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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_mean=-0.

Latest revision as of 16:35, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127080091..127080100,+p4@Stat6
Mm9::chr11:22760432..22760456,-p3@B3gnt2
Mm9::chr15:59480199..59480242,+p1@Trib1
Mm9::chr5:32438831..32438878,+p1@Fosl2
Mm9::chr5:32438894..32438908,+p2@Fosl2
Mm9::chr6:125299825..125299838,+p4@Tnfrsf1a


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:0048295positive regulation of isotype switching to IgE isotypes0.0151579902491918
GO:0002829negative regulation of T-helper 2 type immune response0.0151579902491918
GO:0002828regulation of T-helper 2 type immune response0.0151579902491918
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0151579902491918
GO:0048289isotype switching to IgE isotypes0.0151579902491918
GO:0043120tumor necrosis factor binding0.0151579902491918
GO:0048293regulation of isotype switching to IgE isotypes0.0151579902491918
GO:0005031tumor necrosis factor receptor activity0.0151579902491918
GO:0045893positive regulation of transcription, DNA-dependent0.0151579902491918
GO:0002820negative regulation of adaptive immune response0.0151579902491918
GO:0005035death receptor activity0.0151579902491918
GO:0002823negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0151579902491918
GO:0050777negative regulation of immune response0.0151579902491918
GO:0002683negative regulation of immune system process0.0151579902491918
GO:0042092T-helper 2 type immune response0.0151579902491918
GO:0045941positive regulation of transcription0.0151579902491918
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0151579902491918
GO:0045830positive regulation of isotype switching0.0194908236070853
GO:0031325positive regulation of cellular metabolic process0.0195423438037034
GO:0009893positive regulation of metabolic process0.0195423438037034
GO:0043283biopolymer metabolic process0.0195423438037034
GO:0006357regulation of transcription from RNA polymerase II promoter0.0195423438037034
GO:0045191regulation of isotype switching0.0195423438037034
GO:0006693prostaglandin metabolic process0.0195423438037034
GO:0006692prostanoid metabolic process0.0195423438037034
GO:0006366transcription from RNA polymerase II promoter0.0195423438037034
GO:0043565sequence-specific DNA binding0.0195423438037034
GO:0006355regulation of transcription, DNA-dependent0.0195423438037034
GO:0006351transcription, DNA-dependent0.0195423438037034
GO:0032774RNA biosynthetic process0.0195423438037034
GO:0050729positive regulation of inflammatory response0.0195423438037034
GO:0031349positive regulation of defense response0.0195423438037034
GO:0045449regulation of transcription0.0195423438037034
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0195423438037034
GO:0004860protein kinase inhibitor activity0.0195423438037034
GO:0006350transcription0.0195423438037034
GO:0002208somatic diversification of immunoglobulins during immune response0.0195423438037034
GO:0002204somatic recombination of immunoglobulin genes during immune response0.0195423438037034
GO:0045190isotype switching0.0195423438037034
GO:0002381immunoglobulin production during immune response0.0195423438037034
GO:0019210kinase inhibitor activity0.0195423438037034
GO:0002819regulation of adaptive immune response0.0195423438037034
GO:0002822regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.0.0195423438037034
GO:0010468regulation of gene expression0.0195423438037034
GO:0031323regulation of cellular metabolic process0.0208470082702882
GO:0050871positive regulation of B cell activation0.0208470082702882
GO:0016447somatic recombination of immunoglobulin gene segments0.0208470082702882
GO:0019222regulation of metabolic process0.0208470082702882
GO:0031347regulation of defense response0.0208470082702882
GO:0051241negative regulation of multicellular organismal process0.0208470082702882
GO:0050727regulation of inflammatory response0.0208470082702882
GO:0016444somatic cell DNA recombination0.0208470082702882
GO:0002562somatic diversification of immune receptors via germline recombination within a single locus0.0208470082702882
GO:0016070RNA metabolic process0.0208470082702882
GO:0006690icosanoid metabolic process0.0208470082702882
GO:0016445somatic diversification of immunoglobulins0.0208470082702882
GO:0002200somatic diversification of immune receptors0.0218430977084959
GO:0043170macromolecule metabolic process0.0222453518230858
GO:0050864regulation of B cell activation0.0243899157232587
GO:0002377immunoglobulin production0.0252756617130364
GO:0002440production of molecular mediator of immune response0.0253148365305417
GO:0048522positive regulation of cellular process0.0253148365305417
GO:0048583regulation of response to stimulus0.0271470582401027
GO:0019221cytokine and chemokine mediated signaling pathway0.0273279768087273
GO:0010467gene expression0.0295513593912224
GO:0003700transcription factor activity0.0295513593912224
GO:0048518positive regulation of biological process0.0309642625493989
GO:0044238primary metabolic process0.0336469501789967
GO:0044237cellular metabolic process0.0336585119279058
GO:0051251positive regulation of lymphocyte activation0.0338248111422986
GO:0019887protein kinase regulator activity0.0344361317682002
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0356074807768266
GO:0019955cytokine binding0.0356074807768266
GO:0016064immunoglobulin mediated immune response0.0366900650795972
GO:0019724B cell mediated immunity0.0367149999362538
GO:0006310DNA recombination0.0372632124910298
GO:0019207kinase regulator activity0.0372632124910298
GO:0050794regulation of cellular process0.0404470684666517
GO:0051249regulation of lymphocyte activation0.0407069757311571
GO:0042113B cell activation0.0411267233716689
GO:0050865regulation of cell activation0.0411267233716689
GO:0002250adaptive immune response0.0415255534530609
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0415255534530609
GO:0002449lymphocyte mediated immunity0.0424038110968864
GO:0002443leukocyte mediated immunity0.0450674053215862
GO:0050789regulation of biological process0.0493197986807879
GO:0050776regulation of immune response0.0493197986807879
GO:0002682regulation of immune system process0.0496297266270087



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
gastrointestinal system1.37e-0847
intestine2.12e-0831
endoderm-derived structure2.97e-08118
endoderm2.97e-08118
presumptive endoderm2.97e-08118
digestive system7.50e-08116
digestive tract7.50e-08116
primitive gut7.50e-08116
subdivision of digestive tract3.21e-07114
mucosa4.89e-0715


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)
MA0003.10.276983
MA0004.10.536396
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.10.558098
MA0017.11.00628
MA0019.10.800946
MA0024.12.16928
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
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.895081
MA0058.10.436487
MA0059.11.14076
MA0060.10.275911
MA0061.11.49922
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.753052
MA0074.10.638014
MA0076.11.04996
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.988233
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.12.43957
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.822296
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
MA0139.10.243463
MA0140.10.625902
MA0141.11.07584
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.10.153598
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.21.11803
MA0035.20.630778
MA0039.20.181031
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.37938
MA0065.20.380324
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
MA0162.10.70356
MA0163.11.03138
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.730639
MA0102.21.7182
MA0258.10.290587
MA0259.11.5079
MA0442.10
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