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|sample_strain=
|sample_strain=
|sample_tissue=Visual cortex
|sample_tissue=Visual cortex
|timecourse=Visual_cortex_development
|timecourse=mouse_visualcortex
|top_motifs=POU1F1:3.45691573052;CUX2:3.2129384021;POU3F1..4:2.89684204278;AHR_ARNT_ARNT2:2.84040025334;EGR1..3:2.77382438138;AIRE:2.70338577182;REST:2.66331246453;ZFP161:2.59211808313;NHLH1,2:2.49947590414;HOXA9_MEIS1:2.45359075076;ZBTB6:2.45078826254;PRDM1:2.41893746158;OCT4_SOX2{dimer}:2.40847959416;MYFfamily:2.35262147517;ATF5_CREB3:2.27869191905;EVI1:2.25037406688;PAX4:2.22490331583;KLF4:2.20463910166;MED-1{core}:2.19381542899;ALX1:2.17031292655;UFEwm:2.16247347318;HMGA1,2:2.11217881949;BREu{core}:2.10411900453;PRRX1,2:2.07816364556;LMO2:2.05751970176;POU6F1:2.05066636928;ZBTB16:1.99561591686;PAX6:1.92160128999;JUN:1.91099428271;MTF1:1.86562825469;PBX1:1.83720424101;MAFB:1.82957867618;GZF1:1.79935743593;CREB1:1.79890001419;ATF2:1.79120759764;DBP:1.76594894675;FOXQ1:1.76359261385;PAX8:1.74438417501;MTE{core}:1.68378781102;HIC1:1.63337472732;RFX1:1.62496875724;ZIC1..3:1.61787815942;RREB1:1.61260378705;TEF:1.54422148123;PAX5:1.53656710624;TFAP2B:1.48708554149;CDC5L:1.47690255085;TGIF1:1.43759481024;GATA4:1.43680651506;TFDP1:1.43601087216;NKX6-1,2:1.3596743766;GFI1B:1.337650431;CDX1,2,4:1.33566992231;ARID5B:1.31946406813;HOX{A4,D4}:1.27288506796;MZF1:1.2326399346;NRF1:1.1865842908;IKZF1:1.18479006281;NKX2-3_NKX2-5:1.17450775476;SMAD1..7,9:1.17009511456;NANOG:1.14821022305;MYOD1:1.13885757148;NFIL3:1.13638478144;ZNF384:1.09546475655;GTF2I:1.07891378201;FOXN1:1.07515798592;GLI1..3:1.0694455719;HOX{A5,B5}:1.04059617924;NKX2-2,8:1.01982136431;HAND1,2:0.941639659374;ONECUT1,2:0.940571275109;RFX2..5_RFXANK_RFXAP:0.918992668653;VSX1,2:0.906657102504;NR3C1:0.898850598324;TAL1_TCF{3,4,12}:0.897063661332;NKX3-2:0.8953675429;POU5F1:0.819493946699;TFAP2{A,C}:0.813873757025;STAT1,3:0.795973922897;bHLH_family:0.790047282336;IRF7:0.678734126604;ZEB1:0.669232904923;NFE2L2:0.629393375467;RBPJ:0.623551501528;PATZ1:0.603864497664;RORA:0.595725742737;SPZ1:0.541511783985;FOX{F1,F2,J1}:0.540045648899;NKX3-1:0.517593475414;SOX2:0.480036300991;ATF4:0.439629401427;PPARG:0.415791490713;FOXM1:0.374661986729;SREBF1,2:0.370514521578;FOXP1:0.355633078768;SOX{8,9,10}:0.327159941059;LHX3,4:0.308099677617;MAZ:0.287434795848;BPTF:0.276949061832;HES1:0.235030269369;NFE2L1:0.216420049058;ZNF143:0.213035917923;HIF1A:0.198317937453;GTF2A1,2:0.187142085431;ADNP_IRX_SIX_ZHX:0.142147022289;NFE2:0.0894123506045;STAT2,4,6:0.0838188627372;ESRRA:0.0533850152701;FOXA2:0.0351013081515;EN1,2:0.0311970714198;PAX2:0.0250446361274;FOXP3:0.0109128984416;SNAI1..3:-0.107105466238;MEF2{A,B,C,D}:-0.112484532064;IKZF2:-0.149248493924;HMX1:-0.209956968935;ATF6:-0.228055351604;FOXD3:-0.251957149973;NKX2-1,4:-0.281592914414;CRX:-0.29661259668;TOPORS:-0.331244057679;FOXL1:-0.370266484398;SOX17:-0.416810902647;NANOG{mouse}:-0.476326382408;ZNF238:-0.495377142618;GCM1,2:-0.502090676889;NFATC1..3:-0.518320952869;MYB:-0.526524467557;YY1:-0.629601546908;MYBL2:-0.708726335571;TFAP4:-0.713731037313;ZNF148:-0.728768320983;EP300:-0.72889097454;AR:-0.766660538876;HBP1_HMGB_SSRP1_UBTF:-0.767357629377;TLX2:-0.782037597184;HSF1,2:-0.798951281512;LEF1_TCF7_TCF7L1,2:-0.803190511729;TLX1..3_NFIC{dimer}:-0.812527519917;HNF1A:-0.883414887448;FOS_FOS{B,L1}_JUN{B,D}:-0.902732816981;CEBPA,B_DDIT3:-0.92247520939;RUNX1..3:-0.961011892566;NFKB1_REL_RELA:-0.977102467724;POU2F1..3:-0.981320195001;EBF1:-0.998049815504;GATA6:-1.02586306895;FOSL2:-1.05205452574;ZNF423:-1.0927640623;HNF4A_NR2F1,2:-1.09464832708;SPI1:-1.09680707193;BACH2:-1.17517251232;ALX4:-1.2051262473;SP1:-1.21234912663;SOX5:-1.21395087378;ELK1,4_GABP{A,B1}:-1.22449474194;TFCP2:-1.24141941902;NFY{A,B,C}:-1.24154070358;T:-1.24766508424;XCPE1{core}:-1.27150129328;PITX1..3:-1.30657412507;PAX1,9:-1.31309154206;NR5A1,2:-1.31366074621;NR6A1:-1.31989744268;SPIB:-1.34071015179;GFI1:-1.35855331701;IRF1,2:-1.38959663504;TBX4,5:-1.40233823844;PDX1:-1.40608458007;FOX{I1,J2}:-1.43206133101;ETS1,2:-1.47313468931;HLF:-1.49609203804;TEAD1:-1.5003744474;TBP:-1.51130315416;FOXO1,3,4:-1.54944174034;E2F1..5:-1.60424324683;DMAP1_NCOR{1,2}_SMARC:-1.70855774668;STAT5{A,B}:-1.73177368183;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.76212166106;ELF1,2,4:-1.81009832996;NR1H4:-1.82719081026;RXR{A,B,G}:-1.94248657549;SRF:-1.96915254029;NFIX:-2.04758922055;TP53:-2.1254121333;RXRA_VDR{dimer}:-2.19540858667;ESR1:-2.20563847695;FOX{D1,D2}:-2.34986294385;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-2.50276064766
|top_motifs=POU1F1:3.45691573052;CUX2:3.2129384021;POU3F1..4:2.89684204278;AHR_ARNT_ARNT2:2.84040025334;EGR1..3:2.77382438138;AIRE:2.70338577182;REST:2.66331246453;ZFP161:2.59211808313;NHLH1,2:2.49947590414;HOXA9_MEIS1:2.45359075076;ZBTB6:2.45078826254;PRDM1:2.41893746158;OCT4_SOX2{dimer}:2.40847959416;MYFfamily:2.35262147517;ATF5_CREB3:2.27869191905;EVI1:2.25037406688;PAX4:2.22490331583;KLF4:2.20463910166;MED-1{core}:2.19381542899;ALX1:2.17031292655;UFEwm:2.16247347318;HMGA1,2:2.11217881949;BREu{core}:2.10411900453;PRRX1,2:2.07816364556;LMO2:2.05751970176;POU6F1:2.05066636928;ZBTB16:1.99561591686;PAX6:1.92160128999;JUN:1.91099428271;MTF1:1.86562825469;PBX1:1.83720424101;MAFB:1.82957867618;GZF1:1.79935743593;CREB1:1.79890001419;ATF2:1.79120759764;DBP:1.76594894675;FOXQ1:1.76359261385;PAX8:1.74438417501;MTE{core}:1.68378781102;HIC1:1.63337472732;RFX1:1.62496875724;ZIC1..3:1.61787815942;RREB1:1.61260378705;TEF:1.54422148123;PAX5:1.53656710624;TFAP2B:1.48708554149;CDC5L:1.47690255085;TGIF1:1.43759481024;GATA4:1.43680651506;TFDP1:1.43601087216;NKX6-1,2:1.3596743766;GFI1B:1.337650431;CDX1,2,4:1.33566992231;ARID5B:1.31946406813;HOX{A4,D4}:1.27288506796;MZF1:1.2326399346;NRF1:1.1865842908;IKZF1:1.18479006281;NKX2-3_NKX2-5:1.17450775476;SMAD1..7,9:1.17009511456;NANOG:1.14821022305;MYOD1:1.13885757148;NFIL3:1.13638478144;ZNF384:1.09546475655;GTF2I:1.07891378201;FOXN1:1.07515798592;GLI1..3:1.0694455719;HOX{A5,B5}:1.04059617924;NKX2-2,8:1.01982136431;HAND1,2:0.941639659374;ONECUT1,2:0.940571275109;RFX2..5_RFXANK_RFXAP:0.918992668653;VSX1,2:0.906657102504;NR3C1:0.898850598324;TAL1_TCF{3,4,12}:0.897063661332;NKX3-2:0.8953675429;POU5F1:0.819493946699;TFAP2{A,C}:0.813873757025;STAT1,3:0.795973922897;bHLH_family:0.790047282336;IRF7:0.678734126604;ZEB1:0.669232904923;NFE2L2:0.629393375467;RBPJ:0.623551501528;PATZ1:0.603864497664;RORA:0.595725742737;SPZ1:0.541511783985;FOX{F1,F2,J1}:0.540045648899;NKX3-1:0.517593475414;SOX2:0.480036300991;ATF4:0.439629401427;PPARG:0.415791490713;FOXM1:0.374661986729;SREBF1,2:0.370514521578;FOXP1:0.355633078768;SOX{8,9,10}:0.327159941059;LHX3,4:0.308099677617;MAZ:0.287434795848;BPTF:0.276949061832;HES1:0.235030269369;NFE2L1:0.216420049058;ZNF143:0.213035917923;HIF1A:0.198317937453;GTF2A1,2:0.187142085431;ADNP_IRX_SIX_ZHX:0.142147022289;NFE2:0.0894123506045;STAT2,4,6:0.0838188627372;ESRRA:0.0533850152701;FOXA2:0.0351013081515;EN1,2:0.0311970714198;PAX2:0.0250446361274;FOXP3:0.0109128984416;SNAI1..3:-0.107105466238;MEF2{A,B,C,D}:-0.112484532064;IKZF2:-0.149248493924;HMX1:-0.209956968935;ATF6:-0.228055351604;FOXD3:-0.251957149973;NKX2-1,4:-0.281592914414;CRX:-0.29661259668;TOPORS:-0.331244057679;FOXL1:-0.370266484398;SOX17:-0.416810902647;NANOG{mouse}:-0.476326382408;ZNF238:-0.495377142618;GCM1,2:-0.502090676889;NFATC1..3:-0.518320952869;MYB:-0.526524467557;YY1:-0.629601546908;MYBL2:-0.708726335571;TFAP4:-0.713731037313;ZNF148:-0.728768320983;EP300:-0.72889097454;AR:-0.766660538876;HBP1_HMGB_SSRP1_UBTF:-0.767357629377;TLX2:-0.782037597184;HSF1,2:-0.798951281512;LEF1_TCF7_TCF7L1,2:-0.803190511729;TLX1..3_NFIC{dimer}:-0.812527519917;HNF1A:-0.883414887448;FOS_FOS{B,L1}_JUN{B,D}:-0.902732816981;CEBPA,B_DDIT3:-0.92247520939;RUNX1..3:-0.961011892566;NFKB1_REL_RELA:-0.977102467724;POU2F1..3:-0.981320195001;EBF1:-0.998049815504;GATA6:-1.02586306895;FOSL2:-1.05205452574;ZNF423:-1.0927640623;HNF4A_NR2F1,2:-1.09464832708;SPI1:-1.09680707193;BACH2:-1.17517251232;ALX4:-1.2051262473;SP1:-1.21234912663;SOX5:-1.21395087378;ELK1,4_GABP{A,B1}:-1.22449474194;TFCP2:-1.24141941902;NFY{A,B,C}:-1.24154070358;T:-1.24766508424;XCPE1{core}:-1.27150129328;PITX1..3:-1.30657412507;PAX1,9:-1.31309154206;NR5A1,2:-1.31366074621;NR6A1:-1.31989744268;SPIB:-1.34071015179;GFI1:-1.35855331701;IRF1,2:-1.38959663504;TBX4,5:-1.40233823844;PDX1:-1.40608458007;FOX{I1,J2}:-1.43206133101;ETS1,2:-1.47313468931;HLF:-1.49609203804;TEAD1:-1.5003744474;TBP:-1.51130315416;FOXO1,3,4:-1.54944174034;E2F1..5:-1.60424324683;DMAP1_NCOR{1,2}_SMARC:-1.70855774668;STAT5{A,B}:-1.73177368183;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.76212166106;ELF1,2,4:-1.81009832996;NR1H4:-1.82719081026;RXR{A,B,G}:-1.94248657549;SRF:-1.96915254029;NFIX:-2.04758922055;TP53:-2.1254121333;RXRA_VDR{dimer}:-2.19540858667;ESR1:-2.20563847695;FOX{D1,D2}:-2.34986294385;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-2.50276064766
|xref=
|xref=
}}
}}

Revision as of 19:55, 16 September 2014


Name:visual cortex - wildtype, neonate N15, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs13033
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueVisual cortex
dev stagepostnatal day 15
sexmale
ageP15
cell typemixed
cell lineN/A
companyN/A
collaborationMichela Fagiolini/Alka Saxena/Piero Carninci
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberN/A
catalog numberN/A
sample typeVisual cortex tissue
extraction protocol (Details)Total RNA Trizol Qiagen minElute

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005460
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13033 CAGE DRX009134 DRR010008
Accession ID Mm9

Library idBAMCTSS
CNhs13033 DRZ001433 DRZ002816
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

CNhs13033

00
10.809
100
1000
10000.0342
1001-0.00595
1002-0.0468
10030.44
10040
10050
10060.666
1007-0.259
10080
1009-0.177
101-0.0768
10100
10110.842
10120.587
10130.0876
10140
1015-0.113
1016-0.134
10170
10180
10190
1020
10200.434
10210
1022-0.0704
10230
1024-0.0899
10250
10260
10270.197
10280
10290.252
103-0.0848
10300
1031-0.403
10320.144
10330
10340
10350
1036-0.183
10370
1038-0.0391
10390.0123
1040
1040-0.484
10410



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: CNhs13033

Jaspar motifP-value
MA0002.20.0264
MA0003.10.246
MA0004.10.528
MA0006.10.0956
MA0007.10.305
MA0009.10.879
MA0014.10.605
MA0017.11.89415e-7
MA0018.20.00771
MA0019.10.109
MA0024.10.0336
MA0025.10.375
MA0027.10.0448
MA0028.10.0275
MA0029.10.539
MA0030.10.37
MA0031.10.0161
MA0035.20.0102
MA0038.10.714
MA0039.20.00224
MA0040.10.0605
MA0041.10.393
MA0042.10.587
MA0043.10.763
MA0046.13.86586e-10
MA0047.22.53641e-4
MA0048.10.0568
MA0050.11.40012e-5
MA0051.17.68255e-4
MA0052.10.997
MA0055.10.00837
MA0057.10.471
MA0058.10.305
MA0059.10.295
MA0060.10.0617
MA0061.10.0557
MA0062.23.3502e-5
MA0065.21.4145e-6
MA0066.10.163
MA0067.10.601
MA0068.10.22
MA0069.10.145
MA0070.10.977
MA0071.10.0404
MA0072.10.109
MA0073.10.826
MA0074.10.104
MA0076.10.0443
MA0077.10.77
MA0078.10.974
MA0079.20.823
MA0080.22.01646e-10
MA0081.10.234
MA0083.10.00221
MA0084.10.614
MA0087.10.572
MA0088.10.331
MA0090.10.14
MA0091.10.338
MA0092.10.298
MA0093.10.514
MA0099.23.67271e-4
MA0100.10.378
MA0101.10.0167
MA0102.20.214
MA0103.10.271
MA0104.20.886
MA0105.10.0916
MA0106.10.0792
MA0107.10.0431
MA0108.21.54453e-4
MA0111.10.766
MA0112.20.00104
MA0113.10.169
MA0114.13.14022e-6
MA0115.12.83795e-4
MA0116.10.163
MA0117.10.738
MA0119.10.115
MA0122.10.511
MA0124.10.962
MA0125.10.267
MA0131.10.808
MA0135.10.148
MA0136.11.38507e-11
MA0137.20.0615
MA0138.20.00328
MA0139.10.391
MA0140.10.0017
MA0141.15.7324e-4
MA0142.10.227
MA0143.10.789
MA0144.10.0404
MA0145.10.0693
MA0146.10.00912
MA0147.10.934
MA0148.15.68554e-4
MA0149.10.5
MA0150.10.118
MA0152.10.954
MA0153.14.45823e-10
MA0154.10.061
MA0155.10.331
MA0156.12.24336e-11
MA0157.10.0229
MA0159.10.0048
MA0160.10.00366
MA0162.10.181
MA0163.10.00392
MA0164.10.772
MA0258.10.0473
MA0259.10.758



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: CNhs13033

Novel motifP-value
10.352
100.123
1000.476
1010.52
1020.821
1030.198
1040.949
1050.55
1060.0478
1070.16
1080.492
1090.00232
110.104
1100.0699
1110.451
1120.0191
1130.308
1140.602
1150.794
1160.336
1170.00675
1180.526
1190.189
120.579
1200.912
1210.144
1220.949
1230.00125
1240.0342
1250.978
1260.0431
1270.684
1280.052
1290.432
136.9781e-9
1300.0337
1310.447
1320.51
1330.366
1340.0842
1350.234
1360.0014
1370.547
1380.694
1390.988
140.755
1400.283
1410.659
1420.935
1430.581
1440.666
1456.91146e-4
1460.255
1470.107
1480.759
1490.567
150.289
1500.0352
1510.748
1520.0632
1530.721
1540.911
1550.5
1561.20876e-14
1570.27
1580.375
1590.216
1600.343
1610.0669
1620.602
1630.787
1640.098
1650.21
1660.656
1670.217
1680.578
1690.00369
170.0506
180.821
190.0628
20.975
200.0588
210.231
220.0783
230.648
240.0131
250.958
268.84069e-7
270.59
280.639
290.0487
30.0525
300.927
310.767
320.873
330.187
340.473
350.497
360.617
370.0155
380.332
390.224
40.214
400.105
410.61
420.198
430.121
440.899
450.541
460.246
470.527
480.432
490.324
50.458
500.149
510.723
520.168
530.654
540.918
550.858
560.452
570.848
580.412
590.132
60.981
600.0263
610.0421
620.367
630.123
640.674
650.263
660.494
670.822
680.275
690.309
70.0195
700.458
710.0102
720.518
730.0164
740.571
750.0646
760.693
770.345
780.00316
790.661
80.22
800.971
810.553
820.413
830.03
840.827
850.248
860.162
870.00253
880.453
890.945
90.354
900.525
910.406
920.547
930.658
940.776
950.0166
960.572
970.932
980.534
990.411



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: CNhs13033


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)
0000955 (brain)
0002021 (occipital lobe)
0000411 (visual cortex)
0000956 (cerebral cortex)
0000479 (tissue)
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)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0001950 (neocortex)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000316 (mouse neonate N15 sample)
0011268 (mouse visual cortex from wildtype- neonate N15 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
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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