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{{f5samples
{{f5samples
|id=FF:10159-103A6
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000061,UBERON:0000062,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000489,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001137,UBERON:0002050,UBERON:0002100,UBERON:0002240,UBERON:0002346,UBERON:0002532,UBERON:0003057,UBERON:0003075,UBERON:0003076,UBERON:0003103,UBERON:0004121,UBERON:0005068,UBERON:0005174,UBERON:0005177,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007023,UBERON:0007135,UBERON:0007284
|name=spinal cord, adult, donor10252
|sample_id=10159
|rna_tube_id=103A6
|rna_box=103
|rna_position=A6
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=spinal cord
|sample_donor(cell lot)=donor: 10252
|sample_sex=female
|sample_age=76
|sample_ethnicity=
|rna_rin=
|rna_od260/230=2.24
|rna_od260/280=2.04
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=Peter Heutink
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=49.2225
|rna_concentration=0.6563
|sample_note=
|profile_hcage=CNhs12227,LSID852,release009,COMPLETED
|profile_cagescan=NCig10030,,,
|profile_srnaseq=SRhi10003,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000061,UBERON:0000062,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000489,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001137,UBERON:0002050,UBERON:0002100,UBERON:0002240,UBERON:0002346,UBERON:0002532,UBERON:0003057,UBERON:0003075,UBERON:0003076,UBERON:0003103,UBERON:0004121,UBERON:0005068,UBERON:0005174,UBERON:0005177,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007023,UBERON:0007135,UBERON:0007284
|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:10159-103A6
|is_a=EFO:0002091;;FF:0000002;;FF:0000004;;FF:0000210;;FF:0010159
|is_a=EFO:0002091;;FF:0000002;;FF:0000004;;FF:0000210;;FF:0010159
|name=spinal cord, adult, donor10252
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=NCig10030,,,
|profile_hcage=CNhs12227,LSID852,release009,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=SRhi10003,,,
|rna_box=103
|rna_catalog_number=
|rna_concentration=0.6563
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.24
|rna_od260/280=2.04
|rna_position=A6
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=103A6
|rna_weight_ug=49.2225
|sample_age=76
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=NA
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=Peter Heutink
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=donor: 10252
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10159
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=spinal cord
|top_motifs=SOX2:3.51961377734;NFIX:3.4758119206;EP300:3.02634851096;GATA4:3.01587883798;SOX{8,9,10}:2.98062434898;SOX5:2.9698740497;BPTF:2.79660258958;RREB1:2.72893366293;HOX{A6,A7,B6,B7}:2.48595467957;TGIF1:2.43929579309;PRDM1:2.35588732447;MYFfamily:2.34057614065;RBPJ:2.3171773668;ZFP161:2.29192220121;NKX3-2:2.24804098935;POU6F1:2.11929301838;FOXQ1:2.07776107201;NR3C1:2.04611735393;FOXO1,3,4:2.02048789324;STAT1,3:2.00707325087;GTF2I:1.97839139299;ATF2:1.93876374692;CUX2:1.86761668168;POU5F1:1.86593251494;FOX{I1,J2}:1.84905825203;MED-1{core}:1.83244446081;PATZ1:1.82876508602;FOX{D1,D2}:1.81232252982;MZF1:1.81107629455;FOXD3:1.80038538266;OCT4_SOX2{dimer}:1.78623701329;NHLH1,2:1.76911477161;DBP:1.76187794892;FOXP3:1.75204625003;PRRX1,2:1.72111238654;FOX{F1,F2,J1}:1.71544885674;REST:1.70902122083;AR:1.66727081101;RFX2..5_RFXANK_RFXAP:1.63829610294;MAFB:1.59908517706;SOX17:1.59501559149;MTF1:1.58938694656;SREBF1,2:1.58709649549;PDX1:1.58004778484;MAZ:1.56249433613;MTE{core}:1.55087961664;ZBTB6:1.53905148483;HBP1_HMGB_SSRP1_UBTF:1.52436456225;MYBL2:1.49182897204;POU3F1..4:1.47562326467;SP1:1.46147781263;HIC1:1.46101904861;TFAP2B:1.45442486787;SMAD1..7,9:1.43254393805;PAX6:1.41297779771;STAT2,4,6:1.39557875743;NANOG:1.35758266339;VSX1,2:1.3135258071;FOXP1:1.3091168688;NRF1:1.18533816176;ZNF384:1.17000221757;LMO2:1.14223516764;TLX1..3_NFIC{dimer}:1.13298730942;RFX1:1.10936245172;TLX2:1.09432130219;EGR1..3:1.05439622509;GFI1B:1.04750190149;HSF1,2:1.02583699994;HMGA1,2:1.00868322728;ZNF143:1.00692461648;BREu{core}:1.00190994093;TFAP2{A,C}:0.983464264698;NKX6-1,2:0.972551139968;JUN:0.922065689818;ZNF423:0.898226435306;IRF7:0.889332274428;EBF1:0.8879205842;XBP1:0.88769440241;KLF4:0.851443422887;IKZF2:0.81940234957;PAX5:0.786897031148;ZIC1..3:0.752375798617;GFI1:0.737533420494;FOXM1:0.731967047457;GCM1,2:0.72417585725;HAND1,2:0.70004731651;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.678860871058;T:0.636296622234;NFATC1..3:0.627188244347;LEF1_TCF7_TCF7L1,2:0.60703317788;TOPORS:0.604102720592;RORA:0.565887186872;PBX1:0.514884403031;FOXA2:0.473755151315;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.468953706471;NFY{A,B,C}:0.465447439446;TFCP2:0.43561436386;CREB1:0.430145823651;SPZ1:0.390378895299;IRF1,2:0.347047622239;HOX{A4,D4}:0.317167742296;NFIL3:0.316988605421;NANOG{mouse}:0.294808894337;CDC5L:0.277343253843;CRX:0.264572509393;AHR_ARNT_ARNT2:0.242288684073;GZF1:0.178765377906;TFDP1:0.178056402099;NKX2-3_NKX2-5:0.153485536555;PAX2:0.153368024815;ZBTB16:0.141602009032;HMX1:0.11688123589;GTF2A1,2:0.0946816789792;ETS1,2:0.092189852519;PAX4:0.0865808224524;ATF4:0.0407169242555;PITX1..3:0.0363222059731;ONECUT1,2:0.0334799343947;NFE2L2:0.0334080155336;ARID5B:-0.0159989127662;DMAP1_NCOR{1,2}_SMARC:-0.0267357396129;SPIB:-0.0501004675525;ATF5_CREB3:-0.070515601013;ELF1,2,4:-0.0888628385763;CDX1,2,4:-0.0910478759756;HIF1A:-0.0923229955328;FOXN1:-0.0979928361201;SPI1:-0.0989715251889;MEF2{A,B,C,D}:-0.139362939913;NR6A1:-0.209917265447;POU1F1:-0.221041905354;CEBPA,B_DDIT3:-0.263132370629;NR1H4:-0.274679716644;HNF4A_NR2F1,2:-0.282955379263;HOXA9_MEIS1:-0.352113018806;TFAP4:-0.355305513405;ALX4:-0.356617001756;TP53:-0.357460785546;bHLH_family:-0.370309638923;ATF6:-0.37272666055;LHX3,4:-0.401411392077;TBP:-0.403515908792;ESRRA:-0.42815017982;YY1:-0.448505343046;MYOD1:-0.448951287948;NFE2:-0.450619828446;NFE2L1:-0.461652777027;XCPE1{core}:-0.468896389085;AIRE:-0.469516580349;GATA6:-0.469862652291;IKZF1:-0.517468346062;ALX1:-0.584045256695;NKX2-1,4:-0.590261002767;EVI1:-0.599918023563;ZNF238:-0.619915812125;NR5A1,2:-0.629323154689;SRF:-0.653008899201;NKX3-1:-0.670084700719;ZEB1:-0.678597456342;PAX3,7:-0.692721439702;TEAD1:-0.706572171804;PAX8:-0.738155915894;UFEwm:-0.743053585273;FOSL2:-0.7518082835;TEF:-0.7604765348;ELK1,4_GABP{A,B1}:-0.79323545887;E2F1..5:-0.807198876365;HNF1A:-0.836805179642;NKX2-2,8:-0.856022710173;TBX4,5:-0.86066695108;ADNP_IRX_SIX_ZHX:-0.889576506539;HLF:-0.897442432944;TAL1_TCF{3,4,12}:-0.902208171765;NFKB1_REL_RELA:-0.90235509989;RUNX1..3:-0.903890687332;FOS_FOS{B,L1}_JUN{B,D}:-0.912857929423;BACH2:-0.975763258744;MYB:-1.03223005107;SNAI1..3:-1.03586380635;RXRA_VDR{dimer}:-1.09044215169;RXR{A,B,G}:-1.10982115359;FOXL1:-1.14115555006;ZNF148:-1.26125208647;POU2F1..3:-1.37168229088;PPARG:-1.39363779122;PAX1,9:-1.49857631344;HES1:-1.49897773131;GLI1..3:-1.80926531221;EN1,2:-1.84948698378;ESR1:-1.97280158726;HOX{A5,B5}:-2.06737605874;STAT5{A,B}:-2.32246987152
}}
}}

Revision as of 14:03, 21 March 2012


Name:spinal cord, adult, donor10252
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespinal cord
dev stageNA
sexfemale
age76
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0.113
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.739
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.249
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0.113
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
C115-pituitary-Neural-caudate-putamen-amygdala-medulla-hippocampus0
C116-myeloma-xeroderma-tonsil-CD19-spleen-lymph-trachea0
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C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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: CNhs12227

Jaspar motifP-value
MA0002.20.0754
MA0003.10.22
MA0004.10.461
MA0006.10.399
MA0007.10.507
MA0009.10.299
MA0014.10.787
MA0017.10.00857
MA0018.20.332
MA0019.10.616
MA0024.10.64
MA0025.10.676
MA0027.10.942
MA0028.10.11
MA0029.10.0276
MA0030.10.0214
MA0031.10.00712
MA0035.20.00611
MA0038.10.125
MA0039.20.359
MA0040.10.383
MA0041.10.549
MA0042.10.774
MA0043.10.887
MA0046.10.00343
MA0047.20.789
MA0048.10.126
MA0050.10.656
MA0051.10.592
MA0052.10.556
MA0055.10.00181
MA0057.10.751
MA0058.10.732
MA0059.10.133
MA0060.10.117
MA0061.10.00604
MA0062.20.0238
MA0065.29.20012e-4
MA0066.10.00583
MA0067.10.581
MA0068.10.454
MA0069.10.996
MA0070.10.238
MA0071.10.0255
MA0072.10.752
MA0073.10.68
MA0074.10.135
MA0076.10.267
MA0077.10.00665
MA0078.10.969
MA0079.20.935
MA0080.20.00674
MA0081.10.0893
MA0083.10.153
MA0084.10.222
MA0087.10.0982
MA0088.10.332
MA0090.10.298
MA0091.10.439
MA0092.10.232
MA0093.10.585
MA0099.28.79666e-18
MA0100.10.701
MA0101.10.0071
MA0102.20.99
MA0103.10.00666
MA0104.20.46
MA0105.17.56673e-5
MA0106.10.0204
MA0107.10.005
MA0108.20.862
MA0111.10.735
MA0112.26.34229e-4
MA0113.10.806
MA0114.10.0135
MA0115.10.873
MA0116.10.00281
MA0117.10.984
MA0119.10.149
MA0122.10.419
MA0124.10.202
MA0125.10.147
MA0131.10.933
MA0135.10.027
MA0136.14.36573e-4
MA0137.20.00305
MA0138.20.7
MA0139.10.576
MA0140.10.0203
MA0141.10.00109
MA0142.10.235
MA0143.10.0145
MA0144.10.815
MA0145.10.474
MA0146.10.0384
MA0147.10.204
MA0148.10.543
MA0149.10.0259
MA0150.10.00158
MA0152.10.418
MA0153.10.637
MA0154.10.0455
MA0155.10.599
MA0156.10.00329
MA0157.10.17
MA0159.10.0109
MA0160.10.0325
MA0162.10.12
MA0163.15.67224e-8
MA0164.10.396
MA0258.10.00883
MA0259.10.708



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: CNhs12227

Novel motifP-value
10.0709
100.0663
1000.348
1010.471
1020.842
1030.0297
1040.0667
1050.67
1060.0191
1070.131
1080.547
1090.001
110.0136
1100.0761
1110.105
1120.333
1130.23
1140.0913
1150.721
1160.0729
1170.0153
1180.124
1190.158
120.563
1200.228
1210.893
1220.782
1230.856
1240.317
1250.566
1260.187
1270.451
1280.164
1290.43
130.0102
1300.556
1310.00291
1320.523
1330.0786
1340.436
1350.0592
1360.00116
1370.823
1380.906
1390.14
140.96
1400.393
1410.426
1420.523
1430.0509
1440.969
1450.354
1460.682
1470.675
1480.35
1490.0897
150.0525
1500.0859
1510.665
1520.0658
1530.959
1540.505
1550.621
1560.164
1570.364
1580.0681
1590.00573
160.0317
1600.156
1610.164
1620.969
1630.821
1640.0136
1650.481
1660.934
1670.964
1680.924
1690.0214
170.0497
180.0286
190.377
20.961
200.23
210.0282
220.34
230.565
240.129
250.796
260.00395
270.626
280.872
290.00447
30.0623
300.911
310.856
320.00604
330.0783
340.867
350.485
360.316
370.029
380.561
390.284
40.855
400.109
410.316
420.313
430.185
440.0212
450.763
460.0285
470.0683
480.0551
490.353
50.995
500.653
510.285
520.731
530.557
540.548
550.923
560.601
570.289
580.467
590.0661
60.971
600.174
610.127
620.251
630.285
640.121
650.309
660.23
670.532
680.44
690.344
70.201
700.0125
710.00915
720.382
730.0365
740.594
750.0201
760.182
770.112
780.0039
790.5
80.0274
800.929
810.629
820.571
830.245
840.421
850.473
860.183
871.02689e-4
880.677
890.161
90.63
900.212
910.452
920.65
930.988
940.141
950.00606
960.543
970.913
980.208
990.37



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: CNhs12227


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
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000489 (cavitated compound organ)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001137 (dorsum)
0002050 (embryonic structure)
0002100 (trunk)
0002240 (spinal cord)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0003057 (chordal neural plate)
0003075 (neural plate)
0003076 (posterior neural tube)
0003103 (compound organ)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005174 (dorsal region element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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