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|top_motifs=CRX:4.46620142041;RORA:2.54058790251;SOX{8,9,10}:2.40723303553;TAL1_TCF{3,4,12}:2.31631876775;NANOG:2.29417348937;PITX1..3:2.23195359654;SOX2:2.15219437101;BPTF:2.09739622744;NKX2-1,4:2.00174519958;LHX3,4:1.78423144584;TFDP1:1.77768740792;MZF1:1.67522837447;FOXP1:1.65655467297;TGIF1:1.65606409472;RXR{A,B,G}:1.65245671942;TFAP2B:1.61772755808;MTE{core}:1.58418871857;BREu{core}:1.49741931319;PAX6:1.48711649278;NHLH1,2:1.45996813178;DBP:1.34561665236;NKX6-1,2:1.34288457079;GFI1:1.32596941309;SOX5:1.3240857405;TOPORS:1.30495519877;PATZ1:1.25065719095;SOX17:1.21718325394;HSF1,2:1.20284341038;MED-1{core}:1.20150831728;MAZ:1.18626069789;PRDM1:1.16297853927;ATF2:1.15670707606;ESR1:1.15415255254;RBPJ:1.14847232183;GATA4:1.14592590352;VSX1,2:1.13913664515;ZFP161:1.13430270279;IKZF1:1.12748405439;POU5F1:1.11355542302;HIC1:1.09097479389;POU6F1:1.0867994771;MYBL2:1.08022608006;AHR_ARNT_ARNT2:1.06535766101;KLF4:1.03350318951;GTF2I:1.02246765011;OCT4_SOX2{dimer}:1.02064818104;ZBTB16:1.01864545502;EGR1..3:1.0120632644;HBP1_HMGB_SSRP1_UBTF:1.00937082668;MAFB:0.974943123605;GFI1B:0.971597698886;NKX2-3_NKX2-5:0.963801978327;LEF1_TCF7_TCF7L1,2:0.940472796664;FOX{I1,J2}:0.939082943854;RREB1:0.927389492903;POU1F1:0.900808385796;FOXD3:0.886988768961;NFY{A,B,C}:0.876316241371;POU3F1..4:0.850617783762;MYOD1:0.831002197845;NR3C1:0.823543755495;NANOG{mouse}:0.788676424106;PRRX1,2:0.776104149712;CUX2:0.768554446023;FOXN1:0.731534046507;TFAP2{A,C}:0.723696379269;ZNF384:0.720559366356;E2F1..5:0.717441767;GTF2A1,2:0.702499260713;EP300:0.699058952974;IKZF2:0.679830464913;RFX1:0.679080683233;PAX4:0.65836899415;ZNF143:0.636246437782;NRF1:0.613399012586;SP1:0.605615364594;SMAD1..7,9:0.603638225964;REST:0.58918590576;TFAP4:0.550899597107;MYFfamily:0.550881375814;ZBTB6:0.528231716316;HOX{A5,B5}:0.521079550604;NFIX:0.493371605021;XCPE1{core}:0.482082168851;HES1:0.479826899246;AIRE:0.469607514456;ZIC1..3:0.459311281984;FOXL1:0.458807953127;PAX8:0.436994526614;TEAD1:0.426531020199;GCM1,2:0.413783171141;ONECUT1,2:0.407802893675;PAX1,9:0.388006881657;PAX5:0.387821633224;RFX2..5_RFXANK_RFXAP:0.322591180163;MTF1:0.311068840391;TFCP2:0.31040063809;TBP:0.299164637652;POU2F1..3:0.289694016117;EVI1:0.287924984198;HOX{A4,D4}:0.286023164533;ADNP_IRX_SIX_ZHX:0.285976459786;UFEwm:0.269433563082;CREB1:0.245838085081;NFATC1..3:0.242011980394;LMO2:0.223629523825;PBX1:0.216704141504;HAND1,2:0.207977622866;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.205615530197;HMX1:0.196172191117;ZNF238:0.188000654794;MEF2{A,B,C,D}:0.18096304499;FOXO1,3,4:0.167654161703;NKX3-1:0.132519584182;CDC5L:0.0975922505123;NKX3-2:0.0907303581204;NKX2-2,8:0.0453685258958;JUN:0.0362180794191;HIF1A:0.0287805034983;MYB:0.0229141201629;FOX{D1,D2}:-0.00759508642206;PAX2:-0.00846849876278;EN1,2:-0.0164617704177;ELK1,4_GABP{A,B1}:-0.0208565344414;TLX1..3_NFIC{dimer}:-0.0263680950275;TEF:-0.0406626546996;ATF4:-0.0555147185638;HMGA1,2:-0.070930525291;TLX2:-0.074737808463;NFE2L2:-0.0816554263617;YY1:-0.148762903173;FOXP3:-0.162531432325;CDX1,2,4:-0.165303305915;SREBF1,2:-0.204399202397;TBX4,5:-0.24573741332;ZNF423:-0.255332223406;STAT5{A,B}:-0.258969884062;RXRA_VDR{dimer}:-0.304420953583;IRF7:-0.334534457415;NFE2:-0.335713337604;SRF:-0.345435228492;ATF5_CREB3:-0.355474424941;STAT1,3:-0.359123553236;SNAI1..3:-0.373804749109;T:-0.39992569247;AR:-0.412167496509;FOXA2:-0.427670610583;ATF6:-0.465162371454;FOS_FOS{B,L1}_JUN{B,D}:-0.474378767544;HOXA9_MEIS1:-0.518863560716;TP53:-0.521565895081;NFIL3:-0.535615132016;IRF1,2:-0.53932741615;PPARG:-0.54960228652;ALX4:-0.553884804183;ARID5B:-0.563526359811;PDX1:-0.607367386011;FOSL2:-0.621392796347;BACH2:-0.641401930482;GLI1..3:-0.654352100675;ALX1:-0.695045077316;NFE2L1:-0.701839892448;ZNF148:-0.733632577121;HNF4A_NR2F1,2:-0.75284768973;ZEB1:-0.753731842448;SPIB:-0.763527450337;FOXM1:-0.775091555557;EBF1:-0.791180063663;GATA6:-0.808647191216;SPI1:-0.823304564827;NFKB1_REL_RELA:-0.827027650137;SPZ1:-0.84385975365;HNF1A:-0.860107544233;NR5A1,2:-0.866342643072;STAT2,4,6:-0.86948790662;CEBPA,B_DDIT3:-0.897908310348;ESRRA:-0.902236427549;GZF1:-0.939639018361;ELF1,2,4:-0.942138799624;FOX{F1,F2,J1}:-0.953985501673;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.991825450314;RUNX1..3:-1.02911831288;FOXQ1:-1.09057376171;ETS1,2:-1.13020868711;bHLH_family:-1.17612543061;NR1H4:-1.23835238527;NR6A1:-1.29519892706;DMAP1_NCOR{1,2}_SMARC:-1.36018446718;HLF:-1.47850505155
}}
}}

Revision as of 15:18, 15 February 2012


Name:eyeball, neonate N00, 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 stage0 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
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

CNhs11207

00
10.169
100
1000.149
10000.00486
10010.117
10020.262
10030.0222
10040.205
1005-0.0101
10060.172
10070.143
10080
10090.0934
1010.0287
10100
10110.0617
10120.127
1013-0.105
10140.445
10150.19
10160.301
10170
10180.0807
10190
1020
10200
10210.0558
10220.0103
10230
10240.0286
1025-0.0611
10260.0286
10270.853
10280
10290.266
1030.463
10300
10310.322
10320.0231
10330
10340
10350.0286
10360
10370
10380.0953
1039-0.174
1040
10400.0792
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 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: CNhs11207

Jaspar motifP-value
MA0002.26.99963e-5
MA0003.10.254
MA0004.10.371
MA0006.10.347
MA0007.10.292
MA0009.10.355
MA0014.10.138
MA0017.11.94821e-7
MA0018.20.464
MA0019.10.571
MA0024.10.0065
MA0025.10.0959
MA0027.10.331
MA0028.10.173
MA0029.10.447
MA0030.10.843
MA0031.10.448
MA0035.28.95112e-4
MA0038.10.00621
MA0039.20.0475
MA0040.10.0938
MA0041.10.413
MA0042.10.926
MA0043.10.685
MA0046.16.03816e-23
MA0047.24.00589e-4
MA0048.10.505
MA0050.18.93772e-4
MA0051.10.00624
MA0052.10.733
MA0055.10.641
MA0057.10.129
MA0058.10.349
MA0059.10.245
MA0060.17.96768e-8
MA0061.10.0277
MA0062.20.0028
MA0065.27.51832e-7
MA0066.10.233
MA0067.10.954
MA0068.10.387
MA0069.10.0278
MA0070.10.708
MA0071.10.6
MA0072.10.262
MA0073.10.334
MA0074.10.301
MA0076.10.468
MA0077.10.00755
MA0078.10.833
MA0079.20.528
MA0080.25.42327e-12
MA0081.10.0482
MA0083.10.93
MA0084.10.0734
MA0087.10.185
MA0088.10.0496
MA0090.10.937
MA0091.10.218
MA0092.10.494
MA0093.10.397
MA0099.24.1374e-5
MA0100.10.846
MA0101.10.0657
MA0102.20.489
MA0103.10.00446
MA0104.20.716
MA0105.10.00128
MA0106.10.311
MA0107.10.0786
MA0108.20.0171
MA0111.10.71
MA0112.22.53449e-4
MA0113.10.31
MA0114.13.21659e-6
MA0115.11.91301e-5
MA0116.10.0073
MA0117.10.605
MA0119.10.0498
MA0122.10.894
MA0124.10.522
MA0125.10.00316
MA0131.10.668
MA0135.10.71
MA0136.16.93397e-16
MA0137.20.0111
MA0138.20.856
MA0139.10.0642
MA0140.13.94882e-4
MA0141.11.21139e-4
MA0142.10.567
MA0143.10.123
MA0144.10.0308
MA0145.10.0615
MA0146.10.0587
MA0147.10.5
MA0148.13.90158e-4
MA0149.10.0075
MA0150.10.0348
MA0152.10.335
MA0153.18.08266e-26
MA0154.10.00543
MA0155.10.712
MA0156.17.1723e-7
MA0157.10.216
MA0159.10.00685
MA0160.10.00283
MA0162.10.386
MA0163.14.71896e-4
MA0164.10.993
MA0258.10.00832
MA0259.10.802



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: CNhs11207

Novel motifP-value
10.08
100.105
1000.786
1010.644
1020.779
1030.0248
1040.712
1050.536
1060.11
1070.373
1080.938
1090.00856
110.0357
1100.095
1110.00114
1120.00508
1130.99
1140.0321
1150.88
1160.177
1170.0189
1180.455
1190.0543
120.445
1200.318
1210.515
1220.888
1230.666
1240.588
1250.0804
1260.183
1270.0968
1280.179
1290.409
130.00515
1300.943
1310.225
1320.615
1330.741
1340.527
1350.284
1360.168
1370.794
1380.338
1390.0292
140.9
1400.191
1410.0281
1420.764
1430.184
1440.709
1450.0721
1460.385
1470.498
1480.283
1490.231
150.0462
1500.376
1510.343
1520.0788
1530.608
1540.973
1550.296
1560.941
1570.924
1580.353
1590.748
1600.404
1610.143
1620.979
1630.577
1640.0111
1650.0154
1660.593
1670.739
1680.694
1690.00352
170.0459
180.467
190.296
20.717
200.499
210.307
220.256
230.351
240.0687
250.403
260.0257
270.473
280.317
290.0445
30.0557
300.84
310.52
320.282
330.235
340.768
350.523
360.074
370.0229
380.238
390.544
40.699
400.151
410.253
420.212
430.157
440.0533
450.537
460.142
470.0627
480.0637
490.156
50.0988
500.746
510.578
520.485
530.964
540.65
550.353
560.26
570.55
580.214
590.0337
60.47
600.0749
610.298
620.0845
630.0905
640.4
650.117
660.842
670.983
680.104
690.804
70.0906
700.00462
710.0181
720.164
730.0288
740.566
750.0272
760.564
770.135
780.0384
790.201
80.0353
800.256
810.295
820.0104
830.414
840.445
850.0333
860.167
870.0656
880.6
890.0843
90.627
900.0885
910.855
920.108
930.277
940.393
950.0459
960.413
970.823
980.439
990.518



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: CNhs11207


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)

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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