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MCL coexpression mm9:346: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000221!4.50e-14!44;CL:0000133!4.50e-14!44;CL:0002319!1.59e-13!43;CL:0000055!9.44e-13!49;CL:0000117!3.41e-09!23;CL:0000337!3.41e-09!23;CL:0000540!4.47e-09!33;CL:0000047!4.47e-09!33;CL:0000031!4.47e-09!33;CL:0000404!4.47e-09!33;CL:0000393!1.83e-08!39;CL:0000211!1.83e-08!39;CL:0002453!9.13e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.25e-30!73;UBERON:0001016!7.33e-30!75;UBERON:0004121!2.22e-26!95;UBERON:0000924!2.22e-26!95;UBERON:0006601!2.22e-26!95;UBERON:0002346!7.94e-25!64;UBERON:0003075!7.94e-25!64;UBERON:0007284!7.94e-25!64;UBERON:0000073!8.26e-25!54;UBERON:0001049!9.62e-24!52;UBERON:0005068!9.62e-24!52;UBERON:0006241!9.62e-24!52;UBERON:0007135!9.62e-24!52;UBERON:0010371!4.06e-21!73;UBERON:0000955!7.14e-21!47;UBERON:0006238!7.14e-21!47;UBERON:0002616!2.40e-20!46;UBERON:0010314!8.98e-19!92;UBERON:0003056!2.96e-18!49;UBERON:0003080!4.49e-17!40;UBERON:0002780!1.35e-16!39;UBERON:0001890!1.35e-16!39;UBERON:0006240!1.35e-16!39;UBERON:0002020!3.42e-14!34;UBERON:0003528!1.46e-11!29;UBERON:0002791!1.46e-11!29;UBERON:0001893!1.46e-11!29;UBERON:0004111!3.26e-09!122;UBERON:0000025!1.72e-08!114;UBERON:0000956!6.41e-08!21;UBERON:0001869!6.41e-08!21;UBERON:0000203!6.41e-08!21;UBERON:0002619!8.22e-08!17;UBERON:0003076!2.54e-07!12;UBERON:0003057!2.54e-07!12
}}

Latest revision as of 15:08, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128333291..128333302,+p@chr10:128333291..128333302
+
Mm9::chr10:128333303..128333314,+p@chr10:128333303..128333314
+
Mm9::chr10:77815068..77815204,-p1@Agpat3
Mm9::chr11:105927236..105927268,-p1@uc007lya.1
Mm9::chr11:61318640..61318712,+p1@B9d1
Mm9::chr11:68884292..68884358,+p1@Tmem107
Mm9::chr12:77505391..77505413,+p2@Hspa2
Mm9::chr12:81536158..81536222,+p@chr12:81536158..81536222
+
Mm9::chr15:79604813..79604824,-p2@Dnalc4
Mm9::chr16:90935110..90935130,-p3@1110004E09Rik
Mm9::chr17:56970339..56970428,-p1@Rfx2
Mm9::chr2:105843510..105843543,+p1@ENSMUST00000126340
p1@uc008lli.1
Mm9::chr2:112333409..112333437,-p@chr2:112333409..112333437
-
Mm9::chr2:131000557..131000573,-p1@Spef1
Mm9::chr2:70347324..70347350,-p1@ENSMUST00000150702
Mm9::chr5:117737598..117737632,-p1@Pebp1
Mm9::chr5:137384000..137384044,+p1@Rabl5
Mm9::chr7:148068151..148068171,-p4@Sirt3
Mm9::chr7:4484021..4484072,-p1@6030429G01Rik
Mm9::chr8:108225042..108225090,+p1@Pard6a
Mm9::chr8:13705884..13705952,+p1@4932443I19Rik
Mm9::chr9:21921567..21921618,-p1@Elof1


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>

Uber Anatomy
Ontology termp-valuen
central nervous system2.25e-3073
nervous system7.33e-3075
ectoderm-derived structure2.22e-2695
ectoderm2.22e-2695
presumptive ectoderm2.22e-2695
neurectoderm7.94e-2564
neural plate7.94e-2564
presumptive neural plate7.94e-2564
regional part of nervous system8.26e-2554
neural tube9.62e-2452
neural rod9.62e-2452
future spinal cord9.62e-2452
neural keel9.62e-2452
ecto-epithelium4.06e-2173
brain7.14e-2147
future brain7.14e-2147
regional part of brain2.40e-2046
structure with developmental contribution from neural crest8.98e-1992
pre-chordal neural plate2.96e-1849
anterior neural tube4.49e-1740
regional part of forebrain1.35e-1639
forebrain1.35e-1639
future forebrain1.35e-1639
gray matter3.42e-1434
brain grey matter1.46e-1129
regional part of telencephalon1.46e-1129
telencephalon1.46e-1129
anatomical conduit3.26e-09122
tube1.72e-08114
cerebral cortex6.41e-0821
cerebral hemisphere6.41e-0821
pallium6.41e-0821
regional part of cerebral cortex8.22e-0817
posterior neural tube2.54e-0712
chordal neural plate2.54e-0712


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)
MA0003.11.54906
MA0004.10.444991
MA0006.10.789557
MA0007.10.135697
MA0009.10.483331
MA0014.11.65904
MA0017.10.0678809
MA0019.10.329708
MA0024.10.445298
MA0025.10.694475
MA0027.12.07936
MA0028.11.25253
MA0029.10.426655
MA0030.10.43227
MA0031.10.402033
MA0038.10.683113
MA0040.10.494317
MA0041.10.10094
MA0042.10.312557
MA0043.10.569356
MA0046.10.514989
MA0048.11.15341
MA0050.10.506524
MA0051.10.698522
MA0052.10.501416
MA0055.10.310665
MA0056.10
MA0057.10.0270577
MA0058.10.303016
MA0059.10.659185
MA0060.11.20594
MA0061.10.343057
MA0063.10
MA0066.10.235725
MA0067.10.798606
MA0068.10.0289431
MA0069.10.501715
MA0070.10.493176
MA0071.10.505175
MA0072.10.485733
MA0073.10.807161
MA0074.10.209912
MA0076.11.96185
MA0077.10.466808
MA0078.10.275441
MA0081.10.353705
MA0083.10.568641
MA0084.11.11388
MA0087.10.530004
MA0088.10.333856
MA0089.10
MA0090.10.124244
MA0091.10.153118
MA0092.10.124428
MA0093.10.229794
MA0095.10
MA0098.10
MA0100.12.45519
MA0101.10.333139
MA0103.10.253989
MA0105.10.303135
MA0106.10.281418
MA0107.10.0699845
MA0108.20.348212
MA0109.10
MA0111.10.132626
MA0113.10.720329
MA0114.10.145706
MA0115.10.571881
MA0116.10.788841
MA0117.10.542889
MA0119.10.101951
MA0122.10.560692
MA0124.10.748494
MA0125.11.62725
MA0130.10
MA0131.11.56694
MA0132.10
MA0133.10
MA0135.10.602346
MA0136.10.637057
MA0139.10.0885364
MA0140.10.584015
MA0141.10.991673
MA0142.10.389844
MA0143.10.27232
MA0144.10.621329
MA0145.11.7347
MA0146.11.96294
MA0147.10.162533
MA0148.10.155077
MA0149.10.104621
MA0062.21.94427
MA0035.20.591852
MA0039.20.167402
MA0138.20.319705
MA0002.20.0910543
MA0137.20.581412
MA0104.20.254432
MA0047.20.243248
MA0112.21.38655
MA0065.20.116416
MA0150.10.135628
MA0151.10
MA0152.10.68198
MA0153.10.617506
MA0154.10.201776
MA0155.10.143331
MA0156.10.94766
MA0157.10.363212
MA0158.10
MA0159.10.174007
MA0160.10.156994
MA0161.10
MA0162.10.649913
MA0163.10.192561
MA0164.10.224368
MA0080.20.247073
MA0018.20.231394
MA0099.20.314682
MA0079.20.984167
MA0102.21.16504
MA0258.10.310208
MA0259.10.347953
MA0442.10
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