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MCL coexpression mm9:778: Difference between revisions

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{{MCL_coexpression_mm9
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symporter activity;0.00821782720648661;20512!GO:0005310;dicarboxylic acid transmembrane transporter activity;0.00821782720648661;20512!GO:0006835;dicarboxylic acid transport;0.00821782720648661;20512!GO:0015296;anion:cation symporter activity;0.00936832301539473;20512!GO:0005343;organic acid:sodium symporter activity;0.00936832301539473;20512!GO:0015370;solute:sodium symporter activity;0.0123267408097299;20512!GO:0015294;solute:cation symporter activity;0.0123267408097299;20512!GO:0043025;cell soma;0.0123267408097299;20512!GO:0046943;carboxylic acid transmembrane transporter activity;0.0123267408097299;20512!GO:0005342;organic acid transmembrane transporter activity;0.0123267408097299;20512!GO:0046942;carboxylic acid transport;0.0123267408097299;20512!GO:0015849;organic acid transport;0.0123267408097299;20512!GO:0008509;anion transmembrane transporter activity;0.0212399226259961;20512!GO:0015293;symporter activity;0.0234208075384868;20512!GO:0015291;secondary active transmembrane transporter activity;0.0289267517668328;20512!GO:0006605;protein targeting;0.0289678409028653;20512!GO:0022804;active transmembrane transporter activity;0.0456814512360579;20512!GO:0042995;cell projection;0.0498548183860187;20512!GO:0006886;intracellular protein 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|gostat_on_MCL_coexpression=GO:0017153;sodium:dicarboxylate symporter activity;0.00821782720648661;20512!GO:0005310;dicarboxylic acid transmembrane transporter activity;0.00821782720648661;20512!GO:0006835;dicarboxylic acid transport;0.00821782720648661;20512!GO:0015296;anion:cation symporter activity;0.00936832301539473;20512!GO:0005343;organic acid:sodium symporter activity;0.00936832301539473;20512!GO:0015370;solute:sodium symporter activity;0.0123267408097299;20512!GO:0015294;solute:cation symporter activity;0.0123267408097299;20512!GO:0043025;cell soma;0.0123267408097299;20512!GO:0046943;carboxylic acid transmembrane transporter activity;0.0123267408097299;20512!GO:0005342;organic acid transmembrane transporter activity;0.0123267408097299;20512!GO:0046942;carboxylic acid transport;0.0123267408097299;20512!GO:0015849;organic acid transport;0.0123267408097299;20512!GO:0008509;anion transmembrane transporter activity;0.0212399226259961;20512!GO:0015293;symporter activity;0.0234208075384868;20512!GO:0015291;secondary active transmembrane transporter activity;0.0289267517668328;20512!GO:0006605;protein targeting;0.0289678409028653;20512!GO:0022804;active transmembrane transporter activity;0.0456814512360579;20512!GO:0042995;cell projection;0.0498548183860187;20512!GO:0006886;intracellular protein transport;0.0499557390710107;20512!
|ontology_enrichment_celltype=CL:0002453!4.74e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!4.22e-25!54;UBERON:0000955!2.74e-24!47;UBERON:0006238!2.74e-24!47;UBERON:0001017!9.21e-24!73;UBERON:0001049!2.49e-23!52;UBERON:0005068!2.49e-23!52;UBERON:0006241!2.49e-23!52;UBERON:0007135!2.49e-23!52;UBERON:0002616!2.70e-23!46;UBERON:0001016!1.05e-22!75;UBERON:0002346!8.03e-20!64;UBERON:0003075!8.03e-20!64;UBERON:0007284!8.03e-20!64;UBERON:0003080!6.19e-19!40;UBERON:0004121!3.13e-18!95;UBERON:0000924!3.13e-18!95;UBERON:0006601!3.13e-18!95;UBERON:0002780!5.78e-18!39;UBERON:0001890!5.78e-18!39;UBERON:0006240!5.78e-18!39;UBERON:0010371!1.25e-17!73;UBERON:0003056!6.07e-17!49;UBERON:0010314!1.01e-15!92;UBERON:0003528!5.05e-13!29;UBERON:0002791!5.05e-13!29;UBERON:0001893!5.05e-13!29;UBERON:0002619!6.17e-13!17;UBERON:0002021!1.06e-12!10;UBERON:0000411!1.06e-12!10;UBERON:0001950!1.06e-12!10;UBERON:0002020!2.92e-12!34;UBERON:0000956!2.57e-11!21;UBERON:0001869!2.57e-11!21;UBERON:0000203!2.57e-11!21;UBERON:0000025!2.01e-08!114;UBERON:0004111!4.37e-08!122
}}

Latest revision as of 15:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:115641974..115642002,+p@chr11:115641974..115642002
+
Mm9::chr11:115642012..115642032,+p@chr11:115642012..115642032
+
Mm9::chr14:9129624..9129650,-p@chr14:9129624..9129650
-
Mm9::chr14:9130880..9130889,-p@chr14:9130880..9130889
-
Mm9::chr14:9132143..9132179,-p@chr14:9132143..9132179
-
Mm9::chr14:9142192..9142239,-p1@Fam107a
Mm9::chr14:9142248..9142259,-p3@Fam107a
Mm9::chr14:9142284..9142298,-p2@Fam107a
Mm9::chr15:8660734..8660760,-p2@Slc1a3


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:0017153sodium:dicarboxylate symporter activity0.00821782720648661
GO:0005310dicarboxylic acid transmembrane transporter activity0.00821782720648661
GO:0006835dicarboxylic acid transport0.00821782720648661
GO:0015296anion:cation symporter activity0.00936832301539473
GO:0005343organic acid:sodium symporter activity0.00936832301539473
GO:0015370solute:sodium symporter activity0.0123267408097299
GO:0015294solute:cation symporter activity0.0123267408097299
GO:0043025cell soma0.0123267408097299
GO:0046943carboxylic acid transmembrane transporter activity0.0123267408097299
GO:0005342organic acid transmembrane transporter activity0.0123267408097299
GO:0046942carboxylic acid transport0.0123267408097299
GO:0015849organic acid transport0.0123267408097299
GO:0008509anion transmembrane transporter activity0.0212399226259961
GO:0015293symporter activity0.0234208075384868
GO:0015291secondary active transmembrane transporter activity0.0289267517668328
GO:0006605protein targeting0.0289678409028653
GO:0022804active transmembrane transporter activity0.0456814512360579
GO:0042995cell projection0.0498548183860187
GO:0006886intracellular protein transport0.0499557390710107



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
oligodendrocyte precursor cell4.74e-078

Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.22e-2554
brain2.74e-2447
future brain2.74e-2447
central nervous system9.21e-2473
neural tube2.49e-2352
neural rod2.49e-2352
future spinal cord2.49e-2352
neural keel2.49e-2352
regional part of brain2.70e-2346
nervous system1.05e-2275
neurectoderm8.03e-2064
neural plate8.03e-2064
presumptive neural plate8.03e-2064
anterior neural tube6.19e-1940
ectoderm-derived structure3.13e-1895
ectoderm3.13e-1895
presumptive ectoderm3.13e-1895
regional part of forebrain5.78e-1839
forebrain5.78e-1839
future forebrain5.78e-1839
ecto-epithelium1.25e-1773
pre-chordal neural plate6.07e-1749
structure with developmental contribution from neural crest1.01e-1592
brain grey matter5.05e-1329
regional part of telencephalon5.05e-1329
telencephalon5.05e-1329
regional part of cerebral cortex6.17e-1317
occipital lobe1.06e-1210
visual cortex1.06e-1210
neocortex1.06e-1210
gray matter2.92e-1234
cerebral cortex2.57e-1121
cerebral hemisphere2.57e-1121
pallium2.57e-1121
tube2.01e-08114
anatomical conduit4.37e-08122


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)
MA0003.10.00143485
MA0004.10.394951
MA0006.10.238555
MA0007.12.64186
MA0009.10.82278
MA0014.10.119217
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.837668
MA0043.10.918718
MA0046.10.858391
MA0048.10.281053
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.11.84247
MA0056.10
MA0057.11.39929
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.11.0215
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.12.43733
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.951436
MA0091.10.407455
MA0092.10.95209
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.867731
MA0103.11.37229
MA0105.10.109964
MA0106.10.582805
MA0107.11.35172
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.12.3425
MA0114.10.19245
MA0115.10.921497
MA0116.10.670446
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.11.07908
MA0145.10.200183
MA0146.10.0111657
MA0147.10.205697
MA0148.10.410398
MA0149.10.879199
MA0062.20.113962
MA0035.20.482026
MA0039.20.175249
MA0138.20.630612
MA0002.20.145685
MA0137.20.783415
MA0104.20.157347
MA0047.20.533516
MA0112.20.0543294
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.0631765
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.614411
MA0160.10.413266
MA0161.10
MA0162.10.0143037
MA0163.10.0600297
MA0164.12.18873
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.21.52717
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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