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MCL coexpression mm9:122: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!4.25e-20!29;UBERON:0005057!4.25e-20!29;UBERON:0002193!6.17e-19!48;UBERON:0002405!6.17e-19!48;UBERON:0000077!1.03e-18!35;UBERON:0003408!2.04e-17!24;UBERON:0002370!1.37e-16!23;UBERON:0000974!1.37e-16!23;UBERON:0004807!1.37e-16!23;UBERON:0005058!1.37e-16!23;UBERON:0003351!1.37e-16!23;UBERON:0009113!1.37e-16!23;UBERON:0003295!1.37e-16!23;UBERON:0009722!1.37e-16!23;UBERON:0005562!1.37e-16!23;UBERON:0007690!1.37e-16!23;UBERON:0002390!1.59e-16!45;UBERON:0003061!1.59e-16!45;UBERON:0006562!1.35e-15!24;UBERON:0001557!1.35e-15!24;UBERON:0001042!1.35e-15!24;UBERON:0008814!1.35e-15!24;UBERON:0009145!1.35e-15!24;UBERON:0001004!2.11e-15!42;UBERON:0000065!1.19e-14!41;UBERON:0000072!4.58e-13!27;UBERON:0001041!1.02e-10!80;UBERON:0000063!1.55e-09!35;UBERON:0001007!2.54e-09!116;UBERON:0001555!2.54e-09!116;UBERON:0007026!2.54e-09!116;UBERON:0007811!3.50e-09!36;UBERON:0003081!5.63e-09!87;UBERON:0004119!6.32e-09!118;UBERON:0000925!6.32e-09!118;UBERON:0006595!6.32e-09!118;UBERON:0004921!1.93e-08!114;UBERON:0005911!2.11e-07!69
|ontology_enrichment_uberon=UBERON:0004177!4.25e-20!29;UBERON:0005057!4.25e-20!29;UBERON:0002193!6.17e-19!48;UBERON:0002405!6.17e-19!48;UBERON:0000077!1.03e-18!35;UBERON:0003408!2.04e-17!24;UBERON:0002370!1.37e-16!23;UBERON:0000974!1.37e-16!23;UBERON:0004807!1.37e-16!23;UBERON:0005058!1.37e-16!23;UBERON:0003351!1.37e-16!23;UBERON:0009113!1.37e-16!23;UBERON:0003295!1.37e-16!23;UBERON:0009722!1.37e-16!23;UBERON:0005562!1.37e-16!23;UBERON:0007690!1.37e-16!23;UBERON:0002390!1.59e-16!45;UBERON:0003061!1.59e-16!45;UBERON:0006562!1.35e-15!24;UBERON:0001557!1.35e-15!24;UBERON:0001042!1.35e-15!24;UBERON:0008814!1.35e-15!24;UBERON:0009145!1.35e-15!24;UBERON:0001004!2.11e-15!42;UBERON:0000065!1.19e-14!41;UBERON:0000072!4.58e-13!27;UBERON:0001041!1.02e-10!80;UBERON:0000063!1.55e-09!35;UBERON:0001007!2.54e-09!116;UBERON:0001555!2.54e-09!116;UBERON:0007026!2.54e-09!116;UBERON:0007811!3.50e-09!36;UBERON:0003081!5.63e-09!87;UBERON:0004119!6.32e-09!118;UBERON:0000925!6.32e-09!118;UBERON:0006595!6.32e-09!118;UBERON:0004921!1.93e-08!114;UBERON:0005911!2.11e-07!69
|tfbs_overrepresentation_for_novel_motifs=0.514811,0.627003,0.166552,0.179848,0.558168,0.203724,0.21988,0.219554,0.601604,0.655703,1.28604,0.0316071,0.0986113,0.239012,0.654952,0,0.993445,0.376968,0.167932,0.123628,0.0554904,0.376758,0.237574,0.285326,0.179964,0.139624,0.492072,0.12706,0.329968,0.39993,0.781959,0.0707372,0.661922,0.586882,0.353732,0.0271974,0.0888183,0.815253,0.0314977,0.101379,0.0639907,0.224851,0.356,0.359621,0.23112,0.162549,0.452264,0.661499,1.6246,0.225106,0.934047,0.0632924,0.825978,0.819119,0.435497,0.250544,0.248416,0.332645,0.428935,0.118354,0.0636861,0.351475,0.307278,0.896397,0.269048,0.163992,0.219798,0.477929,0.223154,0.948287,0.704845,0.334558,0.0617705,0.933013,0.38553,0.117527,0.138424,0.428065,0.462329,0.313184,0.583989,0.168759,0.348708,0.0143712,0.333578,0.336792,1.5358,0.309521,0.0230401,0.616279,0.265586,0.339461,0.261453,0.131348,0.451713,0.624742,0.00727812,0.076521,1.47556,0.536553,0.454427,0.247776,0.390729,0.328427,0.326814,0.0493548,0.743753,0.646132,0.209948,0.826115,0.110914,0.124449,0.46264,0.164926,0.270401,0.0310082,0.343046,0.317541,0.640347,0.579966,0.487621,0.0279213,0.0516778,1.41203,0.308442,0.468913,0.23251,0.254327,1.17175,0.217582,0.115453,1.17295,0.581164,0.133029,0.285361,4.91087,0.232591,0.227396,0.251752,0.953976,0.588456,0.633943,0.309531,0.258988,0.316979,0.376754,0.0983591,0.916531,0.37841,0.123695,0.178108,0.125348,0.414884,0.518745,0.0476634,0.177179,0.563391,0.399548,0.339837,0.232008,0.716235,0.680594,0.059326,0.479685,0.312015,0.44949,0.324309,0.199604,0.337287
}}
}}

Revision as of 17:50, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126602396..126602419,+p4@B4galnt1
Mm9::chr10:13685045..13685054,+p@chr10:13685045..13685054
+
Mm9::chr10:13685064..13685085,+p@chr10:13685064..13685085
+
Mm9::chr10:42580501..42580520,+p3@Scml4
Mm9::chr10:77760880..77760891,-p19@Agpat3
Mm9::chr10:77760907..77760929,-p6@Agpat3
Mm9::chr11:103206045..103206073,+p2@Gm11648
Mm9::chr11:103206079..103206126,+p1@Gm11648
Mm9::chr11:106611587..106611660,-p5@Pecam1
Mm9::chr11:106611989..106612004,+p@chr11:106611989..106612004
+
Mm9::chr11:118109821..118109885,-p1@Cyth1
Mm9::chr11:51391390..51391396,+p@chr11:51391390..51391396
+
Mm9::chr11:6289120..6289140,+p5@Zmiz2
Mm9::chr11:75150291..75150312,-p@chr11:75150291..75150312
-
Mm9::chr11:99016486..99016499,+p@chr11:99016486..99016499
+
Mm9::chr12:77187706..77187736,+p@chr12:77187706..77187736
+
Mm9::chr13:112599146..112599226,-p1@Map3k1
Mm9::chr13:24706074..24706083,+p12@Fam65b
Mm9::chr13:24706445..24706452,+p7@Fam65b
Mm9::chr13:24706457..24706472,+p3@Fam65b
Mm9::chr13:67476665..67476693,-p2@Zfp456
Mm9::chr14:57194346..57194371,+p3@Parp4
Mm9::chr14:57194374..57194383,+p4@Parp4
Mm9::chr15:5058469..5058490,-p2@Card6
Mm9::chr15:67008386..67008403,-p3@St3gal1
Mm9::chr15:88977579..88977625,-p@chr15:88977579..88977625
-
Mm9::chr15:97077389..97077435,+p2@Fam113b
Mm9::chr15:97077442..97077483,+p3@Fam113b
Mm9::chr15:97191611..97191656,+p1@Fam113b
Mm9::chr16:23224945..23224996,+p2@St6gal1
Mm9::chr17:25032405..25032430,-p2@Eme2
Mm9::chr17:25032464..25032487,+p2@Mrps34
Mm9::chr17:34324647..34324694,+p2@Tap1
Mm9::chr17:37407200..37407205,+p2@H2-M3
Mm9::chr17:37407206..37407223,+p@chr17:37407206..37407223
+
Mm9::chr17:84580558..84580579,+p@chr17:84580558..84580579
+
Mm9::chr18:32557271..32557332,+p@chr18:32557271..32557332
+
Mm9::chr18:56628862..56628868,+p7@Gramd3
Mm9::chr18:56628869..56628892,+p4@Gramd3
Mm9::chr18:56629164..56629171,+p@chr18:56629164..56629171
+
Mm9::chr18:65574650..65574662,+p@chr18:65574650..65574662
+
Mm9::chr19:25127000..25127009,+p5@Dock8
Mm9::chr19:25127026..25127031,+p8@Dock8
Mm9::chr19:29441762..29441777,-p5@5033414D02Rik
Mm9::chr19:4204194..4204207,+p@chr19:4204194..4204207
+
Mm9::chr19:4204211..4204221,+p@chr19:4204211..4204221
+
Mm9::chr1:193916421..193916500,-p1@Traf5
Mm9::chr1:52289245..52289276,-p4@Gls
Mm9::chr1:52687536..52687601,+p1@Tmem194b
Mm9::chr1:58859336..58859361,+p6@Casp8
Mm9::chr2:150493121..150493157,+p1@E130215H24Rik
Mm9::chr2:165818215..165818226,+p4@Ncoa3
Mm9::chr2:168415791..168415802,-p5@Nfatc2
Mm9::chr2:24240651..24240687,+p5@Psd4
Mm9::chr2:71975181..71975199,+p@chr2:71975181..71975199
+
Mm9::chr2:79095374..79095400,+p11@Itga4
Mm9::chr2:79096094..79096109,+p5@Itga4
Mm9::chr3:101092050..101092065,-p4@Cd2
Mm9::chr3:68930763..68930807,-p4@Kpna4
Mm9::chr4:100937461..100937483,-p@chr4:100937461..100937483
-
Mm9::chr4:105985923..105985934,+p@chr4:105985923..105985934
+
Mm9::chr4:16090758..16090772,-p3@Ripk2
Mm9::chr4:32336396..32336403,+p@chr4:32336396..32336403
+
Mm9::chr5:121161785..121161796,+p@chr5:121161785..121161796
+
Mm9::chr5:37438641..37438657,+p6@Jakmip1
Mm9::chr5:72559357..72559377,-p2@Commd8
Mm9::chr6:38305533..38305551,-p@chr6:38305533..38305551
-
Mm9::chr6:48597207..48597218,+p2@Gimap8
Mm9::chr6:48597223..48597297,+p1@Gimap8
Mm9::chr6:48601771..48601774,+p@chr6:48601771..48601774
+
Mm9::chr6:48658205..48658251,-p1@Gimap6
Mm9::chr6:48688951..48688965,-p@chr6:48688951..48688965
-
Mm9::chr6:48689038..48689095,+p1@Gimap1
Mm9::chr6:48690612..48690631,-p1@ENSMUST00000155906
Mm9::chr6:48696168..48696179,+p4@Gimap5
Mm9::chr6:48696187..48696211,+p2@Gimap5
Mm9::chr7:133428921..133428932,-p@chr7:133428921..133428932
-
Mm9::chr7:90809588..90809600,-p@chr7:90809588..90809600
-
Mm9::chr8:109207033..109207054,+p2@Tmco7
Mm9::chr8:13677775..13677827,+p@chr8:13677775..13677827
+
Mm9::chr8:23816979..23817052,-p1@Ikbkb
Mm9::chr8:3353417..3353468,+p1@A430078G23Rik
Mm9::chr8:3353499..3353525,+p3@A430078G23Rik
Mm9::chr8:47237988..47238002,+p1@ENSMUST00000147206
Mm9::chr8:90812927..90812975,+p1@Adcy7
Mm9::chr8:96958042..96958070,-p1@ENSMUST00000098492
Mm9::chr8:96958159..96958197,-p1@ENSMUST00000057009
Mm9::chr8:96958243..96958254,+p@chr8:96958243..96958254
+
Mm9::chr8:96958278..96958303,+p@chr8:96958278..96958303
+
Mm9::chr9:107453750..107453771,+p7@Rassf1
Mm9::chr9:107985661..107985701,-p4@Rnf123
Mm9::chr9:108953667..108953733,+p1@Shisa5
Mm9::chr9:108955342..108955378,+p4@Shisa5
Mm9::chr9:108955381..108955394,+p10@Shisa5
Mm9::chr9:108955396..108955417,+p7@Shisa5
Mm9::chr9:21936050..21936064,-p@chr9:21936050..21936064
-
Mm9::chrX:104344919..104344944,+p1@A630033H20Rik
Mm9::chrX:156146546..156146574,+p4@Sh3kbp1


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:0030173integral to Golgi membrane0.00374337247082646
GO:0031228intrinsic to Golgi membrane0.00374337247082646
GO:0031301integral to organelle membrane0.0204991446629905
GO:0031300intrinsic to organelle membrane0.0204991446629905
GO:0000139Golgi membrane0.0268998940548663
GO:0051092activation of NF-kappaB transcription factor0.0268998940548663
GO:0043413biopolymer glycosylation0.0341803125074024
GO:0051091positive regulation of transcription factor activity0.0371653898988394
GO:0008373sialyltransferase activity0.0371653898988394



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 cell1.36e-1312
T cell1.70e-1211
pro-T cell1.70e-1211
lymphocyte3.21e-1213
common lymphoid progenitor3.21e-1213
mature alpha-beta T cell4.66e-119
alpha-beta T cell4.66e-119
immature T cell4.66e-119
mature T cell4.66e-119
immature alpha-beta T cell4.66e-119
hematopoietic lineage restricted progenitor cell7.70e-1125
CD4-positive, alpha-beta T cell6.35e-108
nucleate cell3.68e-0916
hematopoietic cell4.00e-0932
hematopoietic oligopotent progenitor cell4.00e-0932
hematopoietic stem cell4.00e-0932
angioblastic mesenchymal cell4.00e-0932
hematopoietic multipotent progenitor cell4.00e-0932
leukocyte2.17e-0817
nongranular leukocyte2.17e-0817
thymocyte1.08e-076
double negative thymocyte1.08e-076
naive T cell1.08e-076
double-positive, alpha-beta thymocyte1.08e-076
CD4-positive, alpha-beta thymocyte1.08e-076
naive thymus-derived CD4-positive, alpha-beta T cell1.08e-076
DN4 thymocyte1.08e-076
DN1 thymic pro-T cell1.08e-076
DN2 thymocyte1.08e-076
DN3 thymocyte1.08e-076
immature single positive thymocyte1.08e-076
early T lineage precursor1.08e-076
mature CD4 single-positive thymocyte1.08e-076
resting double-positive thymocyte1.08e-076
double-positive blast1.08e-076
CD69-positive double-positive thymocyte1.08e-076
CD69-positive, CD4-positive single-positive thymocyte1.08e-076
CD4-positive, CD8-intermediate double-positive thymocyte1.08e-076
CD24-positive, CD4 single-positive thymocyte1.08e-076

Uber Anatomy
Ontology termp-valuen
hemopoietic organ4.25e-2029
immune organ4.25e-2029
hemolymphoid system6.17e-1948
immune system6.17e-1948
mixed endoderm/mesoderm-derived structure1.03e-1835
gland of gut2.04e-1724
thymus1.37e-1623
neck1.37e-1623
respiratory system epithelium1.37e-1623
hemolymphoid system gland1.37e-1623
pharyngeal epithelium1.37e-1623
thymic region1.37e-1623
pharyngeal gland1.37e-1623
entire pharyngeal arch endoderm1.37e-1623
thymus primordium1.37e-1623
early pharyngeal endoderm1.37e-1623
hematopoietic system1.59e-1645
blood island1.59e-1645
pharynx1.35e-1524
upper respiratory tract1.35e-1524
chordate pharynx1.35e-1524
pharyngeal arch system1.35e-1524
pharyngeal region of foregut1.35e-1524
respiratory system2.11e-1542
respiratory tract1.19e-1441
segment of respiratory tract4.58e-1327
foregut1.02e-1080
organ segment1.55e-0935
digestive system2.54e-09116
digestive tract2.54e-09116
primitive gut2.54e-09116
craniocervical region3.50e-0936
lateral plate mesoderm5.63e-0987
endoderm-derived structure6.32e-09118
endoderm6.32e-09118
presumptive endoderm6.32e-09118
subdivision of digestive tract1.93e-08114
endo-epithelium2.11e-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)

{{{tfbs_overrepresentation_jaspar}}}

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