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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008738
|DRA_sample_Accession=CAGE@DRS008738
|accession_numbers=CAGE;DRX008848;DRR009720;DRZ001145;DRZ002530
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002038,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009663,UBERON:0002420,UBERON:0002616,UBERON:0002780,UBERON:0009661,UBERON:0000125,UBERON:0002950,UBERON:0002020,UBERON:0007245,UBERON:0010317,UBERON:0002308,UBERON:0010009,UBERON:0001017,UBERON:0001016,UBERON:0001893,UBERON:0001890,UBERON:0001891,UBERON:0010011,UBERON:0000454
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002038,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009663,UBERON:0002420,UBERON:0002616,UBERON:0002780,UBERON:0009661,UBERON:0000125,UBERON:0002950,UBERON:0002020,UBERON:0007245,UBERON:0010317,UBERON:0002308,UBERON:0010009,UBERON:0001017,UBERON:0001016,UBERON:0001893,UBERON:0001890,UBERON:0001891,UBERON:0010011,UBERON:0000454
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0002614
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0002614
Line 42: Line 43:
|is_a=EFO:0002091;;FF:0000208
|is_a=EFO:0002091;;FF:0000208
|is_obsolete=
|is_obsolete=
|library_id=CNhs12643
|library_ids=CNhs12643
|library_ids=CNhs12643
|name=Mouse Neurons - substantia nigra, donor6
|name=Mouse Neurons - substantia nigra, donor6
Line 85: Line 87:
|top_motifs=REST:2.72995994701;ZBTB6:2.72328419067;MTF1:2.6944485555;HAND1,2:2.17988972289;OCT4_SOX2{dimer}:2.15497278077;ZFP161:2.0746371218;PAX5:2.07276465092;MYFfamily:2.0537101963;EGR1..3:2.02821693656;KLF4:1.98902224135;LMO2:1.98002097474;ZIC1..3:1.93750145384;FOXD3:1.9318729483;TFAP2B:1.92707956663;NHLH1,2:1.89788510145;ATF2:1.88533844606;BREu{core}:1.83408375499;HIC1:1.8184567119;CUX2:1.79270848982;POU6F1:1.78937845492;MED-1{core}:1.78521382589;NFIL3:1.73747225502;FOXM1:1.69754387668;PAX4:1.67004723949;RFX1:1.6420519687;UFEwm:1.5933856444;PRRX1,2:1.55828628904;MAFB:1.45871941151;AHR_ARNT_ARNT2:1.44685777762;EVI1:1.4382630428;MTE{core}:1.42330519702;POU3F1..4:1.32492806082;NKX2-2,8:1.31770499406;PAX6:1.31398072551;ADNP_IRX_SIX_ZHX:1.20902503815;SMAD1..7,9:1.20746535222;TGIF1:1.19804104424;GTF2I:1.19154275431;VSX1,2:1.18152613104;JUN:1.18112078562;PRDM1:1.18043211308;DBP:1.17486074266;PBX1:1.16384607408;HBP1_HMGB_SSRP1_UBTF:1.15572001273;ZNF423:1.1519528065;GFI1B:1.14747098274;TFDP1:1.13592294267;RFX2..5_RFXANK_RFXAP:1.08996646788;ALX1:1.08648315168;HMGA1,2:1.06067104494;CREB1:1.06063758684;NRF1:1.05837452446;RBPJ:1.04282837435;TFAP2{A,C}:1.0378280276;ATF5_CREB3:1.02083793877;SREBF1,2:1.01228541051;IKZF1:1.01060811935;FOXN1:1.00911497081;PATZ1:0.984832092273;RREB1:0.974352631346;STAT1,3:0.954193389424;GATA4:0.938792622826;MYOD1:0.887027508341;ONECUT1,2:0.885854877612;MZF1:0.876821704892;ZEB1:0.839336499005;MAZ:0.82750857233;HOXA9_MEIS1:0.827043822172;PAX8:0.809994479496;FOX{I1,J2}:0.795590193238;LHX3,4:0.794719363142;NANOG:0.781322840634;GTF2A1,2:0.75984809042;ZNF143:0.756698105151;GZF1:0.756008766818;ARID5B:0.748933787211;HSF1,2:0.734609894229;NKX3-2:0.718989907939;CDC5L:0.707922879766;FOXP3:0.677511127618;SOX2:0.670620437032;PAX2:0.651684443649;HES1:0.643145355983;NFE2L2:0.578773662892;NFE2L1:0.524300270325;NKX6-1,2:0.521075459159;POU5F1:0.49056574372;POU1F1:0.479329671224;YY1:0.442482315113;RORA:0.430636185762;GCM1,2:0.413812482951;SOX{8,9,10}:0.40744173835;GLI1..3:0.372589770604;NR5A1,2:0.36279740663;FOXQ1:0.347069158158;ZNF384:0.321813804935;TEF:0.315914997231;SOX5:0.281558296324;TFAP4:0.277407429042;SP1:0.266030065655;FOX{F1,F2,J1}:0.234273401953;EBF1:0.201701473271;AIRE:0.170272233957;NFE2:0.16936646752;ESRRA:0.149353178471;SPZ1:0.140611055763;MYBL2:0.13989359478;HMX1:0.117488694377;CDX1,2,4:0.0888180333813;PAX1,9:0.0875302344293;ATF4:0.0742860843536;SOX17:0.0523034784133;LEF1_TCF7_TCF7L1,2:0.0393121710219;NR3C1:0.0199761277261;ZNF148:0.00571607936596;T:0.000947388874438;TAL1_TCF{3,4,12}:-0.0519817304704;ATF6:-0.0550609871518;NKX2-3_NKX2-5:-0.0637876232682;PPARG:-0.0879768465041;XCPE1{core}:-0.145774655587;RXR{A,B,G}:-0.156806149219;FOXP1:-0.158823795497;TLX1..3_NFIC{dimer}:-0.163456949753;BPTF:-0.197606670022;TFCP2:-0.203622530782;NFATC1..3:-0.2416693483;EN1,2:-0.252281495183;NKX3-1:-0.268406879496;NKX2-1,4:-0.288698432737;FOXA2:-0.293818425272;AR:-0.301560475845;SNAI1..3:-0.332267303866;bHLH_family:-0.335996899573;HOX{A4,D4}:-0.346304303105;ZBTB16:-0.346580453902;CRX:-0.366758691632;TOPORS:-0.407285661293;HIF1A:-0.409489023245;IRF7:-0.439025048542;TBX4,5:-0.445912570446;EP300:-0.476696155379;HOX{A5,B5}:-0.500982446169;MEF2{A,B,C,D}:-0.50281582151;IKZF2:-0.541824235652;FOSL2:-0.568896107688;FOXO1,3,4:-0.603865024047;ESR1:-0.605647354402;STAT2,4,6:-0.622188823179;PDX1:-0.642459227457;HLF:-0.644630866829;NR1H4:-0.64889220473;MYB:-0.659464177856;ZNF238:-0.684870687888;ELK1,4_GABP{A,B1}:-0.725524401182;NFY{A,B,C}:-0.773807446362;CEBPA,B_DDIT3:-0.779576229517;HNF4A_NR2F1,2:-0.7803186892;FOX{D1,D2}:-0.801824541714;BACH2:-0.804130930573;POU2F1..3:-0.814935715848;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.860192452449;SPI1:-0.882939508996;HNF1A:-0.888597735472;TEAD1:-0.90452335231;GATA6:-0.907710431904;RUNX1..3:-0.924679847491;IRF1,2:-0.939942284759;FOXL1:-0.959223791141;FOS_FOS{B,L1}_JUN{B,D}:-1.01991993625;NR6A1:-1.04809566519;RXRA_VDR{dimer}:-1.12974531219;TP53:-1.17328978537;NFKB1_REL_RELA:-1.218659505;ETS1,2:-1.26503613002;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.28260878481;DMAP1_NCOR{1,2}_SMARC:-1.28797092037;TBP:-1.30967478837;ELF1,2,4:-1.3937463628;SPIB:-1.41462884364;ALX4:-1.53581034488;TLX2:-1.54467290088;GFI1:-1.64162176749;PITX1..3:-1.67777688256;E2F1..5:-1.68316280936;NANOG{mouse}:-1.69116298058;NFIX:-1.72196269328;STAT5{A,B}:-1.81450939937;SRF:-1.81563336477
|top_motifs=REST:2.72995994701;ZBTB6:2.72328419067;MTF1:2.6944485555;HAND1,2:2.17988972289;OCT4_SOX2{dimer}:2.15497278077;ZFP161:2.0746371218;PAX5:2.07276465092;MYFfamily:2.0537101963;EGR1..3:2.02821693656;KLF4:1.98902224135;LMO2:1.98002097474;ZIC1..3:1.93750145384;FOXD3:1.9318729483;TFAP2B:1.92707956663;NHLH1,2:1.89788510145;ATF2:1.88533844606;BREu{core}:1.83408375499;HIC1:1.8184567119;CUX2:1.79270848982;POU6F1:1.78937845492;MED-1{core}:1.78521382589;NFIL3:1.73747225502;FOXM1:1.69754387668;PAX4:1.67004723949;RFX1:1.6420519687;UFEwm:1.5933856444;PRRX1,2:1.55828628904;MAFB:1.45871941151;AHR_ARNT_ARNT2:1.44685777762;EVI1:1.4382630428;MTE{core}:1.42330519702;POU3F1..4:1.32492806082;NKX2-2,8:1.31770499406;PAX6:1.31398072551;ADNP_IRX_SIX_ZHX:1.20902503815;SMAD1..7,9:1.20746535222;TGIF1:1.19804104424;GTF2I:1.19154275431;VSX1,2:1.18152613104;JUN:1.18112078562;PRDM1:1.18043211308;DBP:1.17486074266;PBX1:1.16384607408;HBP1_HMGB_SSRP1_UBTF:1.15572001273;ZNF423:1.1519528065;GFI1B:1.14747098274;TFDP1:1.13592294267;RFX2..5_RFXANK_RFXAP:1.08996646788;ALX1:1.08648315168;HMGA1,2:1.06067104494;CREB1:1.06063758684;NRF1:1.05837452446;RBPJ:1.04282837435;TFAP2{A,C}:1.0378280276;ATF5_CREB3:1.02083793877;SREBF1,2:1.01228541051;IKZF1:1.01060811935;FOXN1:1.00911497081;PATZ1:0.984832092273;RREB1:0.974352631346;STAT1,3:0.954193389424;GATA4:0.938792622826;MYOD1:0.887027508341;ONECUT1,2:0.885854877612;MZF1:0.876821704892;ZEB1:0.839336499005;MAZ:0.82750857233;HOXA9_MEIS1:0.827043822172;PAX8:0.809994479496;FOX{I1,J2}:0.795590193238;LHX3,4:0.794719363142;NANOG:0.781322840634;GTF2A1,2:0.75984809042;ZNF143:0.756698105151;GZF1:0.756008766818;ARID5B:0.748933787211;HSF1,2:0.734609894229;NKX3-2:0.718989907939;CDC5L:0.707922879766;FOXP3:0.677511127618;SOX2:0.670620437032;PAX2:0.651684443649;HES1:0.643145355983;NFE2L2:0.578773662892;NFE2L1:0.524300270325;NKX6-1,2:0.521075459159;POU5F1:0.49056574372;POU1F1:0.479329671224;YY1:0.442482315113;RORA:0.430636185762;GCM1,2:0.413812482951;SOX{8,9,10}:0.40744173835;GLI1..3:0.372589770604;NR5A1,2:0.36279740663;FOXQ1:0.347069158158;ZNF384:0.321813804935;TEF:0.315914997231;SOX5:0.281558296324;TFAP4:0.277407429042;SP1:0.266030065655;FOX{F1,F2,J1}:0.234273401953;EBF1:0.201701473271;AIRE:0.170272233957;NFE2:0.16936646752;ESRRA:0.149353178471;SPZ1:0.140611055763;MYBL2:0.13989359478;HMX1:0.117488694377;CDX1,2,4:0.0888180333813;PAX1,9:0.0875302344293;ATF4:0.0742860843536;SOX17:0.0523034784133;LEF1_TCF7_TCF7L1,2:0.0393121710219;NR3C1:0.0199761277261;ZNF148:0.00571607936596;T:0.000947388874438;TAL1_TCF{3,4,12}:-0.0519817304704;ATF6:-0.0550609871518;NKX2-3_NKX2-5:-0.0637876232682;PPARG:-0.0879768465041;XCPE1{core}:-0.145774655587;RXR{A,B,G}:-0.156806149219;FOXP1:-0.158823795497;TLX1..3_NFIC{dimer}:-0.163456949753;BPTF:-0.197606670022;TFCP2:-0.203622530782;NFATC1..3:-0.2416693483;EN1,2:-0.252281495183;NKX3-1:-0.268406879496;NKX2-1,4:-0.288698432737;FOXA2:-0.293818425272;AR:-0.301560475845;SNAI1..3:-0.332267303866;bHLH_family:-0.335996899573;HOX{A4,D4}:-0.346304303105;ZBTB16:-0.346580453902;CRX:-0.366758691632;TOPORS:-0.407285661293;HIF1A:-0.409489023245;IRF7:-0.439025048542;TBX4,5:-0.445912570446;EP300:-0.476696155379;HOX{A5,B5}:-0.500982446169;MEF2{A,B,C,D}:-0.50281582151;IKZF2:-0.541824235652;FOSL2:-0.568896107688;FOXO1,3,4:-0.603865024047;ESR1:-0.605647354402;STAT2,4,6:-0.622188823179;PDX1:-0.642459227457;HLF:-0.644630866829;NR1H4:-0.64889220473;MYB:-0.659464177856;ZNF238:-0.684870687888;ELK1,4_GABP{A,B1}:-0.725524401182;NFY{A,B,C}:-0.773807446362;CEBPA,B_DDIT3:-0.779576229517;HNF4A_NR2F1,2:-0.7803186892;FOX{D1,D2}:-0.801824541714;BACH2:-0.804130930573;POU2F1..3:-0.814935715848;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.860192452449;SPI1:-0.882939508996;HNF1A:-0.888597735472;TEAD1:-0.90452335231;GATA6:-0.907710431904;RUNX1..3:-0.924679847491;IRF1,2:-0.939942284759;FOXL1:-0.959223791141;FOS_FOS{B,L1}_JUN{B,D}:-1.01991993625;NR6A1:-1.04809566519;RXRA_VDR{dimer}:-1.12974531219;TP53:-1.17328978537;NFKB1_REL_RELA:-1.218659505;ETS1,2:-1.26503613002;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.28260878481;DMAP1_NCOR{1,2}_SMARC:-1.28797092037;TBP:-1.30967478837;ELF1,2,4:-1.3937463628;SPIB:-1.41462884364;ALX4:-1.53581034488;TLX2:-1.54467290088;GFI1:-1.64162176749;PITX1..3:-1.67777688256;E2F1..5:-1.68316280936;NANOG{mouse}:-1.69116298058;NFIX:-1.72196269328;STAT5{A,B}:-1.81450939937;SRF:-1.81563336477
|xref=
|xref=
}} {{DRAAccessionNumbers
|DRA_sample_Accession=CAGE@DRS008738
|accession_numbers=DRX008848;DRR009720;DRZ001145;DRZ002530;CAGE
|library_id=CNhs12643
}}
}}

Revision as of 17:27, 17 October 2013


Name:Mouse Neurons - substantia nigra, donor6
Species:Mouse (Mus musculus)
Library ID:CNhs12643
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesubstantia nigra
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companySciencell/3H
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNASUB2
catalog numbercustom
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008738
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
CNhs12643 CAGE DRX008848 DRR009720
CollapseAccession ID Mm9

Library idBAMCTSS
CNhs12643 DRZ001145 DRZ002530
Download raw sequence, BAM & CTSS
CollapseMm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
CollapseMm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs12643



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12643



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12643



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12643


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002614 (neuron of the substantia nigra)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002038 (substantia nigra)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009663 (telencephalic nucleus)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0009661 (midbrain nucleus)
0000125 (neural nucleus)
0002950 (regional part of midbrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0002308 (nucleus of brain)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0001891 (midbrain)
0010011 (collection of basal ganglia)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000208 (mouse neuron of the substantia nigra sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
CL:0000133 (neurectodermal cell)
CL:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)