Personal tools

MCL coexpression mm9:3126

From FANTOM5_SSTAR

Jump to: navigation, search


Phase1 CAGE Peaks

 Short description
Mm9::chr17:88071863..88071920,+p1@Msh2
Mm9::chr17:88374384..88374425,+p1@Msh6
Mm9::chr17:88374426..88374447,+p2@Msh6


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:0032301MutSalpha complex1.10459508071702e-06
GO:0032137guanine/thymine mispair binding1.10459508071702e-06
GO:0032134mispaired DNA binding1.10459508071702e-06
GO:0045910negative regulation of DNA recombination1.32551409686043e-06
GO:0032300mismatch repair complex1.32551409686043e-06
GO:0000018regulation of DNA recombination1.84099180119504e-06
GO:0008340determination of adult life span3.31378524215107e-06
GO:0002566somatic diversification of immune receptors via somatic mutation3.43651802889741e-06
GO:0016446somatic hypermutation of immunoglobulin genes3.43651802889741e-06
GO:0030983mismatched DNA binding3.97654229058129e-06
GO:0010259multicellular organismal aging4.51879805747873e-06
GO:0006298mismatch repair5.06272745328636e-06
GO:0045005maintenance of fidelity during DNA-dependent DNA replication5.60794425594797e-06
GO:0051053negative regulation of DNA metabolic process7.17986802466065e-06
GO:0002208somatic diversification of immunoglobulins during immune response1.15982483475287e-05
GO:0051052regulation of DNA metabolic process1.15982483475287e-05
GO:0002204somatic recombination of immunoglobulin genes during immune response1.15982483475287e-05
GO:0003684damaged DNA binding1.15982483475287e-05
GO:0045190isotype switching1.15982483475287e-05
GO:0003690double-stranded DNA binding1.15982483475287e-05
GO:0002381immunoglobulin production during immune response1.21505458878873e-05
GO:0009411response to UV1.50626601915958e-05
GO:0016447somatic recombination of immunoglobulin gene segments1.68570814492033e-05
GO:0007568aging1.72486770296581e-05
GO:0016444somatic cell DNA recombination1.72486770296581e-05
GO:0002562somatic diversification of immune receptors via germline recombination within a single locus1.72486770296581e-05
GO:0016445somatic diversification of immunoglobulins1.77962540782187e-05
GO:0002200somatic diversification of immune receptors1.95671128584158e-05
GO:0042770DNA damage response, signal transduction2.266324389747e-05
GO:0002377immunoglobulin production2.72834984937105e-05
GO:0002440production of molecular mediator of immune response2.77930375148154e-05
GO:0006261DNA-dependent DNA replication3.57267471419412e-05
GO:0043566structure-specific DNA binding3.77570682136001e-05
GO:0016064immunoglobulin mediated immune response7.84262507309087e-05
GO:0019724B cell mediated immunity7.84262507309087e-05
GO:0009416response to light stimulus8.06354408923426e-05
GO:0006310DNA recombination8.06354408923428e-05
GO:0042113B cell activation0.000103773801004205
GO:0002250adaptive immune response0.000108139858402197
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.000108139858402197
GO:0002449lymphocyte mediated immunity0.000112510898935891
GO:0009314response to radiation0.000112510898935891
GO:0002443leukocyte mediated immunity0.000124613738059495
GO:0006260DNA replication0.000222023611224122
GO:0002252immune effector process0.000222023611224122
GO:0009628response to abiotic stimulus0.000336853473745617
GO:0006281DNA repair0.000408723681888293
GO:0046649lymphocyte activation0.000408838254250388
GO:0032302MutSbeta complex0.000411450396188717
GO:0045321leukocyte activation0.000466470502586799
GO:0001775cell activation0.000526523655141781
GO:0006974response to DNA damage stimulus0.000564299390754764
GO:0002520immune system development0.000636676331246617
GO:0009719response to endogenous stimulus0.000636676331246617
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000650405667073105
GO:0004422hypoxanthine phosphoribosyltransferase activity0.000720018468418099
GO:0031324negative regulation of cellular metabolic process0.000823330291216552
GO:0009892negative regulation of metabolic process0.00100799824090832
GO:0031573intra-S DNA damage checkpoint0.00100799824090832
GO:0019237centromeric DNA binding0.00100799824090832
GO:0042981regulation of apoptosis0.00125630487721288
GO:0043067regulation of programmed cell death0.00125996328253913
GO:0006301postreplication repair0.00125996328253913
GO:0010224response to UV-B0.00125996328253913
GO:0006955immune response0.00192923478666894
GO:0006915apoptosis0.00302761143479985
GO:0006259DNA metabolic process0.00303708417443146
GO:0012501programmed cell death0.00303708417443146
GO:0010165response to X-ray0.00316136667868932
GO:0008219cell death0.00316136667868932
GO:0016265death0.00316136667868932
GO:0002376immune system process0.00394897343835839
GO:0006950response to stress0.00410388848509244
GO:0008630DNA damage response, signal transduction resulting in induction of apoptosis0.00456783940125631
GO:0000077DNA damage checkpoint0.00456783940125631
GO:0048523negative regulation of cellular process0.00485662842114258
GO:0031570DNA integrity checkpoint0.00523391578181307
GO:0010212response to ionizing radiation0.00539547157395146
GO:0048519negative regulation of biological process0.00539547157395146
GO:0043524negative regulation of neuron apoptosis0.00579281417436577
GO:0044428nuclear part0.00638815623589258
GO:0000075cell cycle checkpoint0.00638815623589258
GO:0008629induction of apoptosis by intracellular signals0.0072813443799675
GO:0000790nuclear chromatin0.00743427994164438
GO:0016763transferase activity, transferring pentosyl groups0.0078203772286416
GO:0048468cell development0.00786280319950723
GO:0043523regulation of neuron apoptosis0.00787191588747264
GO:0030183B cell differentiation0.00801113858398435
GO:0051402neuron apoptosis0.00859937199282748
GO:0005524ATP binding0.00930677812585996
GO:0032559adenyl ribonucleotide binding0.00943009814178596
GO:0007050cell cycle arrest0.00984950624419794
GO:0030554adenyl nucleotide binding0.0101680471426959
GO:0006119oxidative phosphorylation0.0109234700143371
GO:0006164purine nucleotide biosynthetic process0.0136196908178191
GO:0032553ribonucleotide binding0.0136196908178191
GO:0032555purine ribonucleotide binding0.0136196908178191
GO:0043234protein complex0.0136196908178191
GO:0044454nuclear chromosome part0.0136196908178191
GO:0017076purine nucleotide binding0.0144140821272926
GO:0048731system development0.0145733056803732
GO:0006163purine nucleotide metabolic process0.0145974080908556
GO:0048869cellular developmental process0.014926117176959
GO:0030154cell differentiation0.014926117176959
GO:0000228nuclear chromosome0.0149452030019608
GO:0000166nucleotide binding0.0172915378599145
GO:0030098lymphocyte differentiation0.0172915378599145
GO:0003677DNA binding0.017417163183156
GO:0003682chromatin binding0.0181611850926484
GO:0048856anatomical structure development0.0181611850926484
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0181611850926484
GO:0032991macromolecular complex0.0189921612564465
GO:0045786negative regulation of progression through cell cycle0.0206311186083919
GO:0001701in utero embryonic development0.0208278894505394
GO:0031323regulation of cellular metabolic process0.0208278894505394
GO:0009165nucleotide biosynthetic process0.0211335987252187
GO:0007275multicellular organismal development0.0214186646059709
GO:0002521leukocyte differentiation0.0214186646059709
GO:0019222regulation of metabolic process0.0214186646059709
GO:0006917induction of apoptosis0.0214186646059709
GO:0012502induction of programmed cell death0.0214186646059709
GO:0044446intracellular organelle part0.0236398165012331
GO:0044422organelle part0.0236398165012331
GO:0043066negative regulation of apoptosis0.0241275812678535
GO:0043069negative regulation of programmed cell death0.0242544955368895
GO:0043065positive regulation of apoptosis0.0259656376627664
GO:0043068positive regulation of programmed cell death0.0260758368641234
GO:0000074regulation of progression through cell cycle0.027900544291027
GO:0009117nucleotide metabolic process0.0281485248832004
GO:0000785chromatin0.0296989949745331
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0296989949745331
GO:0003676nucleic acid binding0.0308758257953824
GO:0030097hemopoiesis0.0313512986094566
GO:0032502developmental process0.0323943610132257
GO:0043009chordate embryonic development0.0328055083993732
GO:0009792embryonic development ending in birth or egg hatching0.0330036116311129
GO:0048534hemopoietic or lymphoid organ development0.0336794882180467
GO:0016757transferase activity, transferring glycosyl groups0.0336794882180467
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0340527432305236
GO:0016887ATPase activity0.0373182871840627
GO:0050794regulation of cellular process0.0386077915932061
GO:0044427chromosomal part0.0422449277084787
GO:0006928cell motility0.0449610239423505
GO:0051674localization of cell0.0449610239423505
GO:0050789regulation of biological process0.0465663462567136
GO:0051726regulation of cell cycle0.0478692544526144
GO:0005694chromosome0.0482161388422169



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
anterior region of body4.27e-0943
hemopoietic organ4.28e-0929
immune organ4.28e-0929
primordium9.29e-08134
craniocervical region2.36e-0736
thymus5.46e-0723
neck5.46e-0723
respiratory system epithelium5.46e-0723
hemolymphoid system gland5.46e-0723
pharyngeal epithelium5.46e-0723
thymic region5.46e-0723
pharyngeal gland5.46e-0723
entire pharyngeal arch endoderm5.46e-0723
thymus primordium5.46e-0723
early pharyngeal endoderm5.46e-0723
gland of gut9.89e-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)
MA0003.10.526413
MA0004.10.801718
MA0006.10.60285
MA0007.13.07498
MA0009.11.27673
MA0014.12.60474
MA0017.10.635031
MA0019.11.08369
MA0024.12.75393
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
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.13.20384
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.121346
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
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
MA0093.10.62555
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
MA0114.10.537669
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
MA0146.11.44443
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.21.06145
MA0035.20.903829
MA0039.23.91141
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.21.81944
MA0102.22.01714
MA0258.10.520639
MA0259.11.34197
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:3126&oldid=3075125"