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{{f5samples
{{f5samples
|id=FF:11222-116B7
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000153,UBERON:0000161,UBERON:0000165,UBERON:0000166,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000930,UBERON:0001004,UBERON:0001007,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0001828,UBERON:0002050,UBERON:0002384,UBERON:0002532,UBERON:0004111,UBERON:0004119,UBERON:0005423,UBERON:0007026
|name=Fibroblast - Gingival, donor4 (GFH2)
|sample_id=11222
|rna_tube_id=116B7
|rna_box=116
|rna_position=B7
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=N/A
|rna_lot_number=
|rna_catalog_number=N/A
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=22 years old adult
|sample_tissue=gum
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=22
|sample_ethnicity=A
|rna_rin=9.6
|rna_od260/230=1.986666667
|rna_od260/280=2.043333333
|sample_cell_type=fibroblast
|sample_cell_line=
|sample_collaboration=Mitsuhiro Ohshima (Nihon University School of Dentistry)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=21.8482
|rna_concentration=0.9931
|sample_note=machine failed, remainder reloaded, low amount
|profile_hcage=CNhs10848,LSID700,release009,COMPLETED
|profile_cagescan=NCig10039,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371,CL:0002552
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371,CL:0002552
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000153,UBERON:0000161,UBERON:0000165,UBERON:0000166,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000930,UBERON:0001004,UBERON:0001007,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0001828,UBERON:0002050,UBERON:0002384,UBERON:0002532,UBERON:0004111,UBERON:0004119,UBERON:0005423,UBERON:0007026
|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:11222-116B7
|is_a=EFO:0002091;;FF:0000002;;FF:0000063;;FF:0000210
|is_a=EFO:0002091;;FF:0000002;;FF:0000063;;FF:0000210
|name=Fibroblast - Gingival, donor4 (GFH2)
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=NCig10039,,,
|profile_hcage=CNhs10848,LSID700,release009,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=116
|rna_catalog_number=N/A
|rna_concentration=0.9931
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.986666667
|rna_od260/280=2.043333333
|rna_position=B7
|rna_rin=9.6
|rna_sample_type=total RNA
|rna_tube_id=116B7
|rna_weight_ug=21.8482
|sample_age=22
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=fibroblast
|sample_collaboration=Mitsuhiro Ohshima (Nihon University School of Dentistry)
|sample_company=N/A
|sample_description=
|sample_dev_stage=22 years old adult
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=A
|sample_experimental_condition=
|sample_id=11222
|sample_note=machine failed, remainder reloaded, low amount
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=gum
|top_motifs=ZNF238:2.23120268032;ESR1:2.20077088531;TAL1_TCF{3,4,12}:1.56675570685;IRF1,2:1.55764858298;HES1:1.53086436786;NKX2-2,8:1.51169454215;SPZ1:1.4546573499;HMGA1,2:1.42690486448;GZF1:1.39426924362;NFIX:1.33181598779;IRF7:1.26132719643;TFAP4:1.21362263543;MYBL2:1.20292922238;TP53:1.19561515596;MAZ:1.17007001631;MAFB:1.15625226572;GLI1..3:1.15536010657;ALX4:1.14585102895;EBF1:1.14210214718;PAX3,7:1.12402212585;TFCP2:1.11585914126;FOXL1:1.09232357498;PATZ1:1.01225486177;LHX3,4:1.00516125503;TFDP1:0.925999130442;NFATC1..3:0.870330063134;KLF4:0.864116968888;TFAP2{A,C}:0.860593164822;FOXO1,3,4:0.859315713463;NKX2-3_NKX2-5:0.856336776221;PAX5:0.786140121167;SREBF1,2:0.771097844273;TEAD1:0.762373798208;PAX1,9:0.759092961888;NKX6-1,2:0.753632354159;TLX1..3_NFIC{dimer}:0.742238222229;HAND1,2:0.740717896137;NHLH1,2:0.733725647291;ZBTB6:0.731270530515;ATF6:0.68424070201;GTF2A1,2:0.673010829881;HMX1:0.668083540223;NKX3-1:0.58467357098;ZNF423:0.57928029673;YY1:0.573633888579;PRDM1:0.546878984576;UFEwm:0.535095721753;GTF2I:0.526342086275;DBP:0.507728701641;TBX4,5:0.487374690148;NFE2L2:0.477689525797;RXR{A,B,G}:0.459496917499;MTF1:0.457921871941;TFAP2B:0.452924964401;EVI1:0.438091549906;NANOG{mouse}:0.433672217137;SOX17:0.422413299598;PPARG:0.420712611352;MZF1:0.411426860741;GFI1:0.410523265967;HBP1_HMGB_SSRP1_UBTF:0.403884223195;PDX1:0.401264688145;NKX3-2:0.396817698209;HIC1:0.393523052041;MYB:0.346986605395;NR3C1:0.32210552749;FOXA2:0.319678017662;EGR1..3:0.304722166278;RREB1:0.297675719978;GATA4:0.296412383435;NR6A1:0.285267336103;LEF1_TCF7_TCF7L1,2:0.245267612557;CEBPA,B_DDIT3:0.244865294793;HSF1,2:0.241519440274;MYFfamily:0.23884093774;MTE{core}:0.238808610955;HOX{A6,A7,B6,B7}:0.227727747637;ZNF148:0.226146189303;SMAD1..7,9:0.223160230289;HLF:0.218584186911;NFIL3:0.195754977725;ADNP_IRX_SIX_ZHX:0.175986974389;GFI1B:0.175413733544;XBP1:0.169887086121;RORA:0.15737095577;SRF:0.153037498524;MED-1{core}:0.131403655653;TBP:0.124352369897;XCPE1{core}:0.0919756752386;PRRX1,2:0.0859007805813;REST:0.0829990758736;HOX{A4,D4}:0.0731624044184;FOX{I1,J2}:0.0695075634209;HNF4A_NR2F1,2:0.0569099822678;STAT2,4,6:0.0532205711126;DMAP1_NCOR{1,2}_SMARC:0.0528940515903;SP1:0.0421029767528;ATF5_CREB3:0.0411241292412;FOS_FOS{B,L1}_JUN{B,D}:0.0320037552997;HNF1A:0.015294463613;BACH2:0.0122783734455;BPTF:0.00968638788455;EN1,2:0.00836000687458;NFKB1_REL_RELA:-0.0162171359473;HOXA9_MEIS1:-0.0358795873106;bHLH_family:-0.0456628203499;RBPJ:-0.0477162844177;NFE2L1:-0.0685137745105;GCM1,2:-0.0717402087379;CDC5L:-0.0850294228453;RUNX1..3:-0.0856506157887;ZFP161:-0.0975428719195;ZIC1..3:-0.135078758678;NFE2:-0.143520935019;NR1H4:-0.149267345744;FOXD3:-0.150315430814;ZNF384:-0.161149226065;FOSL2:-0.179328657929;TEF:-0.196367759171;SOX5:-0.202410474046;NR5A1,2:-0.255283225172;FOX{F1,F2,J1}:-0.265490557175;MEF2{A,B,C,D}:-0.268964105722;TOPORS:-0.292483548729;ESRRA:-0.292688458173;RFX1:-0.294345300875;CREB1:-0.295631661257;ETS1,2:-0.299001753024;IKZF1:-0.312723591219;RFX2..5_RFXANK_RFXAP:-0.333351500525;CRX:-0.337298341993;LMO2:-0.345905817213;PAX2:-0.347170265259;AHR_ARNT_ARNT2:-0.351691455246;PBX1:-0.357521625493;FOX{D1,D2}:-0.379383617835;POU5F1:-0.403578112705;E2F1..5:-0.419102602187;POU3F1..4:-0.431264001178;PAX8:-0.441211414587;NKX2-1,4:-0.460118782008;STAT5{A,B}:-0.466390661207;ATF2:-0.475170967161;BREu{core}:-0.4758150264;HOX{A5,B5}:-0.482465466018;POU6F1:-0.482751562591;JUN:-0.498399240605;GATA6:-0.501318588002;RXRA_VDR{dimer}:-0.503440407186;ZNF143:-0.511898103673;PAX4:-0.512718187108;ATF4:-0.514111143328;ELK1,4_GABP{A,B1}:-0.521948221552;FOXP1:-0.522393898835;ELF1,2,4:-0.53362880579;T:-0.535182772973;SPIB:-0.535464271897;AIRE:-0.563030551545;SPI1:-0.565854765488;NANOG:-0.585692409558;NRF1:-0.591053543395;CDX1,2,4:-0.596137217563;TLX2:-0.624487809822;EP300:-0.638908471454;MYOD1:-0.658347748039;TGIF1:-0.686565811615;ARID5B:-0.692114434618;FOXM1:-0.700366572463;CUX2:-0.730759241364;STAT1,3:-0.733292097507;SOX2:-0.746397283275;SOX{8,9,10}:-0.787718740806;AR:-0.814727370356;HIF1A:-0.828882720117;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.849477369353;OCT4_SOX2{dimer}:-0.883446495889;NFY{A,B,C}:-0.908867358198;ZEB1:-0.920337121413;IKZF2:-0.938970953709;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.943183092192;FOXQ1:-0.976862215079;POU2F1..3:-1.00874979323;FOXN1:-1.0186216736;ALX1:-1.02425803096;SNAI1..3:-1.03792710942;FOXP3:-1.04147257539;ONECUT1,2:-1.12173062473;PITX1..3:-1.12328545115;POU1F1:-1.13518109727;ZBTB16:-1.15656421556;PAX6:-1.21064069048;VSX1,2:-1.60207564264
}}
}}

Revision as of 14:49, 21 March 2012


Name:Fibroblast - Gingival, donor4 (GFH2)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuegum
dev stage22 years old adult
sexmale
age22
cell typefibroblast
cell lineNA
companyN/A
collaborationMitsuhiro Ohshima (Nihon University School of Dentistry)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
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
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-penis-0.168
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
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: CNhs10848

Jaspar motifP-value
MA0002.20.735
MA0003.10.164
MA0004.10.456
MA0006.10.0576
MA0007.10.48
MA0009.10.595
MA0014.10.797
MA0017.10.834
MA0018.29.62262e-4
MA0019.10.823
MA0024.10.00979
MA0025.10.412
MA0027.10.465
MA0028.14.40105e-4
MA0029.10.3
MA0030.10.631
MA0031.10.287
MA0035.20.0532
MA0038.10.711
MA0039.20.0157
MA0040.10.413
MA0041.10.272
MA0042.10.191
MA0043.19.87394e-4
MA0046.10.469
MA0047.20.763
MA0048.10.704
MA0050.13.29274e-17
MA0051.19.44473e-13
MA0052.10.206
MA0055.10.48
MA0057.10.423
MA0058.10.283
MA0059.10.162
MA0060.11.18008e-4
MA0061.10.365
MA0062.24.02308e-8
MA0065.20.598
MA0066.10.272
MA0067.10.00932
MA0068.10.417
MA0069.10.675
MA0070.10.287
MA0071.10.387
MA0072.10.748
MA0073.10.801
MA0074.10.423
MA0076.12.12678e-4
MA0077.10.807
MA0078.10.901
MA0079.20.771
MA0080.21.31473e-5
MA0081.10.297
MA0083.10.191
MA0084.10.0251
MA0087.10.0608
MA0088.10.474
MA0090.10.00604
MA0091.10.0217
MA0092.10.405
MA0093.10.372
MA0099.20.698
MA0100.10.529
MA0101.10.9
MA0102.20.919
MA0103.10.00749
MA0104.20.00552
MA0105.10.89
MA0106.10.0214
MA0107.10.439
MA0108.20.0868
MA0111.10.925
MA0112.20.0153
MA0113.10.548
MA0114.10.917
MA0115.10.0907
MA0116.10.528
MA0117.10.103
MA0119.10.338
MA0122.10.741
MA0124.10.594
MA0125.10.589
MA0131.10.108
MA0135.10.879
MA0136.18.82082e-7
MA0137.20.626
MA0138.20.704
MA0139.10.774
MA0140.10.284
MA0141.10.548
MA0142.10.347
MA0143.10.9
MA0144.10.845
MA0145.10.33
MA0146.10.994
MA0147.10.00226
MA0148.10.642
MA0149.10.789
MA0150.10.207
MA0152.10.0554
MA0153.10.682
MA0154.10.817
MA0155.10.0308
MA0156.12.14397e-6
MA0157.10.219
MA0159.10.0412
MA0160.10.782
MA0162.10.031
MA0163.10.33
MA0164.10.459
MA0258.10.0949
MA0259.10.0123



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: CNhs10848

Novel motifP-value
10.32
100.456
1000.598
1010.725
1020.0385
1030.58
1040.221
1050.638
1060.16
1070.046
1080.535
1090.992
110.963
1100.649
1110.0493
1120.445
1130.887
1140.389
1150.363
1160.293
1170.508
1180.222
1190.665
120.0102
1200.35
1210.264
1220.0262
1230.00442
1240.286
1250.641
1260.54
1270.439
1280.0756
1290.246
130.0248
1300.281
1310.569
1320.197
1330.171
1340.0229
1350.786
1360.69
1370.355
1380.58
1390.19
140.464
1400.0429
1410.0102
1420.889
1430.846
1440.119
1450.986
1460.3
1470.277
1480.834
1490.531
150.688
1500.223
1510.859
1520.0314
1530.661
1540.518
1550.00461
1560.445
1570.781
1580.0551
1590.469
160.151
1600.595
1610.979
1620.126
1630.754
1640.541
1650.664
1660.00686
1670.231
1680.828
1690.0788
170.921
180.123
190.00476
20.0715
200.14
210.484
220.39
230.155
240.814
250.138
260.666
270.537
280.505
290.172
30.566
300.0881
310.289
321.64388e-12
330.652
340.336
350.783
360.0402
370.623
380.537
390.568
40.0779
400.08
410.612
420.706
430.564
440.998
450.323
460.506
470.435
480.531
490.937
50.486
500.514
510.696
520.353
530.556
540.526
550.121
560.72
570.907
580.302
590.048
60.6
600.879
610.724
620.832
630.453
640.693
650.167
660.618
670.819
680.865
690.394
70.0973
700.434
710.605
720.639
730.168
740.242
750.417
760.982
770.21
780.526
790.00423
80.566
800.534
810.53
820.379
830.254
840.631
850.469
860.956
870.458
880.238
890.253
90.354
900.854
910.323
920.286
930.63
940.352
950.552
960.655
970.289
980.292
992.62935e-4



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: CNhs10848


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002552 (fibroblast of gingiva)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000153 (anterior region of body)
0000161 (orifice)
0000165 (mouth)
0000166 (oral opening)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000930 (stomodeum)
0001004 (respiratory system)
0001007 (digestive system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0001828 (gingiva)
0002050 (embryonic structure)
0002384 (connective tissue)
0002532 (epiblast (generic))
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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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