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MCL coexpression mm9:450: Difference between revisions

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{{MCL_coexpression_mm9
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of lipopolysaccharide-mediated signaling pathway;0.0358248189763768;230594!GO:0032088;inhibition of NF-kappaB transcription factor;0.0358248189763768;230594!GO:0043433;negative regulation of transcription factor 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.576985920070998,0.772756742594203,0.654269736176001,0.309464800266008,0.145067179940881,0.625318035789511,0.413546773108342,0.300884327422511,0.247688825192758,0,0.692016017019732,0.648500832987384,0.683002603331745,0,0.0436484939370568,0,0.0925120487913534,0.0896964873768703,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.03606733520158,0.714520353775421,0.768708791565329,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0158508717912236,0,0.104270869053659,0,0,0,0,0,0.0304999548426479,0,0,0,0,0,0,0,0,0,0,0.0469568706916304,0.328399697538505,0,0,0,0,0,0,0,0,0.018591637173385,0.039816537722881,0,0.0829241914504701,0.0858449846883365,0,0,0,0,0.0712192470419816,0,0.0259754887595653,0,0,0,0,0,0,0,0,0.103591721382858,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00585236590271805,0,0,0,0,0,0,0,0,0,0,0,0.0107468382041091,0,0,0,0,0,0,0,0.0150852831465655,0,0,0,0,0,0,0,0,0,0,0.0659019793256198,0.0691813633419548,0.0586723554240733,0,0,0.173700201812769,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.202968298031755,0,0,0.0749511157581746,0.169336129901,0.221208825682355,0.063545408223121,0.0820316904417725,0.0811026744862318,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0853163241331035,0,0.0080747536863872,0.0530480122014902,0.0357618192777494,0.0787037500278776,0.0935585710841254,0.031819465763674,0.131118230744044,0.0760369664416062,0.128532244053129,0.0822687222705835,0.0932803464572988,0.148558490410283,0,0,0,0,0,0,0.0365202021377223,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0243204144142754
|gostat_on_MCL_coexpression=GO:0031664;regulation of lipopolysaccharide-mediated signaling pathway;0.0358248189763768;230594!GO:0032088;inhibition of NF-kappaB transcription factor;0.0358248189763768;230594!GO:0043433;negative regulation of transcription factor activity;0.0477533411195426;230594!
|ontology_enrichment_celltype=CL:0000838!4.89e-17!12;CL:0000791!4.21e-16!9;CL:0000789!4.21e-16!9;CL:0002420!4.21e-16!9;CL:0002419!4.21e-16!9;CL:0000790!4.21e-16!9;CL:0002031!1.47e-15!25;CL:0000542!1.72e-15!13;CL:0000051!1.72e-15!13;CL:0000084!2.65e-15!11;CL:0000827!2.65e-15!11;CL:0000624!2.22e-14!8;CL:0000988!4.91e-14!32;CL:0002032!4.91e-14!32;CL:0000037!4.91e-14!32;CL:0000566!4.91e-14!32;CL:0000837!4.91e-14!32;CL:0002242!5.10e-12!16;CL:0000738!3.88e-11!17;CL:0002087!3.88e-11!17;CL:0000893!4.36e-11!6;CL:0002489!4.36e-11!6;CL:0000898!4.36e-11!6;CL:0000809!4.36e-11!6;CL:0000810!4.36e-11!6;CL:0000895!4.36e-11!6;CL:0000808!4.36e-11!6;CL:0000894!4.36e-11!6;CL:0000806!4.36e-11!6;CL:0000807!4.36e-11!6;CL:0000805!4.36e-11!6;CL:0002425!4.36e-11!6;CL:0002436!4.36e-11!6;CL:0002427!4.36e-11!6;CL:0002428!4.36e-11!6;CL:0002429!4.36e-11!6;CL:0002433!4.36e-11!6;CL:0002431!4.36e-11!6;CL:0002432!4.36e-11!6;CL:0002320!2.34e-09!46;CL:0000134!2.34e-09!46;CL:0000219!4.86e-08!54;CL:0000553!7.23e-08!6;CL:0000556!7.23e-08!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.80e-26!48;UBERON:0002405!1.80e-26!48;UBERON:0004177!1.30e-24!29;UBERON:0005057!1.30e-24!29;UBERON:0002390!1.29e-22!45;UBERON:0003061!1.29e-22!45;UBERON:0000077!2.77e-21!35;UBERON:0002370!2.81e-21!23;UBERON:0000974!2.81e-21!23;UBERON:0004807!2.81e-21!23;UBERON:0005058!2.81e-21!23;UBERON:0003351!2.81e-21!23;UBERON:0009113!2.81e-21!23;UBERON:0003295!2.81e-21!23;UBERON:0009722!2.81e-21!23;UBERON:0005562!2.81e-21!23;UBERON:0007690!2.81e-21!23;UBERON:0006562!3.65e-20!24;UBERON:0003408!3.65e-20!24;UBERON:0001557!3.65e-20!24;UBERON:0001042!3.65e-20!24;UBERON:0008814!3.65e-20!24;UBERON:0009145!3.65e-20!24;UBERON:0000072!2.53e-17!27;UBERON:0000065!9.45e-15!41;UBERON:0001004!2.99e-14!42;UBERON:0003081!1.70e-13!87;UBERON:0000063!3.65e-12!35;UBERON:0007811!1.10e-11!36;UBERON:0001041!2.27e-09!80;UBERON:0002384!2.34e-09!46;UBERON:0000153!5.69e-09!43;UBERON:0000926!5.22e-08!120;UBERON:0004120!5.22e-08!120;UBERON:0006603!5.22e-08!120;UBERON:0005911!6.13e-08!69;UBERON:0003929!1.19e-07!55
}}

Latest revision as of 15:19, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:117347567..117347572,-p@chr10:117347567..117347572
-
Mm9::chr11:99016381..99016399,-p1@Ccr7
Mm9::chr12:85534957..85535017,-p2@C130039O16Rik
Mm9::chr17:45697953..45697957,+p@chr17:45697953..45697957
+
Mm9::chr18:24102351..24102354,+p@chr18:24102351..24102354
+
Mm9::chr19:11560491..11560507,+p@chr19:11560491..11560507
+
Mm9::chr1:16043380..16043381,+p@chr1:16043380..16043381
+
Mm9::chr3:101087080..101087084,-p@chr3:101087080..101087084
-
Mm9::chr3:101091764..101091784,-p3@Cd2
Mm9::chr3:87945895..87945946,+p2@Mef2d
Mm9::chr4:108132386..108132400,+p14@Zcchc11
Mm9::chr5:122682375..122682396,+p@chr5:122682375..122682396
+
Mm9::chr6:48697740..48697754,-p@chr6:48697740..48697754
-
Mm9::chr8:125092248..125092267,-p@chr8:125092248..125092267
-
Mm9::chr9:108954219..108954229,-p@chr9:108954219..108954229
-
Mm9::chrX:104344803..104344839,+p3@A630033H20Rik


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:0031664regulation of lipopolysaccharide-mediated signaling pathway0.0358248189763768
GO:0032088inhibition of NF-kappaB transcription factor0.0358248189763768
GO:0043433negative regulation of transcription factor activity0.0477533411195426



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
lymphoid lineage restricted progenitor cell4.89e-1712
mature alpha-beta T cell4.21e-169
alpha-beta T cell4.21e-169
immature T cell4.21e-169
mature T cell4.21e-169
immature alpha-beta T cell4.21e-169
hematopoietic lineage restricted progenitor cell1.47e-1525
lymphocyte1.72e-1513
common lymphoid progenitor1.72e-1513
T cell2.65e-1511
pro-T cell2.65e-1511
CD4-positive, alpha-beta T cell2.22e-148
hematopoietic cell4.91e-1432
hematopoietic oligopotent progenitor cell4.91e-1432
hematopoietic stem cell4.91e-1432
angioblastic mesenchymal cell4.91e-1432
hematopoietic multipotent progenitor cell4.91e-1432
nucleate cell5.10e-1216
leukocyte3.88e-1117
nongranular leukocyte3.88e-1117
thymocyte4.36e-116
double negative thymocyte4.36e-116
naive T cell4.36e-116
double-positive, alpha-beta thymocyte4.36e-116
CD4-positive, alpha-beta thymocyte4.36e-116
naive thymus-derived CD4-positive, alpha-beta T cell4.36e-116
DN4 thymocyte4.36e-116
DN1 thymic pro-T cell4.36e-116
DN2 thymocyte4.36e-116
DN3 thymocyte4.36e-116
immature single positive thymocyte4.36e-116
early T lineage precursor4.36e-116
mature CD4 single-positive thymocyte4.36e-116
resting double-positive thymocyte4.36e-116
double-positive blast4.36e-116
CD69-positive double-positive thymocyte4.36e-116
CD69-positive, CD4-positive single-positive thymocyte4.36e-116
CD4-positive, CD8-intermediate double-positive thymocyte4.36e-116
CD24-positive, CD4 single-positive thymocyte4.36e-116
connective tissue cell2.34e-0946
mesenchymal cell2.34e-0946
motile cell4.86e-0854
megakaryocyte progenitor cell7.23e-086
megakaryocyte7.23e-086

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.80e-2648
immune system1.80e-2648
hemopoietic organ1.30e-2429
immune organ1.30e-2429
hematopoietic system1.29e-2245
blood island1.29e-2245
mixed endoderm/mesoderm-derived structure2.77e-2135
thymus2.81e-2123
neck2.81e-2123
respiratory system epithelium2.81e-2123
hemolymphoid system gland2.81e-2123
pharyngeal epithelium2.81e-2123
thymic region2.81e-2123
pharyngeal gland2.81e-2123
entire pharyngeal arch endoderm2.81e-2123
thymus primordium2.81e-2123
early pharyngeal endoderm2.81e-2123
pharynx3.65e-2024
gland of gut3.65e-2024
upper respiratory tract3.65e-2024
chordate pharynx3.65e-2024
pharyngeal arch system3.65e-2024
pharyngeal region of foregut3.65e-2024
segment of respiratory tract2.53e-1727
respiratory tract9.45e-1541
respiratory system2.99e-1442
lateral plate mesoderm1.70e-1387
organ segment3.65e-1235
craniocervical region1.10e-1136
foregut2.27e-0980
connective tissue2.34e-0946
anterior region of body5.69e-0943
mesoderm5.22e-08120
mesoderm-derived structure5.22e-08120
presumptive mesoderm5.22e-08120
endo-epithelium6.13e-0869
gut epithelium1.19e-0755


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)
MA0003.10.0116141
MA0004.10.221835
MA0006.10.105852
MA0007.10.604993
MA0009.10.599391
MA0014.10.0122179
MA0017.11.26447
MA0019.10.434009
MA0024.10.558971
MA0025.10.819843
MA0027.12.21717
MA0028.10.360944
MA0029.10.53905
MA0030.11.34526
MA0031.10.512616
MA0038.10.33811
MA0040.10.611015
MA0041.10.498821
MA0042.10.15744
MA0043.10.689898
MA0046.10.632833
MA0048.10.0196258
MA0050.10.701661
MA0051.10.914027
MA0052.10.618515
MA0055.10.0114678
MA0056.10
MA0057.10.381022
MA0058.10.464825
MA0059.11.50458
MA0060.10.0623353
MA0061.12.57484
MA0063.10
MA0066.10.328887
MA0067.10.92691
MA0068.10.394673
MA0069.10.618831
MA0070.10.609808
MA0071.10.70014
MA0072.10.601934
MA0073.15.03745
MA0074.10.299171
MA0076.10.134359
MA0077.10.581866
MA0078.10.37382
MA0081.11.00846
MA0083.12.77346
MA0084.11.24749
MA0087.10.648637
MA0088.10.251567
MA0089.10
MA0090.10.196267
MA0091.10.655274
MA0092.10.571528
MA0093.10.374263
MA0095.10
MA0098.10
MA0100.10.289731
MA0101.10.501038
MA0103.10.128989
MA0105.13.34649
MA0106.10.380511
MA0107.11.28321
MA0108.20.454274
MA0109.10
MA0111.10.206727
MA0113.10.356344
MA0114.10.263654
MA0115.10.692537
MA0116.10.700593
MA0117.10.662171
MA0119.10.16785
MA0122.10.680832
MA0124.10.875485
MA0125.10.804312
MA0130.10
MA0131.10.43
MA0132.10
MA0133.10
MA0135.10.724328
MA0136.10.84684
MA0139.10.0480655
MA0140.10.289637
MA0141.10.437281
MA0142.10.499475
MA0143.10.37032
MA0144.11.43278
MA0145.10.0491125
MA0146.10.0504792
MA0147.10.286569
MA0148.10.23425
MA0149.11.56348
MA0062.20.576052
MA0035.20.796986
MA0039.20.119432
MA0138.20.423003
MA0002.20.413675
MA0137.21.3762
MA0104.20.204256
MA0047.20.337465
MA0112.20.00977202
MA0065.20.479069
MA0150.10.210447
MA0151.10
MA0152.10.337555
MA0153.10.740107
MA0154.10.413095
MA0155.10.32315
MA0156.10.41693
MA0157.10.47062
MA0158.10
MA0159.10.0900717
MA0160.10.23657
MA0161.10
MA0162.10.138028
MA0163.10.348713
MA0164.10.315868
MA0080.20.790324
MA0018.20.323932
MA0099.20.417463
MA0079.20.298654
MA0102.21.29919
MA0258.10.0692929
MA0259.10.0787033
MA0442.10
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