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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS009017
|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 41: Line 42:
|is_a=EFO:0002091;;FF:0011420
|is_a=EFO:0002091;;FF:0011420
|is_obsolete=
|is_obsolete=
|library_ids=CNhs10518
|name=whole body, neonate N10
|name=whole body, neonate N10
|namespace=FANTOM5
|namespace=FANTOM5
Line 83: Line 85:
|top_motifs=MEF2{A,B,C,D}:2.80323910383;FOXL1:2.72468084339;TBP:2.47606531534;ESR1:2.2433557508;SMAD1..7,9:2.20985432401;HOX{A4,D4}:2.20495899248;TFAP4:2.13592758709;TLX2:1.94807032519;TFCP2:1.91300412354;GCM1,2:1.70515688105;NFE2L2:1.70159875066;ZNF238:1.66602352621;NFATC1..3:1.66068905205;TFAP2{A,C}:1.58905909781;GLI1..3:1.52432422895;NKX2-3_NKX2-5:1.51051223567;EBF1:1.50129678498;TAL1_TCF{3,4,12}:1.46770968639;SOX5:1.44543554135;NR5A1,2:1.35337656013;FOSL2:1.30556586257;FOXP3:1.29607807461;ZNF148:1.29595107254;MAFB:1.29320512701;TOPORS:1.29223790227;TGIF1:1.27710959651;STAT2,4,6:1.22827755255;SRF:1.21066375291;MYFfamily:1.21041108672;TLX1..3_NFIC{dimer}:1.17244341913;MYOD1:1.14473076544;SOX{8,9,10}:1.14221378804;NHLH1,2:1.12470227594;HES1:1.10864112159;RXRA_VDR{dimer}:1.10293844155;TEAD1:1.08219124716;PAX1,9:1.02916651666;GFI1:0.957963622087;RXR{A,B,G}:0.933063802209;NR3C1:0.930698855749;EP300:0.884640029966;MYBL2:0.824743845232;MTF1:0.805007064923;ATF6:0.800055514575;GTF2A1,2:0.781441130419;NFE2L1:0.752719247282;ESRRA:0.735284898356;IKZF1:0.658133237052;HSF1,2:0.639159317767;PPARG:0.628854369099;GATA6:0.609188070029;ALX4:0.607860826218;TP53:0.59948501821;RORA:0.585734695703;CEBPA,B_DDIT3:0.582942685641;KLF4:0.581816751212;MAZ:0.580198421903;PAX5:0.565113970601;FOS_FOS{B,L1}_JUN{B,D}:0.529783316323;GFI1B:0.517386894328;FOXQ1:0.494074883555;PATZ1:0.493163602032;SP1:0.476686051157;XCPE1{core}:0.474131716993;PRDM1:0.469553718445;HIC1:0.452432253473;HLF:0.444738186271;FOXA2:0.419192342001;GTF2I:0.404422504369;NFE2:0.398360449629;HIF1A:0.398312381944;YY1:0.391583452498;ALX1:0.34379148953;SPZ1:0.339504372265;RUNX1..3:0.33064269021;LEF1_TCF7_TCF7L1,2:0.324705649786;CRX:0.324081649535;LMO2:0.322427521787;PBX1:0.317288311439;IRF7:0.316463990561;SPIB:0.290663452512;ZIC1..3:0.288409942086;SPI1:0.278859218893;FOX{I1,J2}:0.267351280936;BACH2:0.252679082507;DMAP1_NCOR{1,2}_SMARC:0.247747467672;RREB1:0.24458727361;PAX2:0.24006667197;SREBF1,2:0.237799490082;MTE{core}:0.233478645614;STAT5{A,B}:0.186110615242;ETS1,2:0.178205264117;NR1H4:0.171204727348;UFEwm:0.148804870144;VSX1,2:0.136537284073;TFAP2B:0.135902212097;HMGA1,2:0.126494148817;AR:0.123260863627;EN1,2:0.093912414872;HMX1:0.0896004064106;PDX1:0.0743148773323;MZF1:0.0655682518132;TBX4,5:0.0571134419723;FOXO1,3,4:0.0520125325742;NR6A1:0.0197210710121;GATA4:0.0129181380287;POU3F1..4:0.00203304528926;NFIL3:-0.005117094985;NKX2-2,8:-0.0211067389043;REST:-0.0233686684871;IRF1,2:-0.0244318619339;POU5F1:-0.027977462379;ZNF423:-0.0357569815057;POU2F1..3:-0.0771069247004;NFKB1_REL_RELA:-0.0810517803638;ZNF143:-0.0821965557977;ELF1,2,4:-0.085644613349;NKX3-2:-0.0928423275228;HBP1_HMGB_SSRP1_UBTF:-0.0944845052777;IKZF2:-0.112593896668;E2F1..5:-0.120851597821;FOX{F1,F2,J1}:-0.121671363584;NANOG{mouse}:-0.121822615294;EVI1:-0.136694479445;T:-0.143560217044;NKX2-1,4:-0.15328672953;JUN:-0.156523191962;ZFP161:-0.165166924088;ATF2:-0.18365394511;ZBTB6:-0.196718485877;EGR1..3:-0.217014698799;HOXA9_MEIS1:-0.232190567364;NANOG:-0.232395069508;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.27256277422;MED-1{core}:-0.326008583104;SOX2:-0.339199432212;SOX17:-0.36698232171;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.376405580598;FOX{D1,D2}:-0.378281622971;ATF4:-0.384834730705;PITX1..3:-0.390513067031;CDC5L:-0.406248824278;PRRX1,2:-0.412568508485;HNF4A_NR2F1,2:-0.426607727516;bHLH_family:-0.439112082428;ZNF384:-0.439856759627;HOX{A5,B5}:-0.4442957746;MYB:-0.451983548648;ARID5B:-0.495226030114;BREu{core}:-0.49878689591;POU6F1:-0.498995077124;HNF1A:-0.515677026114;LHX3,4:-0.522415682626;NRF1:-0.523280863556;RFX1:-0.528299385598;CUX2:-0.529691589305;PAX8:-0.555104176871;RFX2..5_RFXANK_RFXAP:-0.562664379562;RBPJ:-0.578033079071;HAND1,2:-0.58013047477;NFY{A,B,C}:-0.592028891047;DBP:-0.594272815287;ATF5_CREB3:-0.599629772239;POU1F1:-0.631508106767;FOXM1:-0.688686850916;TEF:-0.716846063983;SNAI1..3:-0.748978068609;GZF1:-0.761334356603;AHR_ARNT_ARNT2:-0.788260366886;NKX3-1:-0.791075641707;TFDP1:-0.794000718577;ZEB1:-0.856894907041;PAX6:-0.894967752471;PAX4:-0.912921155951;FOXP1:-0.969288184802;OCT4_SOX2{dimer}:-0.97129757895;CREB1:-1.01713215188;NFIX:-1.01871816744;AIRE:-1.14860198871;ELK1,4_GABP{A,B1}:-1.20488981648;ADNP_IRX_SIX_ZHX:-1.27675756429;FOXD3:-1.28134194755;FOXN1:-1.29079430229;STAT1,3:-1.33236730547;NKX6-1,2:-1.36228821431;CDX1,2,4:-1.52092002853;ZBTB16:-1.56603721766;BPTF:-1.69274181558;ONECUT1,2:-1.78540902025
|top_motifs=MEF2{A,B,C,D}:2.80323910383;FOXL1:2.72468084339;TBP:2.47606531534;ESR1:2.2433557508;SMAD1..7,9:2.20985432401;HOX{A4,D4}:2.20495899248;TFAP4:2.13592758709;TLX2:1.94807032519;TFCP2:1.91300412354;GCM1,2:1.70515688105;NFE2L2:1.70159875066;ZNF238:1.66602352621;NFATC1..3:1.66068905205;TFAP2{A,C}:1.58905909781;GLI1..3:1.52432422895;NKX2-3_NKX2-5:1.51051223567;EBF1:1.50129678498;TAL1_TCF{3,4,12}:1.46770968639;SOX5:1.44543554135;NR5A1,2:1.35337656013;FOSL2:1.30556586257;FOXP3:1.29607807461;ZNF148:1.29595107254;MAFB:1.29320512701;TOPORS:1.29223790227;TGIF1:1.27710959651;STAT2,4,6:1.22827755255;SRF:1.21066375291;MYFfamily:1.21041108672;TLX1..3_NFIC{dimer}:1.17244341913;MYOD1:1.14473076544;SOX{8,9,10}:1.14221378804;NHLH1,2:1.12470227594;HES1:1.10864112159;RXRA_VDR{dimer}:1.10293844155;TEAD1:1.08219124716;PAX1,9:1.02916651666;GFI1:0.957963622087;RXR{A,B,G}:0.933063802209;NR3C1:0.930698855749;EP300:0.884640029966;MYBL2:0.824743845232;MTF1:0.805007064923;ATF6:0.800055514575;GTF2A1,2:0.781441130419;NFE2L1:0.752719247282;ESRRA:0.735284898356;IKZF1:0.658133237052;HSF1,2:0.639159317767;PPARG:0.628854369099;GATA6:0.609188070029;ALX4:0.607860826218;TP53:0.59948501821;RORA:0.585734695703;CEBPA,B_DDIT3:0.582942685641;KLF4:0.581816751212;MAZ:0.580198421903;PAX5:0.565113970601;FOS_FOS{B,L1}_JUN{B,D}:0.529783316323;GFI1B:0.517386894328;FOXQ1:0.494074883555;PATZ1:0.493163602032;SP1:0.476686051157;XCPE1{core}:0.474131716993;PRDM1:0.469553718445;HIC1:0.452432253473;HLF:0.444738186271;FOXA2:0.419192342001;GTF2I:0.404422504369;NFE2:0.398360449629;HIF1A:0.398312381944;YY1:0.391583452498;ALX1:0.34379148953;SPZ1:0.339504372265;RUNX1..3:0.33064269021;LEF1_TCF7_TCF7L1,2:0.324705649786;CRX:0.324081649535;LMO2:0.322427521787;PBX1:0.317288311439;IRF7:0.316463990561;SPIB:0.290663452512;ZIC1..3:0.288409942086;SPI1:0.278859218893;FOX{I1,J2}:0.267351280936;BACH2:0.252679082507;DMAP1_NCOR{1,2}_SMARC:0.247747467672;RREB1:0.24458727361;PAX2:0.24006667197;SREBF1,2:0.237799490082;MTE{core}:0.233478645614;STAT5{A,B}:0.186110615242;ETS1,2:0.178205264117;NR1H4:0.171204727348;UFEwm:0.148804870144;VSX1,2:0.136537284073;TFAP2B:0.135902212097;HMGA1,2:0.126494148817;AR:0.123260863627;EN1,2:0.093912414872;HMX1:0.0896004064106;PDX1:0.0743148773323;MZF1:0.0655682518132;TBX4,5:0.0571134419723;FOXO1,3,4:0.0520125325742;NR6A1:0.0197210710121;GATA4:0.0129181380287;POU3F1..4:0.00203304528926;NFIL3:-0.005117094985;NKX2-2,8:-0.0211067389043;REST:-0.0233686684871;IRF1,2:-0.0244318619339;POU5F1:-0.027977462379;ZNF423:-0.0357569815057;POU2F1..3:-0.0771069247004;NFKB1_REL_RELA:-0.0810517803638;ZNF143:-0.0821965557977;ELF1,2,4:-0.085644613349;NKX3-2:-0.0928423275228;HBP1_HMGB_SSRP1_UBTF:-0.0944845052777;IKZF2:-0.112593896668;E2F1..5:-0.120851597821;FOX{F1,F2,J1}:-0.121671363584;NANOG{mouse}:-0.121822615294;EVI1:-0.136694479445;T:-0.143560217044;NKX2-1,4:-0.15328672953;JUN:-0.156523191962;ZFP161:-0.165166924088;ATF2:-0.18365394511;ZBTB6:-0.196718485877;EGR1..3:-0.217014698799;HOXA9_MEIS1:-0.232190567364;NANOG:-0.232395069508;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.27256277422;MED-1{core}:-0.326008583104;SOX2:-0.339199432212;SOX17:-0.36698232171;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.376405580598;FOX{D1,D2}:-0.378281622971;ATF4:-0.384834730705;PITX1..3:-0.390513067031;CDC5L:-0.406248824278;PRRX1,2:-0.412568508485;HNF4A_NR2F1,2:-0.426607727516;bHLH_family:-0.439112082428;ZNF384:-0.439856759627;HOX{A5,B5}:-0.4442957746;MYB:-0.451983548648;ARID5B:-0.495226030114;BREu{core}:-0.49878689591;POU6F1:-0.498995077124;HNF1A:-0.515677026114;LHX3,4:-0.522415682626;NRF1:-0.523280863556;RFX1:-0.528299385598;CUX2:-0.529691589305;PAX8:-0.555104176871;RFX2..5_RFXANK_RFXAP:-0.562664379562;RBPJ:-0.578033079071;HAND1,2:-0.58013047477;NFY{A,B,C}:-0.592028891047;DBP:-0.594272815287;ATF5_CREB3:-0.599629772239;POU1F1:-0.631508106767;FOXM1:-0.688686850916;TEF:-0.716846063983;SNAI1..3:-0.748978068609;GZF1:-0.761334356603;AHR_ARNT_ARNT2:-0.788260366886;NKX3-1:-0.791075641707;TFDP1:-0.794000718577;ZEB1:-0.856894907041;PAX6:-0.894967752471;PAX4:-0.912921155951;FOXP1:-0.969288184802;OCT4_SOX2{dimer}:-0.97129757895;CREB1:-1.01713215188;NFIX:-1.01871816744;AIRE:-1.14860198871;ELK1,4_GABP{A,B1}:-1.20488981648;ADNP_IRX_SIX_ZHX:-1.27675756429;FOXD3:-1.28134194755;FOXN1:-1.29079430229;STAT1,3:-1.33236730547;NKX6-1,2:-1.36228821431;CDX1,2,4:-1.52092002853;ZBTB16:-1.56603721766;BPTF:-1.69274181558;ONECUT1,2:-1.78540902025
|xref=
|xref=
}} {{DRAAccessionNumbers
|DRA_sample_Accession=CAGE@DRS009017
|accession_numbers=DRX009154;DRR010028;DRZ001453;DRZ002836;CAGE
|library_id=CNhs10518
}}
}}

Revision as of 23:49, 16 October 2013


Name:whole body, neonate N10
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage10 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  DRS009017
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{library_id}}} {{{accession_numbers}}}
Accession ID Mm9

Library idBAMCTSS
{{{library_id}}}
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

CNhs10518

00
10.0646
100
1000
10000.435
10010.182
1002-0.0513
10030.162
10040
10050.0881
10060.491
1007-0.0888
10080
10090.144
101-0.0158
10100
10110.0366
10120
1013-0.0689
10140.165
1015-0.0559
10160.0298
10170
10180.0871
10190
1020
10200
10210.0419
10220.55
10230
10240.239
10250
10260.136
10270.152
10280
1029-0.0114
1030.74
10300.165
10310.262
10320.197
10330
10340
10350.285
1036-0.036
10370
1038-0.0453
10390.244
1040
10400.126
10410.49



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: CNhs10518

Jaspar motifP-value
MA0002.20.0662
MA0003.10.0108
MA0004.10.0918
MA0006.10.143
MA0007.10.553
MA0009.10.698
MA0014.10.941
MA0017.10.133
MA0018.20.0181
MA0019.10.112
MA0024.10.0784
MA0025.10.583
MA0027.10.208
MA0028.12.12603e-4
MA0029.10.785
MA0030.10.733
MA0031.10.721
MA0035.20.821
MA0038.10.13
MA0039.20.188
MA0040.10.0696
MA0041.10.309
MA0042.10.49
MA0043.10.0185
MA0046.13.23452e-8
MA0047.20.218
MA0048.10.00154
MA0050.10.147
MA0051.10.665
MA0052.12.10008e-53
MA0055.14.83338e-4
MA0057.10.503
MA0058.10.0519
MA0059.10.0157
MA0060.10.192
MA0061.10.709
MA0062.21.98761e-7
MA0065.20.0252
MA0066.10.799
MA0067.10.166
MA0068.10.956
MA0069.10.289
MA0070.10.755
MA0071.10.836
MA0072.10.307
MA0073.10.611
MA0074.10.845
MA0076.12.39175e-5
MA0077.10.664
MA0078.10.0317
MA0079.20.0283
MA0080.20.66
MA0081.10.893
MA0083.13.17325e-9
MA0084.10.366
MA0087.10.778
MA0088.10.935
MA0090.10.284
MA0091.10.186
MA0092.10.132
MA0093.10.0995
MA0099.20.576
MA0100.10.0235
MA0101.10.458
MA0102.20.457
MA0103.10.00435
MA0104.20.0379
MA0105.10.464
MA0106.10.589
MA0107.10.632
MA0108.21.96658e-42
MA0111.10.843
MA0112.20.00159
MA0113.10.74
MA0114.10.242
MA0115.10.0056
MA0116.10.215
MA0117.10.961
MA0119.10.215
MA0122.10.149
MA0124.10.686
MA0125.10.146
MA0131.10.283
MA0135.10.176
MA0136.10.0036
MA0137.20.0111
MA0138.26.34727e-4
MA0139.10.969
MA0140.10.0119
MA0141.10.178
MA0142.10.226
MA0143.10.107
MA0144.10.381
MA0145.10.0174
MA0146.10.697
MA0147.10.0655
MA0148.10.794
MA0149.10.0199
MA0150.10.937
MA0152.10.367
MA0153.12.10136e-8
MA0154.10.0348
MA0155.10.095
MA0156.10.0027
MA0157.10.824
MA0159.10.663
MA0160.10.416
MA0162.10.201
MA0163.10.135
MA0164.10.112
MA0258.10.0539
MA0259.10.116



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: CNhs10518

Novel motifP-value
10.966
100.546
1000.983
1010.149
1020.758
1030.406
1040.515
1050.105
1060.138
1070.189
1080.678
1090.235
110.691
1100.852
1110.242
1120.663
1130.269
1140.776
1150.823
1160.0882
1170.1
1180.384
1190.412
120.0662
1200.68
1210.754
1220.846
1230.11
1240.725
1250.784
1260.493
1270.377
1280.282
1290.519
130.566
1300.603
1310.312
1320.972
1330.138
1340.827
1350.211
1360.772
1370.168
1380.451
1390.365
140.191
1400.935
1410.241
1420.102
1430.934
1440.0844
1450.309
1460.407
1470.978
1480.98
1490.137
150.549
1500.818
1510.127
1520.0495
1530.539
1540.555
1550.511
1560.798
1570.114
1580.274
1590.146
1600.12
1610.287
1620.811
1630.78
1640.165
1650.191
1660.56
1670.0202
1680.0457
1690.00677
170.437
180.504
190.049
20.0385
200.0289
210.616
220.243
230.36
240.715
250.545
260.63
270.486
280.823
290.156
30.894
300.306
310.501
320.032
330.339
340.098
350.243
360.163
370.263
380.644
390.539
40.881
400.975
410.278
420.68
430.576
440.92
450.214
460.842
470.758
480.94
490.795
50.4
500.48
510.734
520.212
530.142
540.29
550.908
560.399
570.672
580.621
590.00787
60.628
600.349
610.416
620.482
630.336
640.787
650.471
660.465
670.526
680.449
690.305
70.381
700.875
710.425
720.998
730.187
740.435
750.513
760.0181
770.245
780.111
790.308
80.897
800.208
810.166
820.204
830.213
840.493
850.0969
860.671
870.175
880.551
890.347
90.22
900.0614
910.143
920.378
930.385
940.761
950.361
960.808
970.873
980.981
990.342



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: CNhs10518


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)
0000305 (mouse neonate N10 sample)
0011420 (mouse whole body- neonate N10 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)

{{{1}}} Accession numbers
MethodSample accession id
{{{2}}} 
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{4}}} {{{3}}}
Accession ID

Library idBAMCTSS
{{{4}}}
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