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MCL coexpression mm9:178: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.612673655089495,0,0.286963248752788,0,0.0642873521037868,0.180011747370744,0.770523777084444,0,0,0,0,0,0,0.0354470656487682,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.031895734489288,0,0.0403878614760544,0,0.0480053095083702,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0005069;transmembrane receptor protein tyrosine kinase docking protein activity;0.0164352041704131;13449!GO:0016486;peptide hormone processing;0.0219100036200702;20394!GO:0005066;transmembrane receptor protein tyrosine kinase signaling protein activity;0.0219100036200702;13449!GO:0005158;insulin receptor binding;0.02669915869116;13449!GO:0046883;regulation of hormone secretion;0.0328541996086636;20394!GO:0030141;secretory granule;0.0474144436780716;20394!GO:0046879;hormone secretion;0.0474144436780716;20394!GO:0032403;protein complex binding;0.0474144436780716;13449!GO:0051046;regulation of secretion;0.0474144436780716;20394!
|ontology_enrichment_celltype=CL:0000624!4.06e-31!8;CL:0000791!1.06e-27!9;CL:0000789!1.06e-27!9;CL:0002420!1.06e-27!9;CL:0002419!1.06e-27!9;CL:0000790!1.06e-27!9;CL:0000893!9.31e-27!6;CL:0002489!9.31e-27!6;CL:0000898!9.31e-27!6;CL:0000809!9.31e-27!6;CL:0000810!9.31e-27!6;CL:0000895!9.31e-27!6;CL:0000808!9.31e-27!6;CL:0000894!9.31e-27!6;CL:0000806!9.31e-27!6;CL:0000807!9.31e-27!6;CL:0000805!9.31e-27!6;CL:0002425!9.31e-27!6;CL:0002436!9.31e-27!6;CL:0002427!9.31e-27!6;CL:0002428!9.31e-27!6;CL:0002429!9.31e-27!6;CL:0002433!9.31e-27!6;CL:0002431!9.31e-27!6;CL:0002432!9.31e-27!6;CL:0000084!1.01e-22!11;CL:0000827!1.01e-22!11;CL:0000838!7.46e-21!12;CL:0000542!2.86e-19!13;CL:0000051!2.86e-19!13;CL:0002242!1.06e-15!16;CL:0000738!8.61e-15!17;CL:0002087!8.61e-15!17;CL:0000815!2.31e-11!1;CL:0000792!2.31e-11!1;CL:0002031!4.14e-10!25;CL:0000988!6.42e-08!32;CL:0002032!6.42e-08!32;CL:0000037!6.42e-08!32;CL:0000566!6.42e-08!32;CL:0000837!6.42e-08!32
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!1.33e-20!23;UBERON:0000974!1.33e-20!23;UBERON:0004807!1.33e-20!23;UBERON:0005058!1.33e-20!23;UBERON:0003351!1.33e-20!23;UBERON:0009113!1.33e-20!23;UBERON:0003295!1.33e-20!23;UBERON:0009722!1.33e-20!23;UBERON:0005562!1.33e-20!23;UBERON:0007690!1.33e-20!23;UBERON:0006562!9.61e-20!24;UBERON:0003408!9.61e-20!24;UBERON:0001557!9.61e-20!24;UBERON:0001042!9.61e-20!24;UBERON:0008814!9.61e-20!24;UBERON:0009145!9.61e-20!24;UBERON:0000072!1.52e-17!27;UBERON:0004177!2.49e-16!29;UBERON:0005057!2.49e-16!29;UBERON:0000077!1.63e-13!35;UBERON:0000063!1.63e-13!35;UBERON:0007811!3.91e-13!36;UBERON:0000065!1.63e-11!41;UBERON:0001004!3.09e-11!42;UBERON:0000153!5.69e-11!43;UBERON:0002390!1.78e-10!45;UBERON:0003061!1.78e-10!45;UBERON:0002193!8.28e-10!48;UBERON:0002405!8.28e-10!48;UBERON:0003929!1.57e-08!55;UBERON:0002368!8.45e-08!60;UBERON:0002530!3.53e-07!65;UBERON:0000490!4.59e-07!66;UBERON:0005911!9.58e-07!69
|tfbs_overrepresentation_for_novel_motifs=0.146567,0.00636313,0.118789,0.384261,1.5126,1.00732,0.155196,0.270766,0.110866,0.0269746,0.119056,0.0364912,0.0964507,0.166142,0.75553,0,0.119925,0.436127,0.136672,0.368967,2.64778,0.114756,0.0429404,0.171431,0.1265,0.426849,0.437326,0.100074,0.141803,0.160069,0.0904807,0.520292,0.156381,0.232812,0.0130875,0.0088637,0.068548,0.0355502,0.903344,0.0319888,1.82095,0.0214762,0.086399,0.35278,0.00226759,0.183419,0.28339,0.269815,0.640961,0.14583,0.111346,0.824909,0.141435,0.267037,0.279316,0.172691,0.701269,0.134193,0.5416,0.68674,0.4916,0.228818,0.131006,0.105975,0.0486964,0.125874,0.381373,0.678485,0.484984,0.548445,0.0345153,0.596798,0.000845264,0.303448,0.00822345,0.0749232,0.828184,0.570522,0.911492,0.346931,0.60382,0.128756,0.492355,1.15897,0.223497,5.30506e-06,0.0237433,0.483918,0.0853783,0.827384,0.437166,0.643288,0.18296,0.316172,0.0174681,1.55224,0.548727,0.184657,0.0834273,0.16899,1.34641,0.175139,0.254967,0.727656,0.72534,0.0213932,0.141674,0.790947,0.0313293,0.00516177,0.138761,0.256193,0.194611,0.0298842,0.442923,0.163895,0.0012246,0.202643,0.767927,0.560911,0.307398,0.318909,0.430184,0.269363,1.22337,0.155933,1.02771,0.178891,0.380184,0.970977,0.243403,0.0726333,1.67666,0.41462,0.460694,0.040681,0.156161,0.0948934,0.420518,1.17879,0.797769,0.385076,0.787631,0.535494,0.350107,0.444986,0.287001,1.14035,0.158909,0.0361124,0.102243,1.87805e-06,0.739242,0.272261,0.727249,0.327312,1.25519,0.229702,0.143819,0.0119463,0.428211,0.634307,0.156184,0.279093,0.345963,0.0469065,0.390556,0.604303,0.00135716
}}

Latest revision as of 14:50, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128377739..128377750,+p@chr10:128377739..128377750
+
Mm9::chr10:22026200..22026224,-p@chr10:22026200..22026224
-
Mm9::chr10:43549000..43549003,-p@chr10:43549000..43549003
-
Mm9::chr11:100471383..100471386,-p@chr11:100471383..100471386
-
Mm9::chr11:97149062..97149066,-p@chr11:97149062..97149066
-
Mm9::chr14:122329986..122330017,+p@chr14:122329986..122330017
+
Mm9::chr14:53414794..53414801,+p3@ENSMUST00000103582
Mm9::chr14:54565684..54565697,+p1@ENSMUST00000103677
Mm9::chr14:71175978..71175985,+p9@Dok2
Mm9::chr14:71176029..71176038,+p7@Dok2
Mm9::chr17:34084925..34084953,+p@chr17:34084925..34084953
+
Mm9::chr19:57552085..57552092,+p@chr19:57552085..57552092
+
Mm9::chr1:133057843..133057865,+p@chr1:133057843..133057865
+
Mm9::chr1:138477131..138477139,-p@chr1:138477131..138477139
-
Mm9::chr2:101832120..101832141,+p@chr2:101832120..101832141
+
Mm9::chr2:101832319..101832329,+p@chr2:101832319..101832329
+
Mm9::chr2:113669745..113669761,-p5@Scg5
Mm9::chr2:113669769..113669796,-p4@Scg5
Mm9::chr2:113669799..113669833,-p@chr2:113669799..113669833
-
Mm9::chr2:113669834..113669842,-p@chr2:113669834..113669842
-
Mm9::chr2:113972833..113972839,-p@chr2:113972833..113972839
-
Mm9::chr2:165355616..165355619,+p@chr2:165355616..165355619
+
Mm9::chr3:101054539..101054542,-p@chr3:101054539..101054542
-
Mm9::chr3:115677249..115677254,-p@chr3:115677249..115677254
-
Mm9::chr3:39878658..39878665,+p@chr3:39878658..39878665
+
Mm9::chr3:39878699..39878707,+p@chr3:39878699..39878707
+
Mm9::chr3:88992242..88992250,+p@chr3:88992242..88992250
+
Mm9::chr4:116864706..116864725,-p@chr4:116864706..116864725
-
Mm9::chr4:129252879..129252895,+p@chr4:129252879..129252895
+
Mm9::chr4:133674504..133674520,+p@chr4:133674504..133674520
+
Mm9::chr4:154310054..154310101,+p@chr4:154310054..154310101
+
Mm9::chr4:154310687..154310708,-p@chr4:154310687..154310708
-
Mm9::chr4:154310712..154310719,-p@chr4:154310712..154310719
-
Mm9::chr4:154339181..154339210,+p@chr4:154339181..154339210
+
Mm9::chr4:32336248..32336285,+p@chr4:32336248..32336285
+
Mm9::chr5:124713399..124713426,-p4@Mphosph9
Mm9::chr5:150261363..150261373,+p@chr5:150261363..150261373
+
Mm9::chr5:22608195..22608205,+p@chr5:22608195..22608205
+
Mm9::chr5:22608207..22608231,+p@chr5:22608207..22608231
+
Mm9::chr6:146419239..146419243,-p@chr6:146419239..146419243
-
Mm9::chr6:147048074..147048100,+p@chr6:147048074..147048100
+
Mm9::chr6:30252614..30252619,-p@chr6:30252614..30252619
-
Mm9::chr6:48658262..48658273,-p4@Gimap6
Mm9::chr7:104095384..104095412,+p@chr7:104095384..104095412
+
Mm9::chr7:132695647..132695690,-p@chr7:132695647..132695690
-
Mm9::chr7:146420479..146420501,-p@chr7:146420479..146420501
-
Mm9::chr7:75474130..75474170,+p@chr7:75474130..75474170
+
Mm9::chr8:127240594..127240606,-p@chr8:127240594..127240606
-
Mm9::chr8:127240635..127240642,-p@chr8:127240635..127240642
-
Mm9::chr8:14997000..14997016,+p@chr8:14997000..14997016
+
Mm9::chr8:32225510..32225535,+p@chr8:32225510..32225535
+
Mm9::chr8:35209414..35209421,+p@chr8:35209414..35209421
+
Mm9::chr8:35218506..35218510,+p@chr8:35218506..35218510
+
Mm9::chr8:35219934..35219939,+p@chr8:35219934..35219939
+
Mm9::chr9:104756787..104756804,+p@chr9:104756787..104756804
+
Mm9::chr9:44807022..44807033,-p@chr9:44807022..44807033
-
Mm9::chr9:96250310..96250314,-p@chr9:96250310..96250314
-


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:0005069transmembrane receptor protein tyrosine kinase docking protein activity0.0164352041704131
GO:0016486peptide hormone processing0.0219100036200702
GO:0005066transmembrane receptor protein tyrosine kinase signaling protein activity0.0219100036200702
GO:0005158insulin receptor binding0.02669915869116
GO:0046883regulation of hormone secretion0.0328541996086636
GO:0030141secretory granule0.0474144436780716
GO:0046879hormone secretion0.0474144436780716
GO:0032403protein complex binding0.0474144436780716
GO:0051046regulation of secretion0.0474144436780716



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
CD4-positive, alpha-beta T cell4.06e-318
mature alpha-beta T cell1.06e-279
alpha-beta T cell1.06e-279
immature T cell1.06e-279
mature T cell1.06e-279
immature alpha-beta T cell1.06e-279
thymocyte9.31e-276
double negative thymocyte9.31e-276
naive T cell9.31e-276
double-positive, alpha-beta thymocyte9.31e-276
CD4-positive, alpha-beta thymocyte9.31e-276
naive thymus-derived CD4-positive, alpha-beta T cell9.31e-276
DN4 thymocyte9.31e-276
DN1 thymic pro-T cell9.31e-276
DN2 thymocyte9.31e-276
DN3 thymocyte9.31e-276
immature single positive thymocyte9.31e-276
early T lineage precursor9.31e-276
mature CD4 single-positive thymocyte9.31e-276
resting double-positive thymocyte9.31e-276
double-positive blast9.31e-276
CD69-positive double-positive thymocyte9.31e-276
CD69-positive, CD4-positive single-positive thymocyte9.31e-276
CD4-positive, CD8-intermediate double-positive thymocyte9.31e-276
CD24-positive, CD4 single-positive thymocyte9.31e-276
T cell1.01e-2211
pro-T cell1.01e-2211
lymphoid lineage restricted progenitor cell7.46e-2112
lymphocyte2.86e-1913
common lymphoid progenitor2.86e-1913
nucleate cell1.06e-1516
leukocyte8.61e-1517
nongranular leukocyte8.61e-1517
regulatory T cell2.31e-111
CD4-positive, CD25-positive, alpha-beta regulatory T cell2.31e-111
hematopoietic lineage restricted progenitor cell4.14e-1025
hematopoietic cell6.42e-0832
hematopoietic oligopotent progenitor cell6.42e-0832
hematopoietic stem cell6.42e-0832
angioblastic mesenchymal cell6.42e-0832
hematopoietic multipotent progenitor cell6.42e-0832

Uber Anatomy
Ontology termp-valuen
thymus1.33e-2023
neck1.33e-2023
respiratory system epithelium1.33e-2023
hemolymphoid system gland1.33e-2023
pharyngeal epithelium1.33e-2023
thymic region1.33e-2023
pharyngeal gland1.33e-2023
entire pharyngeal arch endoderm1.33e-2023
thymus primordium1.33e-2023
early pharyngeal endoderm1.33e-2023
pharynx9.61e-2024
gland of gut9.61e-2024
upper respiratory tract9.61e-2024
chordate pharynx9.61e-2024
pharyngeal arch system9.61e-2024
pharyngeal region of foregut9.61e-2024
segment of respiratory tract1.52e-1727
hemopoietic organ2.49e-1629
immune organ2.49e-1629
mixed endoderm/mesoderm-derived structure1.63e-1335
organ segment1.63e-1335
craniocervical region3.91e-1336
respiratory tract1.63e-1141
respiratory system3.09e-1142
anterior region of body5.69e-1143
hematopoietic system1.78e-1045
blood island1.78e-1045
hemolymphoid system8.28e-1048
immune system8.28e-1048
gut epithelium1.57e-0855
endocrine gland8.45e-0860
gland3.53e-0765
unilaminar epithelium4.59e-0766
endo-epithelium9.58e-0769


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)
MA0003.11.20587e-07
MA0004.10.385317
MA0006.10.0415473
MA0007.10.0684961
MA0009.10.191265
MA0014.14.95831e-07
MA0017.10.0574655
MA0019.10.0941371
MA0024.10.165161
MA0025.10.353759
MA0027.11.66879
MA0028.10.112771
MA0029.10.907126
MA0030.10.92254
MA0031.12.63955
MA0038.10.748337
MA0040.11.09457
MA0041.12.48611
MA0042.11.5311
MA0043.10.707353
MA0046.10.213856
MA0048.10.015503
MA0050.10.763847
MA0051.10.443149
MA0052.10.204079
MA0055.10.0545838
MA0056.10
MA0057.10.136683
MA0058.10.20194
MA0059.10.61596
MA0060.10.0331132
MA0061.10.112867
MA0063.10
MA0066.10.0481357
MA0067.10.441881
MA0068.11.84818
MA0069.10.204293
MA0070.10.19821
MA0071.10.4718
MA0072.10.563018
MA0073.11.68692
MA0074.10.0377987
MA0076.10.293772
MA0077.10.531185
MA0078.10.505867
MA0081.10.455866
MA0083.10.253734
MA0084.10.727417
MA0087.10.224823
MA0088.10.00571852
MA0089.10
MA0090.10.313647
MA0091.10.215833
MA0092.11.51105
MA0093.10.23438
MA0095.10
MA0098.10
MA0100.10.139252
MA0101.10.23793
MA0103.10.274786
MA0105.10.0180307
MA0106.10.243012
MA0107.10.0605747
MA0108.20.695144
MA0109.10
MA0111.10.0656539
MA0113.10.213388
MA0114.10.00489862
MA0115.10.256201
MA0116.10.0414361
MA0117.10.234357
MA0119.11.63859
MA0122.10.247708
MA0124.10.398961
MA0125.10.341396
MA0130.10
MA0131.10.0921323
MA0132.10
MA0133.10
MA0135.10.279703
MA0136.10.378601
MA0139.10.0445704
MA0140.10.929162
MA0141.10.514108
MA0142.10.806815
MA0143.12.36757
MA0144.10.333842
MA0145.10.0347505
MA0146.13.4955e-05
MA0147.10.235217
MA0148.11.40063
MA0149.10.0419353
MA0062.20.0872273
MA0035.21.35432
MA0039.20.00285408
MA0138.20.0886784
MA0002.21.78431
MA0137.20.171803
MA0104.20.117358
MA0047.20.746198
MA0112.20.100694
MA0065.20.101728
MA0150.10.0684324
MA0151.10
MA0152.10.425503
MA0153.10.291594
MA0154.10.0602218
MA0155.10.0910539
MA0156.10.97201
MA0157.11.76287
MA0158.10
MA0159.10.410675
MA0160.10.224189
MA0161.10
MA0162.18.2523e-06
MA0163.10.000170299
MA0164.10.166928
MA0080.20.431432
MA0018.20.0463256
MA0099.20.0859843
MA0079.20.0030021
MA0102.20.775536
MA0258.10.0417728
MA0259.10.209944
MA0442.10
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