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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=0.107621400158085

Latest revision as of 14:57, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:81091291..81091312,+p7@Ankrd24
Mm9::chr11:75751179..75751224,-p2@Rph3al
Mm9::chr11:97213662..97213677,-p1@Gpr179
Mm9::chr12:74040716..74040745,+p3@Six6
Mm9::chr13:98517328..98517339,-p1@ENSMUST00000123535
Mm9::chr13:98517354..98517369,-p1@ENSMUST00000144993
p1@uc007rof.1
p1@uc007rog.1
Mm9::chr14:18814327..18814334,+p10@Thrb
Mm9::chr14:18814381..18814390,+p7@Thrb
Mm9::chr14:18814402..18814414,+p@chr14:18814402..18814414
+
Mm9::chr16:65520838..65520853,+p1@Pou1f1
Mm9::chr16:65523642..65523649,+p3@Pou1f1
Mm9::chr17:52741567..52741609,+p2@Kcnh8
Mm9::chr17:52741610..52741620,+p6@Kcnh8
Mm9::chr17:56381175..56381209,+p1@uc008dbj.1
Mm9::chr1:167090803..167090816,-p1@Tbx19
Mm9::chr1:167090905..167090912,-p2@Tbx19
Mm9::chr1:167090920..167090924,-p3@Tbx19
Mm9::chr1:74947550..74947553,-p@chr1:74947550..74947553
-
Mm9::chr1:75438947..75438964,+p@chr1:75438947..75438964
+
Mm9::chr2:157366618..157366640,-p@chr2:157366618..157366640
-
Mm9::chr2:174153248..174153264,+p2@Gnas
Mm9::chr2:174154863..174154912,+p@chr2:174154863..174154912
+
Mm9::chr2:26062195..26062206,+p@chr2:26062195..26062206
+
Mm9::chr2:26063801..26063813,-p2@Lhx3
Mm9::chr3:102586593..102586598,-p1@Tshb
Mm9::chr3:102586631..102586638,-p2@Tshb
Mm9::chr5:117863775..117863794,+p4@Ksr2
Mm9::chr5:117863819..117863831,+p8@Ksr2
Mm9::chr6:99619574..99619589,-p@chr6:99619574..99619589
-
Mm9::chr7:52910997..52911006,-p@chr7:52910997..52911006
-
Mm9::chr7:52911010..52911020,-p@chr7:52911010..52911020
-
Mm9::chr7:52911023..52911037,-p@chr7:52911023..52911037
-
Mm9::chr7:86033242..86033245,+p1@Mir7-2
Mm9::chrX:47150877..47150932,-p1@Igsf1


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:0050794regulation of cellular process0.00590710375771117
GO:0050789regulation of biological process0.00590710375771117
GO:0021983pituitary gland development0.00590710375771117
GO:0021536diencephalon development0.00590710375771117
GO:0065007biological regulation0.00590710375771117
GO:0003700transcription factor activity0.00590710375771117
GO:0043565sequence-specific DNA binding0.00642647008083665
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0112185472859472
GO:0007417central nervous system development0.0112364024618341
GO:0045893positive regulation of transcription, DNA-dependent0.0112364024618341
GO:0035270endocrine system development0.0112364024618341
GO:0006355regulation of transcription, DNA-dependent0.0112364024618341
GO:0006351transcription, DNA-dependent0.0112364024618341
GO:0032774RNA biosynthetic process0.0112364024618341
GO:0045449regulation of transcription0.0112364024618341
GO:0032962positive regulation of inositol trisphosphate biosynthetic process0.0112364024618341
GO:0040032post-embryonic body morphogenesis0.0112364024618341
GO:0032958inositol phosphate biosynthetic process0.0112364024618341
GO:0032960regulation of inositol trisphosphate biosynthetic process0.0112364024618341
GO:0032959inositol trisphosphate biosynthetic process0.0112364024618341
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0112364024618341
GO:0045941positive regulation of transcription0.0112364024618341
GO:0006350transcription0.0112364024618341
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0112364024618341
GO:0010468regulation of gene expression0.0124911522910315
GO:0048522positive regulation of cellular process0.0124911522910315
GO:0048732gland development0.0128309556366026
GO:0031323regulation of cellular metabolic process0.0128309556366026
GO:0009966regulation of signal transduction0.0128309556366026
GO:0007275multicellular organismal development0.0128309556366026
GO:0021526medial motor column neuron differentiation0.0128309556366026
GO:0006021inositol biosynthetic process0.0128309556366026
GO:0043647inositol phosphate metabolic process0.0128309556366026
GO:0032957inositol trisphosphate metabolic process0.0128309556366026
GO:0060133somatotropin secreting cell development0.0128309556366026
GO:0019222regulation of metabolic process0.0128309556366026
GO:0031325positive regulation of cellular metabolic process0.0128309556366026
GO:0016070RNA metabolic process0.0138703516458522
GO:0009893positive regulation of metabolic process0.0138703516458522
GO:0048518positive regulation of biological process0.0138703516458522
GO:0006357regulation of transcription from RNA polymerase II promoter0.0147857581625108
GO:0030900forebrain development0.0148460829282235
GO:0045165cell fate commitment0.0148460829282235
GO:0060126somatotropin secreting cell differentiation0.0148460829282235
GO:0021523somatic motor neuron differentiation0.0148460829282235
GO:0004887thyroid hormone receptor activity0.0148460829282235
GO:0043567regulation of insulin-like growth factor receptor signaling pathway0.0148460829282235
GO:0005667transcription factor complex0.0164725702998602
GO:0006366transcription from RNA polymerase II promoter0.0165816177594602
GO:0017158regulation of calcium ion-dependent exocytosis0.0172982678649299
GO:0045913positive regulation of carbohydrate metabolic process0.0172982678649299
GO:0045672positive regulation of osteoclast differentiation0.0172982678649299
GO:0043255regulation of carbohydrate biosynthetic process0.0172982678649299
GO:0048731system development0.0172982678649299
GO:0002521leukocyte differentiation0.0194933648973085
GO:0000155two-component sensor activity0.0202358494253453
GO:0010171body morphogenesis0.0202358494253453
GO:0019899enzyme binding0.0202358494253453
GO:0005515protein binding0.0211253157868178
GO:0010467gene expression0.0211253157868178
GO:0021984adenohypophysis development0.0211253157868178
GO:0006109regulation of carbohydrate metabolic process0.0211253157868178
GO:0021522spinal cord motor neuron differentiation0.0211253157868178
GO:0048701embryonic cranial skeleton morphogenesis0.0211253157868178
GO:0002763positive regulation of myeloid leukocyte differentiation0.0211253157868178
GO:0021517ventral spinal cord development0.0211253157868178
GO:0044451nucleoplasm part0.0221721459452071
GO:0003677DNA binding0.0222761548361811
GO:0045744negative regulation of G-protein coupled receptor protein signaling pathway0.0222761548361811
GO:0008340determination of adult life span0.0222761548361811
GO:0045669positive regulation of osteoblast differentiation0.0222761548361811
GO:0007191dopamine receptor, adenylate cyclase activating pathway0.0222761548361811
GO:0021515cell differentiation in spinal cord0.0222761548361811
GO:0005654nucleoplasm0.0228968227183673
GO:0048856anatomical structure development0.0238193328862061
GO:0032502developmental process0.0238193328862061
GO:0009886post-embryonic morphogenesis0.0238193328862061
GO:0001958endochondral ossification0.0238193328862061
GO:0000160two-component signal transduction system (phosphorelay)0.0254819134731916
GO:0008045motor axon guidance0.0254819134731916
GO:0048009insulin-like growth factor receptor signaling pathway0.0254819134731916
GO:0006020inositol metabolic process0.0254819134731916
GO:0007420brain development0.026621305295221
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0269882116123206
GO:0004673protein histidine kinase activity0.0269882116123206
GO:0010259multicellular organismal aging0.0269882116123206
GO:0007399nervous system development0.0275084067601556
GO:0048704embryonic skeletal morphogenesis0.029003590036877
GO:0031981nuclear lumen0.0307770382413672
GO:0045667regulation of osteoblast differentiation0.0307770382413672
GO:0030097hemopoiesis0.0307770382413672
GO:0048513organ development0.0320697550064008
GO:0045639positive regulation of myeloid cell differentiation0.0320697550064008
GO:0021510spinal cord development0.0320697550064008
GO:0035116embryonic hindlimb morphogenesis0.0338069629820718
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0338069629820718
GO:0048534hemopoietic or lymphoid organ development0.0354718434540506
GO:0045670regulation of osteoclast differentiation0.0354718434540506
GO:0048706embryonic skeletal development0.0374431685213606
GO:0043233organelle lumen0.0377593851977914
GO:0031974membrane-enclosed lumen0.0377593851977914
GO:0002520immune system development0.0387961186000068
GO:0007212dopamine receptor signaling pathway0.0393181365829893
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.0393181365829893
GO:0002761regulation of myeloid leukocyte differentiation0.0393181365829893
GO:0017157regulation of exocytosis0.0393181365829893
GO:0017137Rab GTPase binding0.0411022280316904
GO:0017156calcium ion-dependent exocytosis0.0424588572380158
GO:0030316osteoclast differentiation0.0424588572380158
GO:0040018positive regulation of multicellular organism growth0.0462383828423891
GO:0043234protein complex0.0462383828423891
GO:0048705skeletal morphogenesis0.0462383828423891
GO:0035137hindlimb morphogenesis0.0462383828423891
GO:0001708cell fate specification0.0462383828423891
GO:0019319hexose biosynthetic process0.0462383828423891
GO:0046165alcohol biosynthetic process0.0493702570149621
GO:0046364monosaccharide biosynthetic process0.0493702570149621



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
pituitary gland4.51e-708
gland of diencephalon4.51e-708
neuroendocrine gland4.51e-708
diencephalon4.68e-5610
future diencephalon4.68e-5610
regional part of forebrain3.32e-1439
forebrain3.32e-1439
future forebrain3.32e-1439
anterior neural tube7.68e-1440
regional part of brain5.50e-1246
brain1.01e-1147
future brain1.01e-1147
pre-chordal neural plate3.16e-1149
neural tube1.48e-1052
neural rod1.48e-1052
future spinal cord1.48e-1052
neural keel1.48e-1052
regional part of nervous system3.79e-1054
endocrine gland4.35e-0960
neurectoderm1.73e-0864
neural plate1.73e-0864
presumptive neural plate1.73e-0864
gland2.37e-0865
endocrine system1.72e-0772
ecto-epithelium2.22e-0773
central nervous system2.22e-0773
nervous system3.61e-0775


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)
MA0003.10.130578
MA0004.10.0668523
MA0006.10.0779732
MA0007.11.25431
MA0009.10.895867
MA0014.10.0865794
MA0017.10.0224649
MA0019.10.205515
MA0024.10.303927
MA0025.10.530879
MA0027.11.89129
MA0028.10.215634
MA0029.10.287662
MA0030.10.292547
MA0031.10.266391
MA0038.10.137249
MA0040.10.347276
MA0041.10.0399705
MA0042.10.143421
MA0043.10.415031
MA0046.10.365786
MA0048.12.4522
MA0050.10.0833996
MA0051.10.142335
MA0052.10.353618
MA0055.11.05766
MA0056.10
MA0057.10.400394
MA0058.10.0341303
MA0059.10.0376694
MA0060.10.371749
MA0061.10.466178
MA0063.10
MA0066.10.131108
MA0067.10.629308
MA0068.10.420921
MA0069.10.932273
MA0070.10.346258
MA0071.10.0830235
MA0072.10.339628
MA0073.11.46888
MA0074.10.360358
MA0076.10.112845
MA0077.10.32285
MA0078.10.161775
MA0081.10.171296
MA0083.10.414379
MA0084.10.934141
MA0087.10.379309
MA0088.10.0730061
MA0089.10
MA0090.10.0537918
MA0091.10.252373
MA0092.10.768262
MA0093.10.0207872
MA0095.10
MA0098.10
MA0100.10.106017
MA0101.10.360528
MA0103.12.01541
MA0105.10.677108
MA0106.10.166496
MA0107.10.101094
MA0108.20.629361
MA0109.10
MA0111.10.467988
MA0113.10.149628
MA0114.10.458548
MA0115.10.417336
MA0116.10.951333
MA0117.10.390961
MA0119.10.361635
MA0122.10.407133
MA0124.10.581749
MA0125.10.516802
MA0130.10
MA0131.10.202517
MA0132.10
MA0133.10
MA0135.10.445266
MA0136.10.12239
MA0139.10.458496
MA0140.10.105959
MA0141.10.0297262
MA0142.11.31229
MA0143.10.159321
MA0144.10.720381
MA0145.10.15673
MA0146.10.631427
MA0147.10.0544343
MA0148.10.0735508
MA0149.10.0420811
MA0062.20.0390526
MA0035.20.712602
MA0039.20.469314
MA0138.21.08784
MA0002.20.156814
MA0137.20.120024
MA0104.20.0273993
MA0047.20.136816
MA0112.20.377237
MA0065.21.43952
MA0150.10.0609087
MA0151.10
MA0152.10.424765
MA0153.10.459241
MA0154.10.297862
MA0155.11.34988
MA0156.10.0266647
MA0157.10.233393
MA0158.10
MA0159.11.15511
MA0160.10.259663
MA0161.10
MA0162.10.0802491
MA0163.10.230921
MA0164.10.388159
MA0080.20.0236909
MA0018.20.127843
MA0099.20.193216
MA0079.20.895631
MA0102.20.984244
MA0258.10.1126
MA0259.10.0485446
MA0442.10
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