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Latest revision as of 15:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:20731012..20731056,-p1@1110067D22Rik
Mm9::chr11:20731063..20731077,-p5@1110067D22Rik
Mm9::chr11:79153084..79153137,+p2@Nf1
Mm9::chr11:86570985..86571074,-p1@Cltc
Mm9::chr15:81641878..81641921,+p1@Tef
Mm9::chr18:36440723..36440805,+p1@Pura
Mm9::chr1:59820262..59820306,+p@chr1:59820262..59820306
+
Mm9::chr3:7503423..7503503,+p1@Fam164a
Mm9::chr5:67009875..67009950,-p1@Apbb2


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:0003690double-stranded DNA binding0.0134550899062544
GO:0048522positive regulation of cellular process0.0163456878692465
GO:0048518positive regulation of biological process0.0163456878692465
GO:0043566structure-specific DNA binding0.0163456878692465
GO:0030198extracellular matrix organization and biogenesis0.0163456878692465
GO:0046929negative regulation of neurotransmitter secretion0.0163456878692465
GO:0021897forebrain astrocyte development0.0163456878692465
GO:0021896forebrain astrocyte differentiation0.0163456878692465
GO:0043062extracellular structure organization and biogenesis0.0163456878692465
GO:0022011myelination in the peripheral nervous system0.0163456878692465
GO:0048712negative regulation of astrocyte differentiation0.0163456878692465
GO:0032292ensheathment of axons in the peripheral nervous system0.0163456878692465
GO:0046907intracellular transport0.0163456878692465
GO:0006915apoptosis0.0163456878692465
GO:0014065phosphoinositide 3-kinase cascade0.0163456878692465
GO:0046580negative regulation of Ras protein signal transduction0.0163456878692465
GO:0001937negative regulation of endothelial cell proliferation0.0163456878692465
GO:0048715negative regulation of oligodendrocyte differentiation0.0163456878692465
GO:0035021negative regulation of Rac protein signal transduction0.0163456878692465
GO:0048485sympathetic nervous system development0.0163456878692465
GO:0001953negative regulation of cell-matrix adhesion0.0163456878692465
GO:0014002astrocyte development0.0163456878692465
GO:0035035histone acetyltransferase binding0.0163456878692465
GO:0014044Schwann cell development0.0163456878692465
GO:0048853forebrain morphogenesis0.0163456878692465
GO:0045749negative regulation of S phase of mitotic cell cycle0.0163456878692465
GO:0032320positive regulation of Ras GTPase activity0.0163456878692465
GO:0012501programmed cell death0.0163456878692465
GO:0007399nervous system development0.0163456878692465
GO:0008219cell death0.0163456878692465
GO:0016265death0.0163456878692465
GO:0043525positive regulation of neuron apoptosis0.0163456878692465
GO:0048710regulation of astrocyte differentiation0.0163456878692465
GO:0001938positive regulation of endothelial cell proliferation0.0163456878692465
GO:0051224negative regulation of protein transport0.0163456878692465
GO:0048713regulation of oligodendrocyte differentiation0.0163456878692465
GO:0046823negative regulation of nucleocytoplasmic transport0.0163456878692465
GO:0048854brain morphogenesis0.0163456878692465
GO:0042308negative regulation of protein import into nucleus0.0163456878692465
GO:0042992negative regulation of transcription factor import into nucleus0.0163456878692465
GO:0051932synaptic transmission, GABAergic0.0163456878692465
GO:0032228regulation of synaptic transmission, GABAergic0.0163456878692465
GO:0048745smooth muscle development0.0163456878692465
GO:0022408negative regulation of cell-cell adhesion0.0163456878692465
GO:0043065positive regulation of apoptosis0.0163456878692465
GO:0043068positive regulation of programmed cell death0.0163456878692465
GO:0030029actin filament-based process0.0163456878692465
GO:0048731system development0.0163456878692465
GO:0051649establishment of cellular localization0.0163456878692465
GO:0008284positive regulation of cell proliferation0.0163456878692465
GO:0051641cellular localization0.0163456878692465
GO:0048844artery morphogenesis0.0163456878692465
GO:0031575G1/S transition checkpoint0.0163456878692465
GO:0033261regulation of progression through S phase0.0163456878692465
GO:0045930negative regulation of progression through mitotic cell cycle0.0163456878692465
GO:0030132clathrin coat of coated pit0.0163456878692465
GO:0007090regulation of S phase of mitotic cell cycle0.0163456878692465
GO:0043409negative regulation of MAPKKK cascade0.0163456878692465
GO:0005662DNA replication factor A complex0.0163456878692465
GO:0000074regulation of progression through cell cycle0.0163456878692465
GO:0048646anatomical structure formation0.01699335735862
GO:0008134transcription factor binding0.01699335735862
GO:0014014negative regulation of gliogenesis0.01699335735862
GO:0045686negative regulation of glial cell differentiation0.01699335735862
GO:0001936regulation of endothelial cell proliferation0.01699335735862
GO:0007406negative regulation of neuroblast proliferation0.01699335735862
GO:0035020regulation of Rac protein signal transduction0.01699335735862
GO:0045124regulation of bone resorption0.01699335735862
GO:0051058negative regulation of small GTPase mediated signal transduction0.01699335735862
GO:0048708astrocyte differentiation0.0175351338662379
GO:0051320S phase0.0175351338662379
GO:0001540beta-amyloid binding0.0175351338662379
GO:0046332SMAD binding0.0175351338662379
GO:0000084S phase of mitotic cell cycle0.0175351338662379
GO:0030130clathrin coat of trans-Golgi network vesicle0.0175351338662379
GO:0048483autonomic nervous system development0.0175351338662379
GO:0001952regulation of cell-matrix adhesion0.0175351338662379
GO:0014037Schwann cell differentiation0.0175351338662379
GO:0048523negative regulation of cellular process0.0175794545976659
GO:0000278mitotic cell cycle0.0175794545976659
GO:0012510trans-Golgi network transport vesicle membrane0.0175794545976659
GO:0021987cerebral cortex development0.0175794545976659
GO:0042990regulation of transcription factor import into nucleus0.0175794545976659
GO:0045671negative regulation of osteoclast differentiation0.0175794545976659
GO:0042991transcription factor import into nucleus0.0175794545976659
GO:0050821protein stabilization0.0175794545976659
GO:0001935endothelial cell proliferation0.0175794545976659
GO:0048856anatomical structure development0.0175794545976659
GO:0048519negative regulation of biological process0.0175794545976659
GO:0042306regulation of protein import into nucleus0.0175794545976659
GO:0043601nuclear replisome0.0175794545976659
GO:0045685regulation of glial cell differentiation0.0175794545976659
GO:0031647regulation of protein stability0.0175794545976659
GO:0002762negative regulation of myeloid leukocyte differentiation0.0175794545976659
GO:0014013regulation of gliogenesis0.0175794545976659
GO:0022407regulation of cell-cell adhesion0.0175794545976659
GO:0030894replisome0.0175794545976659
GO:0033157regulation of intracellular protein transport0.0175794545976659
GO:0030325adrenal gland development0.0175794545976659
GO:0032386regulation of intracellular transport0.0175794545976659
GO:0043596nuclear replication fork0.0189606964011911
GO:0021782glial cell development0.0189606964011911
GO:0048709oligodendrocyte differentiation0.0189606964011911
GO:0051223regulation of protein transport0.0197054482809939
GO:0004675transmembrane receptor protein serine/threonine kinase activity0.0197054482809939
GO:0048169regulation of long-term neuronal synaptic plasticity0.0197054482809939
GO:0030660Golgi-associated vesicle membrane0.0197054482809939
GO:0005024transforming growth factor beta receptor activity0.0197054482809939
GO:0030658transport vesicle membrane0.0197054482809939
GO:0022403cell cycle phase0.0202095827569335
GO:0016477cell migration0.0204644015387217
GO:0046822regulation of nucleocytoplasmic transport0.0204644015387217
GO:0051048negative regulation of secretion0.0204644015387217
GO:0030140trans-Golgi network transport vesicle0.0204644015387217
GO:0009888tissue development0.0204644015387217
GO:0007275multicellular organismal development0.0204644015387217
GO:0030125clathrin vesicle coat0.0204644015387217
GO:0007093mitotic cell cycle checkpoint0.0204644015387217
GO:0051349positive regulation of lyase activity0.0204644015387217
GO:0030308negative regulation of cell growth0.0204644015387217
GO:0045762positive regulation of adenylate cyclase activity0.0204644015387217
GO:0007162negative regulation of cell adhesion0.0204644015387217
GO:0031281positive regulation of cyclase activity0.0204644015387217
GO:0021510spinal cord development0.0204644015387217
GO:0021543pallium development0.0215144537072125
GO:0030336negative regulation of cell migration0.0215144537072125
GO:0048168regulation of neuronal synaptic plasticity0.0215144537072125
GO:0045453bone resorption0.0220076795855186
GO:0045670regulation of osteoclast differentiation0.0220076795855186
GO:0016601Rac protein signal transduction0.0220076795855186
GO:0030665clathrin coated vesicle membrane0.0220076795855186
GO:0030048actin filament-based movement0.0220076795855186
GO:0030199collagen fibril organization0.0220076795855186
GO:0048699generation of neurons0.0224068643188616
GO:0042127regulation of cell proliferation0.0225163873294182
GO:0016525negative regulation of angiogenesis0.0227857160623316
GO:0045761regulation of adenylate cyclase activity0.0227857160623316
GO:0006928cell motility0.0228170981353696
GO:0051674localization of cell0.0228170981353696
GO:0048468cell development0.023096674058741
GO:0043407negative regulation of MAP kinase activity0.023096674058741
GO:0009653anatomical structure morphogenesis0.023096674058741
GO:0022008neurogenesis0.023096674058741
GO:0030133transport vesicle0.023096674058741
GO:0031279regulation of cyclase activity0.023096674058741
GO:0048593camera-type eye morphogenesis0.023096674058741
GO:0051051negative regulation of transport0.023096674058741
GO:0043408regulation of MAPKKK cascade0.023096674058741
GO:0051339regulation of lyase activity0.023096674058741
GO:0051271negative regulation of cell motility0.023096674058741
GO:0002761regulation of myeloid leukocyte differentiation0.023096674058741
GO:0046928regulation of neurotransmitter secretion0.023096674058741
GO:0051726regulation of cell cycle0.0237507957228263
GO:0040013negative regulation of locomotion0.0237507957228263
GO:0045792negative regulation of cell size0.0237507957228263
GO:0045638negative regulation of myeloid cell differentiation0.0237507957228263
GO:0030316osteoclast differentiation0.0240709248791205
GO:0050768negative regulation of neurogenesis0.0240709248791205
GO:0050804regulation of synaptic transmission0.0240709248791205
GO:0051969regulation of transmission of nerve impulse0.0240709248791205
GO:0007346regulation of progression through mitotic cell cycle0.0240709248791205
GO:0003697single-stranded DNA binding0.0240709248791205
GO:0001666response to hypoxia0.0248108579845035
GO:0001889liver development0.0248108579845035
GO:0048167regulation of synaptic plasticity0.0248108579845035
GO:0042981regulation of apoptosis0.0251050011782061
GO:0043067regulation of programmed cell death0.0253729548010551
GO:0007632visual behavior0.0253729548010551
GO:0008542visual learning0.0253729548010551
GO:0006886intracellular protein transport0.0259086891893655
GO:0007422peripheral nervous system development0.0259086891893655
GO:0021537telencephalon development0.0259086891893655
GO:0050803regulation of synapse structure and activity0.0259086891893655
GO:0007270nerve-nerve synaptic transmission0.0265699613075102
GO:0005657replication fork0.0265699613075102
GO:0030120vesicle coat0.0265699613075102
GO:0001707mesoderm formation0.0272087109496776
GO:0001894tissue homeostasis0.0272087109496776
GO:0045926negative regulation of growth0.0272087109496776
GO:0048332mesoderm morphogenesis0.0273748186859302
GO:0030662coated vesicle membrane0.0273748186859302
GO:0007405neuroblast proliferation0.0273748186859302
GO:0031644regulation of neurological process0.0273748186859302
GO:0048871multicellular organismal homeostasis0.0273748186859302
GO:0000075cell cycle checkpoint0.0273748186859302
GO:0042552myelination0.0278214804145908
GO:0001649osteoblast differentiation0.0278214804145908
GO:0007088regulation of mitosis0.0278214804145908
GO:0001704formation of primary germ layer0.0278214804145908
GO:0005798Golgi-associated vesicle0.0286953384310088
GO:0007272ensheathment of neurons0.0292533937047309
GO:0046850regulation of bone remodeling0.0292533937047309
GO:0008366axon ensheathment0.0292533937047309
GO:0045765regulation of angiogenesis0.0301011951816067
GO:0009790embryonic development0.0301363014826384
GO:0007010cytoskeleton organization and biogenesis0.0301363014826384
GO:0005905coated pit0.03062586274139
GO:0008283cell proliferation0.0317820467544107
GO:0032318regulation of Ras GTPase activity0.0322634666508231
GO:0030118clathrin coat0.0329049836176353
GO:0043523regulation of neuron apoptosis0.0329049836176353
GO:0032502developmental process0.0332440968863381
GO:0045637regulation of myeloid cell differentiation0.0335335459870207
GO:0006469negative regulation of protein kinase activity0.034149533003231
GO:0033673negative regulation of kinase activity0.034149533003231
GO:0001508regulation of action potential0.034922014638442
GO:0051402neuron apoptosis0.0351769147734034
GO:0051348negative regulation of transferase activity0.0351769147734034
GO:0030659cytoplasmic vesicle membrane0.0351769147734034
GO:0010001glial cell differentiation0.0351769147734034
GO:0002573myeloid leukocyte differentiation0.0368407362901451
GO:0005515protein binding0.0370502388151655
GO:0042063gliogenesis0.0370531235352101
GO:0051325interphase0.0370531235352101
GO:0051329interphase of mitotic cell cycle0.0370531235352101
GO:0048592eye morphogenesis0.0386679777962139
GO:0007050cell cycle arrest0.0397176846146631
GO:0050767regulation of neurogenesis0.0397176846146631
GO:0030155regulation of cell adhesion0.0397176846146631
GO:0001656metanephros development0.0397176846146631
GO:0022402cell cycle process0.0399943934116325
GO:0008017microtubule binding0.0400475292700703
GO:0004702receptor signaling protein serine/threonine kinase activity0.0400475292700703
GO:0043086negative regulation of catalytic activity0.0407287675598444
GO:0035270endocrine system development0.0414036682275784
GO:0044433cytoplasmic vesicle part0.0417032600792224
GO:0007498mesoderm development0.0417032600792224
GO:0007612learning0.0417032600792224
GO:0007269neurotransmitter secretion0.0431004978089489
GO:0050794regulation of cellular process0.0431004978089489
GO:0030117membrane coat0.0431004978089489
GO:0048475coated membrane0.0431004978089489
GO:0030334regulation of cell migration0.0431004978089489
GO:0051046regulation of secretion0.0431004978089489
GO:0048869cellular developmental process0.0441314655668843
GO:0030154cell differentiation0.0441314655668843
GO:0015631tubulin binding0.0445029206157498
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0445029206157498
GO:0001764neuron migration0.0445029206157498
GO:0065008regulation of biological quality0.0445029206157498
GO:0012506vesicle membrane0.0446674617431578
GO:0006606protein import into nucleus0.0446674617431578
GO:0035023regulation of Rho protein signal transduction0.0446674617431578
GO:0051170nuclear import0.0452713279105757
GO:0015031protein transport0.0455026347024982
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.045683542693465
GO:0051270regulation of cell motility0.0462754481709401
GO:0043405regulation of MAP kinase activity0.0466741229496561
GO:0019933cAMP-mediated signaling0.0466741229496561
GO:0007369gastrulation0.0480212347133907
GO:0019935cyclic-nucleotide-mediated signaling0.0482043106355067
GO:0007160cell-matrix adhesion0.0482043106355067
GO:0040012regulation of locomotion0.0482043106355067
GO:0045184establishment of protein localization0.0482043106355067
GO:0045055regulated secretory pathway0.0482043106355067
GO:0043087regulation of GTPase activity0.0482043106355067
GO:0017038protein import0.0482043106355067
GO:0021915neural tube development0.0487597388117101
GO:0044454nuclear chromosome part0.0498570487141844
GO:0031589cell-substrate adhesion0.0498570487141844
GO:0043170macromolecule metabolic process0.0498574753935555



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
ectoderm-derived structure5.56e-1395
ectoderm5.56e-1395
presumptive ectoderm5.56e-1395
ecto-epithelium4.26e-1273
multi-cellular organism4.78e-12333
structure with developmental contribution from neural crest5.86e-1292
anatomical conduit5.91e-12122
regional part of nervous system1.43e-1154
neurectoderm8.25e-1164
neural plate8.25e-1164
presumptive neural plate8.25e-1164
central nervous system1.28e-1073
neural tube1.42e-1052
neural rod1.42e-1052
future spinal cord1.42e-1052
neural keel1.42e-1052
tube1.80e-10114
nervous system2.33e-1075
gray matter5.58e-1034
brain1.06e-0847
future brain1.06e-0847
embryo1.52e-08320
regional part of brain2.97e-0846
brain grey matter4.43e-0829
regional part of telencephalon4.43e-0829
telencephalon4.43e-0829
occipital lobe4.62e-0810
visual cortex4.62e-0810
neocortex4.62e-0810
pre-chordal neural plate1.21e-0749
anterior neural tube1.55e-0740
regional part of forebrain4.80e-0739
forebrain4.80e-0739
future forebrain4.80e-0739


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)
MA0003.15.04139
MA0004.11.02263
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.12.09919
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.11.47862
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.221677
MA0056.10
MA0057.11.93392
MA0058.10.305206
MA0059.10.316585
MA0060.10.9744
MA0061.10.56663
MA0063.10
MA0066.11.29967
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.00108891
MA0074.10.488775
MA0076.10.765781
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.709711
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.720048
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.670446
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.867077
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.442138
MA0146.13.35461
MA0147.11.12076
MA0148.10.410398
MA0149.10.330018
MA0062.20.738221
MA0035.20.482026
MA0039.21.36306
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.926067
MA0047.20.533516
MA0112.20.442124
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.490492
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.13.06145
MA0163.11.53225
MA0164.10.508398
MA0080.20.267388
MA0018.21.28741
MA0099.20.624421
MA0079.25.6867
MA0102.21.5442
MA0258.10.180934
MA0259.11.70624
MA0442.10