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|top_motifs=CRX:6.37842220848;RORA:4.56463435368;NFE2L2:2.57375083509;ESRRA:2.52544813257;NFIL3:1.94113492886;MAFB:1.75213128208;SREBF1,2:1.67899757679;ZEB1:1.63561232295;GCM1,2:1.59709356709;NANOG:1.59452590083;bHLH_family:1.44103980369;MYOD1:1.41426482914;TGIF1:1.40971627016;SNAI1..3:1.35431443768;NKX2-1,4:1.33972995288;NR5A1,2:1.28724077368;PITX1..3:1.265043865;SPZ1:1.26359419233;FOSL2:1.25170401745;SOX5:1.23212472378;FOXP3:1.21961897237;FOXQ1:1.18621450406;NFE2:1.18104290328;PAX1,9:1.13966470777;NFE2L1:1.13322583503;GZF1:1.10180448988;HOX{A4,D4}:1.06282620345;CDC5L:1.04312759247;POU6F1:1.03495328091;TOPORS:0.981195041267;TLX1..3_NFIC{dimer}:0.973090094614;FOXO1,3,4:0.959197475274;SP1:0.949008767047;NHLH1,2:0.924721836247;HIF1A:0.893216904309;SMAD1..7,9:0.880776479712;ADNP_IRX_SIX_ZHX:0.874734536172;NFIX:0.870543455462;TFAP2{A,C}:0.831931032631;ZBTB6:0.792117631984;VSX1,2:0.762135029522;MEF2{A,B,C,D}:0.750499881748;TAL1_TCF{3,4,12}:0.705961305203;PPARG:0.613997804979;TP53:0.611443961247;MYFfamily:0.596139986139;NKX3-2:0.566772630611;REST:0.541864283741;ATF6:0.535023849016;TFCP2:0.532447203885;ARID5B:0.527767061557;NFATC1..3:0.521553188087;FOXA2:0.519804302765;ESR1:0.495710907693;PAX2:0.458075845229;MYBL2:0.456967746103;AHR_ARNT_ARNT2:0.422893076848;GTF2I:0.410541096911;AR:0.400795714917;KLF4:0.399386029297;CUX2:0.393225417812;HIC1:0.384517119842;IRF7:0.382838387354;HSF1,2:0.366521957015;HMX1:0.360851782128;GTF2A1,2:0.35460022916;FOX{I1,J2}:0.311102399431;POU2F1..3:0.3099086588;PAX5:0.309304600664;DBP:0.231714646329;BPTF:0.222569174343;FOS_FOS{B,L1}_JUN{B,D}:0.218419997432;FOXN1:0.214135559605;ZFP161:0.206752997953;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.206211047106;TFAP2B:0.19932048885;PRRX1,2:0.166560834325;STAT5{A,B}:0.157957548852;NKX2-2,8:0.129247179956;BREu{core}:0.125298872784;ATF5_CREB3:0.121457983671;TEAD1:0.12091929426;IKZF1:0.12079544478;RXR{A,B,G}:0.108231524275;ATF2:0.0939378313242;RFX2..5_RFXANK_RFXAP:0.0858437346469;TFAP4:0.0832082923936;XCPE1{core}:0.0823320056024;ZNF143:0.0810695058372;YY1:0.0729451441347;TBP:0.0526887237838;MAZ:0.0497175612317;NKX2-3_NKX2-5:0.0479403966801;MZF1:0.0474905376573;POU1F1:0.0465880617871;FOXL1:0.0447125192137;GFI1B:0.0353892226076;SOX{8,9,10}:0.0274718918838;RXRA_VDR{dimer}:0.0178532046127;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.00659034836423;MED-1{core}:0.00459380268236;HAND1,2:-0.00199144936906;SRF:-0.00765880423198;GFI1:-0.00870243830561;IRF1,2:-0.0499576969826;PATZ1:-0.0781719669639;EGR1..3:-0.0794762800004;ZNF148:-0.0903527456453;TLX2:-0.09116057846;HLF:-0.101745124132;EBF1:-0.103130964015;FOXP1:-0.117831449506;LMO2:-0.128771911928;POU3F1..4:-0.154350389885;FOX{F1,F2,J1}:-0.162675361925;CREB1:-0.164729695535;FOX{D1,D2}:-0.167914241826;MTE{core}:-0.173301497465;TBX4,5:-0.181784448417;PRDM1:-0.201104165124;GATA4:-0.226346442126;RBPJ:-0.231852799228;HNF4A_NR2F1,2:-0.235471236628;HBP1_HMGB_SSRP1_UBTF:-0.249112043984;GATA6:-0.252833289318;RFX1:-0.267385519912;BACH2:-0.313533306428;ATF4:-0.331687857076;CEBPA,B_DDIT3:-0.336604997579;ZIC1..3:-0.344670909958;NR3C1:-0.357390407408;PBX1:-0.358216484664;ALX4:-0.369148352359;MTF1:-0.372654618779;NRF1:-0.378376802341;JUN:-0.406006377028;SOX2:-0.41349645351;LHX3,4:-0.417422918222;T:-0.453937462884;ETS1,2:-0.455509289431;DMAP1_NCOR{1,2}_SMARC:-0.460932877634;FOXD3:-0.480531358615;ZBTB16:-0.498488947609;PAX6:-0.537095763651;STAT2,4,6:-0.543850197629;HMGA1,2:-0.565407655703;ELK1,4_GABP{A,B1}:-0.570066412351;POU5F1:-0.593435665597;HES1:-0.638691739793;HOX{A5,B5}:-0.681924957265;MYB:-0.707730273245;NFKB1_REL_RELA:-0.707761524303;SPI1:-0.712191095869;PAX8:-0.71809245328;RREB1:-0.730617246631;GLI1..3:-0.73094644671;NKX6-1,2:-0.73499504727;SPIB:-0.74087010269;UFEwm:-0.749472219414;LEF1_TCF7_TCF7L1,2:-0.767746308119;SOX17:-0.79578350553;ZNF384:-0.804048374574;NANOG{mouse}:-0.805903334956;PDX1:-0.848071423571;EN1,2:-0.858084886202;HNF1A:-0.874589558845;ELF1,2,4:-0.936342801174;RUNX1..3:-0.94217844609;PAX4:-0.960277799847;EP300:-1.02325011104;TFDP1:-1.07449101341;EVI1:-1.07952103175;ZNF238:-1.114826879;NFY{A,B,C}:-1.12272554474;ONECUT1,2:-1.14110913498;FOXM1:-1.15653718706;NKX3-1:-1.19064615685;NR6A1:-1.24390470809;OCT4_SOX2{dimer}:-1.37737674477;AIRE:-1.41466828425;IKZF2:-1.42506421275;NR1H4:-1.45942534183;ALX1:-1.57715172937;E2F1..5:-1.58410783524;HOXA9_MEIS1:-1.58930437131;TEF:-1.71820357874;STAT1,3:-1.96142432252;ZNF423:-2.11701875703;CDX1,2,4:-3.21381269463
}}
}}

Revision as of 15:18, 15 February 2012


Name:eyeball, adult, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueeyeball
dev stageadult
sexmale
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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs10484

00
10.153
100
1000
10000.424
10010.341
10020.138
10030.208
10040
10050.153
10060.314
1007-0.0381
10080
10090.0225
101-0.0737
10100
10110.0569
10120.0829
10130.339
1014-0.0851
1015-0.303
1016-0.2
10170
10180.0829
10191.677
1020
10200
10210
10220.495
10230
10240.0051
10250
10260
10270.307
10280
10290.217
103-0.0638
10300
1031-0.315
1032-0.101
10330
10340.343
10350.0829
1036-0.365
10371.173
1038-0.0456
10390.284
1040
1040-0.0036
10410.0829



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 no result for this sample


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: CNhs10484

Jaspar motifP-value
MA0002.20.931
MA0003.10.0558
MA0004.10.582
MA0006.10.948
MA0007.10.668
MA0009.10.713
MA0014.10.644
MA0017.10.389
MA0018.20.468
MA0019.10.951
MA0024.11.27734e-7
MA0025.10.0181
MA0027.10.0384
MA0028.11.49023e-4
MA0029.10.94
MA0030.10.274
MA0031.10.306
MA0035.20.464
MA0038.10.0252
MA0039.20.116
MA0040.10.608
MA0041.10.504
MA0042.10.0888
MA0043.10.353
MA0046.11.98545e-14
MA0047.20.763
MA0048.14.65688e-4
MA0050.10.938
MA0051.10.648
MA0052.16.30971e-8
MA0055.10.00698
MA0057.10.747
MA0058.10.55
MA0059.10.0447
MA0060.16.38549e-4
MA0061.11.61497e-4
MA0062.21.51531e-7
MA0065.20.0412
MA0066.10.686
MA0067.10.212
MA0068.10.011
MA0069.10.903
MA0070.10.808
MA0071.10.0127
MA0072.11.08952e-9
MA0073.10.578
MA0074.10.517
MA0076.11.41925e-4
MA0077.10.901
MA0078.10.116
MA0079.20.231
MA0080.27.09869e-6
MA0081.10.00375
MA0083.10.713
MA0084.10.618
MA0087.10.0299
MA0088.10.706
MA0090.10.276
MA0091.10.431
MA0092.10.929
MA0093.10.699
MA0099.20.759
MA0100.10.00791
MA0101.10.00612
MA0102.20.786
MA0103.10.00183
MA0104.20.175
MA0105.11.67433e-8
MA0106.10.549
MA0107.10.0223
MA0108.20.864
MA0111.10.342
MA0112.20.666
MA0113.10.216
MA0114.10.679
MA0115.10.333
MA0116.10.247
MA0117.10.489
MA0119.10.236
MA0122.10.469
MA0124.10.137
MA0125.10.253
MA0131.10.345
MA0135.10.196
MA0136.14.62911e-8
MA0137.20.0433
MA0138.26.86839e-4
MA0139.10.979
MA0140.10.928
MA0141.10.876
MA0142.10.858
MA0143.10.204
MA0144.10.0424
MA0145.10.141
MA0146.10.682
MA0147.10.0328
MA0148.10.332
MA0149.10.926
MA0150.10.0189
MA0152.10.962
MA0153.18.03714e-12
MA0154.10.61
MA0155.10.678
MA0156.11.48912e-6
MA0157.10.91
MA0159.10.437
MA0160.10.0139
MA0162.10.714
MA0163.12.73653e-4
MA0164.10.417
MA0258.10.139
MA0259.10.396



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: CNhs10484

Novel motifP-value
10.658
100.292
1000.819
1010.84
1020.794
1030.921
1040.611
1050.507
1060.764
1070.755
1080.972
1090.761
110.965
1100.411
1110.538
1120.859
1130.289
1140.287
1150.639
1160.138
1170.00583
1180.0212
1190.111
120.0416
1200.219
1210.458
1220.532
1230.298
1240.195
1250.831
1260.406
1270.808
1280.756
1290.546
130.214
1300.607
1310.759
1320.585
1330.785
1340.728
1350.109
1360.156
1370.838
1380.13
1390.34
140.12
1400.777
1410.69
1420.15
1430.0196
1440.512
1450.0596
1460.339
1470.568
1480.708
1490.74
150.817
1500.318
1510.0571
1520.671
1530.869
1540.751
1550.212
1560.892
1570.93
1580.927
1590.63
1600.799
1610.378
1620.658
1630.352
1640.0641
1650.51
1660.813
1670.847
1680.731
1690.569
170.518
180.369
190.339
20.0962
200.0458
210.31
220.302
230.217
240.514
250.944
260.0744
270.233
280.578
290.0735
30.625
300.23
310.767
320.698
330.138
340.873
350.568
360.25
370.735
380.738
390.863
40.328
400.924
410.739
420.513
430.896
440.954
450.236
460.662
470.672
480.88
490.775
50.981
500.921
510.707
520.341
530.0971
540.277
550.242
560.611
570.495
580.731
590.276
60.816
600.596
610.189
620.775
630.633
640.859
650.817
660.528
670.713
680.418
690.124
70.578
700.298
710.0806
720.9
730.116
740.746
750.0435
760.0388
770.339
780.839
790.948
80.29
800.403
810.2
820.437
830.998
840.0715
850.28
860.444
870.914
880.703
890.741
90.5
900.373
910.288
920.535
930.579
940.486
950.0581
960.986
970.742
980.0934
990.965



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: CNhs10484


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000019 (camera-type eye)
0000020 (sense organ)
0000033 (head)
0000047 (simple eye)
0000061 (anatomical structure)
0000062 (organ)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000970 (eye)
0001032 (sensory system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0002104 (visual system)
0004456 (entire sense organ system)
0007023 (adult organism)

FF: FANTOM5
NA

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
NA

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