Personal tools

MCL coexpression mm9:237: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0002346!1.34e-30!64;UBERON:0003075!1.34e-30!64;UBERON:0007284!1.34e-30!64;UBERON:0000073!1.05e-29!54;UBERON:0001049!1.04e-27!52;UBERON:0005068!1.04e-27!52;UBERON:0006241!1.04e-27!52;UBERON:0007135!1.04e-27!52;UBERON:0010371!2.99e-26!73;UBERON:0001016!8.86e-26!75;UBERON:0001017!2.72e-25!73;UBERON:0004121!4.84e-25!95;UBERON:0000924!4.84e-25!95;UBERON:0006601!4.84e-25!95;UBERON:0003056!3.02e-24!49;UBERON:0000955!1.62e-22!47;UBERON:0006238!1.62e-22!47;UBERON:0002616!8.46e-22!46;UBERON:0010314!2.29e-21!92;UBERON:0002020!1.00e-20!34;UBERON:0003080!3.15e-20!40;UBERON:0002780!2.33e-19!39;UBERON:0001890!2.33e-19!39;UBERON:0006240!2.33e-19!39;UBERON:0003528!5.51e-16!29;UBERON:0002791!5.51e-16!29;UBERON:0001893!5.51e-16!29;UBERON:0000956!2.70e-10!21;UBERON:0001869!2.70e-10!21;UBERON:0000203!2.70e-10!21;UBERON:0002021!3.26e-10!10;UBERON:0000411!3.26e-10!10;UBERON:0001950!3.26e-10!10;UBERON:0002619!6.47e-09!17;UBERON:0003076!6.07e-08!12;UBERON:0003057!6.07e-08!12;UBERON:0002240!2.90e-07!6;UBERON:0005174!2.90e-07!6;UBERON:0001137!2.90e-07!6;UBERON:0002420!3.75e-07!8;UBERON:0007245!3.75e-07!8;UBERON:0010009!3.75e-07!8;UBERON:0010011!3.75e-07!8;UBERON:0000454!3.75e-07!8
|ontology_enrichment_uberon=UBERON:0002346!1.34e-30!64;UBERON:0003075!1.34e-30!64;UBERON:0007284!1.34e-30!64;UBERON:0000073!1.05e-29!54;UBERON:0001049!1.04e-27!52;UBERON:0005068!1.04e-27!52;UBERON:0006241!1.04e-27!52;UBERON:0007135!1.04e-27!52;UBERON:0010371!2.99e-26!73;UBERON:0001016!8.86e-26!75;UBERON:0001017!2.72e-25!73;UBERON:0004121!4.84e-25!95;UBERON:0000924!4.84e-25!95;UBERON:0006601!4.84e-25!95;UBERON:0003056!3.02e-24!49;UBERON:0000955!1.62e-22!47;UBERON:0006238!1.62e-22!47;UBERON:0002616!8.46e-22!46;UBERON:0010314!2.29e-21!92;UBERON:0002020!1.00e-20!34;UBERON:0003080!3.15e-20!40;UBERON:0002780!2.33e-19!39;UBERON:0001890!2.33e-19!39;UBERON:0006240!2.33e-19!39;UBERON:0003528!5.51e-16!29;UBERON:0002791!5.51e-16!29;UBERON:0001893!5.51e-16!29;UBERON:0000956!2.70e-10!21;UBERON:0001869!2.70e-10!21;UBERON:0000203!2.70e-10!21;UBERON:0002021!3.26e-10!10;UBERON:0000411!3.26e-10!10;UBERON:0001950!3.26e-10!10;UBERON:0002619!6.47e-09!17;UBERON:0003076!6.07e-08!12;UBERON:0003057!6.07e-08!12;UBERON:0002240!2.90e-07!6;UBERON:0005174!2.90e-07!6;UBERON:0001137!2.90e-07!6;UBERON:0002420!3.75e-07!8;UBERON:0007245!3.75e-07!8;UBERON:0010009!3.75e-07!8;UBERON:0010011!3.75e-07!8;UBERON:0000454!3.75e-07!8
|tfbs_overrepresentation_for_novel_motifs=0.384343,0.0352613,0.144471,0.213815,0.0590063,0.497287,0.104889,0.00292643,0.276028,0.00321295,0.285618,0.0989852,0.624051,0.725079,0.0692062,0,0.227242,0.77646,0.111759,0.31002,0.112337,0.00893652,0.110607,0.0119755,0.349535,0.395728,0.196712,0.254303,0.0200576,0.0529926,0.067173,0.299728,2.30695,0.271358,0.0148828,79.5758,0.133476,0.0972432,0.108318,8.43939,0.152868,0.522569,0.0399019,4.27671,0.0727439,0.0548326,0.175278,0.273217,0.0476321,0.0909817,0.616607,0.140375,0.304948,0.410902,0.425236,0.367773,0.241541,0.092899,0.679403,0.113689,0.284859,0.145755,0.0754323,0.207938,0.120577,0.235321,0.541105,0.859836,0.281425,0.722621,0.0312127,0.0195853,0.0603927,0.453125,0.0090779,0.57912,0.850508,0.971245,0.272308,0.278742,5.41464,0.239205,0.144928,1.43735,0.359152,0.0256378,0.0369392,0.11294,0.178324,1.01435,0.602595,0.363085,0.309353,0.330603,0.00669479,2.66128,0.406006,0.311476,0.175436,8.06732,0.0482794,0.299519,1.81331,0.215832,2.54979,0.243326,0.256395,0.26834,0.0289516,0.0271571,0.370979,0.398154,0.116771,0.0864573,0.608883,1.108,0.00504378,0.0603348,1.20738,4.8574,0.457657,0.194256,0.126502,0.167736,1.5817,0.754951,0.108979,0.304247,0.539782,0.170045,0.383004,0.205841,0.514133,0.121912,0.628232,0.00244215,4.57065,0.0698314,0.584355,1.37293,0.983786,0.545219,0.133089,0.30759,0.605645,2.4478,0.524947,1.33397,0.047831,0.0600404,0.020748,3.0705e-05,1.86624,0.564992,0.12142,0.480377,0.140946,0.0771059,0.0435255,0.707258,0.592794,0.358477,0.27532,0.366734,0.208613,0.374998,0.468292,0.0982188,0.00198914
|tfbs_overrepresentation_for_novel_motifs=0.384343,0.0352613,0.144471,0.213815,0.0590063,0.497287,0.104889,0.00292643,0.276028,0.00321295,0.285618,0.0989852,0.624051,0.725079,0.0692062,0,0.227242,0.77646,0.111759,0.31002,0.112337,0.00893652,0.110607,0.0119755,0.349535,0.395728,0.196712,0.254303,0.0200576,0.0529926,0.067173,0.299728,2.30695,0.271358,0.0148828,79.5758,0.133476,0.0972432,0.108318,8.43939,0.152868,0.522569,0.0399019,4.27671,0.0727439,0.0548326,0.175278,0.273217,0.0476321,0.0909817,0.616607,0.140375,0.304948,0.410902,0.425236,0.367773,0.241541,0.092899,0.679403,0.113689,0.284859,0.145755,0.0754323,0.207938,0.120577,0.235321,0.541105,0.859836,0.281425,0.722621,0.0312127,0.0195853,0.0603927,0.453125,0.0090779,0.57912,0.850508,0.971245,0.272308,0.278742,5.41464,0.239205,0.144928,1.43735,0.359152,0.0256378,0.0369392,0.11294,0.178324,1.01435,0.602595,0.363085,0.309353,0.330603,0.00669479,2.66128,0.406006,0.311476,0.175436,8.06732,0.0482794,0.299519,1.81331,0.215832,2.54979,0.243326,0.256395,0.26834,0.0289516,0.0271571,0.370979,0.398154,0.116771,0.0864573,0.608883,1.108,0.00504378,0.0603348,1.20738,4.8574,0.457657,0.194256,0.126502,0.167736,1.5817,0.754951,0.108979,0.304247,0.539782,0.170045,0.383004,0.205841,0.514133,0.121912,0.628232,0.00244215,4.57065,0.0698314,0.584355,1.37293,0.983786,0.545219,0.133089,0.30759,0.605645,2.4478,0.524947,1.33397,0.047831,0.0600404,0.020748,3.0705e-05,1.86624,0.564992,0.12142,0.480377,0.140946,0.0771059,0.0435255,0.707258,0.592794,0.358477,0.27532,0.366734,0.208613,0.374998,0.468292,0.0982188,0.00198914
|tfbs_overrepresentation_jaspar=MA0003.1;3.37424e-06,MA0004.1;0.0591002,MA0006.1;0.0140831,MA0007.1;0.0536384,MA0009.1;3.24227,MA0014.1;0.0197432,MA0017.1;0.212982,MA0019.1;0.191101,MA0024.1;1.42601,MA0025.1;0.510245,MA0027.1;1.86664,MA0028.1;0.0730902,MA0029.1;0.745712,MA0030.1;0.275727,MA0031.1;0.25021,MA0038.1;1.28582,MA0040.1;0.329301,MA0041.1;0.0344268,MA0042.1;0.030893,MA0043.1;0.395894,MA0046.1;0.347468,MA0048.1;0.000388893,MA0050.1;0.0745234,MA0051.1;0.130333,MA0052.1;0.335523,MA0055.1;0.157523,MA0056.1;0,MA0057.1;2.39764,MA0058.1;0.0291546,MA0059.1;0.0323447,MA0060.1;0.17896,MA0061.1;0.0391257,MA0063.1;0,MA0066.1;0.11962,MA0067.1;0.607746,MA0068.1;0.0312166,MA0069.1;0.335786,MA0070.1;0.328303,MA0071.1;0.257812,MA0072.1;0.321801,MA0073.1;2.36237e-06,MA0074.1;0.101385,MA0076.1;0.0226669,MA0077.1;0.305363,MA0078.1;0.148951,MA0081.1;2.9932,MA0083.1;0.395251,MA0084.1;0.910864,MA0087.1;0.360752,MA0088.1;0.055561,MA0089.1;0,MA0090.1;0.178056,MA0091.1;0.229021,MA0092.1;0.401072,MA0093.1;0.0172904,MA0095.1;0,MA0098.1;0,MA0100.1;0.0958046,MA0101.1;0.139276,MA0103.1;0.0209124,MA0105.1;0.0279902,MA0106.1;0.466516,MA0107.1;0.68868,MA0108.2;0.205936,MA0109.1;0,MA0111.1;0.192705,MA0113.1;0.137307,MA0114.1;0.634231,MA0115.1;0.398164,MA0116.1;0.0662958,MA0117.1;0.372208,MA0119.1;0.139811,MA0122.1;0.388118,MA0124.1;0.560604,MA0125.1;0.496324,MA0130.1;0,MA0131.1;0.188202,MA0132.1;0,MA0133.1;0,MA0135.1;0.425686,MA0136.1;0.726251,MA0139.1;0.0168,MA0140.1;0.0957499,MA0141.1;0.107091,MA0142.1;0.240048,MA0143.1;0.146596,MA0144.1;2.04386,MA0145.1;0.0127105,MA0146.1;0.298608,MA0147.1;0.00888815,MA0148.1;0.0653262,MA0149.1;0.335455,MA0062.2;0.273791,MA0035.2;1.10381,MA0039.2;1.13832e-07,MA0138.2;0.183173,MA0002.2;0.131975,MA0137.2;0.77355,MA0104.2;0.00372163,MA0047.2;0.125063,MA0112.2;0.00385477,MA0065.2;0.125675,MA0150.1;0.0535984,MA0151.1;0,MA0152.1;0.125121,MA0153.1;0.43947,MA0154.1;0.000363185,MA0155.1;0.0456195,MA0156.1;0.45615,MA0157.1;0.218114,MA0158.1;0,MA0159.1;1.41404,MA0160.1;0.235961,MA0161.1;0,MA0162.1;0.000258061,MA0163.1;0.00201546,MA0164.1;0.727093,MA0080.2;2.84498,MA0018.2;0.116511,MA0099.2;0.179217,MA0079.2;0.105779,MA0102.2;0.960792,MA0258.1;0.0322286,MA0259.1;0.0402032,MA0442.1;0
}}
}}

Revision as of 11:24, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:100192609..100192628,-p@chr13:100192609..100192628
-
Mm9::chr14:68704695..68704710,+p@chr14:68704695..68704710
+
Mm9::chr14:68704765..68704777,+p@chr14:68704765..68704777
+
Mm9::chr14:68704851..68704867,-p@chr14:68704851..68704867
-
Mm9::chr14:68705393..68705429,-p@chr14:68705393..68705429
-
Mm9::chr14:68738245..68738248,-p@chr14:68738245..68738248
-
Mm9::chr14:68738345..68738368,-p@chr14:68738345..68738368
-
Mm9::chr14:68738380..68738464,+p@chr14:68738380..68738464
+
Mm9::chr14:68738477..68738488,-p@chr14:68738477..68738488
-
Mm9::chr14:68738545..68738556,-p@chr14:68738545..68738556
-
Mm9::chr14:68738598..68738612,-p@chr14:68738598..68738612
-
Mm9::chr14:68738682..68738750,+p@chr14:68738682..68738750
+
Mm9::chr14:68738766..68738784,-p@chr14:68738766..68738784
-
Mm9::chr14:68738820..68738866,-p@chr14:68738820..68738866
-
Mm9::chr14:68738872..68738899,-p@chr14:68738872..68738899
-
Mm9::chr14:68738878..68738972,+p@chr14:68738878..68738972
+
Mm9::chr14:68738934..68738945,-p@chr14:68738934..68738945
-
Mm9::chr14:68738946..68738957,-p@chr14:68738946..68738957
-
Mm9::chr14:68738978..68739054,+p@chr14:68738978..68739054
+
Mm9::chr14:68739003..68739017,-p@chr14:68739003..68739017
-
Mm9::chr14:68739030..68739042,-p@chr14:68739030..68739042
-
Mm9::chr14:68739123..68739132,-p@chr14:68739123..68739132
-
Mm9::chr14:68739138..68739147,-p@chr14:68739138..68739147
-
Mm9::chr14:68739201..68739215,-p@chr14:68739201..68739215
-
Mm9::chr14:68739376..68739391,-p@chr14:68739376..68739391
-
Mm9::chr14:68739418..68739430,-p@chr14:68739418..68739430
-
Mm9::chr14:68740943..68740970,-p@chr14:68740943..68740970
-
Mm9::chr15:91991841..91991862,+p11@Cntn1
Mm9::chr15:91991895..91991913,+p13@Cntn1
Mm9::chr1:134463580..134463593,-p@chr1:134463580..134463593
-
Mm9::chr2:66279206..66279219,-p3@Scn1a
Mm9::chr3:107699183..107699232,+p4@Gstm5
Mm9::chr6:107479790..107479801,+p2@Lrrn1
Mm9::chr6:30754819..30754824,+p16@uc009bfw.1
Mm9::chrX:117403928..117403942,+p1@Pcdh11x
Mm9::chrX:149078407..149078424,-p10@Shroom2


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:0002089lens morphogenesis in camera-type eye0.019814094486751
GO:0008057eye pigment granule organization and biogenesis0.019814094486751
GO:0043482cellular pigment accumulation0.019814094486751
GO:0043476pigment accumulation0.0297162565983497
GO:0032401establishment of melanosome localization0.0319758323443162
GO:0051905establishment of pigment granule localization0.0319758323443162
GO:0032438melanosome organization and biogenesis0.0319758323443162
GO:0032400melanosome localization0.0319758323443162
GO:0048753pigment granule organization and biogenesis0.0319758323443162
GO:0005874microtubule0.0319758323443162
GO:0051875pigment granule localization0.0319758323443162
GO:0005519cytoskeletal regulatory protein binding0.0319758323443162
GO:0045176apical protein localization0.0319758323443162
GO:0001578microtubule bundle formation0.0333923463558605
GO:0033059cellular pigmentation0.0333923463558605
GO:0008105asymmetric protein localization0.0333923463558605
GO:0051650establishment of vesicle localization0.03435743536712
GO:0030864cortical actin cytoskeleton0.03435743536712
GO:0002088lens development in camera-type eye0.03435743536712
GO:0051648vesicle localization0.0350557751848691
GO:0015630microtubule cytoskeleton0.0350557751848691
GO:0008013beta-catenin binding0.0350557751848691
GO:0006305DNA alkylation0.0370660387790414
GO:0006306DNA methylation0.0370660387790414
GO:0030863cortical cytoskeleton0.038106277368623
GO:0008092cytoskeletal protein binding0.038106277368623
GO:0048593camera-type eye morphogenesis0.038106277368623
GO:0006304DNA modification0.038106277368623
GO:0051656establishment of organelle localization0.0429031570624528
GO:0004364glutathione transferase activity0.0454079412165252
GO:0051015actin filament binding0.0458462077462921
GO:0005913cell-cell adherens junction0.0480988312389123
GO:0051640organelle localization0.0484272292778037
GO:0044448cell cortex part0.0487357391460906



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
CNS neuron (sensu Vertebrata)1.56e-1523
neuroblast (sensu Vertebrata)1.56e-1523
neuron7.14e-1033
neuronal stem cell7.14e-1033
neuroblast7.14e-1033
electrically signaling cell7.14e-1033
electrically responsive cell3.70e-0739
electrically active cell3.70e-0739
ectodermal cell4.14e-0744
neurectodermal cell4.14e-0744
neural cell8.02e-0743

Uber Anatomy
Ontology termp-valuen
neurectoderm1.34e-3064
neural plate1.34e-3064
presumptive neural plate1.34e-3064
regional part of nervous system1.05e-2954
neural tube1.04e-2752
neural rod1.04e-2752
future spinal cord1.04e-2752
neural keel1.04e-2752
ecto-epithelium2.99e-2673
nervous system8.86e-2675
central nervous system2.72e-2573
ectoderm-derived structure4.84e-2595
ectoderm4.84e-2595
presumptive ectoderm4.84e-2595
pre-chordal neural plate3.02e-2449
brain1.62e-2247
future brain1.62e-2247
regional part of brain8.46e-2246
structure with developmental contribution from neural crest2.29e-2192
gray matter1.00e-2034
anterior neural tube3.15e-2040
regional part of forebrain2.33e-1939
forebrain2.33e-1939
future forebrain2.33e-1939
brain grey matter5.51e-1629
regional part of telencephalon5.51e-1629
telencephalon5.51e-1629
cerebral cortex2.70e-1021
cerebral hemisphere2.70e-1021
pallium2.70e-1021
occipital lobe3.26e-1010
visual cortex3.26e-1010
neocortex3.26e-1010
regional part of cerebral cortex6.47e-0917
posterior neural tube6.07e-0812
chordal neural plate6.07e-0812
spinal cord2.90e-076
dorsal region element2.90e-076
dorsum2.90e-076
basal ganglion3.75e-078
nuclear complex of neuraxis3.75e-078
aggregate regional part of brain3.75e-078
collection of basal ganglia3.75e-078
cerebral subcortex3.75e-078


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)
MA0003.13.37424e-06
MA0004.10.0591002
MA0006.10.0140831
MA0007.10.0536384
MA0009.13.24227
MA0014.10.0197432
MA0017.10.212982
MA0019.10.191101
MA0024.11.42601
MA0025.10.510245
MA0027.11.86664
MA0028.10.0730902
MA0029.10.745712
MA0030.10.275727
MA0031.10.25021
MA0038.11.28582
MA0040.10.329301
MA0041.10.0344268
MA0042.10.030893
MA0043.10.395894
MA0046.10.347468
MA0048.10.000388893
MA0050.10.0745234
MA0051.10.130333
MA0052.10.335523
MA0055.10.157523
MA0056.10
MA0057.12.39764
MA0058.10.0291546
MA0059.10.0323447
MA0060.10.17896
MA0061.10.0391257
MA0063.10
MA0066.10.11962
MA0067.10.607746
MA0068.10.0312166
MA0069.10.335786
MA0070.10.328303
MA0071.10.257812
MA0072.10.321801
MA0073.12.36237e-06
MA0074.10.101385
MA0076.10.0226669
MA0077.10.305363
MA0078.10.148951
MA0081.12.9932
MA0083.10.395251
MA0084.10.910864
MA0087.10.360752
MA0088.10.055561
MA0089.10
MA0090.10.178056
MA0091.10.229021
MA0092.10.401072
MA0093.10.0172904
MA0095.10
MA0098.10
MA0100.10.0958046
MA0101.10.139276
MA0103.10.0209124
MA0105.10.0279902
MA0106.10.466516
MA0107.10.68868
MA0108.20.205936
MA0109.10
MA0111.10.192705
MA0113.10.137307
MA0114.10.634231
MA0115.10.398164
MA0116.10.0662958
MA0117.10.372208
MA0119.10.139811
MA0122.10.388118
MA0124.10.560604
MA0125.10.496324
MA0130.10
MA0131.10.188202
MA0132.10
MA0133.10
MA0135.10.425686
MA0136.10.726251
MA0139.10.0168
MA0140.10.0957499
MA0141.10.107091
MA0142.10.240048
MA0143.10.146596
MA0144.12.04386
MA0145.10.0127105
MA0146.10.298608
MA0147.10.00888815
MA0148.10.0653262
MA0149.10.335455
MA0062.20.273791
MA0035.21.10381
MA0039.21.13832e-07
MA0138.20.183173
MA0002.20.131975
MA0137.20.77355
MA0104.20.00372163
MA0047.20.125063
MA0112.20.00385477
MA0065.20.125675
MA0150.10.0535984
MA0151.10
MA0152.10.125121
MA0153.10.43947
MA0154.10.000363185
MA0155.10.0456195
MA0156.10.45615
MA0157.10.218114
MA0158.10
MA0159.11.41404
MA0160.10.235961
MA0161.10
MA0162.10.000258061
MA0163.10.00201546
MA0164.10.727093
MA0080.22.84498
MA0018.20.116511
MA0099.20.179217
MA0079.20.105779
MA0102.20.960792
MA0258.10.0322286
MA0259.10.0402032
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:237&oldid=2573632"