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MCL coexpression mm9:2844: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0048536;spleen development;0.0306150352991968;16468!GO:0048538;thymus development;0.0306150352991968;16468!GO:0001739;sex chromatin;0.0306150352991968;13619!GO:0000803;sex chromosome;0.0306150352991968;13619!GO:0001889;liver development;0.0361001463040186;16468!GO:0005720;nuclear heterochromatin;0.0361001463040186;13619!GO:0000790;nuclear chromatin;0.0397461311794092;13619!GO:0000792;heterochromatin;0.0397461311794092;13619!GO:0016604;nuclear body;0.0397461311794092;13619!
|ontology_enrichment_celltype=CL:0000542!1.09e-12!13;CL:0000051!1.09e-12!13;CL:0000838!1.42e-12!12;CL:0000084!1.32e-11!11;CL:0000827!1.32e-11!11;CL:0000791!1.29e-10!9;CL:0000789!1.29e-10!9;CL:0002420!1.29e-10!9;CL:0002419!1.29e-10!9;CL:0000790!1.29e-10!9;CL:0000624!1.40e-09!8;CL:0002242!2.04e-09!16;CL:0000738!1.35e-08!17;CL:0002087!1.35e-08!17;CL:0000893!1.58e-07!6;CL:0002489!1.58e-07!6;CL:0000898!1.58e-07!6;CL:0000809!1.58e-07!6;CL:0000810!1.58e-07!6;CL:0000895!1.58e-07!6;CL:0000808!1.58e-07!6;CL:0000894!1.58e-07!6;CL:0000806!1.58e-07!6;CL:0000807!1.58e-07!6;CL:0000805!1.58e-07!6;CL:0002425!1.58e-07!6;CL:0002436!1.58e-07!6;CL:0002427!1.58e-07!6;CL:0002428!1.58e-07!6;CL:0002429!1.58e-07!6;CL:0002433!1.58e-07!6;CL:0002431!1.58e-07!6;CL:0002432!1.58e-07!6;CL:0000988!5.68e-07!32;CL:0002032!5.68e-07!32;CL:0000037!5.68e-07!32;CL:0000566!5.68e-07!32;CL:0000837!5.68e-07!32
|ontology_enrichment_disease=
|ontology_enrichment_uberon=
}}

Latest revision as of 19:10, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:44829403..44829438,+p11@Jarid2
Mm9::chr6:122290543..122290561,-p6@Phc1
Mm9::chr7:31933955..31933966,-p@chr7:31933955..31933966
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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:0048536spleen development0.0306150352991968
GO:0048538thymus development0.0306150352991968
GO:0001739sex chromatin0.0306150352991968
GO:0000803sex chromosome0.0306150352991968
GO:0001889liver development0.0361001463040186
GO:0005720nuclear heterochromatin0.0361001463040186
GO:0000790nuclear chromatin0.0397461311794092
GO:0000792heterochromatin0.0397461311794092
GO:0016604nuclear body0.0397461311794092



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><br><br>

Cell Type
Ontology termp-valuen
lymphocyte1.09e-1213
common lymphoid progenitor1.09e-1213
lymphoid lineage restricted progenitor cell1.42e-1212
T cell1.32e-1111
pro-T cell1.32e-1111
mature alpha-beta T cell1.29e-109
alpha-beta T cell1.29e-109
immature T cell1.29e-109
mature T cell1.29e-109
immature alpha-beta T cell1.29e-109
CD4-positive, alpha-beta T cell1.40e-098
nucleate cell2.04e-0916
leukocyte1.35e-0817
nongranular leukocyte1.35e-0817
thymocyte1.58e-076
double negative thymocyte1.58e-076
naive T cell1.58e-076
double-positive, alpha-beta thymocyte1.58e-076
CD4-positive, alpha-beta thymocyte1.58e-076
naive thymus-derived CD4-positive, alpha-beta T cell1.58e-076
DN4 thymocyte1.58e-076
DN1 thymic pro-T cell1.58e-076
DN2 thymocyte1.58e-076
DN3 thymocyte1.58e-076
immature single positive thymocyte1.58e-076
early T lineage precursor1.58e-076
mature CD4 single-positive thymocyte1.58e-076
resting double-positive thymocyte1.58e-076
double-positive blast1.58e-076
CD69-positive double-positive thymocyte1.58e-076
CD69-positive, CD4-positive single-positive thymocyte1.58e-076
CD4-positive, CD8-intermediate double-positive thymocyte1.58e-076
CD24-positive, CD4 single-positive thymocyte1.58e-076
hematopoietic cell5.68e-0732
hematopoietic oligopotent progenitor cell5.68e-0732
hematopoietic stem cell5.68e-0732
angioblastic mesenchymal cell5.68e-0732
hematopoietic multipotent progenitor cell5.68e-0732


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)
MA0003.10.526413
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.896032
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.11.33581
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
MA0077.12.80666
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.11.51475
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.11.04599
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.11.3296
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.46063
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.181475
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.21.44804
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.11.39671
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.22.17326
MA0099.21.06348
MA0079.20.288542
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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