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MCL coexpression mm9:438: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0800187930544913,0,0,0,0,0,0,0,0,0,0.0428469550828748,0,0,0.109123086691028,0,0.0501827898833331,0.0397493170902889,0,0.813300310962814,0.483301582624407,0.736762069307201,0.101668926708099,0.163590153725977,0,0.106932678779961,0,0.115808975689988,0.596188540783974,0.4092716284733,0.0742309351586685,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0606187686764715,0,0,0,0.09889124026805,0.0819907263755358,0.0652962901395099,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0425379529581421,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0646640766951323,0.0481354699899057,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0738741926906438,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0688732037536692,0,0,0,0.161464196262218,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0030688;nucleolar preribosome, small subunit precursor;0.015337422852538;18114!GO:0030685;nucleolar preribosome;0.015337422852538;18114!GO:0030684;preribosome;0.015337422852538;18114!GO:0030308;negative regulation of cell growth;0.0498056716510665;56191!
|ontology_enrichment_celltype=CL:0000117!1.82e-33!23;CL:0000337!1.82e-33!23;CL:0000540!1.83e-22!33;CL:0000047!1.83e-22!33;CL:0000031!1.83e-22!33;CL:0000404!1.83e-22!33;CL:0000393!1.45e-18!39;CL:0000211!1.45e-18!39;CL:0002319!1.43e-16!43;CL:0000221!3.96e-16!44;CL:0000133!3.96e-16!44;CL:0000055!3.46e-14!49;CL:0002610!1.25e-12!3;CL:0002612!4.90e-12!3;CL:0002321!4.62e-09!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!9.22e-29!54;UBERON:0001017!9.92e-25!73;UBERON:0001016!5.76e-24!75;UBERON:0001049!7.70e-24!52;UBERON:0005068!7.70e-24!52;UBERON:0006241!7.70e-24!52;UBERON:0007135!7.70e-24!52;UBERON:0002346!1.08e-18!64;UBERON:0003075!1.08e-18!64;UBERON:0007284!1.08e-18!64;UBERON:0002020!3.28e-18!34;UBERON:0004121!4.32e-18!95;UBERON:0000924!4.32e-18!95;UBERON:0006601!4.32e-18!95;UBERON:0010371!6.13e-16!73;UBERON:0002240!1.80e-15!6;UBERON:0005174!1.80e-15!6;UBERON:0001137!1.80e-15!6;UBERON:0002616!2.47e-14!46;UBERON:0003076!4.95e-14!12;UBERON:0003057!4.95e-14!12;UBERON:0000955!5.73e-14!47;UBERON:0006238!5.73e-14!47;UBERON:0004684!1.25e-12!3;UBERON:0002275!1.25e-12!3;UBERON:0003080!1.65e-12!40;UBERON:0001948!2.22e-12!5;UBERON:0002315!2.22e-12!5;UBERON:0002257!4.90e-12!3;UBERON:0010314!6.93e-12!92;UBERON:0002780!6.59e-11!39;UBERON:0001890!6.59e-11!39;UBERON:0006240!6.59e-11!39;UBERON:0003528!1.48e-10!29;UBERON:0002791!1.48e-10!29;UBERON:0001893!1.48e-10!29;UBERON:0003056!8.97e-10!49;UBERON:0000025!7.16e-09!114;UBERON:0002950!9.80e-09!4;UBERON:0001891!9.80e-09!4;UBERON:0009616!9.80e-09!4;UBERON:0010286!9.80e-09!4;UBERON:0004111!4.82e-08!122;UBERON:0002420!1.04e-07!8;UBERON:0007245!1.04e-07!8;UBERON:0010009!1.04e-07!8;UBERON:0010011!1.04e-07!8;UBERON:0000454!1.04e-07!8;UBERON:0001896!1.17e-07!2;UBERON:0002298!1.17e-07!2;UBERON:0005290!1.17e-07!2;UBERON:0010096!1.17e-07!2;UBERON:0011216!9.88e-07!194
}}

Latest revision as of 15:18, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:77867856..77867866,-p@chr10:77867856..77867866
-
Mm9::chr11:6372235..6372242,-p1@ENSMUST00000175144
Mm9::chr12:110796949..110796955,+p@chr12:110796949..110796955
+
Mm9::chr12:47797986..47798011,-p@chr12:47797986..47798011
-
Mm9::chr18:57632117..57632134,+p@chr18:57632117..57632134
+
Mm9::chr19:5797288..5797301,-p4@ENSMUST00000173314
Mm9::chr1:66486342..66486351,+p@chr1:66486342..66486351
+
Mm9::chr1:66743268..66743289,+p@chr1:66743268..66743289
+
Mm9::chr2:102621960..102621969,+p@chr2:102621960..102621969
+
Mm9::chr3:126639582..126639596,-p@chr3:126639582..126639596
-
Mm9::chr5:31441248..31441260,-p1@Ucn
Mm9::chr5:89666281..89666294,+p@chr5:89666281..89666294
+
Mm9::chr6:30755427..30755442,+p@chr6:30755427..30755442
+
Mm9::chr7:6659121..6659133,-p@chr7:6659121..6659133
-
Mm9::chr7:67121440..67121451,-p@chr7:67121440..67121451
-
Mm9::chr9:67832482..67832485,+p@chr9:67832482..67832485
+
Mm9::chrX:147089410..147089455,-p@chrX:147089410..147089455
-


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:0030688nucleolar preribosome, small subunit precursor0.015337422852538
GO:0030685nucleolar preribosome0.015337422852538
GO:0030684preribosome0.015337422852538
GO:0030308negative regulation of cell growth0.0498056716510665



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
regional part of nervous system9.22e-2954
central nervous system9.92e-2573
nervous system5.76e-2475
neural tube7.70e-2452
neural rod7.70e-2452
future spinal cord7.70e-2452
neural keel7.70e-2452
neurectoderm1.08e-1864
neural plate1.08e-1864
presumptive neural plate1.08e-1864
gray matter3.28e-1834
ectoderm-derived structure4.32e-1895
ectoderm4.32e-1895
presumptive ectoderm4.32e-1895
ecto-epithelium6.13e-1673
spinal cord1.80e-156
dorsal region element1.80e-156
dorsum1.80e-156
regional part of brain2.47e-1446
posterior neural tube4.95e-1412
chordal neural plate4.95e-1412
brain5.73e-1447
future brain5.73e-1447
raphe nuclei1.25e-123
reticular formation1.25e-123
anterior neural tube1.65e-1240
regional part of spinal cord2.22e-125
gray matter of spinal cord2.22e-125
ventral horn of spinal cord4.90e-123
structure with developmental contribution from neural crest6.93e-1292
regional part of forebrain6.59e-1139
forebrain6.59e-1139
future forebrain6.59e-1139
brain grey matter1.48e-1029
regional part of telencephalon1.48e-1029
telencephalon1.48e-1029
pre-chordal neural plate8.97e-1049
tube7.16e-09114
regional part of midbrain9.80e-094
midbrain9.80e-094
presumptive midbrain9.80e-094
midbrain neural tube9.80e-094
anatomical conduit4.82e-08122
basal ganglion1.04e-078
nuclear complex of neuraxis1.04e-078
aggregate regional part of brain1.04e-078
collection of basal ganglia1.04e-078
cerebral subcortex1.04e-078
medulla oblongata1.17e-072
brainstem1.17e-072
myelencephalon1.17e-072
future myelencephalon1.17e-072
organ system subdivision9.88e-07194


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)
MA0003.10.000105157
MA0004.10.206012
MA0006.10.0950487
MA0007.10.195085
MA0009.10.576798
MA0014.10.00023305
MA0017.10.110433
MA0019.10.413421
MA0024.10.536784
MA0025.10.795679
MA0027.12.19092
MA0028.10.100975
MA0029.10.51708
MA0030.10.523021
MA0031.11.23012
MA0038.10.319246
MA0040.10.588314
MA0041.10.152751
MA0042.10.144042
MA0043.10.666547
MA0046.10.609938
MA0048.10.0741002
MA0050.10.235075
MA0051.10.326637
MA0052.11.45222
MA0055.10.00123041
MA0056.10
MA0057.10.0640642
MA0058.10.139612
MA0059.10.147666
MA0060.10.200642
MA0061.10.0684878
MA0063.10
MA0066.10.310219
MA0067.10.902253
MA0068.10.0143498
MA0069.10.59606
MA0070.10.587119
MA0071.10.234437
MA0072.10.579318
MA0073.12.12855e-08
MA0074.10.281183
MA0076.10.122031
MA0077.10.559443
MA0078.10.354249
MA0081.10.163204
MA0083.11.59885
MA0084.11.22195
MA0087.10.625609
MA0088.10.00645469
MA0089.10
MA0090.10.181323
MA0091.10.215731
MA0092.10.535473
MA0093.10.105788
MA0095.10
MA0098.10
MA0100.10.271974
MA0101.10.153616
MA0103.10.373479
MA0105.10.111401
MA0106.10.360817
MA0107.10.113208
MA0108.21.10626
MA0109.10
MA0111.10.191411
MA0113.10.337108
MA0114.10.238352
MA0115.10.669167
MA0116.10.0949327
MA0117.10.639033
MA0119.10.154009
MA0122.10.657549
MA0124.10.851049
MA0125.10.780232
MA0130.10
MA0131.10.409473
MA0132.10
MA0133.10
MA0135.10.700734
MA0136.10.297196
MA0139.10.0414323
MA0140.10.271883
MA0141.10.405018
MA0142.10.477975
MA0143.10.350815
MA0144.10.0688535
MA0145.10.00768581
MA0146.10.00335407
MA0147.10.0750034
MA0148.10.218033
MA0149.10.157322
MA0062.20.0281188
MA0035.20.275617
MA0039.21.69513e-05
MA0138.20.402586
MA0002.20.37393
MA0137.20.127311
MA0104.20.0483916
MA0047.20.853678
MA0112.20.0402239
MA0065.20.115152
MA0150.10.567944
MA0151.10
MA0152.10.853876
MA0153.10.716409
MA0154.10.609154
MA0155.10.0502893
MA0156.10.121496
MA0157.10.4495
MA0158.10
MA0159.10.274824
MA0160.10.220282
MA0161.10
MA0162.10.00501935
MA0163.10.000516301
MA0164.10.297489
MA0080.20.113741
MA0018.20.305372
MA0099.20.397135
MA0079.21.5775e-10
MA0102.21.27355
MA0258.10.0609037
MA0259.10.0696308
MA0442.10
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