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MCL coexpression mm9:389: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!2.27e-28!64;UBERON:0003075!2.27e-28!64;UBERON:0007284!2.27e-28!64;UBERON:0003056!7.30e-24!49;UBERON:0010371!1.62e-23!73;UBERON:0000073!4.73e-23!54;UBERON:0001049!1.15e-22!52;UBERON:0005068!1.15e-22!52;UBERON:0006241!1.15e-22!52;UBERON:0007135!1.15e-22!52;UBERON:0000955!5.90e-21!47;UBERON:0006238!5.90e-21!47;UBERON:0002616!1.00e-19!46;UBERON:0004121!3.67e-19!95;UBERON:0000924!3.67e-19!95;UBERON:0006601!3.67e-19!95;UBERON:0002021!2.50e-17!10;UBERON:0000411!2.50e-17!10;UBERON:0001950!2.50e-17!10;UBERON:0001017!2.89e-17!73;UBERON:0003080!1.17e-16!40;UBERON:0001016!1.51e-16!75;UBERON:0010314!2.01e-16!92;UBERON:0002780!1.66e-15!39;UBERON:0001890!1.66e-15!39;UBERON:0006240!1.66e-15!39;UBERON:0002020!5.31e-15!34;UBERON:0003528!2.14e-13!29;UBERON:0002791!2.14e-13!29;UBERON:0001893!2.14e-13!29;UBERON:0002619!4.91e-13!17;UBERON:0000956!8.77e-12!21;UBERON:0001869!8.77e-12!21;UBERON:0000203!8.77e-12!21;UBERON:0000970!1.84e-08!9;UBERON:0000019!1.84e-08!9;UBERON:0000047!1.84e-08!9;UBERON:0010312!1.84e-08!9;UBERON:0004088!1.84e-08!9;UBERON:0002104!1.84e-08!9;UBERON:0001456!1.84e-08!9;UBERON:0003072!1.84e-08!9;UBERON:0004128!1.84e-08!9;UBERON:0003071!1.84e-08!9
|tfbs_overrepresentation_for_novel_motifs=0.149902,0.00500755,0.415689,1.01095,0.531164,0.188081,0.254787,0.891484,0.140922,0.0966197,0.221763,0.687282,0.130811,0.264234,0.0791346,0,0.42315,0.876905,0.514215,0.245228,0.111207,0.0215888,0.728683,0.527336,0.427698,0.285776,0.486875,0.202945,0.0941661,0.179315,0.192916,0.512187,0.23475,0.221918,0.574198,0.0459596,0.834323,0.242872,0.430935,0.159278,0.521182,0.196576,0.411267,0.578047,0.313944,0.170437,0.355451,0.214351,0.32395,0.317394,0.408111,0.307229,0.063174,0.641205,0.657376,0.269785,0.100694,0.23598,0.242162,0.268198,0.494318,0.314847,0.354886,0.398468,0.278491,0.433342,0.785371,1.12243,0.490165,0.979213,0.12178,0.136992,0.729635,0.6886,0.0208952,0.660397,0.088252,0.346003,1.20472,0.736885,0.138314,0.438213,0.842599,0.542417,0.582029,0.0152094,0.931891,0.0686434,0.944781,1.2816,0.851763,0.586575,0.523661,0.0737837,1.59853,0.677511,0.555715,0.526183,0.355664,0.0526066,0.222463,0.511936,0.625103,0.408622,0.407717,0.196264,0.459578,0.211422,0.116526,0.112248,0.145352,0.626748,0.739879,0.225582,0.858505,0.88475,0.25446,0.180644,0.424276,0.217483,1.6568,0.380657,0.782806,0.913128,0.910454,0.482363,0.261058,0.517583,0.783932,0.553379,0.609469,0.5148,0.75595,0.280468,0.879201,0.0658603,0.471259,0.197578,0.832159,1.64606,1.25025,0.789841,0.804509,0.521565,0.402166,0.196898,0.941495,1.60668,0.156941,0.0717633,0.183779,0.0028093,0.642658,0.0459937,0.27974,0.718834,0.30804,1.01394,1.42746,0.155206,0.841238,0.581248,0.482758,0.442531,0.39934,0.752521,0.0613242,0.244407,0.00460653
|tfbs_overrepresentation_jaspar=MA0003.1;0.000948649,MA0004.1;1.60422,MA0006.1;0.0769247,MA0007.1;0.168178,MA0009.1;0.535932,MA0014.1;0.0140786,MA0017.1;0.6294,MA0019.1;0.376509,MA0024.1;0.496718,MA0025.1;1.77711,MA0027.1;2.14278,MA0028.1;0.0821841,MA0029.1;0.477444,MA0030.1;0.483253,MA0031.1;0.451927,MA0038.1;0.779388,MA0040.1;0.547233,MA0041.1;0.805215,MA0042.1;0.384176,MA0043.1;0.624178,MA0046.1;0.568473,MA0048.1;0.145518,MA0050.1;1.12066,MA0051.1;0.2928,MA0052.1;0.554531,MA0055.1;0.000616504,MA0056.1;0,MA0057.1;0.0454221,MA0058.1;2.43112,MA0059.1;1.85779,MA0060.1;0.0417645,MA0061.1;0.438647,MA0063.1;0,MA0066.1;0.759694,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;0.00518783,MA0074.1;0.249359,MA0076.1;0.101055,MA0077.1;0.518913,MA0078.1;0.319336,MA0081.1;0.138626,MA0083.1;0.623446,MA0084.1;1.1752,MA0087.1;0.583879,MA0088.1;0.0228787,MA0089.1;0,MA0090.1;0.15538,MA0091.1;0.187483,MA0092.1;0.155586,MA0093.1;2.08316,MA0095.1;0,MA0098.1;0,MA0100.1;0.2406,MA0101.1;0.40675,MA0103.1;0.319254,MA0105.1;0.0188009,MA0106.1;0.869465,MA0107.1;0.310214,MA0108.2;0.395878,MA0109.1;0,MA0111.1;0.164756,MA0113.1;0.302851,MA0114.1;0.75813,MA0115.1;0.626759,MA0116.1;0.076822,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;0.0308792,MA0140.1;0.675435,MA0141.1;0.10748,MA0142.1;0.439269,MA0143.1;0.31603,MA0144.1;0.19926,MA0145.1;0.0816911,MA0146.1;0.00163181,MA0147.1;0.813958,MA0148.1;1.66813,MA0149.1;0.133214,MA0062.2;0.0201154,MA0035.2;0.244063,MA0039.2;0.000164924,MA0138.2;1.7073,MA0002.2;0.0318175,MA0137.2;0.3443,MA0104.2;0.955719,MA0047.2;1.41968,MA0112.2;0.0816855,MA0065.2;0.524507,MA0150.1;0.168102,MA0151.1;0,MA0152.1;0.285194,MA0153.1;0.67335,MA0154.1;0.141864,MA0155.1;0.0064214,MA0156.1;0.100572,MA0157.1;0.411541,MA0158.1;0,MA0159.1;0.228388,MA0160.1;0.191754,MA0161.1;0,MA0162.1;0.00257384,MA0163.1;0.00869813,MA0164.1;0.264905,MA0080.2;0.31151,MA0018.2;0.272436,MA0099.2;0.360735,MA0079.2;3.12199e-06,MA0102.2;1.22663,MA0258.1;0.178572,MA0259.1;0.774997,MA0442.1;0
}}

Latest revision as of 15:13, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:110684912..110684948,+p@chr10:110684912..110684948
+
Mm9::chr10:73308096..73308100,+p@chr10:73308096..73308100
+
Mm9::chr10:74010609..74010633,+p@chr10:74010609..74010633
+
Mm9::chr11:78104371..78104386,+p2@BC030499
Mm9::chr11:78110831..78110835,+p@chr11:78110831..78110835
+
Mm9::chr13:118513706..118513707,+p@chr13:118513706..118513707
+
Mm9::chr13:92901773..92901792,-p1@ENSMUST00000146492
Mm9::chr13:96020223..96020286,-p1@Pde8b
Mm9::chr14:65199596..65199607,+p@chr14:65199596..65199607
+
Mm9::chr16:67519751..67519767,-p@chr16:67519751..67519767
-
Mm9::chr18:43037587..43037592,-p@chr18:43037587..43037592
-
Mm9::chr3:36121224..36121240,-p1@Qrfpr
Mm9::chr4:154932219..154932224,+p@chr4:154932219..154932224
+
Mm9::chr5:22414151..22414177,+p@chr5:22414151..22414177
+
Mm9::chr7:97668047..97668051,+p@chr7:97668047..97668051
+
Mm9::chr9:45284419..45284424,+p@chr9:45284419..45284424
+
Mm9::chr9:45403762..45403808,+p@chr9:45403762..45403808
+
Mm9::chr9:57454001..57454012,-p2@Cplx3
Mm9::chr9:57454041..57454067,-p1@Cplx3


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

no results for this coexpression

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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neurectoderm2.27e-2864
neural plate2.27e-2864
presumptive neural plate2.27e-2864
pre-chordal neural plate7.30e-2449
ecto-epithelium1.62e-2373
regional part of nervous system4.73e-2354
neural tube1.15e-2252
neural rod1.15e-2252
future spinal cord1.15e-2252
neural keel1.15e-2252
brain5.90e-2147
future brain5.90e-2147
regional part of brain1.00e-1946
ectoderm-derived structure3.67e-1995
ectoderm3.67e-1995
presumptive ectoderm3.67e-1995
occipital lobe2.50e-1710
visual cortex2.50e-1710
neocortex2.50e-1710
central nervous system2.89e-1773
anterior neural tube1.17e-1640
nervous system1.51e-1675
structure with developmental contribution from neural crest2.01e-1692
regional part of forebrain1.66e-1539
forebrain1.66e-1539
future forebrain1.66e-1539
gray matter5.31e-1534
brain grey matter2.14e-1329
regional part of telencephalon2.14e-1329
telencephalon2.14e-1329
regional part of cerebral cortex4.91e-1317
cerebral cortex8.77e-1221
cerebral hemisphere8.77e-1221
pallium8.77e-1221
eye1.84e-089
camera-type eye1.84e-089
simple eye1.84e-089
immature eye1.84e-089
ocular region1.84e-089
visual system1.84e-089
face1.84e-089
optic cup1.84e-089
optic vesicle1.84e-089
eye primordium1.84e-089


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)
MA0003.10.000948649
MA0004.11.60422
MA0006.10.0769247
MA0007.10.168178
MA0009.10.535932
MA0014.10.0140786
MA0017.10.6294
MA0019.10.376509
MA0024.10.496718
MA0025.11.77711
MA0027.12.14278
MA0028.10.0821841
MA0029.10.477444
MA0030.10.483253
MA0031.10.451927
MA0038.10.779388
MA0040.10.547233
MA0041.10.805215
MA0042.10.384176
MA0043.10.624178
MA0046.10.568473
MA0048.10.145518
MA0050.11.12066
MA0051.10.2928
MA0052.10.554531
MA0055.10.000616504
MA0056.10
MA0057.10.0454221
MA0058.12.43112
MA0059.11.85779
MA0060.10.0417645
MA0061.10.438647
MA0063.10
MA0066.10.759694
MA0067.10.857286
MA0068.10.0481248
MA0069.10.554839
MA0070.10.54606
MA0071.10.592012
MA0072.10.538403
MA0073.10.00518783
MA0074.10.249359
MA0076.10.101055
MA0077.10.518913
MA0078.10.319336
MA0081.10.138626
MA0083.10.623446
MA0084.11.1752
MA0087.10.583879
MA0088.10.0228787
MA0089.10
MA0090.10.15538
MA0091.10.187483
MA0092.10.155586
MA0093.12.08316
MA0095.10
MA0098.10
MA0100.10.2406
MA0101.10.40675
MA0103.10.319254
MA0105.10.0188009
MA0106.10.869465
MA0107.10.310214
MA0108.20.395878
MA0109.10
MA0111.10.164756
MA0113.10.302851
MA0114.10.75813
MA0115.10.626759
MA0116.10.076822
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
MA0139.10.0308792
MA0140.10.675435
MA0141.10.10748
MA0142.10.439269
MA0143.10.31603
MA0144.10.19926
MA0145.10.0816911
MA0146.10.00163181
MA0147.10.813958
MA0148.11.66813
MA0149.10.133214
MA0062.20.0201154
MA0035.20.244063
MA0039.20.000164924
MA0138.21.7073
MA0002.20.0318175
MA0137.20.3443
MA0104.20.955719
MA0047.21.41968
MA0112.20.0816855
MA0065.20.524507
MA0150.10.168102
MA0151.10
MA0152.10.285194
MA0153.10.67335
MA0154.10.141864
MA0155.10.0064214
MA0156.10.100572
MA0157.10.411541
MA0158.10
MA0159.10.228388
MA0160.10.191754
MA0161.10
MA0162.10.00257384
MA0163.10.00869813
MA0164.10.264905
MA0080.20.31151
MA0018.20.272436
MA0099.20.360735
MA0079.23.12199e-06
MA0102.21.22663
MA0258.10.178572
MA0259.10.774997
MA0442.10
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