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MCL coexpression mm9:360: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0.032256856393288,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.277030587599628,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0400093965272457,0,0.106603619640227,0,0,0,0,0,0,0,0.0428469550828748,0.0549981337564001,0,0.196259654667371,0.12277748593221,0.1155407506158,0.0929615792816322,0,0.322458878535173,0.424871088552468,0.403362349605198,0.0538027986792206,0.0891514400963616,0,0.264238928079949,0.260679637160558,0.314696953870186,0.112145192034931,0.154458983811568,0.165254141453003,0.0158508717912236,0.0158196551188907,0,0,0,0,0,0,0.107511441879825,0,0,0,0,0,0,0,0,0,0,0.0469568706916304,0,0.0601091194109999,0,0,0,0,0.0482820047261801,0,0,0,0,0,0,0,0,0.111524892460631,0.0825867363219064,0,0,0,0,0.469421148328001,1.2229039998334,0.341002287980196,0.839479737193607,0.834964724940937,0.578908646702791,0.943573048075894,0,0.0254617646470484,0,0.0829439327499637,0,0,0.0359524366705627,0.0609639314262262,0.0680361098787663,0.075710578475264,0.0388988969149198,0.140512702207538,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0516064421988255,0.0479619276176895,0.0661618130246221,0,0.0169266687412288,0,0.0430998257964463,0,0.520246267719603,0.0812786020093627,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.29298744963777,0.286489064868473,0,0,0,0,0,0,0,0,0,0,0,1.36419973448506,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0709019855629759,0,0.0330788872378041,0,0,0,0,0,0,0.0254340553719351,0,0,0,0.262941939391299,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.692050026556408,0.648016961191465,0.673493476426646,0.582847718906277,0.73577985293809,0.742910698304561,0.699388331856161,0.640641847918435,0.775784146084503,0.665048084301853,0,0,0.034229042449623,0.0945084131504676,0,0,0.0871588832444397,0.081359932135904,0.0604381279967265,0.0489230553888678,0,0.0375226752578547,0.106359930872542,0.0876640865387502,0.0898139621139603,0,0.0476191773904887,0.0766073954291401,0.14986111676545,0.0596387295197733,0,0.0709519923534245,0.092873634605593,0.0589368614163519,0.0914477891695676,0.0982434449953899,0.0729583017401753,0,0.104353329269123,0,0.0486884105045233,0.0780974029773103,0,0.117229416500102,0.0383032227056179,0.0968441960560167,0.0456455446387725,0.0845301845292944,0.0380084440794953,0,0
|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000117!5.00e-12!23;CL:0000337!5.00e-12!23;CL:0000540!2.30e-07!33;CL:0000047!2.30e-07!33;CL:0000031!2.30e-07!33;CL:0000404!2.30e-07!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!3.89e-26!54;UBERON:0002346!3.87e-25!64;UBERON:0003075!3.87e-25!64;UBERON:0007284!3.87e-25!64;UBERON:0001049!4.24e-24!52;UBERON:0005068!4.24e-24!52;UBERON:0006241!4.24e-24!52;UBERON:0007135!4.24e-24!52;UBERON:0002020!3.26e-22!34;UBERON:0001016!5.52e-22!75;UBERON:0010371!5.97e-22!73;UBERON:0001017!3.60e-21!73;UBERON:0004121!3.84e-21!95;UBERON:0000924!3.84e-21!95;UBERON:0006601!3.84e-21!95;UBERON:0000955!5.29e-20!47;UBERON:0006238!5.29e-20!47;UBERON:0003056!6.38e-20!49;UBERON:0010314!2.74e-19!92;UBERON:0002616!6.13e-19!46;UBERON:0003528!7.76e-18!29;UBERON:0002791!7.76e-18!29;UBERON:0001893!7.76e-18!29;UBERON:0003080!4.36e-17!40;UBERON:0002780!3.62e-16!39;UBERON:0001890!3.62e-16!39;UBERON:0006240!3.62e-16!39;UBERON:0000956!8.69e-13!21;UBERON:0001869!8.69e-13!21;UBERON:0000203!8.69e-13!21;UBERON:0002021!2.74e-12!10;UBERON:0000411!2.74e-12!10;UBERON:0001950!2.74e-12!10;UBERON:0002619!9.92e-12!17;UBERON:0003076!1.13e-07!12;UBERON:0003057!1.13e-07!12;UBERON:0000025!6.56e-07!114
}}

Latest revision as of 15:10, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:38607360..38607387,+p7@Dgkb
Mm9::chr12:39271879..39271883,+p@chr12:39271879..39271883
+
Mm9::chr13:65005257..65005303,-p1@Cntnap3
Mm9::chr14:14286644..14286659,+p5@Synpr
Mm9::chr14:14286708..14286747,+p4@Synpr
Mm9::chr15:98638737..98638749,-p7@Ddn
Mm9::chr15:99534536..99534555,+p@chr15:99534536..99534555
+
Mm9::chr15:99534567..99534579,+p@chr15:99534567..99534579
+
Mm9::chr15:99534602..99534618,+p@chr15:99534602..99534618
+
Mm9::chr17:17963911..17963928,+p@chr17:17963911..17963928
+
Mm9::chr17:3482467..3482489,+p@chr17:3482467..3482489
+
Mm9::chr18:23200054..23200067,-p3@Nol4
Mm9::chr2:107130735..107130743,+p3@Kcna4
Mm9::chr4:126429834..126429846,-p@chr4:126429834..126429846
-
Mm9::chr5:89363356..89363370,+p4@Slc4a4
Mm9::chr6:140439637..140439648,+p@chr6:140439637..140439648
+
Mm9::chr8:96790986..96791001,+p@chr8:96790986..96791001
+
Mm9::chr8:98202106..98202116,+p8@Ndrg4
Mm9::chr8:98202130..98202159,+p4@Ndrg4
Mm9::chr8:98202164..98202188,+p3@Ndrg4
Mm9::chr8:98202189..98202196,+p7@Ndrg4
Mm9::chr8:98202219..98202230,+p6@Ndrg4


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
CNS neuron (sensu Vertebrata)5.00e-1223
neuroblast (sensu Vertebrata)5.00e-1223
neuron2.30e-0733
neuronal stem cell2.30e-0733
neuroblast2.30e-0733
electrically signaling cell2.30e-0733

Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.89e-2654
neurectoderm3.87e-2564
neural plate3.87e-2564
presumptive neural plate3.87e-2564
neural tube4.24e-2452
neural rod4.24e-2452
future spinal cord4.24e-2452
neural keel4.24e-2452
gray matter3.26e-2234
nervous system5.52e-2275
ecto-epithelium5.97e-2273
central nervous system3.60e-2173
ectoderm-derived structure3.84e-2195
ectoderm3.84e-2195
presumptive ectoderm3.84e-2195
brain5.29e-2047
future brain5.29e-2047
pre-chordal neural plate6.38e-2049
structure with developmental contribution from neural crest2.74e-1992
regional part of brain6.13e-1946
brain grey matter7.76e-1829
regional part of telencephalon7.76e-1829
telencephalon7.76e-1829
anterior neural tube4.36e-1740
regional part of forebrain3.62e-1639
forebrain3.62e-1639
future forebrain3.62e-1639
cerebral cortex8.69e-1321
cerebral hemisphere8.69e-1321
pallium8.69e-1321
occipital lobe2.74e-1210
visual cortex2.74e-1210
neocortex2.74e-1210
regional part of cerebral cortex9.92e-1217
posterior neural tube1.13e-0712
chordal neural plate1.13e-0712
tube6.56e-07114


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)
MA0003.10.132368
MA0004.10.144883
MA0006.10.2064
MA0007.10.135697
MA0009.10.483331
MA0014.10.0690682
MA0017.10.0678809
MA0019.10.329708
MA0024.10.445298
MA0025.10.694475
MA0027.12.07936
MA0028.10.477663
MA0029.10.426655
MA0030.10.43227
MA0031.10.402033
MA0038.10.243815
MA0040.10.494317
MA0041.10.10094
MA0042.10.0939798
MA0043.10.569356
MA0046.10.514989
MA0048.10.844903
MA0050.10.169675
MA0051.10.250459
MA0052.10.501416
MA0055.14.80874
MA0056.10
MA0057.10.523647
MA0058.10.0904678
MA0059.10.659185
MA0060.10.521938
MA0061.10.0375479
MA0063.10
MA0066.10.235725
MA0067.10.798606
MA0068.12.2211
MA0069.10.501715
MA0070.10.493176
MA0071.10.169125
MA0072.10.485733
MA0073.128.5816
MA0074.10.209912
MA0076.10.0767377
MA0077.10.466808
MA0078.10.275441
MA0081.10.353705
MA0083.10.568641
MA0084.11.11388
MA0087.10.530004
MA0088.10.732432
MA0089.10
MA0090.10.124244
MA0091.10.908402
MA0092.10.124428
MA0093.10.0643828
MA0095.10
MA0098.10
MA0100.10.201797
MA0101.10.101635
MA0103.10.54098
MA0105.10.0554491
MA0106.10.281418
MA0107.10.0699845
MA0108.20.348212
MA0109.10
MA0111.11.33098
MA0113.10.259904
MA0114.10.0367677
MA0115.10.571881
MA0116.10.0563303
MA0117.10.542889
MA0119.11.13093
MA0122.10.560692
MA0124.10.748494
MA0125.10.67944
MA0130.10
MA0131.10.870354
MA0132.10
MA0133.10
MA0135.10.602346
MA0136.10.224107
MA0139.11.40989
MA0140.10.201717
MA0141.10.0822433
MA0142.10.389844
MA0143.10.27232
MA0144.10.344625
MA0145.10.115721
MA0146.10.0539901
MA0147.10.0420513
MA0148.10.155077
MA0149.10.104621
MA0062.20.0591193
MA0035.20.205003
MA0039.20.786572
MA0138.21.54433
MA0002.20.434007
MA0137.20.276466
MA0104.20.254432
MA0047.20.243248
MA0112.20.799281
MA0065.20.373593
MA0150.10.135628
MA0151.10
MA0152.10.68198
MA0153.10.617506
MA0154.10.093399
MA0155.12.33817
MA0156.10.0763253
MA0157.10.363212
MA0158.10
MA0159.10.392761
MA0160.10.156994
MA0161.10
MA0162.13.34481
MA0163.14.82828
MA0164.10.224368
MA0080.20.0703895
MA0018.20.231394
MA0099.20.314682
MA0079.215.8741
MA0102.21.16504
MA0258.10.567108
MA0259.10.0383313
MA0442.10
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