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MCL coexpression mm9:452: Difference between revisions

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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-0

Latest revision as of 15:19, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:19311758..19311893,+p1@Ifngr1
Mm9::chr15:76073831..76073878,-p1@Parp10
Mm9::chr17:34324273..34324290,-p1@Psmb9
Mm9::chr17:34324296..34324325,-p2@Psmb9
Mm9::chr17:34324734..34324773,+p1@Tap1
Mm9::chr17:34335287..34335329,+p1@Psmb8
Mm9::chr17:34335330..34335345,+p2@Psmb8
Mm9::chr17:34341452..34341518,+p1@Tap2
Mm9::chr19:46380069..46380117,-p1@uc008hss.1
Mm9::chr5:38871392..38871478,-p1@Slc2a9
Mm9::chr6:125181666..125181707,-p2@Tapbpl
Mm9::chr6:54766777..54766813,+p3@Znrf2
Mm9::chr7:4610585..4610628,-p1@Ppp6r1
Mm9::chr8:123260252..123260264,+p1@Irf8
Mm9::chr8:91159958..91160015,-p1@Snx20
Mm9::chr9:95855239..95855262,+p2@Xrn1


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:0002376immune system process0.000126456316580598
GO:0006955immune response0.000216050847144709
GO:0019882antigen processing and presentation0.000216050847144709
GO:0015198oligopeptide transporter activity0.000239109370773241
GO:0015197peptide transporter activity0.000239109370773241
GO:0006857oligopeptide transport0.000239109370773241
GO:0005839proteasome core complex (sensu Eukaryota)0.00124764663859537
GO:0004298threonine endopeptidase activity0.00133988942907512
GO:0000502proteasome complex (sensu Eukaryota)0.00213944119925394
GO:0015833peptide transport0.00357056488411637
GO:0043231intracellular membrane-bound organelle0.0067041546691773
GO:0043227membrane-bound organelle0.0067041546691773
GO:0022804active transmembrane transporter activity0.00816039369193958
GO:00045345'-3' exoribonuclease activity0.0143469667541324
GO:0043229intracellular organelle0.0143469667541324
GO:0043226organelle0.0143469667541324
GO:0043492ATPase activity, coupled to movement of substances0.0143469667541324
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0143469667541324
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0143469667541324
GO:0006511ubiquitin-dependent protein catabolic process0.0143469667541324
GO:0019941modification-dependent protein catabolic process0.0143469667541324
GO:0043632modification-dependent macromolecule catabolic process0.0143469667541324
GO:0051603proteolysis involved in cellular protein catabolic process0.0143469667541324
GO:0044257cellular protein catabolic process0.0143469667541324
GO:0015399primary active transmembrane transporter activity0.0143469667541324
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0143469667541324
GO:0019883antigen processing and presentation of endogenous antigen0.0143469667541324
GO:0002483antigen processing and presentation of endogenous peptide antigen0.0143469667541324
GO:0019885antigen processing and presentation of endogenous peptide antigen via MHC class I0.0143469667541324
GO:0044444cytoplasmic part0.0158273200625474
GO:0016787hydrolase activity0.0162258501755409
GO:00084095'-3' exonuclease activity0.0162484168177538
GO:0030163protein catabolic process0.0225127277997454
GO:0005783endoplasmic reticulum0.0281356080350887
GO:0005355glucose transmembrane transporter activity0.0296747923763085
GO:0015145monosaccharide transmembrane transporter activity0.0308702147567943
GO:0015149hexose transmembrane transporter activity0.0308702147567943
GO:0042623ATPase activity, coupled0.0310720046932331
GO:0044265cellular macromolecule catabolic process0.0310720046932331
GO:0043285biopolymer catabolic process0.0313768624398188
GO:0007569cell aging0.0313768624398188
GO:0016896exoribonuclease activity, producing 5'-phosphomonoesters0.0313768624398188
GO:0004532exoribonuclease activity0.0313768624398188
GO:0044424intracellular part0.0326666036173901
GO:0005887integral to plasma membrane0.0335838026201669
GO:0016887ATPase activity0.0335838026201669
GO:0031226intrinsic to plasma membrane0.0335838026201669
GO:0022857transmembrane transporter activity0.0335838026201669
GO:0005622intracellular0.0335838026201669
GO:0005737cytoplasm0.0335838026201669
GO:0032200telomere organization and biogenesis0.0338962854418947
GO:0000723telomere maintenance0.0338962854418947
GO:0016796exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.0352043359394095
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0364253721357344
GO:0009057macromolecule catabolic process0.0364253721357344
GO:0022892substrate-specific transporter activity0.0381679905325293
GO:0005829cytosol0.0462239333408587
GO:0015758glucose transport0.0474632960498069
GO:0008645hexose transport0.0474632960498069
GO:0015749monosaccharide transport0.0474632960498069
GO:0007568aging0.0474632960498069



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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.55e-18118
endoderm5.55e-18118
presumptive endoderm5.55e-18118
digestive system6.18e-18116
digestive tract6.18e-18116
primitive gut6.18e-18116
hemolymphoid system2.29e-1748
immune system2.29e-1748
subdivision of digestive tract7.92e-17114
hematopoietic system1.43e-1545
blood island1.43e-1545
unilaminar epithelium7.77e-1266
gut epithelium1.68e-1155
endo-epithelium3.65e-1169
connective tissue3.58e-1046
organ component layer2.17e-0924
intestine2.68e-0931
mucosa5.86e-0915
gastrointestinal system6.20e-0947
mixed endoderm/mesoderm-derived structure9.10e-0935
hemopoietic organ1.66e-0829
immune organ1.66e-0829
bone marrow3.12e-0816
lateral plate mesoderm5.11e-0887
intestinal mucosa7.92e-0813
anatomical wall7.92e-0813
wall of intestine7.92e-0813
gastrointestinal system mucosa7.92e-0813
foregut1.07e-0780
musculoskeletal system1.44e-0732
gland of gut2.23e-0724
thymus3.62e-0723
neck3.62e-0723
respiratory system epithelium3.62e-0723
hemolymphoid system gland3.62e-0723
pharyngeal epithelium3.62e-0723
thymic region3.62e-0723
pharyngeal gland3.62e-0723
entire pharyngeal arch endoderm3.62e-0723
thymus primordium3.62e-0723
early pharyngeal endoderm3.62e-0723
pharynx5.42e-0724
upper respiratory tract5.42e-0724
chordate pharynx5.42e-0724
pharyngeal arch system5.42e-0724
pharyngeal region of foregut5.42e-0724


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)
MA0003.10.831544
MA0004.10.631712
MA0006.10.344361
MA0007.10.604993
MA0009.10.599391
MA0014.10.382659
MA0017.10.122138
MA0019.10.434009
MA0024.11.3747
MA0025.10.819843
MA0027.12.21717
MA0028.10.112137
MA0029.10.53905
MA0030.10.545058
MA0031.10.512616
MA0038.10.897243
MA0040.10.611015
MA0041.10.498821
MA0042.10.476352
MA0043.10.689898
MA0046.10.632833
MA0048.11.01579
MA0050.17.73958
MA0051.19.01479
MA0052.10.618515
MA0055.10.189769
MA0056.10
MA0057.10.939001
MA0058.10.90709
MA0059.11.50458
MA0060.10.485984
MA0061.10.956293
MA0063.10
MA0066.11.57697
MA0067.10.92691
MA0068.11.33583
MA0069.10.618831
MA0070.11.48175
MA0071.10.251158
MA0072.10.601934
MA0073.10.267464
MA0074.10.299171
MA0076.10.134359
MA0077.10.581866
MA0078.10.37382
MA0081.10.525479
MA0083.10.68915
MA0084.11.24749
MA0087.10.648637
MA0088.10.437739
MA0089.10
MA0090.10.570974
MA0091.10.655274
MA0092.10.571528
MA0093.10.752955
MA0095.10
MA0098.10
MA0100.10.788514
MA0101.10.167439
MA0103.10.404646
MA0105.10.556586
MA0106.11.75755
MA0107.10.394565
MA0108.20.454274
MA0109.10
MA0111.10.206727
MA0113.10.356344
MA0114.10.263654
MA0115.10.692537
MA0116.10.105729
MA0117.10.662171
MA0119.10.16785
MA0122.10.680832
MA0124.10.875485
MA0125.10.804312
MA0130.10
MA0131.11.92675
MA0132.10
MA0133.10
MA0135.10.724328
MA0136.10.84684
MA0139.11.558
MA0140.10.289637
MA0141.10.437281
MA0142.10.499475
MA0143.10.37032
MA0144.10.0778672
MA0145.12.23255
MA0146.12.51051
MA0147.10.599447
MA0148.10.23425
MA0149.10.171305
MA0062.20.134374
MA0035.20.293466
MA0039.22.50641
MA0138.20.423003
MA0002.21.11938
MA0137.20.852405
MA0104.20.783486
MA0047.20.337465
MA0112.20.135501
MA0065.20.278863
MA0150.10.210447
MA0151.10
MA0152.10.337555
MA0153.10.740107
MA0154.10.676749
MA0155.10.32315
MA0156.10.41693
MA0157.10.47062
MA0158.10
MA0159.10.0900717
MA0160.10.23657
MA0161.10
MA0162.10.787943
MA0163.12.23838
MA0164.10.315868
MA0080.20.790324
MA0018.20.323932
MA0099.20.417463
MA0079.26.65935
MA0102.21.29919
MA0258.10.0692929
MA0259.11.98685
MA0442.10
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