Personal tools

MCL coexpression mm9:401: 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!8.28e-34!64;UBERON:0003075!8.28e-34!64;UBERON:0007284!8.28e-34!64;UBERON:0000073!5.35e-30!54;UBERON:0001017!2.06e-29!73;UBERON:0010371!4.91e-29!73;UBERON:0001016!5.58e-29!75;UBERON:0004121!3.83e-28!95;UBERON:0000924!3.83e-28!95;UBERON:0006601!3.83e-28!95;UBERON:0001049!5.47e-28!52;UBERON:0005068!5.47e-28!52;UBERON:0006241!5.47e-28!52;UBERON:0007135!5.47e-28!52;UBERON:0003056!2.18e-24!49;UBERON:0000955!6.99e-23!47;UBERON:0006238!6.99e-23!47;UBERON:0002020!2.76e-22!34;UBERON:0002616!4.15e-22!46;UBERON:0010314!4.38e-20!92;UBERON:0003080!4.87e-20!40;UBERON:0002780!3.98e-19!39;UBERON:0001890!3.98e-19!39;UBERON:0006240!3.98e-19!39;UBERON:0003528!2.37e-17!29;UBERON:0002791!2.37e-17!29;UBERON:0001893!2.37e-17!29;UBERON:0000956!8.66e-11!21;UBERON:0001869!8.66e-11!21;UBERON:0000203!8.66e-11!21;UBERON:0002619!2.76e-09!17;UBERON:0003076!2.01e-08!12;UBERON:0003057!2.01e-08!12;UBERON:0002021!2.37e-08!10;UBERON:0000411!2.37e-08!10;UBERON:0001950!2.37e-08!10;UBERON:0002420!4.00e-08!8;UBERON:0007245!4.00e-08!8;UBERON:0010009!4.00e-08!8;UBERON:0010011!4.00e-08!8;UBERON:0000454!4.00e-08!8;UBERON:0002240!3.41e-07!6;UBERON:0005174!3.41e-07!6;UBERON:0001137!3.41e-07!6
|ontology_enrichment_uberon=UBERON:0002346!8.28e-34!64;UBERON:0003075!8.28e-34!64;UBERON:0007284!8.28e-34!64;UBERON:0000073!5.35e-30!54;UBERON:0001017!2.06e-29!73;UBERON:0010371!4.91e-29!73;UBERON:0001016!5.58e-29!75;UBERON:0004121!3.83e-28!95;UBERON:0000924!3.83e-28!95;UBERON:0006601!3.83e-28!95;UBERON:0001049!5.47e-28!52;UBERON:0005068!5.47e-28!52;UBERON:0006241!5.47e-28!52;UBERON:0007135!5.47e-28!52;UBERON:0003056!2.18e-24!49;UBERON:0000955!6.99e-23!47;UBERON:0006238!6.99e-23!47;UBERON:0002020!2.76e-22!34;UBERON:0002616!4.15e-22!46;UBERON:0010314!4.38e-20!92;UBERON:0003080!4.87e-20!40;UBERON:0002780!3.98e-19!39;UBERON:0001890!3.98e-19!39;UBERON:0006240!3.98e-19!39;UBERON:0003528!2.37e-17!29;UBERON:0002791!2.37e-17!29;UBERON:0001893!2.37e-17!29;UBERON:0000956!8.66e-11!21;UBERON:0001869!8.66e-11!21;UBERON:0000203!8.66e-11!21;UBERON:0002619!2.76e-09!17;UBERON:0003076!2.01e-08!12;UBERON:0003057!2.01e-08!12;UBERON:0002021!2.37e-08!10;UBERON:0000411!2.37e-08!10;UBERON:0001950!2.37e-08!10;UBERON:0002420!4.00e-08!8;UBERON:0007245!4.00e-08!8;UBERON:0010009!4.00e-08!8;UBERON:0010011!4.00e-08!8;UBERON:0000454!4.00e-08!8;UBERON:0002240!3.41e-07!6;UBERON:0005174!3.41e-07!6;UBERON:0001137!3.41e-07!6
|tfbs_overrepresentation_for_novel_motifs=2.0659,1.80443,1.33525,0.178048,0.0709145,0.188081,0.708527,0.032132,0.32877,1.94794,1.18299,0.24561,0.564861,0.264234,0.0791346,0,1.08407,0.0671461,0.514215,1.66406,0.111207,0.283788,0.263535,0.070175,0.427698,0.285776,0.260094,0.202945,1.07713,0.353285,0.562931,0.512187,0.505999,0.424507,1.44793,0.738124,3.59368,0.680922,0.194199,1.01461,0.243076,1.08493,0.867463,0.0801495,1.07932,0.170437,0.935739,1.15441,0.32395,0.653986,0.408111,0.307229,0.55993,0.641205,0.657376,0.269785,0.330626,0.23598,0.242162,0.268198,0.494318,0.845221,0.637374,1.03032,2.14133,0.433342,0.785371,1.12243,0.490165,0.979213,1.26216,0.919753,1.009,0.6886,2.89655,1.35318,0.692891,0.346003,0.479091,0.113666,0.588345,0.438213,0.31368,0.0300873,0.582029,1.07062,0.931891,1.23462,0.944781,1.2816,0.851763,0.586575,0.523661,0.256716,2.12094,0.0436985,0.555715,0.526183,0.936209,0.498538,0.222463,0.511936,0.625103,0.408622,1.0505,0.196264,0.459578,0.211422,1.79101,2.37957,0.875636,0.626748,0.366686,0.640523,0.858505,0.516755,2.84398,1.02142,0.424276,0.0601654,1.6568,0.380657,0.287218,0.345253,0.910454,0.482363,0.261058,0.517583,0.783932,0.0752496,0.609469,0.5148,0.75595,0.280468,0.879201,0.277969,0.471259,1.71251,0.832159,1.64606,1.25025,0.789841,0.296788,0.521565,1.0384,0.572489,0.358053,1.60668,0.156941,2.48518,1.25243,1.8383,0.642658,0.174823,0.27974,0.718834,0.30804,0.288843,0.14831,0.917139,0.841238,0.581248,0.482758,0.143905,0.39934,0.273933,0.220881,0.244407,1.92944
|tfbs_overrepresentation_for_novel_motifs=2.0659,1.80443,1.33525,0.178048,0.0709145,0.188081,0.708527,0.032132,0.32877,1.94794,1.18299,0.24561,0.564861,0.264234,0.0791346,0,1.08407,0.0671461,0.514215,1.66406,0.111207,0.283788,0.263535,0.070175,0.427698,0.285776,0.260094,0.202945,1.07713,0.353285,0.562931,0.512187,0.505999,0.424507,1.44793,0.738124,3.59368,0.680922,0.194199,1.01461,0.243076,1.08493,0.867463,0.0801495,1.07932,0.170437,0.935739,1.15441,0.32395,0.653986,0.408111,0.307229,0.55993,0.641205,0.657376,0.269785,0.330626,0.23598,0.242162,0.268198,0.494318,0.845221,0.637374,1.03032,2.14133,0.433342,0.785371,1.12243,0.490165,0.979213,1.26216,0.919753,1.009,0.6886,2.89655,1.35318,0.692891,0.346003,0.479091,0.113666,0.588345,0.438213,0.31368,0.0300873,0.582029,1.07062,0.931891,1.23462,0.944781,1.2816,0.851763,0.586575,0.523661,0.256716,2.12094,0.0436985,0.555715,0.526183,0.936209,0.498538,0.222463,0.511936,0.625103,0.408622,1.0505,0.196264,0.459578,0.211422,1.79101,2.37957,0.875636,0.626748,0.366686,0.640523,0.858505,0.516755,2.84398,1.02142,0.424276,0.0601654,1.6568,0.380657,0.287218,0.345253,0.910454,0.482363,0.261058,0.517583,0.783932,0.0752496,0.609469,0.5148,0.75595,0.280468,0.879201,0.277969,0.471259,1.71251,0.832159,1.64606,1.25025,0.789841,0.296788,0.521565,1.0384,0.572489,0.358053,1.60668,0.156941,2.48518,1.25243,1.8383,0.642658,0.174823,0.27974,0.718834,0.30804,0.288843,0.14831,0.917139,0.841238,0.581248,0.482758,0.143905,0.39934,0.273933,0.220881,0.244407,1.92944
|tfbs_overrepresentation_jaspar=MA0003.1;1.65122,MA0004.1;0.178381,MA0006.1;0.952171,MA0007.1;0.168178,MA0009.1;0.535932,MA0014.1;1.89506,MA0017.1;0.0906268,MA0019.1;0.376509,MA0024.1;0.496718,MA0025.1;0.751694,MA0027.1;2.14278,MA0028.1;0.280241,MA0029.1;0.477444,MA0030.1;0.483253,MA0031.1;0.451927,MA0038.1;0.285714,MA0040.1;0.547233,MA0041.1;1.89679,MA0042.1;1.82974,MA0043.1;0.624178,MA0046.1;0.568473,MA0048.1;1.45051,MA0050.1;0.205672,MA0051.1;0.2928,MA0052.1;0.554531,MA0055.1;1.4457,MA0056.1;0,MA0057.1;0.262449,MA0058.1;0.117003,MA0059.1;0.392739,MA0060.1;0.369051,MA0061.1;0.0537092,MA0063.1;0,MA0066.1;0.277072,MA0067.1;0.857286,MA0068.1;0.0481248,MA0069.1;0.554839,MA0070.1;0.54606,MA0071.1;0.592012,MA0072.1;0.538403,MA0073.1;0.0405835,MA0074.1;0.249359,MA0076.1;0.101055,MA0077.1;0.518913,MA0078.1;0.319336,MA0081.1;0.429201,MA0083.1;0.623446,MA0084.1;1.1752,MA0087.1;0.583879,MA0088.1;0.705351,MA0089.1;0,MA0090.1;0.471234,MA0091.1;0.549843,MA0092.1;0.471747,MA0093.1;0.0864726,MA0095.1;0,MA0098.1;0,MA0100.1;0.2406,MA0101.1;0.12981,MA0103.1;0.0964586,MA0105.1;0.672551,MA0106.1;0.325663,MA0107.1;0.093115,MA0108.2;0.395878,MA0109.1;0,MA0111.1;0.494436,MA0113.1;0.302851,MA0114.1;0.0527257,MA0115.1;0.626759,MA0116.1;0.951399,MA0117.1;0.597086,MA0119.1;0.130171,MA0122.1;0.615314,MA0124.1;0.80652,MA0125.1;0.736412,MA0130.1;0,MA0131.1;0.372683,MA0132.1;0,MA0133.1;0,MA0135.1;0.657882,MA0136.1;0.264624,MA0139.1;1.25918,MA0140.1;0.240513,MA0141.1;0.708661,MA0142.1;0.439269,MA0143.1;0.31603,MA0144.1;0.0540242,MA0145.1;0.0816911,MA0146.1;1.27781,MA0147.1;0.215066,MA0148.1;0.189643,MA0149.1;0.823515,MA0062.2;0.0201154,MA0035.2;0.68369,MA0039.2;0.875155,MA0138.2;2.57183,MA0002.2;0.560759,MA0137.2;0.105829,MA0104.2;0.337396,MA0047.2;0.285109,MA0112.2;0.0816855,MA0065.2;0.0821754,MA0150.1;0.168102,MA0151.1;0,MA0152.1;0.285194,MA0153.1;0.67335,MA0154.1;0.494059,MA0155.1;1.9396,MA0156.1;0.100572,MA0157.1;0.411541,MA0158.1;0,MA0159.1;0.0638985,MA0160.1;1.06584,MA0161.1;0,MA0162.1;1.18735,MA0163.1;0.853384,MA0164.1;0.264905,MA0080.2;0.0935932,MA0018.2;2.11047,MA0099.2;0.360735,MA0079.2;1.88076,MA0102.2;1.22663,MA0258.1;0.401444,MA0259.1;0.774997,MA0442.1;0
}}
}}

Revision as of 11:41, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:106575390..106575401,+p2@uc007oyh.1
Mm9::chr12:91051249..91051258,+p4@LOC100505240
p5@Nrxn3
Mm9::chr15:4325574..4325623,+p2@Plcxd3
Mm9::chr1:107253057..107253093,-p2@Rnf152
Mm9::chr1:84692551..84692569,-p2@Dner
Mm9::chr1:84692741..84692753,-p7@Dner
Mm9::chr1:84692757..84692777,-p3@Dner
Mm9::chr3:97692834..97692852,-p14@Pde4dip
Mm9::chr4:154719787..154719798,-p5@Prkcz
Mm9::chr4:49857757..49857759,-p@chr4:49857757..49857759
-
Mm9::chr5:151062497..151062511,+p7@Fry
Mm9::chr5:27231364..27231415,+p5@Dpp6
Mm9::chr5:69732910..69732924,-p2@Kctd8
Mm9::chr5:69732938..69732953,-p3@Kctd8
Mm9::chr6:63206101..63206120,+p3@Grid2
Mm9::chr7:148667927..148667985,+p@chr7:148667927..148667985
+
Mm9::chr9:107302127..107302180,+p1@Cacna2d2
Mm9::chr9:107302189..107302203,+p3@Cacna2d2
Mm9::chr9:64233453..64233464,+p2@Megf11


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:0060134prepulse inhibition0.000470719502175586
GO:0048585negative regulation of response to stimulus0.000470719502175586
GO:0032102negative regulation of response to external stimulus0.000470719502175586
GO:0032101regulation of response to external stimulus0.000604812928979771
GO:0001964startle response0.00088618439085382
GO:0005216ion channel activity0.00103108625907904
GO:0022838substrate specific channel activity0.00103108625907904
GO:0004970ionotropic glutamate receptor activity0.00103108625907904
GO:0022803passive transmembrane transporter activity0.00103108625907904
GO:0015267channel activity0.00103108625907904
GO:0008066glutamate receptor activity0.00488962419320737
GO:0048583regulation of response to stimulus0.00488962419320737
GO:0005261cation channel activity0.00488962419320737
GO:0050905neuromuscular process0.00488962419320737
GO:0015075ion transmembrane transporter activity0.00488962419320737
GO:0022836gated channel activity0.00546079721263632
GO:0043025cell soma0.00578478784144084
GO:0006811ion transport0.00578478784144084
GO:0046873metal ion transmembrane transporter activity0.00578478784144084
GO:0045179apical cortex0.00578478784144084
GO:0022891substrate-specific transmembrane transporter activity0.00578478784144084
GO:0048741skeletal muscle fiber development0.00578478784144084
GO:0048747muscle fiber development0.00578478784144084
GO:0005262calcium channel activity0.00607398701555443
GO:0022857transmembrane transporter activity0.0087235199092231
GO:0004700atypical protein kinase C activity0.00945423206658046
GO:0030001metal ion transport0.0102199130653923
GO:0007519skeletal muscle development0.0102199130653923
GO:0044425membrane part0.0102199130653923
GO:0022892substrate-specific transporter activity0.0102199130653923
GO:0006816calcium ion transport0.0110408241806702
GO:0007220Notch receptor processing0.0115191890431605
GO:0045211postsynaptic membrane0.0115985942305008
GO:0022843voltage-gated cation channel activity0.0125769220468412
GO:0008324cation transmembrane transporter activity0.0125769220468412
GO:0006812cation transport0.0125769220468412
GO:0044456synapse part0.0125769220468412
GO:0014706striated muscle development0.0125769220468412
GO:0060024rhythmic synaptic transmission0.0125987378246049
GO:0015674di-, tri-valent inorganic cation transport0.0141581877252212
GO:0004972N-methyl-D-aspartate selective glutamate receptor activity0.0175386307102534
GO:0005112Notch binding0.0175386307102534
GO:0004274dipeptidyl-peptidase IV activity0.0192244577366487
GO:0007517muscle development0.0192244577366487
GO:0022832voltage-gated channel activity0.0192244577366487
GO:0005244voltage-gated ion channel activity0.0192244577366487
GO:0016021integral to membrane0.0225795367769959
GO:0051605protein maturation via proteolysis0.0225795367769959
GO:0031224intrinsic to membrane0.0225795367769959
GO:0051604protein maturation0.0245271979983456
GO:0008239dipeptidyl-peptidase activity0.0282851177934602
GO:0016806dipeptidyl-peptidase and tripeptidyl-peptidase activity0.0282851177934602
GO:0005891voltage-gated calcium channel complex0.032247943507392
GO:0044459plasma membrane part0.032247943507392
GO:0004697protein kinase C activity0.033400420144724
GO:0016020membrane0.0342180268267809
GO:0005515protein binding0.0342180268267809
GO:0001565phorbol ester receptor activity0.0352681340964569
GO:0005234extracellular-glutamate-gated ion channel activity0.0352681340964569
GO:0051969regulation of transmission of nerve impulse0.0394518387140763
GO:0007528neuromuscular junction development0.0394518387140763
GO:0050804regulation of synaptic transmission0.0394518387140763
GO:0005245voltage-gated calcium channel activity0.0407557438701065
GO:0031644regulation of neurological process0.0496031471657009



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>

Uber Anatomy
Ontology termp-valuen
neurectoderm8.28e-3464
neural plate8.28e-3464
presumptive neural plate8.28e-3464
regional part of nervous system5.35e-3054
central nervous system2.06e-2973
ecto-epithelium4.91e-2973
nervous system5.58e-2975
ectoderm-derived structure3.83e-2895
ectoderm3.83e-2895
presumptive ectoderm3.83e-2895
neural tube5.47e-2852
neural rod5.47e-2852
future spinal cord5.47e-2852
neural keel5.47e-2852
pre-chordal neural plate2.18e-2449
brain6.99e-2347
future brain6.99e-2347
gray matter2.76e-2234
regional part of brain4.15e-2246
structure with developmental contribution from neural crest4.38e-2092
anterior neural tube4.87e-2040
regional part of forebrain3.98e-1939
forebrain3.98e-1939
future forebrain3.98e-1939
brain grey matter2.37e-1729
regional part of telencephalon2.37e-1729
telencephalon2.37e-1729
cerebral cortex8.66e-1121
cerebral hemisphere8.66e-1121
pallium8.66e-1121
regional part of cerebral cortex2.76e-0917
posterior neural tube2.01e-0812
chordal neural plate2.01e-0812
occipital lobe2.37e-0810
visual cortex2.37e-0810
neocortex2.37e-0810
basal ganglion4.00e-088
nuclear complex of neuraxis4.00e-088
aggregate regional part of brain4.00e-088
collection of basal ganglia4.00e-088
cerebral subcortex4.00e-088
spinal cord3.41e-076
dorsal region element3.41e-076
dorsum3.41e-076


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)
MA0003.11.65122
MA0004.10.178381
MA0006.10.952171
MA0007.10.168178
MA0009.10.535932
MA0014.11.89506
MA0017.10.0906268
MA0019.10.376509
MA0024.10.496718
MA0025.10.751694
MA0027.12.14278
MA0028.10.280241
MA0029.10.477444
MA0030.10.483253
MA0031.10.451927
MA0038.10.285714
MA0040.10.547233
MA0041.11.89679
MA0042.11.82974
MA0043.10.624178
MA0046.10.568473
MA0048.11.45051
MA0050.10.205672
MA0051.10.2928
MA0052.10.554531
MA0055.11.4457
MA0056.10
MA0057.10.262449
MA0058.10.117003
MA0059.10.392739
MA0060.10.369051
MA0061.10.0537092
MA0063.10
MA0066.10.277072
MA0067.10.857286
MA0068.10.0481248
MA0069.10.554839
MA0070.10.54606
MA0071.10.592012
MA0072.10.538403
MA0073.10.0405835
MA0074.10.249359
MA0076.10.101055
MA0077.10.518913
MA0078.10.319336
MA0081.10.429201
MA0083.10.623446
MA0084.11.1752
MA0087.10.583879
MA0088.10.705351
MA0089.10
MA0090.10.471234
MA0091.10.549843
MA0092.10.471747
MA0093.10.0864726
MA0095.10
MA0098.10
MA0100.10.2406
MA0101.10.12981
MA0103.10.0964586
MA0105.10.672551
MA0106.10.325663
MA0107.10.093115
MA0108.20.395878
MA0109.10
MA0111.10.494436
MA0113.10.302851
MA0114.10.0527257
MA0115.10.626759
MA0116.10.951399
MA0117.10.597086
MA0119.10.130171
MA0122.10.615314
MA0124.10.80652
MA0125.10.736412
MA0130.10
MA0131.10.372683
MA0132.10
MA0133.10
MA0135.10.657882
MA0136.10.264624
MA0139.11.25918
MA0140.10.240513
MA0141.10.708661
MA0142.10.439269
MA0143.10.31603
MA0144.10.0540242
MA0145.10.0816911
MA0146.11.27781
MA0147.10.215066
MA0148.10.189643
MA0149.10.823515
MA0062.20.0201154
MA0035.20.68369
MA0039.20.875155
MA0138.22.57183
MA0002.20.560759
MA0137.20.105829
MA0104.20.337396
MA0047.20.285109
MA0112.20.0816855
MA0065.20.0821754
MA0150.10.168102
MA0151.10
MA0152.10.285194
MA0153.10.67335
MA0154.10.494059
MA0155.11.9396
MA0156.10.100572
MA0157.10.411541
MA0158.10
MA0159.10.0638985
MA0160.11.06584
MA0161.10
MA0162.11.18735
MA0163.10.853384
MA0164.10.264905
MA0080.20.0935932
MA0018.22.11047
MA0099.20.360735
MA0079.21.88076
MA0102.21.22663
MA0258.10.401444
MA0259.10.774997
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:401&oldid=2573796"