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MCL coexpression mm9:1226: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0005681;spliceosome;0.00661407924265768;66125,20638!GO:0008380;RNA splicing;0.00661407924265768;66125,20638!GO:0006397;mRNA processing;0.00688011728768921;66125,20638!GO:0016071;mRNA metabolic process;0.00688011728768921;66125,20638!GO:0006396;RNA processing;0.00993700490759503;66125,20638!GO:0032991;macromolecular complex;0.00993700490759503;69833,66125,20638!GO:0030529;ribonucleoprotein complex;0.0107381397348516;66125,20638!GO:0016070;RNA metabolic process;0.0107381397348516;69833,66125,20638!GO:0030880;RNA polymerase complex;0.0113878965286287;69833!GO:0010467;gene expression;0.0147241541606693;69833,66125,20638!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0179963855922899;69833,66125,20638!GO:0003899;DNA-directed RNA polymerase activity;0.0223120998489921;69833!GO:0044428;nuclear part;0.0303298318377121;66125,20638!GO:0005634;nucleus;0.0342785404752569;69833,66125,20638!GO:0043283;biopolymer metabolic process;0.0350646740319669;69833,66125,20638!}}
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Latest revision as of 16:35, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:12728248..12728325,+p1@Sf3b5
Mm9::chr13:34254822..34254902,+p1@Psmg4
Mm9::chr15:78971754..78971788,+p1@Polr2f
Mm9::chr2:130005046..130005112,-p1@Snrpb
Mm9::chr7:133839456..133839523,+p1@Bola2
Mm9::chr8:72655226..72655291,+p1@Nr2c2ap


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:0005681spliceosome0.00661407924265768
GO:0008380RNA splicing0.00661407924265768
GO:0006397mRNA processing0.00688011728768921
GO:0016071mRNA metabolic process0.00688011728768921
GO:0006396RNA processing0.00993700490759503
GO:0032991macromolecular complex0.00993700490759503
GO:0030529ribonucleoprotein complex0.0107381397348516
GO:0016070RNA metabolic process0.0107381397348516
GO:0030880RNA polymerase complex0.0113878965286287
GO:0010467gene expression0.0147241541606693
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0179963855922899
GO:0003899DNA-directed RNA polymerase activity0.0223120998489921
GO:0044428nuclear part0.0303298318377121
GO:0005634nucleus0.0342785404752569
GO:0043283biopolymer metabolic process0.0350646740319669



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
animal cell2.80e-35115
eukaryotic cell2.80e-35115
somatic cell5.73e-34118
stem cell7.76e-3097
somatic stem cell5.37e-2791
multi fate stem cell5.37e-2791
motile cell1.60e-2554
connective tissue cell6.09e-2146
mesenchymal cell6.09e-2146
hematopoietic cell2.44e-1632
hematopoietic oligopotent progenitor cell2.44e-1632
hematopoietic stem cell2.44e-1632
angioblastic mesenchymal cell2.44e-1632
hematopoietic multipotent progenitor cell2.44e-1632
hematopoietic lineage restricted progenitor cell2.06e-1225
embryonic cell2.53e-1270
non-terminally differentiated cell9.35e-1149
common myeloid progenitor1.06e-1019
ectodermal cell2.08e-0944
neurectodermal cell2.08e-0944
leukocyte3.54e-0917
nongranular leukocyte3.54e-0917
neural cell3.76e-0943
myeloid cell7.10e-0916
nucleate cell1.99e-0816
myeloid lineage restricted progenitor cell4.30e-0713
lymphocyte8.51e-0713
common lymphoid progenitor8.51e-0713

Uber Anatomy
Ontology termp-valuen
connective tissue6.09e-2146
bone marrow2.89e-0916
hematopoietic system2.20e-0845
blood island2.20e-0845
hemolymphoid system4.03e-0848
immune system4.03e-0848


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)
MA0003.10.135108
MA0004.10.536396
MA0006.11.68531
MA0007.10.52077
MA0009.10.987341
MA0014.10.12867
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.11.41229
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.00638767
MA0074.10.638014
MA0076.11.85013
MA0077.10.968053
MA0078.10.729877
MA0081.11.19271
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.682297
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.829535
MA0145.10.379391
MA0146.10.990842
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.25.05991
MA0035.20.630778
MA0039.20.328366
MA0138.20.788113
MA0002.20.689262
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.37938
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.132921
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.11.08528
MA0163.10.372305
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.0520572
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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