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MCL coexpression mm9:222: Difference between revisions

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{{MCL_coexpression_mm9
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metabolic process;0.000579663125793403;22589,109331,81702,21969,94246!GO:0005694;chromosome;0.00116694694797247;22589,109331,21969,94246!GO:0006261;DNA-dependent DNA replication;0.00897090187905303;81702,21969!GO:0043231;intracellular membrane-bound organelle;0.00917410638940051;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043227;membrane-bound organelle;0.00917410638940051;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043229;intracellular organelle;0.0171860332599524;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043226;organelle;0.0171860332599524;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0003682;chromatin binding;0.0171860332599524;22589,94246!GO:0003676;nucleic acid binding;0.0171860332599524;22589,20658,67039,81702,21969,94246!GO:0043204;perikaryon;0.0185730418610017;21969!GO:0003677;DNA binding;0.0185730418610017;22589,20658,81702,21969,94246!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0198003208463124;22589,109331,67039,81702,21969,94246!GO:0003917;DNA topoisomerase type I activity;0.0200732190252243;21969!GO:0006260;DNA replication;0.0200732190252243;81702,21969!GO:0003918;DNA topoisomerase (ATP-hydrolyzing) activity;0.0222346756453473;21969!GO:0016853;isomerase activity;0.0226901522085912;21969,228005!GO:0040016;embryonic cleavage;0.0237111410404715;21969!GO:0003916;DNA topoisomerase activity;0.0246049051280258;21969!GO:0006281;DNA repair;0.0246049051280258;22589,81702!GO:0000785;chromatin;0.0246049051280258;22589,94246!GO:0006265;DNA topological change;0.0246049051280258;21969!GO:0030983;mismatched DNA binding;0.0246049051280258;81702!GO:0032392;DNA geometric change;0.0246049051280258;21969!GO:0006268;DNA unwinding during replication;0.0246049051280258;21969!GO:0032508;DNA duplex unwinding;0.0246049051280258;21969!GO:0043232;intracellular non-membrane-bound organelle;0.026948408889325;22589,109331,21969,94246!GO:0043228;non-membrane-bound organelle;0.026948408889325;22589,109331,21969,94246!GO:0006298;mismatch repair;0.026948408889325;81702!GO:0045005;maintenance of fidelity during DNA-dependent DNA replication;0.0279557744820937;81702!GO:0006974;response to DNA damage stimulus;0.0279557744820937;22589,81702!GO:0051301;cell division;0.0279557744820937;21969,100710!GO:0044424;intracellular part;0.029801112072005;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0009719;response to endogenous stimulus;0.0299004299360272;22589,81702!GO:0016363;nuclear matrix;0.0304182013251265;11737!GO:0005622;intracellular;0.0305396399708874;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0006325;establishment and/or maintenance of chromatin architecture;0.0305396399708874;109331,94246!GO:0043170;macromolecule metabolic process;0.0305396399708874;22589,109331,67039,81702,21969,228005,94246!GO:0007492;endoderm development;0.0305396399708874;81702!GO:0006323;DNA 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|gostat_on_MCL_coexpression=GO:0005634;nucleus;0.000579663125793403;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0006259;DNA metabolic process;0.000579663125793403;22589,109331,81702,21969,94246!GO:0005694;chromosome;0.00116694694797247;22589,109331,21969,94246!GO:0006261;DNA-dependent DNA replication;0.00897090187905303;81702,21969!GO:0043231;intracellular membrane-bound organelle;0.00917410638940051;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043227;membrane-bound organelle;0.00917410638940051;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043229;intracellular organelle;0.0171860332599524;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043226;organelle;0.0171860332599524;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0003682;chromatin binding;0.0171860332599524;22589,94246!GO:0003676;nucleic acid binding;0.0171860332599524;22589,20658,67039,81702,21969,94246!GO:0043204;perikaryon;0.0185730418610017;21969!GO:0003677;DNA binding;0.0185730418610017;22589,20658,81702,21969,94246!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0198003208463124;22589,109331,67039,81702,21969,94246!GO:0003917;DNA topoisomerase type I activity;0.0200732190252243;21969!GO:0006260;DNA replication;0.0200732190252243;81702,21969!GO:0003918;DNA topoisomerase (ATP-hydrolyzing) activity;0.0222346756453473;21969!GO:0016853;isomerase activity;0.0226901522085912;21969,228005!GO:0040016;embryonic cleavage;0.0237111410404715;21969!GO:0003916;DNA topoisomerase activity;0.0246049051280258;21969!GO:0006281;DNA repair;0.0246049051280258;22589,81702!GO:0000785;chromatin;0.0246049051280258;22589,94246!GO:0006265;DNA topological change;0.0246049051280258;21969!GO:0030983;mismatched DNA binding;0.0246049051280258;81702!GO:0032392;DNA geometric change;0.0246049051280258;21969!GO:0006268;DNA unwinding during replication;0.0246049051280258;21969!GO:0032508;DNA duplex unwinding;0.0246049051280258;21969!GO:0043232;intracellular non-membrane-bound organelle;0.026948408889325;22589,109331,21969,94246!GO:0043228;non-membrane-bound organelle;0.026948408889325;22589,109331,21969,94246!GO:0006298;mismatch repair;0.026948408889325;81702!GO:0045005;maintenance of fidelity during DNA-dependent DNA replication;0.0279557744820937;81702!GO:0006974;response to DNA damage stimulus;0.0279557744820937;22589,81702!GO:0051301;cell division;0.0279557744820937;21969,100710!GO:0044424;intracellular part;0.029801112072005;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0009719;response to endogenous stimulus;0.0299004299360272;22589,81702!GO:0016363;nuclear matrix;0.0304182013251265;11737!GO:0005622;intracellular;0.0305396399708874;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0006325;establishment and/or maintenance of chromatin architecture;0.0305396399708874;109331,94246!GO:0043170;macromolecule metabolic process;0.0305396399708874;22589,109331,67039,81702,21969,228005,94246!GO:0007492;endoderm development;0.0305396399708874;81702!GO:0006323;DNA packaging;0.0305396399708874;109331,94246!GO:0043283;biopolymer metabolic process;0.0343721912992878;22589,109331,67039,81702,21969,94246!GO:0044427;chromosomal part;0.0343721912992878;22589,94246!GO:0003690;double-stranded DNA binding;0.0346113957404018;81702!GO:0003725;double-stranded RNA binding;0.0418267428160646;20658!GO:0051276;chromosome organization and biogenesis;0.0498164078999933;109331,94246!
}}

Latest revision as of 14:55, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:107697886..107697901,+p@chr10:107697886..107697901
+
Mm9::chr11:117623812..117623827,+p@chr11:117623812..117623827
+
Mm9::chr11:75555748..75555764,+p@chr11:75555748..75555764
+
Mm9::chr11:94158437..94158452,-p7@Luc7l3
Mm9::chr11:94159097..94159133,-p4@Luc7l3
Mm9::chr11:94159135..94159150,-p8@Luc7l3
Mm9::chr11:94161291..94161382,-p5@Luc7l3
Mm9::chr11:94162886..94162899,-p@chr11:94162886..94162899
-
Mm9::chr11:94170962..94170981,-p@chr11:94170962..94170981
-
Mm9::chr12:60172455..60172477,+p@chr12:60172455..60172477
+
Mm9::chr12:60172575..60172590,+p@chr12:60172575..60172590
+
Mm9::chr12:84992240..84992272,+p@chr12:84992240..84992272
+
Mm9::chr12:85001540..85001595,+p@chr12:85001540..85001595
+
Mm9::chr12:85009144..85009225,-p@chr12:85009144..85009225
-
Mm9::chr13:14279165..14279179,+p@chr13:14279165..14279179
+
Mm9::chr14:75276101..75276106,-p@chr14:75276101..75276106
-
Mm9::chr14:75723653..75723658,+p@chr14:75723653..75723658
+
Mm9::chr14:75730228..75730246,+p@chr14:75730228..75730246
+
Mm9::chr16:91654866..91654920,+p3@Son
Mm9::chr17:32350640..32350672,-p@chr17:32350640..32350672
-
Mm9::chr18:32020264..32020279,+p@chr18:32020264..32020279
+
Mm9::chr19:53697535..53697548,+p@chr19:53697535..53697548
+
Mm9::chr19:55539264..55539277,+p@chr19:55539264..55539277
+
Mm9::chr2:160495855..160495908,+p6@Top1
Mm9::chr2:69587083..69587094,+p@chr2:69587083..69587094
+
Mm9::chr2:69587115..69587134,+p@chr2:69587115..69587134
+
Mm9::chr2:69587435..69587461,+p@chr2:69587435..69587461
+
Mm9::chr4:49662964..49662982,+p2@Rnf20
Mm9::chr4:58496493..58496514,-p1@ENSMUST00000119701
Mm9::chr5:151603420..151603434,+p@chr5:151603420..151603434
+
Mm9::chr5:42223804..42223826,-p@chr5:42223804..42223826
-
Mm9::chr5:90672804..90672850,-p@chr5:90672804..90672850
-
Mm9::chr5:90692406..90692420,-p5@Ankrd17
Mm9::chr8:125537100..125537114,-p@chr8:125537100..125537114
-
Mm9::chr9:20285349..20285363,-p@chr9:20285349..20285363
-
Mm9::chr9:62221442..62221455,+p8@Anp32a
Mm9::chr9:82794408..82794451,-p@chr9:82794408..82794451
-
Mm9::chrX:103070746..103070764,-p5@Atrx
Mm9::chrX:34640120..34640124,-p@chrX:34640120..34640124
-


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:0005634nucleus0.000579663125793403
GO:0006259DNA metabolic process0.000579663125793403
GO:0005694chromosome0.00116694694797247
GO:0006261DNA-dependent DNA replication0.00897090187905303
GO:0043231intracellular membrane-bound organelle0.00917410638940051
GO:0043227membrane-bound organelle0.00917410638940051
GO:0043229intracellular organelle0.0171860332599524
GO:0043226organelle0.0171860332599524
GO:0003682chromatin binding0.0171860332599524
GO:0003676nucleic acid binding0.0171860332599524
GO:0043204perikaryon0.0185730418610017
GO:0003677DNA binding0.0185730418610017
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0198003208463124
GO:0003917DNA topoisomerase type I activity0.0200732190252243
GO:0006260DNA replication0.0200732190252243
GO:0003918DNA topoisomerase (ATP-hydrolyzing) activity0.0222346756453473
GO:0016853isomerase activity0.0226901522085912
GO:0040016embryonic cleavage0.0237111410404715
GO:0003916DNA topoisomerase activity0.0246049051280258
GO:0006281DNA repair0.0246049051280258
GO:0000785chromatin0.0246049051280258
GO:0006265DNA topological change0.0246049051280258
GO:0030983mismatched DNA binding0.0246049051280258
GO:0032392DNA geometric change0.0246049051280258
GO:0006268DNA unwinding during replication0.0246049051280258
GO:0032508DNA duplex unwinding0.0246049051280258
GO:0043232intracellular non-membrane-bound organelle0.026948408889325
GO:0043228non-membrane-bound organelle0.026948408889325
GO:0006298mismatch repair0.026948408889325
GO:0045005maintenance of fidelity during DNA-dependent DNA replication0.0279557744820937
GO:0006974response to DNA damage stimulus0.0279557744820937
GO:0051301cell division0.0279557744820937
GO:0044424intracellular part0.029801112072005
GO:0009719response to endogenous stimulus0.0299004299360272
GO:0016363nuclear matrix0.0304182013251265
GO:0005622intracellular0.0305396399708874
GO:0006325establishment and/or maintenance of chromatin architecture0.0305396399708874
GO:0043170macromolecule metabolic process0.0305396399708874
GO:0007492endoderm development0.0305396399708874
GO:0006323DNA packaging0.0305396399708874
GO:0043283biopolymer metabolic process0.0343721912992878
GO:0044427chromosomal part0.0343721912992878
GO:0003690double-stranded DNA binding0.0346113957404018
GO:0003725double-stranded RNA binding0.0418267428160646
GO:0051276chromosome organization and biogenesis0.0498164078999933



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
embryo6.00e-08320
multi-cellular organism1.50e-07333
primordium6.05e-07134
occipital lobe7.94e-0710
visual cortex7.94e-0710
neocortex7.94e-0710


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)
MA0003.11.97127e-10
MA0004.10.184728
MA0006.10.142703
MA0007.10.384663
MA0009.10.295418
MA0014.12.4938e-07
MA0017.10.176909
MA0019.10.511584
MA0024.10.263595
MA0025.10.48174
MA0027.11.83212
MA0028.10.0579302
MA0029.11.2835
MA0030.11.30072
MA0031.10.228273
MA0038.10.109925
MA0040.10.822451
MA0041.11.62057
MA0042.10.773378
MA0043.10.369607
MA0046.10.32239
MA0048.10.00186738
MA0050.10.489958
MA0051.10.114454
MA0052.10.836068
MA0055.10.0187927
MA0056.10
MA0057.10.00600452
MA0058.10.0230527
MA0059.10.264983
MA0060.10.019438
MA0061.10.0293946
MA0063.10
MA0066.10.340713
MA0067.10.577859
MA0068.10.00148638
MA0069.10.31103
MA0070.10.820264
MA0071.11.27426
MA0072.11.46446
MA0073.18.32938e-13
MA0074.10.614782
MA0076.10.0175818
MA0077.10.281511
MA0078.10.817761
MA0081.10.880688
MA0083.10.368979
MA0084.10.878418
MA0087.10.891033
MA0088.10.0364594
MA0089.10
MA0090.10.151401
MA0091.10.43862
MA0092.10.151694
MA0093.10.0627068
MA0095.10
MA0098.10
MA0100.10.0824768
MA0101.10.116255
MA0103.10.191785
MA0105.10.0049716
MA0106.10.136153
MA0107.10.183235
MA0108.20.185867
MA0109.10
MA0111.10.164809
MA0113.10.76969
MA0114.10.338492
MA0115.10.971884
MA0116.10.010499
MA0117.10.346488
MA0119.10.116736
MA0122.10.362012
MA0124.11.31617
MA0125.10.468049
MA0130.10
MA0131.10.168986
MA0132.10
MA0133.10
MA0135.13.72634
MA0136.10.320131
MA0139.10.00178035
MA0140.10.589362
MA0141.10.689449
MA0142.11.82729
MA0143.10.80811
MA0144.10.0886256
MA0145.10.000418296
MA0146.17.60916e-06
MA0147.10.0345488
MA0148.10.775803
MA0149.10.0292146
MA0062.20.00559468
MA0035.21.00811
MA0039.22.468e-12
MA0138.20.164211
MA0002.20.516387
MA0137.20.019155
MA0104.20.0156277
MA0047.20.354114
MA0112.20.0457301
MA0065.20.238153
MA0150.10.169655
MA0151.10
MA0152.11.18244
MA0153.11.06037
MA0154.10.000201169
MA0155.10.00355102
MA0156.10.202379
MA0157.10.197497
MA0158.10
MA0159.10.111377
MA0160.10.450634
MA0161.10
MA0162.11.92674e-05
MA0163.11.39118e-06
MA0164.10.0969555
MA0080.20.0708729
MA0018.20.101591
MA0099.20.16046
MA0079.20
MA0102.20.928086
MA0258.10.719571
MA0259.10.00546925
MA0442.10
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