Personal tools

FF:659-23C6: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005246
|DRA_sample_Accession=CAGE@SAMD00005246
|accession_numbers=CAGE;DRX009152;DRR010026;DRZ001451;DRZ002834
|accession_numbers=CAGE;DRX009152;DRR010026;DRZ001451;DRZ002834;DRZ012801;DRZ014184
|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 97: Line 97:
|top_motifs=TFAP4:2.51694928964;ESR1:2.26547511963;MEF2{A,B,C,D}:2.26071325147;FOXL1:2.19972438626;TFCP2:2.16638852236;TBP:2.13764941834;TFAP2{A,C}:2.11148475452;EP300:2.09711430681;SMAD1..7,9:2.00504136179;MYOD1:2.00175686666;HOX{A4,D4}:1.96014047097;SOX5:1.92786336754;IKZF1:1.92697936953;GCM1,2:1.90888577026;ZNF238:1.89772892224;TGIF1:1.83253963191;ZNF148:1.73892814933;NFATC1..3:1.60026752985;TEAD1:1.5833689742;MAFB:1.55144231311;NKX2-3_NKX2-5:1.54638863941;GLI1..3:1.45824689632;FOSL2:1.44762760335;NHLH1,2:1.41051429842;TOPORS:1.39816189897;RXR{A,B,G}:1.38831484967;MAZ:1.37090405622;NR3C1:1.35224137226;FOS_FOS{B,L1}_JUN{B,D}:1.32479494003;SRF:1.32013412459;RXRA_VDR{dimer}:1.3196539041;TAL1_TCF{3,4,12}:1.29477982955;NKX3-2:1.26369757431;MYFfamily:1.25783644447;TLX2:1.23225760368;HMX1:1.21375572088;ATF6:1.19634106554;EBF1:1.16429379295;FOXO1,3,4:1.1566384299;AR:1.1009574494;UFEwm:1.08694963874;PAX5:1.08562438766;PRDM1:1.08176836748;KLF4:1.07446952815;PATZ1:1.06943806947;MYBL2:1.06296173417;STAT2,4,6:1.05217995633;HMGA1,2:1.02801466668;PAX2:1.02649620293;GFI1B:0.994046636156;MTF1:0.97651407591;ZNF423:0.971122253623;GTF2I:0.939610410094;XCPE1{core}:0.939506826484;NKX2-1,4:0.937731218217;RREB1:0.918502024911;HIC1:0.904569444339;TLX1..3_NFIC{dimer}:0.882035709024;ZIC1..3:0.86689199111;MZF1:0.862796895744;SP1:0.8600587009;NR1H4:0.856753804955;MTE{core}:0.793317256469;GATA4:0.790707251669;NANOG{mouse}:0.780413148149;NFE2L2:0.767380733353;HES1:0.74380071131;SOX{8,9,10}:0.718090342367;FOXP3:0.716715831656;NFE2L1:0.701762461808;TFAP2B:0.665397262316;FOX{D1,D2}:0.658740019078;VSX1,2:0.658245758185;TP53:0.625777418192;ESRRA:0.586626957742;HIF1A:0.540582144826;PITX1..3:0.539418338742;NR5A1,2:0.537035934585;LEF1_TCF7_TCF7L1,2:0.514628305058;GTF2A1,2:0.513476197919;NFE2:0.511842621287;ATF2:0.502356558408;ZBTB6:0.468724051671;STAT5{A,B}:0.456313314589;HSF1,2:0.442633730851;EGR1..3:0.439632949368;T:0.409726483881;CRX:0.342514699752;BACH2:0.328198719268;EN1,2:0.324024688848;HLF:0.323724309397;IKZF2:0.319630756899;ALX1:0.289917159535;PAX1,9:0.282471386538;IRF7:0.280569390974;MED-1{core}:0.27577320944;SPZ1:0.271486733823;ALX4:0.266620755289;HOX{A5,B5}:0.264536053162;CEBPA,B_DDIT3:0.262093241958;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.240933330629;REST:0.23917363529;HOXA9_MEIS1:0.201766771538;TBX4,5:0.195726580497;RORA:0.194045812183;FOXA2:0.190751634146;CUX2:0.16653888466;SREBF1,2:0.161616663433;DMAP1_NCOR{1,2}_SMARC:0.0698298434068;EVI1:0.0477857236312;BREu{core}:0.0473513314726;SPIB:0.0466557001843;FOX{I1,J2}:0.0360270572048;POU3F1..4:0.00940868754311;LMO2:-0.0194866050421;SPI1:-0.0261900733885;GFI1:-0.0268147175253;ZFP161:-0.0585324350081;AHR_ARNT_ARNT2:-0.0617945096682;JUN:-0.0691235598392;RUNX1..3:-0.0755626065006;HBP1_HMGB_SSRP1_UBTF:-0.0805907224212;SNAI1..3:-0.113355876405;SOX2:-0.128038852425;PPARG:-0.151420816707;POU5F1:-0.167937727208;RBPJ:-0.193736378463;NKX2-2,8:-0.198503875691;NANOG:-0.207576018599;ETS1,2:-0.210438596647;RFX2..5_RFXANK_RFXAP:-0.233479414266;NFKB1_REL_RELA:-0.233699690006;HAND1,2:-0.237671754232;DBP:-0.243114637207;PDX1:-0.249306659472;FOX{F1,F2,J1}:-0.263193564486;YY1:-0.271518541427;POU6F1:-0.28959568322;PAX4:-0.302919635341;ZNF384:-0.308920911431;NR6A1:-0.349161632346;SOX17:-0.357977360552;ATF4:-0.361953418629;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.387540012294;PAX6:-0.388094076392;PBX1:-0.420887043775;CDC5L:-0.442860127514;HNF4A_NR2F1,2:-0.470035988473;IRF1,2:-0.479768381131;TFDP1:-0.505424957899;GZF1:-0.512539366696;FOXP1:-0.520225936746;NFIX:-0.530027701261;RFX1:-0.541246469225;AIRE:-0.577486524225;FOXN1:-0.617583101921;ZEB1:-0.625300904731;FOXM1:-0.634955639589;HNF1A:-0.64052647165;FOXQ1:-0.644366357508;NFIL3:-0.651352001855;ZNF143:-0.654807208404;CREB1:-0.659809199982;ELF1,2,4:-0.663415793029;ATF5_CREB3:-0.673574702374;BPTF:-0.673664190287;E2F1..5:-0.675154556136;MYB:-0.688887763283;OCT4_SOX2{dimer}:-0.717354620627;PRRX1,2:-0.721331678311;NKX6-1,2:-0.724313724402;POU2F1..3:-0.729642292144;TEF:-0.740199815228;NKX3-1:-0.740357114303;bHLH_family:-0.801213859164;NRF1:-0.838381272283;PAX8:-0.840605638737;LHX3,4:-0.89603774208;ADNP_IRX_SIX_ZHX:-1.01623518293;GATA6:-1.02352008478;POU1F1:-1.05598122455;FOXD3:-1.08818385015;ONECUT1,2:-1.11112885224;CDX1,2,4:-1.2289400909;ELK1,4_GABP{A,B1}:-1.25047189217;NFY{A,B,C}:-1.44320082993;ARID5B:-1.55904029073;ZBTB16:-1.60361447555;STAT1,3:-1.98729079086
|top_motifs=TFAP4:2.51694928964;ESR1:2.26547511963;MEF2{A,B,C,D}:2.26071325147;FOXL1:2.19972438626;TFCP2:2.16638852236;TBP:2.13764941834;TFAP2{A,C}:2.11148475452;EP300:2.09711430681;SMAD1..7,9:2.00504136179;MYOD1:2.00175686666;HOX{A4,D4}:1.96014047097;SOX5:1.92786336754;IKZF1:1.92697936953;GCM1,2:1.90888577026;ZNF238:1.89772892224;TGIF1:1.83253963191;ZNF148:1.73892814933;NFATC1..3:1.60026752985;TEAD1:1.5833689742;MAFB:1.55144231311;NKX2-3_NKX2-5:1.54638863941;GLI1..3:1.45824689632;FOSL2:1.44762760335;NHLH1,2:1.41051429842;TOPORS:1.39816189897;RXR{A,B,G}:1.38831484967;MAZ:1.37090405622;NR3C1:1.35224137226;FOS_FOS{B,L1}_JUN{B,D}:1.32479494003;SRF:1.32013412459;RXRA_VDR{dimer}:1.3196539041;TAL1_TCF{3,4,12}:1.29477982955;NKX3-2:1.26369757431;MYFfamily:1.25783644447;TLX2:1.23225760368;HMX1:1.21375572088;ATF6:1.19634106554;EBF1:1.16429379295;FOXO1,3,4:1.1566384299;AR:1.1009574494;UFEwm:1.08694963874;PAX5:1.08562438766;PRDM1:1.08176836748;KLF4:1.07446952815;PATZ1:1.06943806947;MYBL2:1.06296173417;STAT2,4,6:1.05217995633;HMGA1,2:1.02801466668;PAX2:1.02649620293;GFI1B:0.994046636156;MTF1:0.97651407591;ZNF423:0.971122253623;GTF2I:0.939610410094;XCPE1{core}:0.939506826484;NKX2-1,4:0.937731218217;RREB1:0.918502024911;HIC1:0.904569444339;TLX1..3_NFIC{dimer}:0.882035709024;ZIC1..3:0.86689199111;MZF1:0.862796895744;SP1:0.8600587009;NR1H4:0.856753804955;MTE{core}:0.793317256469;GATA4:0.790707251669;NANOG{mouse}:0.780413148149;NFE2L2:0.767380733353;HES1:0.74380071131;SOX{8,9,10}:0.718090342367;FOXP3:0.716715831656;NFE2L1:0.701762461808;TFAP2B:0.665397262316;FOX{D1,D2}:0.658740019078;VSX1,2:0.658245758185;TP53:0.625777418192;ESRRA:0.586626957742;HIF1A:0.540582144826;PITX1..3:0.539418338742;NR5A1,2:0.537035934585;LEF1_TCF7_TCF7L1,2:0.514628305058;GTF2A1,2:0.513476197919;NFE2:0.511842621287;ATF2:0.502356558408;ZBTB6:0.468724051671;STAT5{A,B}:0.456313314589;HSF1,2:0.442633730851;EGR1..3:0.439632949368;T:0.409726483881;CRX:0.342514699752;BACH2:0.328198719268;EN1,2:0.324024688848;HLF:0.323724309397;IKZF2:0.319630756899;ALX1:0.289917159535;PAX1,9:0.282471386538;IRF7:0.280569390974;MED-1{core}:0.27577320944;SPZ1:0.271486733823;ALX4:0.266620755289;HOX{A5,B5}:0.264536053162;CEBPA,B_DDIT3:0.262093241958;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.240933330629;REST:0.23917363529;HOXA9_MEIS1:0.201766771538;TBX4,5:0.195726580497;RORA:0.194045812183;FOXA2:0.190751634146;CUX2:0.16653888466;SREBF1,2:0.161616663433;DMAP1_NCOR{1,2}_SMARC:0.0698298434068;EVI1:0.0477857236312;BREu{core}:0.0473513314726;SPIB:0.0466557001843;FOX{I1,J2}:0.0360270572048;POU3F1..4:0.00940868754311;LMO2:-0.0194866050421;SPI1:-0.0261900733885;GFI1:-0.0268147175253;ZFP161:-0.0585324350081;AHR_ARNT_ARNT2:-0.0617945096682;JUN:-0.0691235598392;RUNX1..3:-0.0755626065006;HBP1_HMGB_SSRP1_UBTF:-0.0805907224212;SNAI1..3:-0.113355876405;SOX2:-0.128038852425;PPARG:-0.151420816707;POU5F1:-0.167937727208;RBPJ:-0.193736378463;NKX2-2,8:-0.198503875691;NANOG:-0.207576018599;ETS1,2:-0.210438596647;RFX2..5_RFXANK_RFXAP:-0.233479414266;NFKB1_REL_RELA:-0.233699690006;HAND1,2:-0.237671754232;DBP:-0.243114637207;PDX1:-0.249306659472;FOX{F1,F2,J1}:-0.263193564486;YY1:-0.271518541427;POU6F1:-0.28959568322;PAX4:-0.302919635341;ZNF384:-0.308920911431;NR6A1:-0.349161632346;SOX17:-0.357977360552;ATF4:-0.361953418629;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.387540012294;PAX6:-0.388094076392;PBX1:-0.420887043775;CDC5L:-0.442860127514;HNF4A_NR2F1,2:-0.470035988473;IRF1,2:-0.479768381131;TFDP1:-0.505424957899;GZF1:-0.512539366696;FOXP1:-0.520225936746;NFIX:-0.530027701261;RFX1:-0.541246469225;AIRE:-0.577486524225;FOXN1:-0.617583101921;ZEB1:-0.625300904731;FOXM1:-0.634955639589;HNF1A:-0.64052647165;FOXQ1:-0.644366357508;NFIL3:-0.651352001855;ZNF143:-0.654807208404;CREB1:-0.659809199982;ELF1,2,4:-0.663415793029;ATF5_CREB3:-0.673574702374;BPTF:-0.673664190287;E2F1..5:-0.675154556136;MYB:-0.688887763283;OCT4_SOX2{dimer}:-0.717354620627;PRRX1,2:-0.721331678311;NKX6-1,2:-0.724313724402;POU2F1..3:-0.729642292144;TEF:-0.740199815228;NKX3-1:-0.740357114303;bHLH_family:-0.801213859164;NRF1:-0.838381272283;PAX8:-0.840605638737;LHX3,4:-0.89603774208;ADNP_IRX_SIX_ZHX:-1.01623518293;GATA6:-1.02352008478;POU1F1:-1.05598122455;FOXD3:-1.08818385015;ONECUT1,2:-1.11112885224;CDX1,2,4:-1.2289400909;ELK1,4_GABP{A,B1}:-1.25047189217;NFY{A,B,C}:-1.44320082993;ARID5B:-1.55904029073;ZBTB16:-1.60361447555;STAT1,3:-1.98729079086
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:659-23C6;search_select_hide=table117:659-23C6
}}
}}

Latest revision as of 19:19, 4 June 2020


Name:whole body, neonate N01
Species:Mouse (Mus musculus)
Library ID:CNhs10576
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage1 day 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  SAMD00005246
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10576 CAGE DRX009152 DRR010026
Accession ID Mm9

Library idBAMCTSS
CNhs10576 DRZ001451 DRZ002834
Accession ID Mm10

Library idBAMCTSS
CNhs10576 DRZ012801 DRZ014184
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs10576

00
10.076
100
1000
10000.417
10010.228
10020.12
10030.323
10040
10050.0432
10060.464
1007-0.0102
10080
10090.168
101-0.0143
10100
10110.141
10120
1013-0.0868
10140.425
1015-0.101
10160.182
10170
10180.247
10190
1020
10200
10210
10220.541
10230
10240.281
10250
10260.257
10270.186
10280
10290.217
1030.856
10300
10310.335
10320.124
10330
10340
10350.076
1036-0.0791
10370
1038-0.0034
10390.142
1040
10400.316
10410.247



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: CNhs10576

Jaspar motifP-value
MA0002.20.174
MA0003.10.0662
MA0004.10.052
MA0006.10.247
MA0007.10.926
MA0009.10.573
MA0014.10.315
MA0017.19.00354e-5
MA0018.20.00644
MA0019.10.898
MA0024.10.0061
MA0025.10.328
MA0027.10.292
MA0028.15.64394e-10
MA0029.10.595
MA0030.10.502
MA0031.10.437
MA0035.20.0117
MA0038.10.966
MA0039.20.968
MA0040.10.598
MA0041.10.633
MA0042.10.848
MA0043.10.063
MA0046.16.1736e-12
MA0047.20.105
MA0048.16.68495e-4
MA0050.11.91433e-4
MA0051.10.00408
MA0052.11.06638e-35
MA0055.19.53084e-6
MA0057.10.794
MA0058.10.0151
MA0059.17.11451e-4
MA0060.11.69234e-5
MA0061.10.448
MA0062.21.30901e-15
MA0065.20.828
MA0066.10.789
MA0067.10.107
MA0068.10.233
MA0069.10.444
MA0070.10.191
MA0071.10.0726
MA0072.10.0486
MA0073.10.577
MA0074.10.62
MA0076.17.32157e-11
MA0077.10.557
MA0078.10.169
MA0079.20.0107
MA0080.24.62952e-5
MA0081.10.21
MA0083.15.89067e-11
MA0084.10.619
MA0087.10.239
MA0088.10.0325
MA0090.10.0297
MA0091.10.782
MA0092.10.372
MA0093.10.0405
MA0099.20.272
MA0100.10.00265
MA0101.10.0514
MA0102.20.71
MA0103.10.00886
MA0104.20.0146
MA0105.10.716
MA0106.10.185
MA0107.10.212
MA0108.24.41876e-22
MA0111.10.817
MA0112.20.392
MA0113.10.817
MA0114.11.13502e-4
MA0115.10.00237
MA0116.10.831
MA0117.10.395
MA0119.10.905
MA0122.10.794
MA0124.10.254
MA0125.10.125
MA0131.10.288
MA0135.10.148
MA0136.16.89067e-8
MA0137.20.00467
MA0138.20.00144
MA0139.10.157
MA0140.10.00988
MA0141.10.264
MA0142.10.0375
MA0143.10.14
MA0144.10.204
MA0145.10.0475
MA0146.10.993
MA0147.10.0188
MA0148.10.092
MA0149.10.00606
MA0150.10.0976
MA0152.10.34
MA0153.12.91015e-12
MA0154.10.438
MA0155.10.0914
MA0156.11.5524e-12
MA0157.10.273
MA0159.10.278
MA0160.10.183
MA0162.10.42
MA0163.10.838
MA0164.10.322
MA0258.10.732
MA0259.10.129



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: CNhs10576

Novel motifP-value
10.337
100.157
1000.997
1010.316
1020.995
1030.0373
1040.893
1050.388
1060.176
1070.0598
1080.374
1090.625
110.402
1100.515
1110.262
1120.139
1130.751
1140.951
1150.259
1160.287
1170.0293
1180.179
1190.799
120.25
1200.958
1210.211
1220.396
1230.268
1240.709
1250.761
1260.06
1270.341
1280.254
1290.412
130.234
1300.751
1310.349
1320.721
1330.679
1340.475
1350.419
1360.51
1370.778
1380.198
1390.409
140.411
1400.737
1410.33
1420.979
1430.486
1440.0249
1450.127
1460.996
1470.911
1480.351
1490.532
150.0172
1500.906
1510.656
1520.0468
1530.242
1540.564
1550.27
1560.021
1570.482
1580.0481
1590.526
1600.384
1610.0232
1620.894
1630.638
1640.111
1650.913
1660.316
1670.0269
1680.0324
1690.0919
170.356
180.513
190.323
20.00814
200.0579
210.777
220.522
230.469
240.461
250.462
260.29
270.998
280.52
290.0146
30.218
300.214
310.541
320.139
330.176
340.134
350.11
360.0406
370.749
380.699
390.905
40.846
400.0688
410.211
420.264
430.901
440.343
450.162
460.927
470.47
480.22
490.31
50.991
500.194
510.966
520.185
530.398
540.355
550.881
560.552
570.42
580.766
590.0442
60.271
600.318
610.283
620.647
630.421
640.65
650.866
660.838
670.683
680.262
690.188
70.818
700.595
710.371
720.437
730.629
740.943
750.107
760.0359
770.224
780.659
790.171
80.289
800.557
810.355
820.345
830.876
840.453
850.117
860.709
870.739
880.856
890.476
90.247
900.0123
910.453
920.575
930.0405
940.882
950.536
960.76
970.518
980.599
990.381



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: CNhs10576


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)
0000304 (mouse neonate N0 sample)
0000734 (mouse neonate N1 sample)
0011399 (mouse whole body- neonate N01 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)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:659-23C6&oldid=4578551"