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|top_motifs=LHX3,4:3.03370255737;PAX6:2.53095880054;BREu{core}:2.48504654228;ADNP_IRX_SIX_ZHX:2.41447715877;POU6F1:2.39758868841;AHR_ARNT_ARNT2:2.25247441476;ZFP161:2.20276086432;VSX1,2:2.16782628935;OCT4_SOX2{dimer}:2.10049975253;TFDP1:2.09761633999;MED-1{core}:2.07149244185;SOX{8,9,10}:2.00928140717;SOX2:2.0071175338;FOXD3:1.97045029918;MTE{core}:1.87751815535;UFEwm:1.86125004624;HMX1:1.83653738625;MZF1:1.80547897423;KLF4:1.78344267914;ZBTB6:1.73325307503;LEF1_TCF7_TCF7L1,2:1.73127807973;FOXQ1:1.72677316623;LMO2:1.71446787867;REST:1.70039609861;NKX6-1,2:1.68033854802;POU5F1:1.65983228959;RREB1:1.6591139389;ALX1:1.64075178019;NRF1:1.57093259118;NANOG:1.48854916269;PATZ1:1.4850583207;HIC1:1.48496299869;ZIC1..3:1.45194476605;SOX17:1.45012257451;PRRX1,2:1.41418998045;RFX1:1.40047735165;ONECUT1,2:1.37777355828;PRDM1:1.37144867816;SMAD1..7,9:1.36676649997;TFAP2B:1.28411121793;EGR1..3:1.27015284118;NHLH1,2:1.24490267462;PAX8:1.23651732564;NKX2-1,4:1.22222430339;DBP:1.21954036901;POU3F1..4:1.21638001779;NR5A1,2:1.21157723308;ATF2:1.20438912834;POU2F1..3:1.20257460387;GFI1B:1.16706231975;ZNF423:1.15445619953;NFE2L1:1.12777278802;MYFfamily:1.03438946708;TGIF1:0.994118525804;ZNF143:0.982735256696;GTF2I:0.946512229776;JUN:0.933082821244;RFX2..5_RFXANK_RFXAP:0.920128449194;HOX{A5,B5}:0.90929842126;NKX3-1:0.899555031623;FOX{I1,J2}:0.847441661613;HOXA9_MEIS1:0.781260388189;RORA:0.774232403358;CUX2:0.744974142442;EP300:0.733115006204;RXR{A,B,G}:0.711192122077;FOXL1:0.685108462827;FOXM1:0.679335788472;PAX5:0.671360639429;YY1:0.628315883472;EN1,2:0.614952781271;NKX3-2:0.600743465289;MTF1:0.592950362205;CDX1,2,4:0.58202764391;GATA4:0.575724488116;BPTF:0.527998908832;RBPJ:0.521814027614;ATF5_CREB3:0.498286235962;HSF1,2:0.4847192909;HES1:0.470984021001;PAX4:0.452468287822;NFIX:0.447974044175;PBX1:0.433229881013;MAZ:0.417690911303;NKX2-3_NKX2-5:0.413204385661;HMGA1,2:0.369006673952;SOX5:0.349378170813;PAX2:0.325182449041;HOX{A4,D4}:0.296055505751;NANOG{mouse}:0.266924765813;CREB1:0.252582815781;MAFB:0.237198883582;HAND1,2:0.231829694312;GTF2A1,2:0.226786733053;TBX4,5:0.226472673365;NFY{A,B,C}:0.219956140211;NR3C1:0.20571368611;CDC5L:0.192712851963;HBP1_HMGB_SSRP1_UBTF:0.150507181407;ELK1,4_GABP{A,B1}:0.131641190389;FOXP3:0.0710477436056;MYOD1:0.0517398881966;EVI1:0.0509425541096;TEF:0.0493852651905;HIF1A:0.039984561028;FOX{F1,F2,J1}:0.0223954870916;GZF1:0.0174434690852;CRX:-0.0970407366161;TFAP2{A,C}:-0.0991958773347;IKZF2:-0.108219385842;ATF4:-0.110549092895;TAL1_TCF{3,4,12}:-0.11440678962;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.12151173668;ZNF384:-0.164563569443;ARID5B:-0.176994624062;ZEB1:-0.187958549473;TFAP4:-0.189974954147;PPARG:-0.198001779963;bHLH_family:-0.215936333253;ATF6:-0.245941645306;MYB:-0.268321095058;ZBTB16:-0.28003224354;NFIL3:-0.287939425012;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.30359928145;SNAI1..3:-0.332663723529;STAT5{A,B}:-0.342143536737;T:-0.356322364868;SP1:-0.370832888147;GFI1:-0.383143464653;ESR1:-0.387521046777;TOPORS:-0.431066888437;FOXP1:-0.449443388357;STAT1,3:-0.467698519499;RUNX1..3:-0.523458880189;POU1F1:-0.543733434056;GCM1,2:-0.548421813051;ZNF238:-0.549834224633;SPZ1:-0.56471054691;PAX1,9:-0.57898318203;HNF4A_NR2F1,2:-0.584539200068;TLX1..3_NFIC{dimer}:-0.596060403828;GLI1..3:-0.597544363528;XCPE1{core}:-0.612525739225;CEBPA,B_DDIT3:-0.641773284025;MEF2{A,B,C,D}:-0.700879445326;GATA6:-0.718775257835;NR1H4:-0.729265647698;HNF1A:-0.742338187742;ESRRA:-0.780852718733;E2F1..5:-0.783733359367;NFE2L2:-0.786725444763;TBP:-0.794618912121;ZNF148:-0.80436014617;RXRA_VDR{dimer}:-0.811291370515;IKZF1:-0.814355653711;HLF:-0.816585029903;NFKB1_REL_RELA:-0.819606689529;SPI1:-0.843163133306;AIRE:-0.852240988779;FOXA2:-0.897761676893;AR:-0.908111849788;SREBF1,2:-0.921367738968;TP53:-0.969545347787;PITX1..3:-1.00178611005;SPIB:-1.0198543303;EBF1:-1.03593542365;ELF1,2,4:-1.09147109868;MYBL2:-1.12686457178;NFE2:-1.17849861504;FOS_FOS{B,L1}_JUN{B,D}:-1.19681763086;BACH2:-1.21296033061;ALX4:-1.2239589029;NKX2-2,8:-1.22487777567;TEAD1:-1.24683519058;FOXN1:-1.24744063691;FOSL2:-1.26879816325;TFCP2:-1.27463600691;ETS1,2:-1.27604509062;TLX2:-1.30109786078;NFATC1..3:-1.35126657989;FOXO1,3,4:-1.41301299906;NR6A1:-1.48704461368;PDX1:-1.50891698486;SRF:-1.65019988342;IRF1,2:-1.69737402921;IRF7:-1.73449491855;FOX{D1,D2}:-1.75313747509;STAT2,4,6:-1.75450013749;DMAP1_NCOR{1,2}_SMARC:-1.76028183929
}}
}}

Revision as of 15:17, 15 February 2012


Name:Mouse Granule cells, donor2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexNA
ageNA
cell typeneuron, granule cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMG3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
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

CNhs12357

00
10.413
100
1000.494
1000-0.0355
1001-0.0749
10020.151
10030.0974
10040
1005-0.115
10060.336
1007-0.107
10080
1009-0.2
101-0.197
10100
10110.227
10120
1013-0.154
10140
10150.362
10160.197
10170
10180
10190
1020
10200.562
10210
1022-0.134
10230
1024-0.247
1025-0.0611
10260
10270.184
10280
1029-0.176
103-0.0848
10300
1031-0.627
10320.211
10330.0032
10340
10350
1036-0.252
10370
10380.0152
1039-0.183
1040
1040-0.216
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: CNhs12357

Jaspar motifP-value
MA0002.20.00349
MA0003.10.211
MA0004.10.569
MA0006.10.0629
MA0007.10.162
MA0009.10.899
MA0014.10.467
MA0017.11.45937e-5
MA0018.20.0319
MA0019.10.387
MA0024.10.938
MA0025.10.568
MA0027.10.729
MA0028.10.279
MA0029.10.467
MA0030.10.378
MA0031.10.0463
MA0035.20.155
MA0038.10.458
MA0039.20.00738
MA0040.10.548
MA0041.10.258
MA0042.10.472
MA0043.10.161
MA0046.12.42967e-7
MA0047.24.22493e-4
MA0048.10.252
MA0050.13.20303e-10
MA0051.11.9644e-5
MA0052.10.0494
MA0055.10.322
MA0057.10.147
MA0058.10.549
MA0059.10.486
MA0060.10.0118
MA0061.10.0545
MA0062.20.0184
MA0065.23.13063e-5
MA0066.10.207
MA0067.10.859
MA0068.10.589
MA0069.10.107
MA0070.10.495
MA0071.10.228
MA0072.10.205
MA0073.10.971
MA0074.10.425
MA0076.10.713
MA0077.10.007
MA0078.10.0886
MA0079.20.955
MA0080.21.29088e-10
MA0081.10.214
MA0083.10.00362
MA0084.10.343
MA0087.10.609
MA0088.10.182
MA0090.10.00756
MA0091.10.232
MA0092.10.163
MA0093.10.583
MA0099.26.08273e-5
MA0100.10.7
MA0101.10.0263
MA0102.20.84
MA0103.10.229
MA0104.20.521
MA0105.10.0989
MA0106.10.0629
MA0107.10.0226
MA0108.20.231
MA0111.10.87
MA0112.21.17131e-4
MA0113.10.323
MA0114.16.30025e-5
MA0115.10.0107
MA0116.10.131
MA0117.10.671
MA0119.10.0712
MA0122.10.49
MA0124.10.97
MA0125.10.185
MA0131.10.91
MA0135.10.37
MA0136.13.7893e-9
MA0137.20.0162
MA0138.20.0845
MA0139.10.426
MA0140.10.00273
MA0141.10.03
MA0142.10.0135
MA0143.10.0113
MA0144.10.0124
MA0145.10.0494
MA0146.10.039
MA0147.10.54
MA0148.13.02231e-6
MA0149.10.0817
MA0150.10.0282
MA0152.10.0866
MA0153.11.26413e-6
MA0154.10.0225
MA0155.10.795
MA0156.11.12519e-7
MA0157.10.0292
MA0159.10.00311
MA0160.10.0832
MA0162.10.345
MA0163.10.00525
MA0164.10.833
MA0258.10.0143
MA0259.10.504



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: CNhs12357

Novel motifP-value
10.156
100.102
1000.779
1010.932
1020.992
1030.0767
1040.987
1050.135
1060.00469
1070.0344
1080.448
1090.00272
110.0782
1100.0938
1110.101
1120.00373
1130.908
1140.481
1150.639
1160.482
1170.0299
1180.516
1190.137
120.498
1200.659
1210.28
1220.783
1230.0943
1240.416
1250.518
1260.245
1270.0462
1280.0304
1290.239
131.92126e-6
1300.178
1310.793
1320.98
1330.39
1340.43
1350.962
1360.144
1370.317
1380.548
1390.106
140.676
1400.0639
1410.319
1420.0441
1430.488
1440.877
1450.00936
1460.369
1470.711
1480.406
1490.212
150.157
1500.11
1510.451
1520.0262
1530.702
1540.64
1550.843
1560.0106
1570.0663
1580.164
1590.0356
1600.331
1610.481
1620.708
1630.421
1640.0163
1650.0198
1660.825
1670.954
1680.609
1690.00482
170.0198
180.449
190.0557
20.95
200.32
210.395
220.0918
230.362
240.0256
250.82
264.14059e-4
270.958
280.345
290.151
30.0777
300.663
310.849
320.523
330.165
340.557
350.381
360.487
370.0086
380.341
390.237
40.605
400.347
410.873
420.233
430.126
440.977
450.536
460.143
470.263
480.11
490.138
50.178
500.212
510.518
520.0966
530.74
540.752
550.975
560.431
570.73
580.231
590.105
60.829
600.0117
610.155
620.118
630.109
640.952
650.317
660.851
670.882
680.184
690.651
70.0151
700.0348
710.0132
720.418
730.0111
740.456
750.119
760.519
770.246
780.0256
790.688
80.125
800.977
810.787
820.202
830.158
840.685
850.191
860.228
870.192
880.337
890.382
90.261
900.217
910.284
920.284
930.0727
940.867
950.0363
960.397
970.91
980.955
990.365



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: CNhs12357


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000117 (CNS neuron (sensu Vertebrata))
0000120 (granule cell)
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000337 (neuroblast (sensu Vertebrata))
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)

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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