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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS009016
|DRA_sample_Accession=CAGE@DRS009016
|accession_numbers=CAGE;DRX009153;DRR010027;DRZ001452;DRZ002835
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
Line 42: Line 43:
|is_a=EFO:0002091;;FF:0011405
|is_a=EFO:0002091;;FF:0011405
|is_obsolete=
|is_obsolete=
|library_id=CNhs10515
|library_ids=CNhs10515
|library_ids=CNhs10515
|name=whole body, neonate N06
|name=whole body, neonate N06
Line 85: Line 87:
|top_motifs=TBP:3.61580461955;HOX{A4,D4}:2.56527698743;SMAD1..7,9:2.51043625328;FOXL1:2.37666021884;ALX1:2.35807434858;ESR1:2.29781351319;MEF2{A,B,C,D}:2.27814580608;TFCP2:2.27396124057;TFAP4:2.23526176882;GLI1..3:2.08749725989;GCM1,2:2.04568872473;ZNF148:1.97034539092;MYOD1:1.90043073937;FOSL2:1.88269826869;TFAP2{A,C}:1.84912224615;ZNF238:1.78143010192;PAX1,9:1.71473425355;NFE2L2:1.691751673;EBF1:1.55250942437;FOXP3:1.50153870557;NFATC1..3:1.44670847242;MYFfamily:1.44028181279;TAL1_TCF{3,4,12}:1.40161132358;FOX{I1,J2}:1.39886773112;LEF1_TCF7_TCF7L1,2:1.33450696238;TEAD1:1.27610322224;FOS_FOS{B,L1}_JUN{B,D}:1.27414279606;TLX2:1.27074726117;NKX2-3_NKX2-5:1.17255486488;SOX5:1.14017589898;ATF6:1.13894691507;TLX1..3_NFIC{dimer}:1.12285225247;TOPORS:1.10921338842;XCPE1{core}:1.10729380464;MAFB:1.09121873801;PAX5:1.08392103529;SRF:1.07430811796;RXRA_VDR{dimer}:1.04672067235;TGIF1:1.04503390897;ZNF423:1.02653879844;GTF2A1,2:0.994385344886;MAZ:0.981977124436;VSX1,2:0.968598576242;IKZF1:0.957817388718;MTF1:0.956323540724;NANOG:0.950495047453;TP53:0.932742876775;STAT2,4,6:0.923083630548;SP1:0.919232079337;NHLH1,2:0.916149302991;SOX{8,9,10}:0.888195948508;EN1,2:0.86002782377;EP300:0.856784967501;HES1:0.848739318754;CEBPA,B_DDIT3:0.826103348416;GTF2I:0.804701346143;MYBL2:0.788982153925;PATZ1:0.769097179357;FOXA2:0.763323697059;HMX1:0.744489703447;BACH2:0.731290525331;HSF1,2:0.714613927982;GFI1B:0.675025034873;HLF:0.653690009554;KLF4:0.623352087305;NR5A1,2:0.612951553773;PPARG:0.611490058718;HIC1:0.590992893397;NFE2L1:0.573792341751;GFI1:0.556598688547;TBX4,5:0.554181184386;LMO2:0.552568318889;RXR{A,B,G}:0.481398231355;RREB1:0.477872518267;TFAP2B:0.470326610669;ESRRA:0.466800757998;NKX2-1,4:0.435643925329;NR3C1:0.427056741687;T:0.414399700214;GATA6:0.395715772772;CRX:0.378605416167;PAX2:0.375177351891;NFE2:0.369873907228;ZIC1..3:0.368380972611;PRDM1:0.333875223893;SPZ1:0.330395401771;RORA:0.330311013683;NKX3-2:0.30043788695;RUNX1..3:0.285006108358;ZBTB6:0.27491407879;MTE{core}:0.266657006608;REST:0.262668198745;HIF1A:0.252694532018;HMGA1,2:0.252333583838;SREBF1,2:0.23669556674;GATA4:0.183432397482;MZF1:0.176700483548;SPI1:0.166151320184;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.162611619942;GZF1:0.158727117553;FOX{F1,F2,J1}:0.152892320742;SNAI1..3:0.130863473289;SPIB:0.107536107508;NR1H4:0.106318151918;STAT5{A,B}:0.10382434826;DMAP1_NCOR{1,2}_SMARC:0.0930439203393;IRF7:0.0924498935544;ALX4:0.0636833581989;PDX1:0.0625871875495;EGR1..3:0.0567594034772;UFEwm:0.052625645516;ETS1,2:0.0494824480689;ATF2:0.0470362848986;IKZF2:0.0351162933459;POU3F1..4:0.0187596334328;HOXA9_MEIS1:0.0123830502205;NKX2-2,8:0.0109314651948;FOX{D1,D2}:-0.0453895329073;NFIL3:-0.0555420767264;NFKB1_REL_RELA:-0.115280268584;POU2F1..3:-0.15987066058;SOX2:-0.163903261414;MED-1{core}:-0.186939034467;YY1:-0.188368129428;POU5F1:-0.189752344197;HOX{A5,B5}:-0.192342986033;FOXQ1:-0.204018592509;PRRX1,2:-0.206104571411;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.21614412786;E2F1..5:-0.217407013529;ZFP161:-0.22113980061;HNF1A:-0.226477543642;FOXO1,3,4:-0.234734318039;CUX2:-0.269273986785;HNF4A_NR2F1,2:-0.27535791591;JUN:-0.279540135945;ZEB1:-0.30018227749;NANOG{mouse}:-0.302769074931;IRF1,2:-0.317599189792;HAND1,2:-0.322019767274;BREu{core}:-0.326726995675;SOX17:-0.329939157907;EVI1:-0.351675971179;ATF4:-0.406139785367;DBP:-0.429115099094;LHX3,4:-0.430114132624;FOXN1:-0.437695938817;TFDP1:-0.451824220219;NR6A1:-0.455547152616;POU6F1:-0.463859384762;FOXM1:-0.467093613767;ZNF143:-0.469951848796;NKX3-1:-0.485301241081;MYB:-0.532378007106;TEF:-0.536784681494;NFIX:-0.547955864037;RFX1:-0.568958261668;ZNF384:-0.587797242908;bHLH_family:-0.594375410944;PAX6:-0.601134817031;ELF1,2,4:-0.607407536778;RBPJ:-0.681561602125;RFX2..5_RFXANK_RFXAP:-0.701783443504;AR:-0.732091263483;CDC5L:-0.776548359213;NFY{A,B,C}:-0.850165909163;ATF5_CREB3:-0.850934526498;AHR_ARNT_ARNT2:-0.873281179786;PBX1:-0.885913781914;HBP1_HMGB_SSRP1_UBTF:-0.887009910426;PITX1..3:-0.909852357574;PAX4:-0.911198190091;FOXP1:-0.991114423879;NRF1:-0.991961786386;OCT4_SOX2{dimer}:-1.00163416311;PAX8:-1.028836624;BPTF:-1.15176776487;NKX6-1,2:-1.1585524407;STAT1,3:-1.19364342198;ADNP_IRX_SIX_ZHX:-1.21235327903;CREB1:-1.2135722232;POU1F1:-1.28116879681;AIRE:-1.32647117626;ARID5B:-1.38000094947;FOXD3:-1.44673878613;ELK1,4_GABP{A,B1}:-1.47138434406;ONECUT1,2:-1.65775264557;CDX1,2,4:-1.73968725906;ZBTB16:-1.91133068796
|top_motifs=TBP:3.61580461955;HOX{A4,D4}:2.56527698743;SMAD1..7,9:2.51043625328;FOXL1:2.37666021884;ALX1:2.35807434858;ESR1:2.29781351319;MEF2{A,B,C,D}:2.27814580608;TFCP2:2.27396124057;TFAP4:2.23526176882;GLI1..3:2.08749725989;GCM1,2:2.04568872473;ZNF148:1.97034539092;MYOD1:1.90043073937;FOSL2:1.88269826869;TFAP2{A,C}:1.84912224615;ZNF238:1.78143010192;PAX1,9:1.71473425355;NFE2L2:1.691751673;EBF1:1.55250942437;FOXP3:1.50153870557;NFATC1..3:1.44670847242;MYFfamily:1.44028181279;TAL1_TCF{3,4,12}:1.40161132358;FOX{I1,J2}:1.39886773112;LEF1_TCF7_TCF7L1,2:1.33450696238;TEAD1:1.27610322224;FOS_FOS{B,L1}_JUN{B,D}:1.27414279606;TLX2:1.27074726117;NKX2-3_NKX2-5:1.17255486488;SOX5:1.14017589898;ATF6:1.13894691507;TLX1..3_NFIC{dimer}:1.12285225247;TOPORS:1.10921338842;XCPE1{core}:1.10729380464;MAFB:1.09121873801;PAX5:1.08392103529;SRF:1.07430811796;RXRA_VDR{dimer}:1.04672067235;TGIF1:1.04503390897;ZNF423:1.02653879844;GTF2A1,2:0.994385344886;MAZ:0.981977124436;VSX1,2:0.968598576242;IKZF1:0.957817388718;MTF1:0.956323540724;NANOG:0.950495047453;TP53:0.932742876775;STAT2,4,6:0.923083630548;SP1:0.919232079337;NHLH1,2:0.916149302991;SOX{8,9,10}:0.888195948508;EN1,2:0.86002782377;EP300:0.856784967501;HES1:0.848739318754;CEBPA,B_DDIT3:0.826103348416;GTF2I:0.804701346143;MYBL2:0.788982153925;PATZ1:0.769097179357;FOXA2:0.763323697059;HMX1:0.744489703447;BACH2:0.731290525331;HSF1,2:0.714613927982;GFI1B:0.675025034873;HLF:0.653690009554;KLF4:0.623352087305;NR5A1,2:0.612951553773;PPARG:0.611490058718;HIC1:0.590992893397;NFE2L1:0.573792341751;GFI1:0.556598688547;TBX4,5:0.554181184386;LMO2:0.552568318889;RXR{A,B,G}:0.481398231355;RREB1:0.477872518267;TFAP2B:0.470326610669;ESRRA:0.466800757998;NKX2-1,4:0.435643925329;NR3C1:0.427056741687;T:0.414399700214;GATA6:0.395715772772;CRX:0.378605416167;PAX2:0.375177351891;NFE2:0.369873907228;ZIC1..3:0.368380972611;PRDM1:0.333875223893;SPZ1:0.330395401771;RORA:0.330311013683;NKX3-2:0.30043788695;RUNX1..3:0.285006108358;ZBTB6:0.27491407879;MTE{core}:0.266657006608;REST:0.262668198745;HIF1A:0.252694532018;HMGA1,2:0.252333583838;SREBF1,2:0.23669556674;GATA4:0.183432397482;MZF1:0.176700483548;SPI1:0.166151320184;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.162611619942;GZF1:0.158727117553;FOX{F1,F2,J1}:0.152892320742;SNAI1..3:0.130863473289;SPIB:0.107536107508;NR1H4:0.106318151918;STAT5{A,B}:0.10382434826;DMAP1_NCOR{1,2}_SMARC:0.0930439203393;IRF7:0.0924498935544;ALX4:0.0636833581989;PDX1:0.0625871875495;EGR1..3:0.0567594034772;UFEwm:0.052625645516;ETS1,2:0.0494824480689;ATF2:0.0470362848986;IKZF2:0.0351162933459;POU3F1..4:0.0187596334328;HOXA9_MEIS1:0.0123830502205;NKX2-2,8:0.0109314651948;FOX{D1,D2}:-0.0453895329073;NFIL3:-0.0555420767264;NFKB1_REL_RELA:-0.115280268584;POU2F1..3:-0.15987066058;SOX2:-0.163903261414;MED-1{core}:-0.186939034467;YY1:-0.188368129428;POU5F1:-0.189752344197;HOX{A5,B5}:-0.192342986033;FOXQ1:-0.204018592509;PRRX1,2:-0.206104571411;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.21614412786;E2F1..5:-0.217407013529;ZFP161:-0.22113980061;HNF1A:-0.226477543642;FOXO1,3,4:-0.234734318039;CUX2:-0.269273986785;HNF4A_NR2F1,2:-0.27535791591;JUN:-0.279540135945;ZEB1:-0.30018227749;NANOG{mouse}:-0.302769074931;IRF1,2:-0.317599189792;HAND1,2:-0.322019767274;BREu{core}:-0.326726995675;SOX17:-0.329939157907;EVI1:-0.351675971179;ATF4:-0.406139785367;DBP:-0.429115099094;LHX3,4:-0.430114132624;FOXN1:-0.437695938817;TFDP1:-0.451824220219;NR6A1:-0.455547152616;POU6F1:-0.463859384762;FOXM1:-0.467093613767;ZNF143:-0.469951848796;NKX3-1:-0.485301241081;MYB:-0.532378007106;TEF:-0.536784681494;NFIX:-0.547955864037;RFX1:-0.568958261668;ZNF384:-0.587797242908;bHLH_family:-0.594375410944;PAX6:-0.601134817031;ELF1,2,4:-0.607407536778;RBPJ:-0.681561602125;RFX2..5_RFXANK_RFXAP:-0.701783443504;AR:-0.732091263483;CDC5L:-0.776548359213;NFY{A,B,C}:-0.850165909163;ATF5_CREB3:-0.850934526498;AHR_ARNT_ARNT2:-0.873281179786;PBX1:-0.885913781914;HBP1_HMGB_SSRP1_UBTF:-0.887009910426;PITX1..3:-0.909852357574;PAX4:-0.911198190091;FOXP1:-0.991114423879;NRF1:-0.991961786386;OCT4_SOX2{dimer}:-1.00163416311;PAX8:-1.028836624;BPTF:-1.15176776487;NKX6-1,2:-1.1585524407;STAT1,3:-1.19364342198;ADNP_IRX_SIX_ZHX:-1.21235327903;CREB1:-1.2135722232;POU1F1:-1.28116879681;AIRE:-1.32647117626;ARID5B:-1.38000094947;FOXD3:-1.44673878613;ELK1,4_GABP{A,B1}:-1.47138434406;ONECUT1,2:-1.65775264557;CDX1,2,4:-1.73968725906;ZBTB16:-1.91133068796
|xref=
|xref=
}} {{DRAAccessionNumbers
|DRA_sample_Accession=CAGE@DRS009016
|accession_numbers=DRX009153;DRR010027;DRZ001452;DRZ002835;CAGE
|library_id=CNhs10515
}}
}}

Revision as of 16:35, 17 October 2013


Name:whole body, neonate N06
Species:Mouse (Mus musculus)
Library ID:CNhs10515
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage6 days neonate
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS009016
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10515 CAGE DRX009153 DRR010027
Accession ID Mm9

Library idBAMCTSS
CNhs10515 DRZ001452 DRZ002835
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
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

CNhs10515

00
10.0866
100
1000
10000.52
10010.0833
1002-0.00349
10030.176
10040
10050.147
10060.422
1007-0.0287
10080
10090.238
101-0.0672
10100
10110.0512
10120
1013-0.0387
10140.187
1015-0.0837
10160.122
10170
10180.159
10190
1020
10200
10210.0373
10220.562
10230
10240.316
10250
10260
10270.223
10280
1029-0.0123
1030.862
10300
10310.262
10320.17
1033-0.0665
10340
10350.0866
1036-0.0433
10370.0866
10380.122
10390.0972
1040
10400.214
10410.275



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: CNhs10515

Jaspar motifP-value
MA0002.20.186
MA0003.10.0188
MA0004.10.122
MA0006.10.138
MA0007.10.487
MA0009.10.436
MA0014.10.832
MA0017.10.0851
MA0018.20.00365
MA0019.10.725
MA0024.10.116
MA0025.10.872
MA0027.10.205
MA0028.11.74082e-6
MA0029.10.53
MA0030.10.274
MA0031.10.991
MA0035.20.835
MA0038.10.726
MA0039.20.0738
MA0040.10.0801
MA0041.10.405
MA0042.10.449
MA0043.10.0153
MA0046.10.0278
MA0047.20.491
MA0048.10.00188
MA0050.10.029
MA0051.10.092
MA0052.13.84795e-39
MA0055.14.9752e-5
MA0057.10.26
MA0058.10.0682
MA0059.10.0159
MA0060.10.0806
MA0061.10.941
MA0062.24.2411e-11
MA0065.20.134
MA0066.10.868
MA0067.10.177
MA0068.10.502
MA0069.10.498
MA0070.10.724
MA0071.10.3
MA0072.10.499
MA0073.10.921
MA0074.10.885
MA0076.11.69328e-7
MA0077.10.883
MA0078.10.131
MA0079.20.00434
MA0080.20.00908
MA0081.10.363
MA0083.11.14204e-8
MA0084.10.861
MA0087.10.758
MA0088.10.53
MA0090.10.161
MA0091.10.661
MA0092.10.104
MA0093.10.123
MA0099.20.00904
MA0100.10.0167
MA0101.10.216
MA0102.20.765
MA0103.10.261
MA0104.20.0329
MA0105.10.785
MA0106.10.535
MA0107.10.472
MA0108.23.32065e-73
MA0111.10.861
MA0112.20.0173
MA0113.10.321
MA0114.10.193
MA0115.10.0135
MA0116.10.301
MA0117.10.716
MA0119.10.358
MA0122.10.183
MA0124.10.619
MA0125.10.00263
MA0131.10.183
MA0135.10.106
MA0136.19.65978e-7
MA0137.20.00597
MA0138.21.25411e-4
MA0139.10.573
MA0140.10.0772
MA0141.10.955
MA0142.10.0579
MA0143.10.176
MA0144.10.457
MA0145.10.0186
MA0146.10.564
MA0147.10.0327
MA0148.10.966
MA0149.10.0337
MA0150.10.993
MA0152.10.78
MA0153.16.4136e-4
MA0154.10.0481
MA0155.10.118
MA0156.11.96907e-7
MA0157.10.645
MA0159.10.66
MA0160.10.97
MA0162.10.364
MA0163.10.376
MA0164.10.0685
MA0258.10.252
MA0259.10.0728



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: CNhs10515

Novel motifP-value
10.951
100.293
1000.726
1010.0592
1020.932
1030.404
1040.357
1050.199
1060.046
1070.0301
1080.324
1090.451
110.858
1100.979
1110.275
1120.581
1130.539
1140.775
1150.659
1160.0306
1170.0932
1180.479
1190.558
120.206
1200.567
1210.925
1220.612
1230.141
1240.748
1250.85
1260.43
1270.276
1280.211
1290.784
130.81
1300.811
1310.175
1320.858
1330.333
1340.725
1350.368
1360.468
1370.397
1380.813
1390.955
140.223
1400.947
1410.295
1420.462
1430.878
1440.0522
1450.726
1460.292
1470.981
1480.827
1490.288
150.168
1500.65
1510.429
1520.021
1530.552
1540.458
1550.214
1560.35
1570.115
1580.0927
1590.251
1600.149
1610.144
1620.86
1630.865
1640.177
1650.882
1660.462
1670.00367
1680.037
1690.0243
170.302
180.5
190.105
20.0107
200.0112
210.738
220.285
230.251
240.956
250.951
260.938
270.546
280.819
290.137
30.875
300.122
310.555
320.0095
330.36
340.102
350.194
360.0789
370.373
380.908
390.293
40.871
400.656
410.519
420.928
430.628
440.747
450.145
460.678
470.774
480.969
490.684
50.699
500.34
510.55
520.101
530.173
540.299
550.57
560.378
570.797
580.701
590.00531
60.997
600.148
610.551
620.657
630.299
640.884
650.478
660.796
670.422
680.207
690.0792
70.666
700.934
710.72
720.794
730.201
740.524
750.367
760.00497
770.121
780.152
790.348
80.81
800.463
810.371
820.325
830.765
840.202
850.0907
860.661
870.084
880.608
890.167
90.17
900.0174
910.421
920.439
930.0246
940.85
950.689
960.941
970.932
980.864
990.184



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: CNhs10515


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000312 (mouse neonate N6 sample)
0011405 (mouse whole body- neonate N06 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
FF:0000294 (mouse embryonic day 11 sample)

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