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MCL coexpression mm9:226: Difference between revisions

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{{MCL_coexpression_mm9
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mesoderm morphogenesis;0.024058502285053;21423!GO:0046022;positive regulation of transcription from RNA polymerase II promoter, mitotic;0.024058502285053;21423!GO:0046021;regulation of transcription from RNA polymerase II promoter, mitotic;0.024058502285053;21423!GO:0045896;regulation of transcription, mitotic;0.024058502285053;21423!GO:0045897;positive regulation of transcription, mitotic;0.024058502285053;21423!GO:0043034;costamere;0.0300607723093566;11465!GO:0048318;axial mesoderm development;0.0300607723093566;21423!GO:0008595;determination of anterior/posterior axis, embryo;0.0300607723093566;21423!GO:0000578;embryonic axis specification;0.0300607723093566;21423!GO:0007351;tripartite regional subdivision;0.0300607723093566;21423!GO:0007350;blastoderm segmentation;0.0327890781787929;21423!GO:0048863;stem cell differentiation;0.0400645629037455;21423!GO:0045214;sarcomere organization;0.0462156796374634;11465!GO:0009948;anterior/posterior axis 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0.00691197873106515,0,0,0.0254682189080574,0,0,0,0,0,0.00329716094707887,0,0.0194385692658993,0,0.0163762769337066,0,0,0,0.0355566442923187,0.0173948374702491,0,0,0,0.0272915817193143,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00239442116604468,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.4191363211702,0,0,0.0113669391818926,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0311452867210519,0,0.0669038710297777,0,0,0.0140742167710327,0.000757748910863145,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0169989595124911,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0048319;axial mesoderm morphogenesis;0.024058502285053;21423!GO:0046022;positive regulation of transcription from RNA polymerase II promoter, mitotic;0.024058502285053;21423!GO:0046021;regulation of transcription from RNA polymerase II promoter, mitotic;0.024058502285053;21423!GO:0045896;regulation of transcription, mitotic;0.024058502285053;21423!GO:0045897;positive regulation of transcription, mitotic;0.024058502285053;21423!GO:0043034;costamere;0.0300607723093566;11465!GO:0048318;axial mesoderm development;0.0300607723093566;21423!GO:0008595;determination of anterior/posterior axis, embryo;0.0300607723093566;21423!GO:0000578;embryonic axis specification;0.0300607723093566;21423!GO:0007351;tripartite regional subdivision;0.0300607723093566;21423!GO:0007350;blastoderm segmentation;0.0327890781787929;21423!GO:0048863;stem cell differentiation;0.0400645629037455;21423!GO:0045214;sarcomere organization;0.0462156796374634;11465!GO:0009948;anterior/posterior axis specification;0.0471995502937702;21423!GO:0008013;beta-catenin binding;0.0494508628401405;21423!GO:0030239;myofibril assembly;0.0494508628401405;11465!GO:0055002;striated muscle cell development;0.0494508628401405;11465!
|ontology_enrichment_celltype=CL:0000553!8.95e-09!6;CL:0000556!8.95e-09!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001962!2.02e-12!2;UBERON:0001961!2.02e-12!2;UBERON:0001744!2.02e-12!2;UBERON:0001155!2.61e-12!2;UBERON:0000059!2.61e-12!2;UBERON:0000160!1.10e-10!31;UBERON:0002465!1.42e-08!3;UBERON:0001153!2.75e-07!1;UBERON:0001045!2.75e-07!1;UBERON:0003199!6.93e-07!1;UBERON:0005409!9.73e-07!47
}}

Latest revision as of 14:55, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:72664273..72664275,+p1@ENSMUST00000171003
Mm9::chr11:120209809..120209822,-p2@Actg1
p2@Gm12715
Mm9::chr11:6315833..6315870,+p1@Ppia
Mm9::chr11:69485809..69485834,-p1@Eif4a1
Mm9::chr11:96787494..96787502,+p@chr11:96787494..96787502
+
Mm9::chr12:115461536..115461545,-p1@ENSMUST00000103477
Mm9::chr13:98530587..98530588,-p2@Gm10260
Mm9::chr14:46011354..46011362,+p@chr14:46011354..46011362
+
Mm9::chr14:46703699..46703701,+p1@Gm1821
Mm9::chr14:48343717..48343719,-p@chr14:48343717..48343719
-
Mm9::chr14:93595014..93595015,-p@chr14:93595014..93595015
-
Mm9::chr15:36155970..36155974,+p@chr15:36155970..36155974
+
Mm9::chr15:38167654..38167656,+p@chr15:38167654..38167656
+
Mm9::chr15:98764869..98764875,-p3@Gm5620
p3@Tuba1b
Mm9::chr16:17222378..17222389,+p@chr16:17222378..17222389
+
Mm9::chr17:74429612..74429635,-p@chr17:74429612..74429635
-
Mm9::chr17:82188702..82188707,-p@chr17:82188702..82188707
-
Mm9::chr18:44716456..44716461,+p@chr18:44716456..44716461
+
Mm9::chr19:28938256..28938257,-p1@ENSMUST00000161562
Mm9::chr19:8035658..8035660,-p@chr19:8035658..8035660
-
Mm9::chr1:193615281..193615282,-p@chr1:193615281..193615282
-
Mm9::chr1:57035338..57035355,-p@chr1:57035338..57035355
-
Mm9::chr1:57035378..57035388,-p@chr1:57035378..57035388
-
Mm9::chr1:60957704..60957705,+p1@ENSMUST00000121555
Mm9::chr1:85008653..85008660,+p1@ENSMUST00000076377
Mm9::chr2:62236000..62236005,+p@chr2:62236000..62236005
+
Mm9::chr3:127395464..127395466,-p1@ENSMUST00000159343
Mm9::chr3:132429535..132429538,+p@chr3:132429535..132429538
+
Mm9::chr3:87454882..87454885,+p@chr3:87454882..87454885
+
Mm9::chr4:145167237..145167239,-p1@ENSMUST00000117838
Mm9::chr4:82849680..82849681,-p@chr4:82849680..82849681
-
Mm9::chr6:70009225..70009230,-p1@ENSMUST00000103376
Mm9::chr6:70167443..70167446,-p1@ENSMUST00000103384
Mm9::chr6:72580544..72580553,-p12@Tcf7l1
Mm9::chr6:75248132..75248139,-p@chr6:75248132..75248139
-
Mm9::chr7:26262601..26262613,-p1@Ceacam1
Mm9::chr8:109097361..109097362,-p1@Gm10073
p2@Gm11942
Mm9::chrX:77149697..77149702,+p@chrX:77149697..77149702
+


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:0048319axial mesoderm morphogenesis0.024058502285053
GO:0046022positive regulation of transcription from RNA polymerase II promoter, mitotic0.024058502285053
GO:0046021regulation of transcription from RNA polymerase II promoter, mitotic0.024058502285053
GO:0045896regulation of transcription, mitotic0.024058502285053
GO:0045897positive regulation of transcription, mitotic0.024058502285053
GO:0043034costamere0.0300607723093566
GO:0048318axial mesoderm development0.0300607723093566
GO:0008595determination of anterior/posterior axis, embryo0.0300607723093566
GO:0000578embryonic axis specification0.0300607723093566
GO:0007351tripartite regional subdivision0.0300607723093566
GO:0007350blastoderm segmentation0.0327890781787929
GO:0048863stem cell differentiation0.0400645629037455
GO:0045214sarcomere organization0.0462156796374634
GO:0009948anterior/posterior axis specification0.0471995502937702
GO:0008013beta-catenin binding0.0494508628401405
GO:0030239myofibril assembly0.0494508628401405
GO:0055002striated muscle cell development0.0494508628401405



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
megakaryocyte progenitor cell8.95e-096
megakaryocyte8.95e-096

Uber Anatomy
Ontology termp-valuen
gut-associated lymphoid tissue2.02e-122
mucosa-associated lymphoid tissue2.02e-122
lymphoid tissue2.02e-122
colon2.61e-122
large intestine2.61e-122
intestine1.10e-1031
lymphoid system1.42e-083
caecum2.75e-071
midgut2.75e-071
egg chamber6.93e-071
gastrointestinal system9.73e-0747


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)
MA0003.10.0143899
MA0004.10.430714
MA0006.10.152656
MA0007.10.0472506
MA0009.10.819044
MA0014.10.0125468
MA0017.10.611641
MA0019.10.177916
MA0024.10.271054
MA0025.10.490939
MA0027.11.84332
MA0028.10.0625976
MA0029.10.255531
MA0030.10.260188
MA0031.10.235297
MA0038.10.368052
MA0040.11.51904
MA0041.10.538021
MA0042.10.502856
MA0043.10.37807
MA0046.10.880169
MA0048.10.335427
MA0050.10.236395
MA0051.10.119487
MA0052.10.318728
MA0055.10.120236
MA0056.10
MA0057.10.00705236
MA0058.10.485005
MA0059.10.825883
MA0060.10.0678139
MA0061.10.00591714
MA0063.10
MA0066.10.353399
MA0067.10.587517
MA0068.10.0237618
MA0069.10.318986
MA0070.10.311646
MA0071.10.235445
MA0072.10.823673
MA0073.12.83084e-05
MA0074.10.307062
MA0076.10.0191324
MA0077.10.289168
MA0078.10.425865
MA0081.10.135744
MA0083.10.984233
MA0084.10.888928
MA0087.10.343502
MA0088.10.00192623
MA0089.10
MA0090.10.159786
MA0091.10.456729
MA0092.10.366076
MA0093.10.349892
MA0095.10
MA0098.10
MA0100.10.292642
MA0101.10.123457
MA0103.10.649267
MA0105.10.00574628
MA0106.11.38697
MA0107.10.0756049
MA0108.20.56139
MA0109.10
MA0111.10.391982
MA0113.10.397366
MA0114.10.827689
MA0115.10.380305
MA0116.10.0564712
MA0117.10.354763
MA0119.10.123955
MA0122.10.370415
MA0124.11.33622
MA0125.10.477172
MA0130.10
MA0131.10.175114
MA0132.10
MA0133.10
MA0135.10.407424
MA0136.10.10138
MA0139.10.350089
MA0140.10.609996
MA0141.10.719674
MA0142.10.640103
MA0143.10.135052
MA0144.10.0326392
MA0145.10.0239734
MA0146.10.0245201
MA0147.10.632221
MA0148.10.462917
MA0149.10.128169
MA0062.20.024102
MA0035.20.298329
MA0039.20.010521
MA0138.20.507946
MA0002.20.110912
MA0137.20.0208018
MA0104.20.248341
MA0047.21.21458
MA0112.20.0987329
MA0065.20.381556
MA0150.10.178585
MA0151.10
MA0152.10.114512
MA0153.11.07945
MA0154.10.0622189
MA0155.10.0347642
MA0156.10.214558
MA0157.11.11446
MA0158.10
MA0159.10.250066
MA0160.10.812694
MA0161.10
MA0162.10.0217528
MA0163.10.00321149
MA0164.10.332928
MA0080.20.196012
MA0018.20.10631
MA0099.20.498573
MA0079.27.9709e-06
MA0102.20.938682
MA0258.10.321845
MA0259.10.2096
MA0442.10
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