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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=AHR_ARNT_ARNT2:2.78866744439;REST:2.77539731241;NHLH1,2:2.70575641281;ZBTB6:2.67182358543;CUX2:2.54157662165;ZFP161:2.50877582434;MTF1:2.46714789619;EGR1..3:2.42594571106;MED-1{core}:2.39705515294;MYFfamily:2.38947275654;HOXA9_MEIS1:2.32908399563;PRRX1,2:2.27271662251;ATF2:2.25123799074;BREu{core}:2.18993861803;ATF5_CREB3:2.18115798033;LMO2:2.07417620494;PBX1:2.07273048527;OCT4_SOX2{dimer}:2.03476229765;MTE{core}:1.99010592793;HAND1,2:1.98163477313;CREB1:1.92269995252;MAFB:1.88500258009;POU3F1..4:1.82384066781;PAX4:1.81874755734;SPZ1:1.81266636973;GZF1:1.77468428619;TFAP2B:1.76658847645;POU6F1:1.75939803017;HIC1:1.74661828498;PAX6:1.73996357291;PRDM1:1.72758852237;JUN:1.71031840001;HMGA1,2:1.70190058048;NFIL3:1.64821416246;PAX5:1.60198732814;RFX1:1.57386298058;TAL1_TCF{3,4,12}:1.56886426166;CDC5L:1.55705155441;TGIF1:1.5269135668;NKX3-2:1.51954682454;TEF:1.48779389368;STAT1,3:1.48230648075;PAX8:1.43304712796;GLI1..3:1.43024944974;HOX{A5,B5}:1.40668194389;ARID5B:1.3940232704;UFEwm:1.38587226535;ZIC1..3:1.36724058206;DBP:1.2961659456;POU1F1:1.29050725089;TFDP1:1.27584853767;NFE2L2:1.27417215516;RORA:1.25578157092;KLF4:1.24322912876;ALX1:1.23633832202;NRF1:1.22541830771;GFI1B:1.17305578678;RREB1:1.13708210309;RFX2..5_RFXANK_RFXAP:1.06495457407;HIF1A:1.04280398171;ZEB1:1.0047686001;IKZF1:0.992438337079;FOXN1:0.986346921883;SMAD1..7,9:0.982415172903;EVI1:0.964984886618;HOX{A4,D4}:0.964178589733;AIRE:0.945736926145;GTF2I:0.942405071238;MYOD1:0.927609393033;FOXM1:0.927099288156;NANOG:0.923588315594;NKX6-1,2:0.870908709346;MZF1:0.837326660482;TFAP2{A,C}:0.802205988042;RBPJ:0.794914712389;EN1,2:0.792481742511;FOX{F1,F2,J1}:0.789731036606;ZBTB16:0.778561468954;FOXQ1:0.763338498258;bHLH_family:0.762632288431;NKX2-2,8:0.75103943988;VSX1,2:0.730300829169;GATA4:0.71945937975;HES1:0.696986018845;SREBF1,2:0.677470890431;ONECUT1,2:0.64528227348;POU5F1:0.624369130128;NFE2:0.595906865106;FOXD3:0.555565501583;CDX1,2,4:0.555327821711;ATF4:0.498342206701;NR3C1:0.496432024972;NKX2-3_NKX2-5:0.477707190612;ZNF143:0.452588019292;NFE2L1:0.406225699173;ZNF384:0.352909064261;PATZ1:0.346117020228;GTF2A1,2:0.258076768856;SOX2:0.187441692026;FOXA2:0.167445687145;ADNP_IRX_SIX_ZHX:0.12794385087;ESRRA:0.109774859226;MAZ:0.109356768271;SNAI1..3:0.0405854499698;HBP1_HMGB_SSRP1_UBTF:0.000338141873553;SOX{8,9,10}:-0.00205026661183;MEF2{A,B,C,D}:-0.0112161918163;FOXP1:-0.0823373811666;STAT2,4,6:-0.0850123143372;BPTF:-0.0964577324286;NFATC1..3:-0.111891622546;YY1:-0.139527876526;SOX17:-0.157165696457;IRF7:-0.197515968336;LHX3,4:-0.215519217501;FOSL2:-0.23016426286;HMX1:-0.345748704499;PAX2:-0.363027264284;MYB:-0.370673024216;ATF6:-0.383470870703;LEF1_TCF7_TCF7L1,2:-0.387190202302;GCM1,2:-0.47401397132;FOXP3:-0.481021609099;ZNF238:-0.517722628306;PPARG:-0.519086671027;FOXL1:-0.525282842887;MYBL2:-0.554914469541;HSF1,2:-0.58697416352;HLF:-0.642171442459;NKX2-1,4:-0.661326289627;POU2F1..3:-0.669761037162;CEBPA,B_DDIT3:-0.674332516732;EBF1:-0.674832590545;PAX1,9:-0.681931988242;TFAP4:-0.689011170412;ZNF148:-0.695030048453;FOS_FOS{B,L1}_JUN{B,D}:-0.750828264198;NKX3-1:-0.766864972901;ZNF423:-0.786920153848;RUNX1..3:-0.796467258812;TLX2:-0.818265312207;NANOG{mouse}:-0.822454797165;IKZF2:-0.824663624297;TLX1..3_NFIC{dimer}:-0.825629221586;HNF1A:-0.825896074248;ELK1,4_GABP{A,B1}:-0.854173197457;SOX5:-0.854247100312;AR:-0.880947555655;STAT5{A,B}:-0.885951179746;NFKB1_REL_RELA:-0.945421558323;SPI1:-0.949319616337;PDX1:-0.958208682436;CRX:-0.969211586505;GATA6:-0.982770515498;HNF4A_NR2F1,2:-0.999903765322;BACH2:-1.0237825411;NR5A1,2:-1.02683627627;TOPORS:-1.02795983704;SP1:-1.151024033;NR6A1:-1.15880576099;NFY{A,B,C}:-1.20690094652;IRF1,2:-1.25424525139;EP300:-1.30621852561;XCPE1{core}:-1.33828522427;TBX4,5:-1.34401795319;FOX{I1,J2}:-1.37257700334;TEAD1:-1.39139004049;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.40371542818;ETS1,2:-1.40523498508;TFCP2:-1.40800365841;RXRA_VDR{dimer}:-1.43998786239;TBP:-1.50159501835;GFI1:-1.51841850175;SPIB:-1.54383751202;ESR1:-1.57667013743;ELF1,2,4:-1.5977908894;PITX1..3:-1.60512423592;E2F1..5:-1.61930854229;ALX4:-1.65121101829;NR1H4:-1.67937324174;T:-1.71266701388;FOXO1,3,4:-1.75642342559;TP53:-1.77624379569;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.77762692107;FOX{D1,D2}:-1.84201709024;DMAP1_NCOR{1,2}_SMARC:-1.90742088908;SRF:-2.00664144306;RXR{A,B,G}:-2.1271445206;NFIX:-2.32130693718
|top_motifs=AHR_ARNT_ARNT2:2.78866744439;REST:2.77539731241;NHLH1,2:2.70575641281;ZBTB6:2.67182358543;CUX2:2.54157662165;ZFP161:2.50877582434;MTF1:2.46714789619;EGR1..3:2.42594571106;MED-1{core}:2.39705515294;MYFfamily:2.38947275654;HOXA9_MEIS1:2.32908399563;PRRX1,2:2.27271662251;ATF2:2.25123799074;BREu{core}:2.18993861803;ATF5_CREB3:2.18115798033;LMO2:2.07417620494;PBX1:2.07273048527;OCT4_SOX2{dimer}:2.03476229765;MTE{core}:1.99010592793;HAND1,2:1.98163477313;CREB1:1.92269995252;MAFB:1.88500258009;POU3F1..4:1.82384066781;PAX4:1.81874755734;SPZ1:1.81266636973;GZF1:1.77468428619;TFAP2B:1.76658847645;POU6F1:1.75939803017;HIC1:1.74661828498;PAX6:1.73996357291;PRDM1:1.72758852237;JUN:1.71031840001;HMGA1,2:1.70190058048;NFIL3:1.64821416246;PAX5:1.60198732814;RFX1:1.57386298058;TAL1_TCF{3,4,12}:1.56886426166;CDC5L:1.55705155441;TGIF1:1.5269135668;NKX3-2:1.51954682454;TEF:1.48779389368;STAT1,3:1.48230648075;PAX8:1.43304712796;GLI1..3:1.43024944974;HOX{A5,B5}:1.40668194389;ARID5B:1.3940232704;UFEwm:1.38587226535;ZIC1..3:1.36724058206;DBP:1.2961659456;POU1F1:1.29050725089;TFDP1:1.27584853767;NFE2L2:1.27417215516;RORA:1.25578157092;KLF4:1.24322912876;ALX1:1.23633832202;NRF1:1.22541830771;GFI1B:1.17305578678;RREB1:1.13708210309;RFX2..5_RFXANK_RFXAP:1.06495457407;HIF1A:1.04280398171;ZEB1:1.0047686001;IKZF1:0.992438337079;FOXN1:0.986346921883;SMAD1..7,9:0.982415172903;EVI1:0.964984886618;HOX{A4,D4}:0.964178589733;AIRE:0.945736926145;GTF2I:0.942405071238;MYOD1:0.927609393033;FOXM1:0.927099288156;NANOG:0.923588315594;NKX6-1,2:0.870908709346;MZF1:0.837326660482;TFAP2{A,C}:0.802205988042;RBPJ:0.794914712389;EN1,2:0.792481742511;FOX{F1,F2,J1}:0.789731036606;ZBTB16:0.778561468954;FOXQ1:0.763338498258;bHLH_family:0.762632288431;NKX2-2,8:0.75103943988;VSX1,2:0.730300829169;GATA4:0.71945937975;HES1:0.696986018845;SREBF1,2:0.677470890431;ONECUT1,2:0.64528227348;POU5F1:0.624369130128;NFE2:0.595906865106;FOXD3:0.555565501583;CDX1,2,4:0.555327821711;ATF4:0.498342206701;NR3C1:0.496432024972;NKX2-3_NKX2-5:0.477707190612;ZNF143:0.452588019292;NFE2L1:0.406225699173;ZNF384:0.352909064261;PATZ1:0.346117020228;GTF2A1,2:0.258076768856;SOX2:0.187441692026;FOXA2:0.167445687145;ADNP_IRX_SIX_ZHX:0.12794385087;ESRRA:0.109774859226;MAZ:0.109356768271;SNAI1..3:0.0405854499698;HBP1_HMGB_SSRP1_UBTF:0.000338141873553;SOX{8,9,10}:-0.00205026661183;MEF2{A,B,C,D}:-0.0112161918163;FOXP1:-0.0823373811666;STAT2,4,6:-0.0850123143372;BPTF:-0.0964577324286;NFATC1..3:-0.111891622546;YY1:-0.139527876526;SOX17:-0.157165696457;IRF7:-0.197515968336;LHX3,4:-0.215519217501;FOSL2:-0.23016426286;HMX1:-0.345748704499;PAX2:-0.363027264284;MYB:-0.370673024216;ATF6:-0.383470870703;LEF1_TCF7_TCF7L1,2:-0.387190202302;GCM1,2:-0.47401397132;FOXP3:-0.481021609099;ZNF238:-0.517722628306;PPARG:-0.519086671027;FOXL1:-0.525282842887;MYBL2:-0.554914469541;HSF1,2:-0.58697416352;HLF:-0.642171442459;NKX2-1,4:-0.661326289627;POU2F1..3:-0.669761037162;CEBPA,B_DDIT3:-0.674332516732;EBF1:-0.674832590545;PAX1,9:-0.681931988242;TFAP4:-0.689011170412;ZNF148:-0.695030048453;FOS_FOS{B,L1}_JUN{B,D}:-0.750828264198;NKX3-1:-0.766864972901;ZNF423:-0.786920153848;RUNX1..3:-0.796467258812;TLX2:-0.818265312207;NANOG{mouse}:-0.822454797165;IKZF2:-0.824663624297;TLX1..3_NFIC{dimer}:-0.825629221586;HNF1A:-0.825896074248;ELK1,4_GABP{A,B1}:-0.854173197457;SOX5:-0.854247100312;AR:-0.880947555655;STAT5{A,B}:-0.885951179746;NFKB1_REL_RELA:-0.945421558323;SPI1:-0.949319616337;PDX1:-0.958208682436;CRX:-0.969211586505;GATA6:-0.982770515498;HNF4A_NR2F1,2:-0.999903765322;BACH2:-1.0237825411;NR5A1,2:-1.02683627627;TOPORS:-1.02795983704;SP1:-1.151024033;NR6A1:-1.15880576099;NFY{A,B,C}:-1.20690094652;IRF1,2:-1.25424525139;EP300:-1.30621852561;XCPE1{core}:-1.33828522427;TBX4,5:-1.34401795319;FOX{I1,J2}:-1.37257700334;TEAD1:-1.39139004049;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.40371542818;ETS1,2:-1.40523498508;TFCP2:-1.40800365841;RXRA_VDR{dimer}:-1.43998786239;TBP:-1.50159501835;GFI1:-1.51841850175;SPIB:-1.54383751202;ESR1:-1.57667013743;ELF1,2,4:-1.5977908894;PITX1..3:-1.60512423592;E2F1..5:-1.61930854229;ALX4:-1.65121101829;NR1H4:-1.67937324174;T:-1.71266701388;FOXO1,3,4:-1.75642342559;TP53:-1.77624379569;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.77762692107;FOX{D1,D2}:-1.84201709024;DMAP1_NCOR{1,2}_SMARC:-1.90742088908;SRF:-2.00664144306;RXR{A,B,G}:-2.1271445206;NFIX:-2.32130693718
|xref=
|xref=
}}
}}

Revision as of 19:56, 16 September 2014


Name:visual cortex - wildtype, neonate N30, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs13034
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueVisual cortex
dev stagepostnatal day 30
sexmale
ageP30
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  SAMD00005503
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13034 CAGE DRX009136 DRR010010
Accession ID Mm9

Library idBAMCTSS
CNhs13034 DRZ001435 DRZ002818
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

CNhs13034

00
10.813
100
1000
1000-0.0355
1001-0.0595
1002-0.116
10030.289
10040
10050
10060.74
1007-0.231
10080
1009-0.19
101-0.0876
10100
10110.995
10120.375
10130.158
1014-0.0874
1015-0.192
1016-0.379
10170
10180
10190
1020
10200.618
10210
10220
10230
1024-0.14
1025-0.0611
10260
10270.396
10280
10290.128
103-0.0848
10300
1031-0.684
10320.195
10330
10340
10350
1036-0.183
10370
10380.0022
10390.0697
1040
1040-0.279
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: CNhs13034

Jaspar motifP-value
MA0002.20.0112
MA0003.10.314
MA0004.10.567
MA0006.10.0988
MA0007.10.388
MA0009.10.923
MA0014.10.691
MA0017.15.12468e-7
MA0018.20.003
MA0019.10.161
MA0024.10.0321
MA0025.10.0108
MA0027.10.137
MA0028.10.0735
MA0029.10.805
MA0030.10.532
MA0031.10.0534
MA0035.20.00852
MA0038.10.925
MA0039.20.00378
MA0040.10.075
MA0041.10.115
MA0042.10.282
MA0043.10.121
MA0046.19.71351e-9
MA0047.22.20919e-4
MA0048.10.0454
MA0050.11.10185e-5
MA0051.10.00363
MA0052.10.403
MA0055.10.00969
MA0057.10.45
MA0058.10.434
MA0059.10.323
MA0060.10.0574
MA0061.10.0364
MA0062.20.00105
MA0065.22.96916e-6
MA0066.10.0584
MA0067.10.465
MA0068.10.253
MA0069.10.0426
MA0070.10.929
MA0071.10.0887
MA0072.10.354
MA0073.10.851
MA0074.10.156
MA0076.10.155
MA0077.10.538
MA0078.10.91
MA0079.20.977
MA0080.21.33197e-10
MA0081.10.212
MA0083.10.00304
MA0084.10.892
MA0087.10.311
MA0088.10.298
MA0090.10.221
MA0091.10.21
MA0092.10.29
MA0093.10.578
MA0099.20.00454
MA0100.10.42
MA0101.10.0137
MA0102.20.27
MA0103.10.411
MA0104.20.864
MA0105.10.036
MA0106.10.0535
MA0107.10.023
MA0108.21.04482e-4
MA0111.10.66
MA0112.29.75766e-4
MA0113.10.207
MA0114.14.35608e-6
MA0115.11.57509e-4
MA0116.10.13
MA0117.10.764
MA0119.10.114
MA0122.10.426
MA0124.10.798
MA0125.10.444
MA0131.10.707
MA0135.10.455
MA0136.11.15175e-11
MA0137.20.192
MA0138.20.00278
MA0139.10.53
MA0140.14.81602e-4
MA0141.10.00263
MA0142.10.385
MA0143.10.642
MA0144.10.127
MA0145.10.0883
MA0146.10.00993
MA0147.10.887
MA0148.11.50989e-4
MA0149.10.42
MA0150.10.281
MA0152.10.562
MA0153.13.29286e-9
MA0154.10.049
MA0155.10.342
MA0156.17.55339e-10
MA0157.10.0347
MA0159.10.0134
MA0160.10.00697
MA0162.10.197
MA0163.10.00645
MA0164.10.988
MA0258.10.0328
MA0259.10.816



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: CNhs13034

Novel motifP-value
10.36
100.0946
1000.418
1010.579
1020.889
1030.164
1040.791
1050.682
1060.0518
1070.141
1080.381
1090.00276
110.0988
1100.0461
1110.403
1120.00603
1130.337
1140.615
1150.934
1160.293
1170.00459
1180.517
1190.306
120.83
1200.785
1210.158
1220.992
1230.00211
1240.0187
1250.662
1260.0626
1270.422
1280.0332
1290.231
139.79521e-9
1300.0603
1310.529
1320.55
1330.5
1340.056
1350.307
1360.0427
1370.539
1380.649
1390.994
140.944
1400.217
1410.929
1420.894
1430.699
1440.568
1455.03722e-5
1460.186
1470.113
1480.403
1490.467
150.261
1500.0367
1510.822
1520.067
1530.96
1540.94
1550.431
1560.00218
1570.134
1580.124
1590.907
1600.237
1610.12
1620.574
1630.921
1640.127
1650.227
1660.464
1670.367
1680.438
1690.00336
170.0591
180.816
190.0558
20.923
200.0446
210.273
220.0843
230.671
240.0165
250.993
261.96553e-6
270.458
280.655
290.0305
30.0509
300.933
310.854
320.888
330.28
340.493
350.523
360.522
370.0186
380.438
390.188
40.16
400.188
410.741
420.171
430.135
440.738
450.567
460.227
470.5
480.358
490.313
50.308
500.136
510.817
520.156
530.603
540.95
550.955
560.512
570.813
580.367
590.124
60.966
600.0362
610.0379
620.324
630.113
640.624
650.449
660.476
670.643
680.192
690.142
70.0175
700.485
710.0132
720.675
730.025
740.895
750.0593
760.702
770.373
780.00227
790.417
80.167
800.712
810.719
820.485
830.0597
840.97
850.235
860.199
870.0549
880.572
890.959
90.35
900.415
910.208
920.604
930.284
940.932
950.0192
960.5
970.932
980.367
990.563



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: CNhs13034


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)
0000310 (mouse neonate N30 sample)
0011269 (mouse visual cortex from wildtype- neonate N30 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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