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Line 88: Line 88:
 
|sample_tissue=Visual cortex
 
|sample_tissue=Visual cortex
 
|time= neonate N30
 
|time= neonate N30
|timecourse=mouse_visualcortex
+
|timecourse=Visual_cortex_development
 
|top_motifs=AHR_ARNT_ARNT2:2.87594215809;PBX1:2.83367803989;CUX2:2.77172505817;REST:2.75435639192;PAX4:2.62200059079;POU3F1..4:2.57420629072;POU6F1:2.54819694238;HOXA9_MEIS1:2.5318903561;EGR1..3:2.53003757045;OCT4_SOX2{dimer}:2.4917914643;ZFP161:2.48848136045;MTF1:2.38372167694;NHLH1,2:2.3647547911;HMGA1,2:2.29536251709;ZBTB6:2.27123865603;FOXQ1:2.20641593849;ATF5_CREB3:2.14200715203;BREu{core}:2.13982607024;MYFfamily:2.12983247409;LMO2:2.06941655167;PRRX1,2:2.05794452151;MED-1{core}:2.02739474514;CREB1:1.94094804337;GZF1:1.92789556505;AIRE:1.90294872924;STAT1,3:1.89833816448;MAFB:1.86616802279;PRDM1:1.83625660756;DBP:1.83617927716;JUN:1.814683713;POU1F1:1.8075471398;HIC1:1.79660277116;ATF2:1.77026352622;NKX3-2:1.72295718974;MTE{core}:1.71632232804;ZIC1..3:1.66998529905;PAX5:1.62417396149;TFAP2B:1.6169611126;TAL1_TCF{3,4,12}:1.56978710088;PAX6:1.56743378439;ALX1:1.54638718442;UFEwm:1.53918941661;RFX1:1.53058374936;NFIL3:1.47321815951;KLF4:1.44638787556;HOX{A4,D4}:1.44334983735;TGIF1:1.4156164602;NKX6-1,2:1.39163431606;GFI1B:1.37259644395;HIF1A:1.27167340291;NKX2-2,8:1.25202536921;GLI1..3:1.20895468404;NANOG:1.18915723379;TFDP1:1.1890977125;EVI1:1.18152434655;GATA4:1.14304044229;HAND1,2:1.11790838384;TEF:1.11760009795;MYOD1:1.10618931218;NRF1:1.10603219981;PAX8:1.10494566411;RFX2..5_RFXANK_RFXAP:1.09034328747;RORA:1.09013414007;RREB1:1.08135317328;RBPJ:1.01574936642;SMAD1..7,9:0.99258434313;GTF2I:0.986945018299;EN1,2:0.980021872935;MZF1:0.975272026055;VSX1,2:0.967128750543;FOXN1:0.965502987426;SPZ1:0.963067940779;IKZF1:0.905576915503;SREBF1,2:0.898990500764;FOXM1:0.874585502426;ONECUT1,2:0.859644865396;PPARG:0.840924142748;NFE2L2:0.838127738904;ZBTB16:0.836183695521;POU5F1:0.784122893429;CDC5L:0.782508223389;bHLH_family:0.727114223632;FOXD3:0.711957179996;ZEB1:0.665839537899;ARID5B:0.642470999254;CDX1,2,4:0.624169844486;NKX2-3_NKX2-5:0.582365615788;FOX{F1,F2,J1}:0.556283698387;IRF7:0.515475491807;FOXP1:0.497694072049;ATF4:0.486410562779;HES1:0.48360427505;PATZ1:0.479400728824;ZNF384:0.475306854298;TFAP2{A,C}:0.456334318537;NR3C1:0.437071298278;ADNP_IRX_SIX_ZHX:0.408008451802;FOXP3:0.40389778367;GTF2A1,2:0.363434237748;BPTF:0.361481771255;FOXA2:0.340460398496;PAX2:0.332716036065;NFE2L1:0.306932127512;SOX2:0.211172380149;MAZ:0.18981123707;NFE2:0.188842309323;ZNF143:0.156591869999;YY1:0.0963321139449;SNAI1..3:0.0624133671888;NKX3-1:-0.0835138781663;LHX3,4:-0.100608080303;MEF2{A,B,C,D}:-0.104103471152;SOX{8,9,10}:-0.123439494707;HSF1,2:-0.196720779619;HBP1_HMGB_SSRP1_UBTF:-0.198613568031;HOX{A5,B5}:-0.212361901874;FOSL2:-0.231593748851;ZNF423:-0.253159031084;SOX17:-0.256179620442;STAT2,4,6:-0.268029445772;FOXL1:-0.31790500398;NFATC1..3:-0.340054754482;MYBL2:-0.399234688998;MYB:-0.418673678891;CRX:-0.427643244189;NKX2-1,4:-0.427739523437;ESRRA:-0.476605805223;EBF1:-0.480250307761;GCM1,2:-0.535483230652;IKZF2:-0.565846546082;LEF1_TCF7_TCF7L1,2:-0.586787777379;FOS_FOS{B,L1}_JUN{B,D}:-0.676752864908;ZNF238:-0.683059675132;TLX1..3_NFIC{dimer}:-0.693416672043;ATF6:-0.719991613045;HMX1:-0.746700431939;CEBPA,B_DDIT3:-0.779174564783;NR5A1,2:-0.78360815765;POU2F1..3:-0.788568413967;EP300:-0.804458888893;BACH2:-0.819269938286;SOX5:-0.826015823215;RUNX1..3:-0.840375192379;HNF1A:-0.871943290887;TFCP2:-0.881582344573;STAT5{A,B}:-0.89692030513;PAX1,9:-0.89874009361;TBX4,5:-0.915341230509;ELK1,4_GABP{A,B1}:-0.920290043697;NANOG{mouse}:-0.93889045336;T:-0.962565775253;HNF4A_NR2F1,2:-1.01010049268;TFAP4:-1.01070147284;HLF:-1.05881387502;SPI1:-1.06557247532;GATA6:-1.06729341695;NFKB1_REL_RELA:-1.11279490174;ZNF148:-1.11362244542;SP1:-1.12357279309;XCPE1{core}:-1.16599548292;ALX4:-1.18418252415;PDX1:-1.19703552056;TOPORS:-1.20575776559;NR6A1:-1.2082753263;IRF1,2:-1.21682286664;TLX2:-1.222581001;TEAD1:-1.34368059677;NFY{A,B,C}:-1.39671111964;FOX{I1,J2}:-1.41662965852;ETS1,2:-1.43056156133;SPIB:-1.53270110328;AR:-1.57642443238;TBP:-1.59766852388;ESR1:-1.66955310394;ELF1,2,4:-1.71912751895;E2F1..5:-1.78774794796;GFI1:-1.81317649294;SRF:-1.88538151155;DMAP1_NCOR{1,2}_SMARC:-1.89341943096;FOX{D1,D2}:-1.92595233816;FOXO1,3,4:-1.93211616467;NR1H4:-1.94198767935;PITX1..3:-1.94405888702;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.94841084138;RXR{A,B,G}:-1.97905983328;TP53:-2.0148869704;RXRA_VDR{dimer}:-2.03808675287;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-2.18545154795;NFIX:-2.19008073737
 
|top_motifs=AHR_ARNT_ARNT2:2.87594215809;PBX1:2.83367803989;CUX2:2.77172505817;REST:2.75435639192;PAX4:2.62200059079;POU3F1..4:2.57420629072;POU6F1:2.54819694238;HOXA9_MEIS1:2.5318903561;EGR1..3:2.53003757045;OCT4_SOX2{dimer}:2.4917914643;ZFP161:2.48848136045;MTF1:2.38372167694;NHLH1,2:2.3647547911;HMGA1,2:2.29536251709;ZBTB6:2.27123865603;FOXQ1:2.20641593849;ATF5_CREB3:2.14200715203;BREu{core}:2.13982607024;MYFfamily:2.12983247409;LMO2:2.06941655167;PRRX1,2:2.05794452151;MED-1{core}:2.02739474514;CREB1:1.94094804337;GZF1:1.92789556505;AIRE:1.90294872924;STAT1,3:1.89833816448;MAFB:1.86616802279;PRDM1:1.83625660756;DBP:1.83617927716;JUN:1.814683713;POU1F1:1.8075471398;HIC1:1.79660277116;ATF2:1.77026352622;NKX3-2:1.72295718974;MTE{core}:1.71632232804;ZIC1..3:1.66998529905;PAX5:1.62417396149;TFAP2B:1.6169611126;TAL1_TCF{3,4,12}:1.56978710088;PAX6:1.56743378439;ALX1:1.54638718442;UFEwm:1.53918941661;RFX1:1.53058374936;NFIL3:1.47321815951;KLF4:1.44638787556;HOX{A4,D4}:1.44334983735;TGIF1:1.4156164602;NKX6-1,2:1.39163431606;GFI1B:1.37259644395;HIF1A:1.27167340291;NKX2-2,8:1.25202536921;GLI1..3:1.20895468404;NANOG:1.18915723379;TFDP1:1.1890977125;EVI1:1.18152434655;GATA4:1.14304044229;HAND1,2:1.11790838384;TEF:1.11760009795;MYOD1:1.10618931218;NRF1:1.10603219981;PAX8:1.10494566411;RFX2..5_RFXANK_RFXAP:1.09034328747;RORA:1.09013414007;RREB1:1.08135317328;RBPJ:1.01574936642;SMAD1..7,9:0.99258434313;GTF2I:0.986945018299;EN1,2:0.980021872935;MZF1:0.975272026055;VSX1,2:0.967128750543;FOXN1:0.965502987426;SPZ1:0.963067940779;IKZF1:0.905576915503;SREBF1,2:0.898990500764;FOXM1:0.874585502426;ONECUT1,2:0.859644865396;PPARG:0.840924142748;NFE2L2:0.838127738904;ZBTB16:0.836183695521;POU5F1:0.784122893429;CDC5L:0.782508223389;bHLH_family:0.727114223632;FOXD3:0.711957179996;ZEB1:0.665839537899;ARID5B:0.642470999254;CDX1,2,4:0.624169844486;NKX2-3_NKX2-5:0.582365615788;FOX{F1,F2,J1}:0.556283698387;IRF7:0.515475491807;FOXP1:0.497694072049;ATF4:0.486410562779;HES1:0.48360427505;PATZ1:0.479400728824;ZNF384:0.475306854298;TFAP2{A,C}:0.456334318537;NR3C1:0.437071298278;ADNP_IRX_SIX_ZHX:0.408008451802;FOXP3:0.40389778367;GTF2A1,2:0.363434237748;BPTF:0.361481771255;FOXA2:0.340460398496;PAX2:0.332716036065;NFE2L1:0.306932127512;SOX2:0.211172380149;MAZ:0.18981123707;NFE2:0.188842309323;ZNF143:0.156591869999;YY1:0.0963321139449;SNAI1..3:0.0624133671888;NKX3-1:-0.0835138781663;LHX3,4:-0.100608080303;MEF2{A,B,C,D}:-0.104103471152;SOX{8,9,10}:-0.123439494707;HSF1,2:-0.196720779619;HBP1_HMGB_SSRP1_UBTF:-0.198613568031;HOX{A5,B5}:-0.212361901874;FOSL2:-0.231593748851;ZNF423:-0.253159031084;SOX17:-0.256179620442;STAT2,4,6:-0.268029445772;FOXL1:-0.31790500398;NFATC1..3:-0.340054754482;MYBL2:-0.399234688998;MYB:-0.418673678891;CRX:-0.427643244189;NKX2-1,4:-0.427739523437;ESRRA:-0.476605805223;EBF1:-0.480250307761;GCM1,2:-0.535483230652;IKZF2:-0.565846546082;LEF1_TCF7_TCF7L1,2:-0.586787777379;FOS_FOS{B,L1}_JUN{B,D}:-0.676752864908;ZNF238:-0.683059675132;TLX1..3_NFIC{dimer}:-0.693416672043;ATF6:-0.719991613045;HMX1:-0.746700431939;CEBPA,B_DDIT3:-0.779174564783;NR5A1,2:-0.78360815765;POU2F1..3:-0.788568413967;EP300:-0.804458888893;BACH2:-0.819269938286;SOX5:-0.826015823215;RUNX1..3:-0.840375192379;HNF1A:-0.871943290887;TFCP2:-0.881582344573;STAT5{A,B}:-0.89692030513;PAX1,9:-0.89874009361;TBX4,5:-0.915341230509;ELK1,4_GABP{A,B1}:-0.920290043697;NANOG{mouse}:-0.93889045336;T:-0.962565775253;HNF4A_NR2F1,2:-1.01010049268;TFAP4:-1.01070147284;HLF:-1.05881387502;SPI1:-1.06557247532;GATA6:-1.06729341695;NFKB1_REL_RELA:-1.11279490174;ZNF148:-1.11362244542;SP1:-1.12357279309;XCPE1{core}:-1.16599548292;ALX4:-1.18418252415;PDX1:-1.19703552056;TOPORS:-1.20575776559;NR6A1:-1.2082753263;IRF1,2:-1.21682286664;TLX2:-1.222581001;TEAD1:-1.34368059677;NFY{A,B,C}:-1.39671111964;FOX{I1,J2}:-1.41662965852;ETS1,2:-1.43056156133;SPIB:-1.53270110328;AR:-1.57642443238;TBP:-1.59766852388;ESR1:-1.66955310394;ELF1,2,4:-1.71912751895;E2F1..5:-1.78774794796;GFI1:-1.81317649294;SRF:-1.88538151155;DMAP1_NCOR{1,2}_SMARC:-1.89341943096;FOX{D1,D2}:-1.92595233816;FOXO1,3,4:-1.93211616467;NR1H4:-1.94198767935;PITX1..3:-1.94405888702;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.94841084138;RXR{A,B,G}:-1.97905983328;TP53:-2.0148869704;RXRA_VDR{dimer}:-2.03808675287;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-2.18545154795;NFIX:-2.19008073737
 
|xref=
 
|xref=
 
}}
 
}}

Revision as of 10:09, 5 March 2015


Name:visual cortex - wildtype
Species:Mouse (Mus musculus)
Library ID:CNhs13036
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  SAMD00005545
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13036 CAGE DRX009138 DRR010012
Accession ID Mm9

Library idBAMCTSS
CNhs13036 DRZ001437 DRZ002820
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

CNhs13036

00
10.817
100
1000
10000
1001-0.0275
1002-0.116
10030.146
10040
10050
10060.611
1007-0.145
10080
1009-0.15
101-0.0855
10100
10110.926
10120.224
10130.304
10140.139
1015-0.0136
1016-0.293
10170
10180
10190
1020
10200.568
10210
1022-0.0704
10230
10240.0845
10250
10260
10270.521
10280
10290.0472
103-0.0861
10300
1031-0.489
10320.0404
10330
10340
10350
1036-0.183
10370
10380.0728
10390.0167
1040
1040-0.466
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: CNhs13036

Jaspar motifP-value
MA0002.20.0132
MA0003.10.273
MA0004.10.562
MA0006.10.0891
MA0007.10.332
MA0009.10.794
MA0014.10.633
MA0017.15.96451e-7
MA0018.20.00378
MA0019.10.152
MA0024.10.0146
MA0025.10.179
MA0027.10.0416
MA0028.10.0457
MA0029.10.573
MA0030.10.307
MA0031.10.0193
MA0035.20.0348
MA0038.10.789
MA0039.20.00276
MA0040.10.0518
MA0041.10.453
MA0042.10.534
MA0043.10.41
MA0046.12.29168e-10
MA0047.22.86369e-4
MA0048.10.062
MA0050.16.00889e-5
MA0051.10.00208
MA0052.10.751
MA0055.10.0169
MA0057.10.552
MA0058.10.402
MA0059.10.321
MA0060.10.0201
MA0061.10.0331
MA0062.21.12357e-4
MA0065.23.88928e-6
MA0066.10.0853
MA0067.10.488
MA0068.10.336
MA0069.10.0886
MA0070.10.718
MA0071.10.0419
MA0072.10.291
MA0073.10.94
MA0074.10.132
MA0076.10.0807
MA0077.10.698
MA0078.10.999
MA0079.20.894
MA0080.21.45221e-10
MA0081.10.172
MA0083.10.00237
MA0084.10.488
MA0087.10.446
MA0088.10.324
MA0090.10.172
MA0091.10.331
MA0092.10.28
MA0093.10.581
MA0099.20.00175
MA0100.10.331
MA0101.10.00783
MA0102.20.284
MA0103.10.355
MA0104.20.881
MA0105.10.0576
MA0106.10.0687
MA0107.10.0186
MA0108.24.42869e-5
MA0111.10.859
MA0112.20.00206
MA0113.10.148
MA0114.16.02031e-6
MA0115.13.60278e-4
MA0116.10.171
MA0117.10.806
MA0119.10.114
MA0122.10.808
MA0124.10.884
MA0125.10.246
MA0131.10.778
MA0135.10.178
MA0136.13.22146e-12
MA0137.20.145
MA0138.20.00201
MA0139.10.578
MA0140.10.00246
MA0141.10.00204
MA0142.10.26
MA0143.10.879
MA0144.10.049
MA0145.10.0891
MA0146.10.0112
MA0147.10.959
MA0148.12.4784e-4
MA0149.10.302
MA0150.10.222
MA0152.10.826
MA0153.13.68464e-9
MA0154.10.0656
MA0155.10.403
MA0156.11.20027e-11
MA0157.10.0382
MA0159.10.00659
MA0160.10.00242
MA0162.10.191
MA0163.10.00419
MA0164.10.827
MA0258.10.0556
MA0259.10.757



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: CNhs13036

Novel motifP-value
10.434
100.115
1000.406
1010.554
1020.935
1030.183
1040.872
1050.616
1060.0455
1070.12
1080.46
1090.00251
110.103
1100.0546
1110.456
1120.0134
1130.366
1140.689
1150.896
1160.28
1170.00472
1180.522
1190.266
120.712
1200.944
1210.177
1220.992
1237.36134e-4
1240.0354
1250.877
1260.025
1270.444
1280.0315
1290.46
134.67443e-9
1300.0296
1310.36
1320.556
1330.401
1340.119
1350.294
1360.00749
1370.527
1380.65
1390.771
140.953
1400.268
1410.952
1420.888
1430.729
1440.533
1451.54892e-4
1460.2
1470.0972
1480.515
1490.58
150.358
1500.0416
1510.82
1520.0662
1530.863
1540.937
1550.283
1564.71686e-10
1570.209
1580.23
1590.882
1600.249
1610.0384
1620.602
1630.864
1640.112
1650.0866
1660.547
1670.243
1680.744
1690.00388
170.0675
180.806
190.0559
20.922
200.0629
210.287
220.0919
230.625
240.0199
250.952
264.58806e-7
270.475
280.671
290.0472
30.0681
300.887
310.915
320.845
330.257
340.405
350.455
360.594
370.021
380.311
390.213
40.177
400.133
410.684
420.175
430.138
440.808
450.559
460.266
470.527
480.348
490.394
50.462
500.145
510.758
520.163
530.603
540.97
550.973
560.514
570.894
580.471
590.127
60.957
600.0336
610.0341
620.392
630.134
640.69
650.266
660.489
670.976
680.245
690.219
70.014
700.458
710.0118
720.681
730.0237
740.952
750.0532
760.794
770.352
788.65183e-4
790.593
80.196
800.684
810.729
820.422
830.123
840.953
850.203
860.188
870.0275
880.486
890.922
90.346
900.625
910.33
920.64
930.819
940.811
950.0122
960.629
970.939
980.423
990.44



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: CNhs13036


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)