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MCL coexpression mm9:475: Difference between revisions

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{{MCL_coexpression_mm9
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matrix structural constituent conferring tensile strength;0.00121006827987927;12825,12831!GO:0005581;collagen;0.00121006827987927;12825,12831!GO:0005201;extracellular matrix structural constituent;0.00224040548834851;12825,12831!GO:0006817;phosphate transport;0.00224040548834851;12825,12831!GO:0044420;extracellular matrix part;0.0033840341444891;12825,12831!GO:0015698;inorganic anion transport;0.00620766434194275;12825,12831!GO:0044421;extracellular region part;0.00620766434194275;51795,21809,12825,12831!GO:0006820;anion transport;0.00620766434194275;12825,12831!GO:0005588;collagen type V;0.00620766434194275;12831!GO:0005583;fibrillar collagen;0.00744838094941756;12831!GO:0005160;transforming growth factor beta receptor binding;0.010154657312649;21809!GO:0005578;proteinaceous extracellular matrix;0.0127967149823794;12825,12831!GO:0030879;mammary gland development;0.0314502842176471;21809!GO:0022610;biological adhesion;0.0440224212608831;12825,12831!GO:0007155;cell adhesion;0.0440224212608831;12825,12831!GO:0005615;extracellular 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|gostat_on_MCL_coexpression=GO:0030020;extracellular matrix structural constituent conferring tensile strength;0.00121006827987927;12825,12831!GO:0005581;collagen;0.00121006827987927;12825,12831!GO:0005201;extracellular matrix structural constituent;0.00224040548834851;12825,12831!GO:0006817;phosphate transport;0.00224040548834851;12825,12831!GO:0044420;extracellular matrix part;0.0033840341444891;12825,12831!GO:0015698;inorganic anion transport;0.00620766434194275;12825,12831!GO:0044421;extracellular region part;0.00620766434194275;51795,21809,12825,12831!GO:0006820;anion transport;0.00620766434194275;12825,12831!GO:0005588;collagen type V;0.00620766434194275;12831!GO:0005583;fibrillar collagen;0.00744838094941756;12831!GO:0005160;transforming growth factor beta receptor binding;0.010154657312649;21809!GO:0005578;proteinaceous extracellular matrix;0.0127967149823794;12825,12831!GO:0030879;mammary gland development;0.0314502842176471;21809!GO:0022610;biological adhesion;0.0440224212608831;12825,12831!GO:0007155;cell adhesion;0.0440224212608831;12825,12831!GO:0005615;extracellular space;0.0451027695374246;51795,21809,12831!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000479!3.42e-07!349
}}

Latest revision as of 15:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126627037..126627127,-p1@Arhgef25
Mm9::chr12:87419853..87419891,-p1@Tgfb3
Mm9::chr16:17797310..17797321,+p2@Scarf2
Mm9::chr1:45368469..45368483,+p1@Col3a1
Mm9::chr1:45378434..45378486,+p@chr1:45378434..45378486
+
Mm9::chr1:45394139..45394159,+p@chr1:45394139..45394159
+
Mm9::chr1:45394262..45394284,+p@chr1:45394262..45394284
+
Mm9::chr1:45458939..45458951,+p@chr1:45458939..45458951
+
Mm9::chr2:27741904..27741915,+p4@Col5a1
Mm9::chr2:27741936..27741960,+p3@Col5a1
Mm9::chr2:27741964..27741981,+p1@Col5a1
Mm9::chr2:27741999..27742013,+p2@Col5a1
Mm9::chr2:84888644..84888660,+p@chr2:84888644..84888660
+
Mm9::chr8:107779000..107779057,-p1@B3gnt9-ps
Mm9::chrX:9694723..9694803,-p1@Srpx


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:0030020extracellular matrix structural constituent conferring tensile strength0.00121006827987927
GO:0005581collagen0.00121006827987927
GO:0005201extracellular matrix structural constituent0.00224040548834851
GO:0006817phosphate transport0.00224040548834851
GO:0044420extracellular matrix part0.0033840341444891
GO:0015698inorganic anion transport0.00620766434194275
GO:0044421extracellular region part0.00620766434194275
GO:0006820anion transport0.00620766434194275
GO:0005588collagen type V0.00620766434194275
GO:0005583fibrillar collagen0.00744838094941756
GO:0005160transforming growth factor beta receptor binding0.010154657312649
GO:0005578proteinaceous extracellular matrix0.0127967149823794
GO:0030879mammary gland development0.0314502842176471
GO:0022610biological adhesion0.0440224212608831
GO:0007155cell adhesion0.0440224212608831
GO:0005615extracellular space0.0451027695374246



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
tissue3.42e-07349


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)
MA0003.13.82304
MA0004.10.239244
MA0006.10.118059
MA0007.11.20517
MA0009.10.623671
MA0014.11.72656
MA0017.10.135289
MA0019.10.456268
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.10.12472
MA0029.10.562703
MA0030.10.568779
MA0031.10.535959
MA0038.10.942753
MA0040.10.635404
MA0041.10.18185
MA0042.10.172351
MA0043.10.71494
MA0046.10.657417
MA0048.10.473865
MA0050.10.270164
MA0051.10.366328
MA0052.10.642973
MA0055.10.229093
MA0056.10
MA0057.11.0364
MA0058.10.501197
MA0059.10.522737
MA0060.10.910192
MA0061.10.0877629
MA0063.10
MA0066.10.349199
MA0067.10.953264
MA0068.10.724284
MA0069.11.55187
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.17.22657
MA0074.10.854077
MA0076.10.148159
MA0077.10.605975
MA0078.11.02284
MA0081.10.193203
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.11.07775
MA0089.10
MA0090.10.610307
MA0091.10.24961
MA0092.10.610874
MA0093.10.40751
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.538493
MA0103.10.439015
MA0105.11.85166
MA0106.10.401864
MA0107.10.428571
MA0108.20.476838
MA0109.10
MA0111.10.223614
MA0113.10.377232
MA0114.10.0864402
MA0115.10.717599
MA0116.10.117928
MA0117.10.686999
MA0119.10.183219
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.16.39485
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.10.335579
MA0139.11.19638
MA0140.10.30902
MA0141.10.472769
MA0142.10.522654
MA0143.10.391481
MA0144.10.617592
MA0145.10.819767
MA0146.10.780669
MA0147.10.0952713
MA0148.10.252062
MA0149.10.18682
MA0062.20.0394542
MA0035.20.312946
MA0039.21.17724
MA0138.20.445088
MA0002.20.458095
MA0137.20.467774
MA0104.20.229221
MA0047.20.357963
MA0112.20.819738
MA0065.20.543457
MA0150.10.227466
MA0151.10
MA0152.10.358055
MA0153.10.765498
MA0154.10.10034
MA0155.13.16082
MA0156.10.147567
MA0157.10.493416
MA0158.10
MA0159.10.101261
MA0160.10.254455
MA0161.10
MA0162.11.18203
MA0163.18.31018
MA0164.10.335886
MA0080.20.13897
MA0018.20.344133
MA0099.20.439458
MA0079.27.61497
MA0102.21.32652
MA0258.10.572032
MA0259.10.621948
MA0442.10
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