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{{f5samples
{{f5samples
|id=FF:12-14D5
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000470,UBERON:0000479,UBERON:0000480,UBERON:0001062,UBERON:0001851,UBERON:0005889,UBERON:0007023
|name=cortex, adult
|sample_id=12
|rna_tube_id=14D5
|rna_box=14
|rna_position=D5
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_dev_stage=adult
|sample_tissue=cortex
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=
|rna_concentration=
|sample_note=
|profile_hcage=CNhs10473,LSID646,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000470,UBERON:0000479,UBERON:0000480,UBERON:0001062,UBERON:0001851,UBERON:0005889,UBERON:0007023
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:12-14D5
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011525
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011525
|name=cortex, adult
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10473,LSID646,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=14
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=D5
|rna_rin=
|rna_sample_type=
|rna_tube_id=14D5
|rna_weight_ug=
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=
|sample_description=
|sample_dev_stage=adult
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=12
|sample_note=
|sample_sex=male
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=cortex
|top_motifs=CUX2:3.20415798773;EGR1..3:3.14779670647;REST:2.98862595283;AHR_ARNT_ARNT2:2.92414621027;PRRX1,2:2.79257787349;ATF2:2.75138759055;NHLH1,2:2.73815081153;POU6F1:2.7061832824;ZFP161:2.64951900112;STAT1,3:2.63092232538;MYFfamily:2.59858753748;MTF1:2.55333466654;ZBTB6:2.47337062945;HAND1,2:2.44615239723;PBX1:2.42896243063;MED-1{core}:2.40844695055;BREu{core}:2.38809272251;MAFB:2.3704136007;POU3F1..4:2.17310153453;PRDM1:2.16910820836;ATF5_CREB3:2.12743790054;TFAP2B:2.12179625603;OCT4_SOX2{dimer}:2.10262894412;HIC1:2.04165718153;NFIL3:1.99475409619;LMO2:1.99371236963;MTE{core}:1.98776458602;CREB1:1.92696060813;SMAD1..7,9:1.842157627;TGIF1:1.81488391885;RFX1:1.7719709362;PAX5:1.73438210398;JUN:1.72690134752;RBPJ:1.65910347159;PAX6:1.64536388881;DBP:1.60521278283;HOXA9_MEIS1:1.60260289098;GTF2I:1.57352128165;NKX3-2:1.5525834186;TFDP1:1.52675086449;SREBF1,2:1.4751133688;MZF1:1.44795877095;TEF:1.42667390173;NANOG:1.40721735028;HMGA1,2:1.40621822659;RREB1:1.37307568646;HOX{A4,D4}:1.3625559133;PAX8:1.32010690229;FOXN1:1.31662707018;NFE2L2:1.26792144556;TAL1_TCF{3,4,12}:1.25801421471;NRF1:1.24958473568;GZF1:1.2403447217;HBP1_HMGB_SSRP1_UBTF:1.23165438337;KLF4:1.2162524799;RFX2..5_RFXANK_RFXAP:1.2084658995;GFI1B:1.20203151538;SPZ1:1.1801827088;PAX4:1.17615733463;TFAP2{A,C}:1.1711161606;ZIC1..3:1.13526535459;FOXQ1:1.0591032252;FOXD3:1.05395810767;GTF2A1,2:1.0396082133;CDX1,2,4:0.990099507922;ZEB1:0.984648270331;FOX{F1,F2,J1}:0.96000831865;PATZ1:0.94067111452;ZNF143:0.933767937553;VSX1,2:0.917808665887;AIRE:0.841637990754;MAZ:0.837735000633;CDC5L:0.827243198326;NFE2:0.818320613868;NR3C1:0.804441554426;LHX3,4:0.798512829436;MYOD1:0.793527022521;SOX2:0.764587993657;HES1:0.763597720189;ADNP_IRX_SIX_ZHX:0.729351708842;POU1F1:0.712677430902;bHLH_family:0.706127665365;FOXM1:0.702932418966;FOXA2:0.681724063001;POU5F1:0.650227176972;RORA:0.643618531812;GLI1..3:0.642891382362;ONECUT1,2:0.628488288809;HIF1A:0.62271283857;NKX2-3_NKX2-5:0.562527364201;IKZF1:0.557196011643;EVI1:0.491341563527;HOX{A5,B5}:0.483549486559;FOXP1:0.474399419408;EN1,2:0.447648485027;NKX6-1,2:0.44193011882;GCM1,2:0.431473543803;ATF4:0.429022217823;AR:0.427111279856;FOXP3:0.424716002661;EBF1:0.418607855346;ZNF423:0.402717669066;UFEwm:0.36788790552;ARID5B:0.344182619276;ALX1:0.299263096647;SOX{8,9,10}:0.288751521363;NFE2L1:0.282405418825;PPARG:0.26953508559;YY1:0.269443505479;GATA4:0.253836474575;NKX2-2,8:0.142137575446;EP300:0.0503892595099;HMX1:0.0438752840949;ESRRA:0.0248510541965;TFAP4:-0.0285203405282;PAX2:-0.0354133028224;ZNF148:-0.039824723341;MEF2{A,B,C,D}:-0.0431166249361;SNAI1..3:-0.0529505275788;LEF1_TCF7_TCF7L1,2:-0.0810955163636;ZNF384:-0.0940876284521;ZNF238:-0.0948374107951;HSF1,2:-0.099395773349;MYBL2:-0.115299717836;SP1:-0.122685996735;NFATC1..3:-0.164185049547;TLX1..3_NFIC{dimer}:-0.167939716405;BPTF:-0.195264065283;ZBTB16:-0.219412248928;FOSL2:-0.236362710216;SOX17:-0.240942475086;ATF6:-0.291054937993;FOXL1:-0.343670783246;CRX:-0.350338013326;STAT2,4,6:-0.356600047149;FOS_FOS{B,L1}_JUN{B,D}:-0.390512732911;XCPE1{core}:-0.400357741766;TFCP2:-0.412746811005;NANOG{mouse}:-0.447890188312;TOPORS:-0.525228663597;NKX2-1,4:-0.549971817587;FOX{I1,J2}:-0.578429477264;MYB:-0.585564762866;ELK1,4_GABP{A,B1}:-0.609190045176;T:-0.643016271014;IRF7:-0.657800225775;HLF:-0.727738527538;TLX2:-0.73480339363;SPI1:-0.755041577367;SOX5:-0.760296555962;TBX4,5:-0.807533974852;CEBPA,B_DDIT3:-0.810624177125;NFY{A,B,C}:-0.868266325917;NKX3-1:-0.878919082958;BACH2:-0.879846497802;HNF1A:-0.890627907693;PAX1,9:-0.890794196349;IKZF2:-0.894697820651;POU2F1..3:-0.917196952945;RUNX1..3:-0.920657982019;GATA6:-0.921125310424;PDX1:-0.944175170238;HNF4A_NR2F1,2:-0.97859564931;NR5A1,2:-1.00021700183;NFKB1_REL_RELA:-1.0080163206;IRF1,2:-1.01522958805;ESR1:-1.06711194683;ETS1,2:-1.08752199533;SPIB:-1.12365994503;FOX{D1,D2}:-1.21395594037;TEAD1:-1.2349927307;GFI1:-1.30844605186;ELF1,2,4:-1.32957794937;TP53:-1.34233184658;TBP:-1.52549235661;STAT5{A,B}:-1.55465059164;PITX1..3:-1.61908697174;NR1H4:-1.66811849449;RXRA_VDR{dimer}:-1.6849771081;E2F1..5:-1.7057642065;ALX4:-1.72868512535;SRF:-1.75718832379;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.76742573765;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.79061265789;RXR{A,B,G}:-1.83812536406;FOXO1,3,4:-1.90105482283;DMAP1_NCOR{1,2}_SMARC:-1.90443985756;NR6A1:-1.93418545724;NFIX:-2.08004492257
}}
}}

Revision as of 15:06, 21 March 2012


Name:cortex, adult
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuecortex
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

CNhs10473

00
10.839
100
1000
10000
10010
1002-0.0592
10030.265
10040
10050.13
10060.739
1007-0.0572
10080
1009-0.0774
101-0.05
10100
10110.985
10120.34
10130.147
1014-0.0155
1015-0.133
1016-0.166
10170
10180
10190
1020
10200
1021-0.0487
1022-0.016
10230
10240
1025-0.0312
10260
10270.375
10280
1029-0.0369
103-0.0861
10300
1031-0.502
10320.0951
10330.0696
10340
10350.0106
1036-0.255
10370
10380.0186
10390.092
1040
1040-0.165
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: CNhs10473

Jaspar motifP-value
MA0002.20.00288
MA0003.10.298
MA0004.10.596
MA0006.10.137
MA0007.10.382
MA0009.10.792
MA0014.10.711
MA0017.17.90756e-7
MA0018.20.00495
MA0019.10.312
MA0024.10.0641
MA0025.10.00195
MA0027.10.0669
MA0028.10.0928
MA0029.10.964
MA0030.10.902
MA0031.10.183
MA0035.20.0157
MA0038.10.397
MA0039.20.0312
MA0040.10.128
MA0041.10.274
MA0042.10.35
MA0043.10.0695
MA0046.13.20088e-10
MA0047.24.70009e-4
MA0048.10.0549
MA0050.11.95729e-4
MA0051.10.0278
MA0052.10.459
MA0055.10.0112
MA0057.10.522
MA0058.10.456
MA0059.10.147
MA0060.10.651
MA0061.10.035
MA0062.20.0033
MA0065.21.03847e-6
MA0066.10.032
MA0067.10.518
MA0068.10.615
MA0069.10.0531
MA0070.10.498
MA0071.10.0195
MA0072.10.138
MA0073.10.856
MA0074.10.132
MA0076.10.223
MA0077.10.675
MA0078.10.704
MA0079.20.376
MA0080.21.84505e-9
MA0081.10.321
MA0083.10.0231
MA0084.10.832
MA0087.10.485
MA0088.10.346
MA0090.10.157
MA0091.10.165
MA0092.10.271
MA0093.10.638
MA0099.20.0116
MA0100.10.317
MA0101.10.0218
MA0102.20.51
MA0103.10.205
MA0104.20.886
MA0105.10.0117
MA0106.10.0518
MA0107.10.0423
MA0108.27.43124e-4
MA0111.10.917
MA0112.25.77001e-4
MA0113.10.355
MA0114.14.51823e-6
MA0115.12.2026e-5
MA0116.10.0683
MA0117.10.908
MA0119.10.11
MA0122.10.907
MA0124.10.522
MA0125.10.0383
MA0131.10.778
MA0135.10.496
MA0136.18.37649e-11
MA0137.20.283
MA0138.29.61154e-4
MA0139.10.643
MA0140.12.20598e-4
MA0141.14.62552e-4
MA0142.10.473
MA0143.10.623
MA0144.10.148
MA0145.10.138
MA0146.10.0178
MA0147.10.765
MA0148.12.81477e-4
MA0149.10.0903
MA0150.10.209
MA0152.10.302
MA0153.18.39011e-11
MA0154.10.0472
MA0155.10.338
MA0156.12.94094e-7
MA0157.10.11
MA0159.10.00121
MA0160.10.00331
MA0162.10.145
MA0163.16.3365e-4
MA0164.10.957
MA0258.10.0168
MA0259.10.921



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: CNhs10473

Novel motifP-value
10.215
100.0492
1000.39
1010.698
1020.925
1030.0467
1040.94
1050.881
1060.059
1070.195
1080.599
1090.00468
110.086
1100.0612
1110.118
1120.00607
1130.38
1140.38
1150.975
1160.302
1170.00367
1180.373
1190.249
120.993
1200.921
1210.517
1220.772
1230.0026
1240.0629
1250.223
1260.0206
1270.361
1280.038
1290.223
131.43024e-7
1300.112
1310.622
1320.756
1330.833
1340.106
1350.373
1360.063
1370.692
1380.874
1390.305
140.952
1400.0479
1410.667
1420.837
1430.391
1440.731
1453.06758e-4
1460.279
1470.256
1480.399
1490.553
150.195
1500.0579
1510.826
1520.125
1530.831
1540.983
1550.294
1560.00336
1570.289
1580.131
1590.902
1600.17
1610.093
1620.67
1630.699
1640.0699
1650.0916
1660.884
1670.674
1680.549
1690.00363
170.0497
180.756
190.0911
20.775
200.0483
210.244
220.142
230.731
240.0315
250.779
264.52714e-7
270.53
280.712
290.0234
30.0406
300.829
310.967
320.55
330.216
340.679
350.895
360.25
370.0203
380.551
390.252
40.172
400.12
410.524
420.15
430.141
440.398
450.717
460.133
470.463
480.323
490.213
50.186
500.243
510.777
520.25
530.434
540.92
550.903
560.468
570.657
580.364
590.114
60.952
600.0368
610.028
620.284
630.156
640.632
650.464
660.769
670.614
680.789
690.15
70.016
700.0963
710.00606
720.59
730.0339
740.893
750.0427
760.501
770.307
780.00306
790.633
80.0648
800.626
810.904
820.238
830.0947
840.73
850.163
860.195
870.16
880.467
890.798
90.506
900.215
910.0789
920.258
930.195
940.806
950.0262
960.45
970.972
980.496
990.429



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: CNhs10473


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
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000470 (cell part)
0000479 (tissue)
0000480 (anatomical group)
0001062 (anatomical entity)
0001851 (cortex)
0005889 (zygote cortex)
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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