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MCL coexpression mm9:235: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.08e-30!54;UBERON:0001049!9.46e-30!52;UBERON:0005068!9.46e-30!52;UBERON:0006241!9.46e-30!52;UBERON:0007135!9.46e-30!52;UBERON:0002020!9.15e-28!34;UBERON:0000955!4.46e-25!47;UBERON:0006238!4.46e-25!47;UBERON:0001017!3.44e-24!73;UBERON:0002616!1.93e-23!46;UBERON:0001016!2.52e-23!75;UBERON:0003528!6.88e-23!29;UBERON:0002791!6.88e-23!29;UBERON:0001893!6.88e-23!29;UBERON:0002346!9.80e-23!64;UBERON:0003075!9.80e-23!64;UBERON:0007284!9.80e-23!64;UBERON:0003080!2.80e-21!40;UBERON:0002021!4.75e-21!10;UBERON:0000411!4.75e-21!10;UBERON:0001950!4.75e-21!10;UBERON:0002780!7.82e-20!39;UBERON:0001890!7.82e-20!39;UBERON:0006240!7.82e-20!39;UBERON:0002619!2.35e-19!17;UBERON:0010371!5.42e-19!73;UBERON:0000956!8.72e-18!21;UBERON:0001869!8.72e-18!21;UBERON:0000203!8.72e-18!21;UBERON:0004121!1.09e-16!95;UBERON:0000924!1.09e-16!95;UBERON:0006601!1.09e-16!95;UBERON:0003056!2.74e-16!49;UBERON:0010314!1.64e-13!92;UBERON:0000025!1.76e-09!114;UBERON:0003076!7.27e-09!12;UBERON:0003057!7.27e-09!12;UBERON:0004111!2.20e-08!122;UBERON:0002950!2.22e-08!4;UBERON:0001891!2.22e-08!4;UBERON:0009616!2.22e-08!4;UBERON:0010286!2.22e-08!4;UBERON:0002240!1.29e-07!6;UBERON:0005174!1.29e-07!6;UBERON:0001137!1.29e-07!6
}}

Latest revision as of 14:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:98378743..98378761,+p@chr10:98378743..98378761
+
Mm9::chr11:76322923..76322937,-p13@Abr
Mm9::chr11:78511087..78511107,-p6@Nlk
Mm9::chr12:38607250..38607266,+p14@Dgkb
Mm9::chr12:83271300..83271328,+p6@Sipa1l1
Mm9::chr13:16072231..16072236,-p@chr13:16072231..16072236
-
Mm9::chr14:70476975..70476997,+p2@Egr3
Mm9::chr15:16658662..16658676,+p@chr15:16658662..16658676
+
Mm9::chr15:98634231..98634235,-p@chr15:98634231..98634235
-
Mm9::chr15:98638321..98638339,-p1@Ddn
Mm9::chr15:98638341..98638363,-p2@Ddn
Mm9::chr15:98638371..98638387,-p3@Ddn
Mm9::chr15:98638393..98638407,-p4@Ddn
Mm9::chr15:98638426..98638433,-p6@Ddn
Mm9::chr16:9995601..9995612,-p@chr16:9995601..9995612
-
Mm9::chr17:71110733..71110746,-p@chr17:71110733..71110746
-
Mm9::chr18:61145396..61145407,+p@chr18:61145396..61145407
+
Mm9::chr19:45890497..45890566,-p1@Kcnip2
Mm9::chr19:45890729..45890742,-p3@Kcnip2
Mm9::chr1:156731300..156731309,-p@chr1:156731300..156731309
-
Mm9::chr1:182413541..182413616,-p1@6330403A02Rik
Mm9::chr2:102498385..102498396,+p16@Slc1a2
Mm9::chr2:12933299..12933313,-p1@C1ql3
Mm9::chr2:61986030..61986033,+p10@Slc4a10
Mm9::chr2:80421664..80421676,-p11@Nckap1
Mm9::chr3:136333533..136333547,+p8@Ppp3ca
Mm9::chr3:67868320..67868329,+p16@Schip1
Mm9::chr4:128798478..128798559,-p1@Hpca
Mm9::chr4:17563333..17563339,-p@chr4:17563333..17563339
-
Mm9::chr5:129325928..129325957,-p7@Rimbp2
Mm9::chr5:24565260..24565271,-p@chr5:24565260..24565271
-
Mm9::chr5:73771769..73771785,+p@chr5:73771769..73771785
+
Mm9::chr5:73771821..73771831,+p@chr5:73771821..73771831
+
Mm9::chr6:96066965..96066998,-p@chr6:96066965..96066998
-
Mm9::chr7:125587063..125587085,-p4@Syt17
Mm9::chr7:68708036..68708039,-p@chr7:68708036..68708039
-


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
regional part of nervous system1.08e-3054
neural tube9.46e-3052
neural rod9.46e-3052
future spinal cord9.46e-3052
neural keel9.46e-3052
gray matter9.15e-2834
brain4.46e-2547
future brain4.46e-2547
central nervous system3.44e-2473
regional part of brain1.93e-2346
nervous system2.52e-2375
brain grey matter6.88e-2329
regional part of telencephalon6.88e-2329
telencephalon6.88e-2329
neurectoderm9.80e-2364
neural plate9.80e-2364
presumptive neural plate9.80e-2364
anterior neural tube2.80e-2140
occipital lobe4.75e-2110
visual cortex4.75e-2110
neocortex4.75e-2110
regional part of forebrain7.82e-2039
forebrain7.82e-2039
future forebrain7.82e-2039
regional part of cerebral cortex2.35e-1917
ecto-epithelium5.42e-1973
cerebral cortex8.72e-1821
cerebral hemisphere8.72e-1821
pallium8.72e-1821
ectoderm-derived structure1.09e-1695
ectoderm1.09e-1695
presumptive ectoderm1.09e-1695
pre-chordal neural plate2.74e-1649
structure with developmental contribution from neural crest1.64e-1392
tube1.76e-09114
posterior neural tube7.27e-0912
chordal neural plate7.27e-0912
anatomical conduit2.20e-08122
regional part of midbrain2.22e-084
midbrain2.22e-084
presumptive midbrain2.22e-084
midbrain neural tube2.22e-084
spinal cord1.29e-076
dorsal region element1.29e-076
dorsum1.29e-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)
MA0003.10.123095
MA0004.10.811946
MA0006.10.578071
MA0007.10.198103
MA0009.10.319708
MA0014.10.889802
MA0017.10.0841017
MA0019.10.191101
MA0024.10.286848
MA0025.10.510245
MA0027.11.86664
MA0028.10.37014
MA0029.10.745712
MA0030.10.275727
MA0031.10.25021
MA0038.10.78965
MA0040.10.329301
MA0041.10.0344268
MA0042.10.126435
MA0043.10.395894
MA0046.10.918045
MA0048.10.393553
MA0050.10.258806
MA0051.10.810968
MA0052.10.335523
MA0055.10.438764
MA0056.10
MA0057.10.491437
MA0058.10.0291546
MA0059.10.0323447
MA0060.10.17896
MA0061.10.235617
MA0063.10
MA0066.10.11962
MA0067.10.607746
MA0068.11.18195
MA0069.10.335786
MA0070.10.328303
MA0071.10.0741713
MA0072.10.321801
MA0073.114.501
MA0074.10.101385
MA0076.10.242571
MA0077.10.305363
MA0078.10.455196
MA0081.10.35127
MA0083.11.02329
MA0084.10.910864
MA0087.10.360752
MA0088.10.175426
MA0089.10
MA0090.10.400464
MA0091.10.0641166
MA0092.10.178376
MA0093.10.390267
MA0095.10
MA0098.10
MA0100.10.0958046
MA0101.10.139276
MA0103.10.229489
MA0105.10.594068
MA0106.10.466516
MA0107.10.68868
MA0108.24.15029
MA0109.10
MA0111.10.428131
MA0113.10.137307
MA0114.10.109325
MA0115.10.398164
MA0116.10.868087
MA0117.10.372208
MA0119.10.59299
MA0122.10.388118
MA0124.10.560604
MA0125.10.496324
MA0130.10
MA0131.10.188202
MA0132.10
MA0133.10
MA0135.10.425686
MA0136.10.358809
MA0139.11.82028
MA0140.10.317342
MA0141.10.107091
MA0142.10.674352
MA0143.10.146596
MA0144.10.415649
MA0145.10.20594
MA0146.10.100076
MA0147.10.126822
MA0148.10.0653262
MA0149.10.0363416
MA0062.20.0776294
MA0035.20.0979998
MA0039.20.958264
MA0138.20.183173
MA0002.20.00287416
MA0137.20.256217
MA0104.20.0219024
MA0047.20.125063
MA0112.20.613424
MA0065.20.808776
MA0150.10.0535984
MA0151.10
MA0152.10.125121
MA0153.10.43947
MA0154.12.19643
MA0155.10.547908
MA0156.10.097518
MA0157.10.218114
MA0158.10
MA0159.10.283903
MA0160.10.235961
MA0161.10
MA0162.11.39431
MA0163.12.20306
MA0164.11.74739
MA0080.21.02115
MA0018.20.116511
MA0099.20.179217
MA0079.26.78402
MA0102.20.960792
MA0258.10.0950215
MA0259.10.114494
MA0442.10
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