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{{f5samples
{{f5samples
|id=FF:10810-111A9
|F5samples=
|name=adrenal cortex adenocarcinoma cell line:SW-13
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|sample_company=JAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
|rna_lot_number=
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|sample_species=Human (Homo sapiens)
|sample_strain=
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|sample_tissue=adrenal gland
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|sample_cell_type=adrenal cortex cell
|sample_cell_line=SW-13
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=adenocarcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0000949,UBERON:0001062,UBERON:0001235,UBERON:0001851,UBERON:0002050,UBERON:0002100,UBERON:0002342,UBERON:0002346,UBERON:0002368,UBERON:0002369,UBERON:0002417,UBERON:0002530,UBERON:0002532,UBERON:0003075,UBERON:0004120,UBERON:0004121,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005423,UBERON:0006598,UBERON:0007284
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:299,DOID:305,DOID:4,DOID:7
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:299,DOID:305,DOID:4,DOID:7
|sample_description=
|comment=
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|fonse_cell_line=FF:0101120
|fonse_cell_line=FF:0101120
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|fonse_cell_line_closure=FF:0101120
Line 66: Line 34:
|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:10810-111A9
|is_a=DOID:7;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100167;;UBERON:0001235
|is_a=DOID:7;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100167;;UBERON:0001235
|name=adrenal cortex adenocarcinoma cell line:SW-13
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11893,LSID830,release010,COMPLETED
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|rna_concentration=1.94439
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.18
|rna_od260/280=2.05
|rna_position=A9
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=111A9
|rna_weight_ug=145.82925
|sample_age=unknown
|sample_cell_catalog=jcrb9069
|sample_cell_line=SW-13
|sample_cell_lot=
|sample_cell_type=adrenal cortex cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=JAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
|sample_description=
|sample_dev_stage=
|sample_disease=adenocarcinoma
|sample_donor(cell lot)=
|sample_ethnicity=unknown
|sample_experimental_condition=
|sample_id=10810
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=adrenal gland
|top_motifs=NRF1:2.27862748454;ELK1,4_GABP{A,B1}:1.985631442;CRX:1.7582384136;PPARG:1.71771821788;ZNF143:1.66885138691;NANOG:1.59145877697;NFY{A,B,C}:1.48400984147;VSX1,2:1.4415073775;GFI1:1.42292769238;PAX8:1.33369678592;E2F1..5:1.27153384789;TFDP1:1.22193738226;ALX1:1.21437588511;NKX2-3_NKX2-5:1.13734680921;PAX4:1.03704747859;POU1F1:1.00782782659;PBX1:1.0006606723;STAT1,3:0.989935733115;PAX1,9:0.971228801936;HOX{A6,A7,B6,B7}:0.940686148101;ONECUT1,2:0.924556431255;RFX1:0.842219889962;LHX3,4:0.794525910687;NKX6-1,2:0.779049531738;AIRE:0.712896675565;MYB:0.687919078819;ARID5B:0.666041896853;SOX17:0.665622536125;FOXQ1:0.650281064083;HOX{A4,D4}:0.62747508164;YY1:0.609377861381;HIC1:0.575928284826;BREu{core}:0.527811037255;EVI1:0.52740722478;HOX{A5,B5}:0.521647003832;T:0.51258467067;OCT4_SOX2{dimer}:0.508162970826;RBPJ:0.504747158101;TEF:0.479186654898;GATA6:0.422979278139;PRRX1,2:0.412242125126;FOX{I1,J2}:0.393944226519;SOX{8,9,10}:0.369738148203;CDX1,2,4:0.34717279035;STAT5{A,B}:0.341224537571;HMGA1,2:0.340026803484;ZNF384:0.324903456898;FOXM1:0.315842855118;PAX3,7:0.31193649109;EN1,2:0.287810239912;LEF1_TCF7_TCF7L1,2:0.238259655838;NR5A1,2:0.23599108503;NR6A1:0.232352583208;PITX1..3:0.230534913895;ADNP_IRX_SIX_ZHX:0.20503996838;HNF4A_NR2F1,2:0.201895179425;HBP1_HMGB_SSRP1_UBTF:0.195633473582;HSF1,2:0.19375550215;ZFP161:0.193192537261;CUX2:0.178879855849;IKZF1:0.163349275795;IKZF2:0.15612287272;ZEB1:0.122591524536;SP1:0.101966626926;POU6F1:0.0815153974945;POU2F1..3:0.0708605350342;KLF4:0.024201833253;HAND1,2:0.0238503015365;FOXA2:0.0234841442728;SREBF1,2:0.0193419295879;GCM1,2:0.0191830657247;ATF5_CREB3:0.0181135623924;EGR1..3:0.00705710380978;REST:-0.0127749997867;GFI1B:-0.0308193546161;DMAP1_NCOR{1,2}_SMARC:-0.0338030648298;FOXP3:-0.034142922726;FOXN1:-0.0351303595437;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0472635458934;TFAP2B:-0.0666832776353;GTF2A1,2:-0.0669982645724;FOXP1:-0.0917479459679;TEAD1:-0.100222540673;ESRRA:-0.137829752094;CREB1:-0.154027163687;NKX2-1,4:-0.176115219049;CDC5L:-0.188492686843;TGIF1:-0.202828175553;FOXL1:-0.202949713015;PATZ1:-0.210510669909;RORA:-0.22704028649;SNAI1..3:-0.232088131984;RUNX1..3:-0.236151959085;ZBTB16:-0.246925452666;ZBTB6:-0.250108087985;HNF1A:-0.278300423534;HOXA9_MEIS1:-0.295303419132;HES1:-0.299229777288;RREB1:-0.310055607252;LMO2:-0.311009450182;AHR_ARNT_ARNT2:-0.313463560235;MYOD1:-0.316670320503;ELF1,2,4:-0.320718485869;NKX3-2:-0.322538958081;NFKB1_REL_RELA:-0.331498011717;PDX1:-0.337506078281;DBP:-0.351429109429;NFE2L2:-0.352774883809;TP53:-0.365037590395;POU3F1..4:-0.366016290037;UFEwm:-0.376395808771;bHLH_family:-0.382753997328;SOX2:-0.402873682212;MEF2{A,B,C,D}:-0.408263600642;XBP1:-0.417406332081;RXR{A,B,G}:-0.418685953327;MZF1:-0.421304539278;RFX2..5_RFXANK_RFXAP:-0.42856818849;FOS_FOS{B,L1}_JUN{B,D}:-0.435341449237;FOSL2:-0.46819096424;PAX5:-0.488814274748;PRDM1:-0.49193060081;JUN:-0.501841414196;SRF:-0.505948888139;NFE2L1:-0.509627603754;SPIB:-0.517863626108;ATF2:-0.531757509433;PAX6:-0.534515220097;SPI1:-0.538085217915;AR:-0.553623713032;NR3C1:-0.554478689406;NANOG{mouse}:-0.556788391002;NFE2:-0.558162707072;ATF4:-0.567365997577;TOPORS:-0.568884427105;HLF:-0.569962065265;BACH2:-0.582818900429;XCPE1{core}:-0.588466373635;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.590255472496;NHLH1,2:-0.601935297364;MED-1{core}:-0.630420764188;TAL1_TCF{3,4,12}:-0.66239441003;MTE{core}:-0.674738961763;PAX2:-0.684924230513;ZIC1..3:-0.695608010784;SOX5:-0.698298079247;FOX{D1,D2}:-0.705943006118;ZNF148:-0.722138068552;GATA4:-0.724766687438;FOXD3:-0.736998487825;TLX1..3_NFIC{dimer}:-0.753965875352;ESR1:-0.757668310934;GTF2I:-0.776778810093;MYBL2:-0.783153215615;NKX3-1:-0.785376893874;POU5F1:-0.79111070154;NFIX:-0.793899730809;MTF1:-0.886437397112;ALX4:-0.891560767863;FOXO1,3,4:-0.915868690151;BPTF:-0.933167230516;ETS1,2:-0.940395531867;NFIL3:-0.941591272632;FOX{F1,F2,J1}:-0.962486661269;NKX2-2,8:-0.970981838627;IRF7:-0.974314450478;TFAP2{A,C}:-0.994624285089;MYFfamily:-1.04265004254;ZNF423:-1.06032027298;NFATC1..3:-1.0692906736;TLX2:-1.07670625323;SPZ1:-1.08479737025;GLI1..3:-1.10203362322;CEBPA,B_DDIT3:-1.13242628214;ZNF238:-1.13468500785;EP300:-1.14577049006;NR1H4:-1.17165450435;TFAP4:-1.21307014736;IRF1,2:-1.26273301411;STAT2,4,6:-1.26410828874;EBF1:-1.27638544596;MAZ:-1.29028614029;TFCP2:-1.3371682509;ATF6:-1.35026832235;HMX1:-1.35042397375;GZF1:-1.35566603468;HIF1A:-1.38977492823;SMAD1..7,9:-1.53097223013;TBP:-1.59874586588;RXRA_VDR{dimer}:-1.65517122003;MAFB:-1.73823918554;TBX4,5:-1.96209347971
}}
}}

Revision as of 14:15, 21 March 2012


Name:adrenal cortex adenocarcinoma cell line:SW-13
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueadrenal gland
dev stageNA
sexfemale
ageunknown
cell typeadrenal cortex cell
cell lineSW-13
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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
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-penis0.116
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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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: CNhs11893

Jaspar motifP-value
MA0002.20.0066
MA0003.10.246
MA0004.10.794
MA0006.10.36
MA0007.10.759
MA0009.10.513
MA0014.10.856
MA0017.10.0552
MA0018.20.383
MA0019.10.94
MA0024.13.41186e-4
MA0025.10.817
MA0027.10.342
MA0028.15.874e-6
MA0029.10.289
MA0030.10.00344
MA0031.10.205
MA0035.20.145
MA0038.12.08091e-5
MA0039.20.321
MA0040.10.266
MA0041.10.791
MA0042.10.503
MA0043.10.539
MA0046.10.142
MA0047.20.255
MA0048.10.323
MA0050.13.99956e-9
MA0051.13.29211e-6
MA0052.10.0027
MA0055.10.0039
MA0057.10.81
MA0058.10.898
MA0059.10.876
MA0060.15.81915e-16
MA0061.10.0532
MA0062.21.43517e-7
MA0065.20.317
MA0066.10.675
MA0067.10.98
MA0068.10.647
MA0069.10.768
MA0070.10.481
MA0071.10.846
MA0072.10.108
MA0073.10.606
MA0074.10.186
MA0076.11.21815e-7
MA0077.10.97
MA0078.10.737
MA0079.20.717
MA0080.28.75972e-11
MA0081.10.34
MA0083.10.0973
MA0084.10.351
MA0087.10.417
MA0088.10.0287
MA0090.10.414
MA0091.10.00474
MA0092.10.157
MA0093.10.628
MA0099.23.42688e-13
MA0100.10.192
MA0101.10.836
MA0102.21.80134e-4
MA0103.10.928
MA0104.20.208
MA0105.10.0102
MA0106.10.521
MA0107.10.395
MA0108.24.54337e-7
MA0111.10.974
MA0112.22.73272e-4
MA0113.10.0309
MA0114.10.939
MA0115.10.808
MA0116.10.0454
MA0117.10.801
MA0119.10.0836
MA0122.10.95
MA0124.10.742
MA0125.10.351
MA0131.10.158
MA0135.10.87
MA0136.11.51305e-6
MA0137.20.262
MA0138.20.549
MA0139.10.0356
MA0140.10.171
MA0141.10.447
MA0142.10.942
MA0143.10.0459
MA0144.10.0189
MA0145.10.103
MA0146.10.411
MA0147.10.126
MA0148.10.196
MA0149.10.565
MA0150.15.49666e-4
MA0152.10.343
MA0153.10.161
MA0154.10.0144
MA0155.10.309
MA0156.10.321
MA0157.10.46
MA0159.10.123
MA0160.10.695
MA0162.10.0449
MA0163.10.164
MA0164.10.778
MA0258.10.0228
MA0259.10.0728



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: CNhs11893

Novel motifP-value
10.93
100.782
1000.474
1010.806
1020.656
1030.446
1040.666
1050.575
1061.176e-7
1070.00217
1080.533
1090.563
110.623
1100.87
1110.825
1120.00651
1130.0486
1140.234
1150.399
1160.733
1170.966
1180.327
1190.814
120.709
1200.857
1210.297
1220.81
1230.914
1240.59
1250.733
1260.97
1270.773
1280.00213
1290.745
130.953
1300.0235
1310.0316
1320.585
1330.117
1340.0785
1350.0212
1360.268
1370.276
1380.422
1390.025
140.471
1400.0534
1410.56
1420.976
1430.169
1440.95
1450.638
1460.389
1470.89
1480.00466
1490.0553
150.417
1500.276
1510.247
1520.029
1530.534
1540.7
1550.672
1560.736
1570.277
1580.746
1590.421
160.352
1600.197
1610.774
1620.784
1630.0641
1640.441
1650.186
1660.124
1670.142
1680.114
1690.0129
170.155
180.0719
190.072
20.0501
200.247
210.468
220.18
230.0032
240.886
250.634
260.456
270.124
280.899
290.751
30.363
300.453
310.677
320.0325
330.776
340.333
350.798
360.235
370.15
380.56
390.439
40.208
400.316
410.408
420.823
430.199
440.665
450.323
460.109
470.789
480.932
490.472
50.357
500.768
510.744
520.00476
530.351
540.603
550.766
560.577
570.978
580.142
590.0635
60.967
600.00138
610.835
620.0736
630.205
640.82
650.058
660.00976
670.806
680.039
690.72
70.787
700.338
710.163
720.181
730.177
740.435
750.862
760.714
770.0911
780.56
790.327
80.477
800.0662
810.45
820.0935
830.575
840.528
850.00418
860.427
870.667
880.614
890.28
90.0861
900.492
910.00716
920.161
930.231
940.141
950.167
960.394
970.808
980.728
990.665



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: CNhs11893


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
299 (adenocarcinoma)
305 (carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001062 (anatomical entity)
0001235 (adrenal cortex)
0001851 (cortex)
0002050 (embryonic structure)
0002100 (trunk)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002369 (adrenal gland)
0002417 (abdominal segment of trunk)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
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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