mature T cell4.66e-139
immature alpha-beta T cell4.66e-139
lymphocyte3.23e-1213
common lymphoid progenitor3.23e-1213
hematopoietic lineage restricted progenitor cell3.61e-1225
T cell4.04e-1211
pro-T cell4.04e-1211
CD4-positive, alpha-beta T cell1.01e-118
hematopoietic cell1.81e-0932
hematopoietic oligopotent progenitor cell1.81e-0932
hematopoietic stem cell1.81e-0932
angioblastic mesenchymal cell1.81e-0932
hematopoietic multipotent progenitor cell1.81e-0932
nucleate cell2.39e-0916
thymocyte5.39e-096
double negative thymocyte5.39e-096
naive T cell5.39e-096
double-positive, alpha-beta thymocyte5.39e-096
CD4-positive, alpha-beta thymocyte5.39e-096
naive thymus-derived CD4-positive, alpha-beta T cell5.39e-096
DN4 thymocyte5.39e-096
DN1 thymic pro-T cell5.39e-096
DN2 thymocyte5.39e-096
DN3 thymocyte5.39e-096
immature single positive thymocyte5.39e-096
early T lineage precursor5.39e-096
mature CD4 single-positive thymocyte5.39e-096
resting double-positive thymocyte5.39e-096
double-positive blast5.39e-096
CD69-positive double-positive thymocyte5.39e-096
CD69-positive, CD4-positive single-positive thymocyte5.39e-096
CD4-positive, CD8-intermediate double-positive thymocyte5.39e-096
CD24-positive, CD4 single-positive thymocyte5.39e-096
leukocyte1.27e-0817
nongranular leukocyte1.27e-0817
megakaryocyte progenitor cell8.62e-076
megakaryocyte8.62e-076

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.10e-2348
immune system1.10e-2348
hemopoietic organ2.53e-2329
immune organ2.53e-2329
hematopoietic system1.65e-2045
blood island1.65e-2045
thymus2.79e-1823
neck2.79e-1823
respiratory system epithelium2.79e-1823
hemolymphoid system gland2.79e-1823
pharyngeal epithelium2.79e-1823
thymic region2.79e-1823
pharyngeal gland2.79e-1823
entire pharyngeal arch endoderm2.79e-1823
thymus primordium2.79e-1823
early pharyngeal endoderm2.79e-1823
mixed endoderm/mesoderm-derived structure5.30e-1835
pharynx2.86e-1724
gland of gut2.86e-1724
upper respiratory tract2.86e-1724
chordate pharynx2.86e-1724
pharyngeal arch system2.86e-1724
pharyngeal region of foregut2.86e-1724
respiratory tract1.36e-1641
respiratory system5.23e-1642
segment of respiratory tract1.07e-1427
foregut6.80e-1380
organ segment2.79e-1135
lateral plate mesoderm4.69e-1087
digestive system9.41e-10116
digestive tract9.41e-10116
primitive gut9.41e-10116
craniocervical region1.28e-0936
endoderm-derived structure2.12e-09118
endoderm2.12e-09118
presumptive endoderm2.12e-09118
endo-epithelium4.19e-0969
subdivision of digestive tract1.14e-08114
anterior region of body3.33e-0743


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)
MA0003.10.0390462
MA0004.10.279808
MA0006.10.451962
MA0007.10.267314
MA0009.10.678286
MA0014.10.00137258
MA0017.10.499735
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.155127
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.10.405578
MA0040.10.690239
MA0041.10.218039
MA0042.10.598261
MA0043.10.771094
MA0046.10.712646
MA0048.10.142843
MA0050.12.31269
MA0051.10.413609
MA0052.10.697946
MA0055.11.06788
MA0056.10
MA0057.10.302463
MA0058.10.202403
MA0059.10.212009
MA0060.10.0941959
MA0061.11.76228
MA0063.10
MA0066.10.395746
MA0067.11.01206
MA0068.11.749
MA0069.10.698271
MA0070.10.688999
MA0071.10.838726
MA0072.10.680902
MA0073.11.16238
MA0074.10.954464
MA0076.10.534535
MA0077.11.58726
MA0078.10.443468
MA0081.10.651709
MA0083.10.77033
MA0084.11.33532
MA0087.11.72985
MA0088.10.204026
MA0089.10
MA0090.10.251458
MA0091.10.290854
MA0092.10.70143
MA0093.10.161141
MA0095.10
MA0098.10
MA0100.10.353762
MA0101.11.83027
MA0103.10.174916
MA0105.10.0530438
MA0106.10.450539
MA0107.12.22374
MA0108.20.527977
MA0109.10
MA0111.10.263095
MA0113.11.088
MA0114.10.727901
MA0115.10.773793
MA0116.10.147513
MA0117.10.742722
MA0119.10.626271
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.262087
MA0140.11.66422
MA0141.11.05803
MA0142.10.575041
MA0143.11.12007
MA0144.10.365041
MA0145.10.698105
MA0146.10.0462894
MA0147.10.121834
MA0148.10.796977
MA0149.10.223436
MA0062.20.783196
MA0035.20.940904
MA0039.20.0682581
MA0138.20.495254
MA0002.20.0773396
MA0137.20.55008
MA0104.20.0856657
MA0047.20.404891
MA0112.20.223965
MA0065.20.0897174
MA0150.10.737147
MA0151.10
MA0152.10.404987
MA0153.10.822355
MA0154.10.139881
MA0155.10.258579
MA0156.11.02086
MA0157.10.545026
MA0158.10
MA0159.10.128669
MA0160.10.80274
MA0161.10
MA0162.10.137604
MA0163.10.386747
MA0164.10.381832
MA0080.22.22871
MA0018.20.390455
MA0099.20.489441
MA0079.20.12524
MA0102.21.38728
MA0258.10.103004
MA0259.10.114734
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:553&oldid=2573948"