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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005366
|DRA_sample_Accession=CAGE@SAMD00005366
|accession_numbers=CAGE;DRX008004;DRR008876;DRZ000301;DRZ001686
|accession_numbers=CAGE;DRX008004;DRR008876;DRZ000301;DRZ001686;DRZ011651;DRZ013036
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000002,UBERON:0000995,UBERON:0003134,UBERON:0001560,UBERON:0005156,UBERON:0000064,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003133,UBERON:0003975,UBERON:0004175,UBERON:0010317,UBERON:0003100,UBERON:0000474
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|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|fonse_treatment_closure=
|fonse_treatment_closure=
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|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/small%2520cell%2520cervical%2520cancer%2520cell%2520line%253aHCSC-1.CNhs11885.10800-110I8.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/small%2520cell%2520cervical%2520cancer%2520cell%2520line%253aHCSC-1.CNhs11885.10800-110I8.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/small%2520cell%2520cervical%2520cancer%2520cell%2520line%253aHCSC-1.CNhs11885.10800-110I8.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/small%2520cell%2520cervical%2520cancer%2520cell%2520line%253aHCSC-1.CNhs11885.10800-110I8.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/small%2520cell%2520cervical%2520cancer%2520cell%2520line%253aHCSC-1.CNhs11885.10800-110I8.hg38.nobarcode.ctss.bed.gz
|id=FF:10800-110I8
|id=FF:10800-110I8
|is_a=EFO:0002091;;FF:0000210;;FF:0101967
|is_a=EFO:0002091;;FF:0000210;;FF:0101967
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|library_id=CNhs11885
|library_id=CNhs11885
|library_id_phase_based=2:CNhs11885
|library_id_phase_based=2:CNhs11885
|microRNAs=
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|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10800
|name=small cell cervical cancer cell line:HCSC-1
|name=small cell cervical cancer cell line:HCSC-1
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
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Line 91: Line 100:
|top_motifs=SOX{8,9,10}:2.67140496793;BREu{core}:2.64330386909;TFDP1:2.53923686829;NFY{A,B,C}:2.47087395195;LMO2:2.33791059256;SNAI1..3:1.99993315932;NKX2-3_NKX2-5:1.98611150017;GFI1:1.97268602278;ZEB1:1.88942463557;E2F1..5:1.83634874443;PBX1:1.66478245738;FOXM1:1.64961779119;NRF1:1.6395351992;XCPE1{core}:1.61818090852;VSX1,2:1.57404760582;ELK1,4_GABP{A,B1}:1.48995501444;ZNF143:1.46440801678;T:1.37115257605;DBP:1.2952265449;SOX2:1.28707086289;POU1F1:1.22947464263;SOX17:1.21914486858;PRRX1,2:1.19969820358;FOXA2:1.18547200175;HOXA9_MEIS1:1.13023413521;FOXQ1:1.12697202121;ADNP_IRX_SIX_ZHX:1.12149011694;MTE{core}:1.08202272116;FOXL1:1.06641349131;HOX{A6,A7,B6,B7}:1.04435903459;ATF4:1.03443658771;POU6F1:1.00260028088;MYOD1:1.00185887378;FOX{F1,F2,J1}:0.999358383964;ZFP161:0.983268407663;HIC1:0.971980601086;ZIC1..3:0.945159822711;bHLH_family:0.94004374315;TFAP2B:0.928817378468;TEF:0.917861735873;NANOG:0.87371771951;PAX8:0.840095715132;EGR1..3:0.829218476673;PAX3,7:0.822698519967;MED-1{core}:0.775210489429;HOX{A4,D4}:0.767149778062;SP1:0.727366142933;OCT4_SOX2{dimer}:0.725714657229;ZNF384:0.72147498364;SREBF1,2:0.691916034461;LHX3,4:0.652864260791;POU2F1..3:0.645702557507;FOXP1:0.633580633723;ATF5_CREB3:0.601824059219;PATZ1:0.59942948769;PDX1:0.596235942536;PPARG:0.55141019175;RFX1:0.550077005341;JUN:0.531139545901;YY1:0.520137024733;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.514160359616;NKX3-1:0.486405125964;CREB1:0.475134465201;ARID5B:0.454061830794;POU5F1:0.431754340376;NR5A1,2:0.411222406397;REST:0.39062784572;HBP1_HMGB_SSRP1_UBTF:0.38846707517;PAX5:0.387654926727;ZNF423:0.372854093376;FOXD3:0.366058237397;MYB:0.329974100052;IKZF2:0.312775388519;LEF1_TCF7_TCF7L1,2:0.309362433246;NHLH1,2:0.238838841434;NKX6-1,2:0.234384892534;MTF1:0.229158583167;ONECUT1,2:0.227341482611;PITX1..3:0.186759474492;PAX4:0.185127067742;PAX6:0.173053214127;EN1,2:0.155101296239;EVI1:0.0997984587943;CUX2:0.0844510285779;PAX1,9:0.0813105922665;AHR_ARNT_ARNT2:0.0808587102969;STAT5{A,B}:0.05130320779;GATA6:0.0489544112163;FOXN1:-0.00993956789664;FOX{D1,D2}:-0.0434090882182;HNF1A:-0.0444294879226;ZBTB16:-0.0478920822389;NKX2-1,4:-0.0531792686741;TOPORS:-0.0574580942554;RBPJ:-0.0586518696898;FOX{I1,J2}:-0.0618149956084;CRX:-0.0645961902801;TBX4,5:-0.0730062238267;FOXP3:-0.0748739340167;MEF2{A,B,C,D}:-0.0775964353798;TGIF1:-0.0799814905359;HNF4A_NR2F1,2:-0.118238125358;AIRE:-0.130714549625;HAND1,2:-0.138703487977;ALX1:-0.149166017727;RFX2..5_RFXANK_RFXAP:-0.159497878413;NKX2-2,8:-0.163252019796;GATA4:-0.18998460393;MAZ:-0.207576901227;MZF1:-0.221473404399;TP53:-0.239987823848;ZBTB6:-0.241218943026;GTF2I:-0.244800693609;MYFfamily:-0.24597711659;ESR1:-0.277105055481;CDX1,2,4:-0.290119352812;FOXO1,3,4:-0.311795307157;ATF2:-0.324962007183;UFEwm:-0.33634259529;NKX3-2:-0.351648171318;GFI1B:-0.358648507748;SOX5:-0.378563354526;HOX{A5,B5}:-0.400686892875;AR:-0.433896247525;DMAP1_NCOR{1,2}_SMARC:-0.434493147451;FOSL2:-0.450160409586;SPIB:-0.452753221595;IKZF1:-0.476443674758;NFKB1_REL_RELA:-0.489539393897;BPTF:-0.523772051901;TFAP2{A,C}:-0.534322544682;RORA:-0.544530250028;HLF:-0.563832696438;SPI1:-0.565150493113;NR6A1:-0.569829774006;TBP:-0.602062576418;HES1:-0.625866890241;NFIX:-0.632639967693;FOS_FOS{B,L1}_JUN{B,D}:-0.637366170209;KLF4:-0.6454343905;CDC5L:-0.658442880088;MAFB:-0.679435474926;BACH2:-0.695794623349;STAT1,3:-0.696647363835;EP300:-0.709168064948;IRF7:-0.710591368188;HIF1A:-0.786081491432;RUNX1..3:-0.792690649746;NFE2L2:-0.794399738298;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.832801704169;PAX2:-0.847179559396;CEBPA,B_DDIT3:-0.856679454127;GTF2A1,2:-0.857089246676;XBP1:-0.871844602807;NFIL3:-0.882799054871;MYBL2:-0.890503503009;ELF1,2,4:-0.902190246748;ATF6:-0.905232005904;ZNF148:-0.918281671128;NFE2L1:-0.920164938722;TAL1_TCF{3,4,12}:-0.936495353917;RREB1:-0.938308074785;TFCP2:-0.94340651918;HMGA1,2:-0.951554939299;ETS1,2:-0.957303954484;EBF1:-0.97011640747;NFE2:-0.973442642623;HMX1:-0.976739124415;NANOG{mouse}:-1.03645925038;PRDM1:-1.09060525466;NR3C1:-1.09291080378;SRF:-1.12842251494;ESRRA:-1.14171729742;POU3F1..4:-1.14477636549;HSF1,2:-1.1604404241;TFAP4:-1.18854119708;GCM1,2:-1.20044986229;TEAD1:-1.21992095601;ALX4:-1.22225129893;GZF1:-1.22362050297;NR1H4:-1.22683640135;TLX1..3_NFIC{dimer}:-1.24565309149;IRF1,2:-1.24641677067;NFATC1..3:-1.51289481132;STAT2,4,6:-1.54817938568;GLI1..3:-1.68048099351;TLX2:-1.69156938676;ZNF238:-1.70155330391;SMAD1..7,9:-1.73209262834;RXR{A,B,G}:-1.84381301906;SPZ1:-1.92066776537;RXRA_VDR{dimer}:-1.92689959449
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10800-110I8;search_select_hide=table117:FF:10800-110I8
}}
}}

Latest revision as of 15:05, 3 June 2020

Name:small cell cervical cancer cell line:HCSC-1
Species:Human (Homo sapiens)
Library ID:CNhs11885
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuecervix
dev stageNA
sexfemale
age48
cell typeunclassifiable
cell lineHCSC-1
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005366
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11885 CAGE DRX008004 DRR008876
Accession ID Hg19

Library idBAMCTSS
CNhs11885 DRZ000301 DRZ001686
Accession ID Hg38

Library idBAMCTSS
CNhs11885 DRZ011651 DRZ013036
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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
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C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
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



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: CNhs11885

Jaspar motifP-value
MA0002.24.68161e-5
MA0003.10.152
MA0004.10.47
MA0006.10.653
MA0007.10.433
MA0009.10.583
MA0014.10.636
MA0017.10.0116
MA0018.20.00114
MA0019.10.861
MA0024.11.97879e-5
MA0025.10.101
MA0027.10.474
MA0028.10.132
MA0029.10.442
MA0030.10.69
MA0031.10.817
MA0035.20.718
MA0038.17.72198e-5
MA0039.20.493
MA0040.10.884
MA0041.10.584
MA0042.10.821
MA0043.10.00167
MA0046.10.615
MA0047.20.719
MA0048.10.607
MA0050.17.92616e-5
MA0051.10.00209
MA0052.10.564
MA0055.10.722
MA0057.10.395
MA0058.10.504
MA0059.10.829
MA0060.13.34785e-19
MA0061.10.0152
MA0062.20.0566
MA0065.20.0157
MA0066.10.0576
MA0067.10.711
MA0068.10.198
MA0069.10.469
MA0070.10.075
MA0071.10.379
MA0072.10.823
MA0073.10.619
MA0074.10.249
MA0076.10.0218
MA0077.10.0014
MA0078.10.329
MA0079.20.292
MA0080.24.42155e-9
MA0081.10.0748
MA0083.10.15
MA0084.10.401
MA0087.10.843
MA0088.10.681
MA0090.17.34431e-4
MA0091.10.0446
MA0092.10.144
MA0093.10.392
MA0099.26.16145e-12
MA0100.10.219
MA0101.10.137
MA0102.20.534
MA0103.10.0454
MA0104.20.475
MA0105.13.38587e-4
MA0106.10.304
MA0107.10.0717
MA0108.20.0347
MA0111.10.587
MA0112.21.79658e-5
MA0113.10.0105
MA0114.10.0826
MA0115.10.993
MA0116.10.00141
MA0117.10.787
MA0119.10.00927
MA0122.10.417
MA0124.10.998
MA0125.10.0495
MA0131.10.297
MA0135.10.172
MA0136.11.34336e-5
MA0137.20.0274
MA0138.20.861
MA0139.10.3
MA0140.10.618
MA0141.10.126
MA0142.10.326
MA0143.10.888
MA0144.10.0379
MA0145.10.137
MA0146.10.0725
MA0147.10.685
MA0148.10.705
MA0149.10.139
MA0150.10.00179
MA0152.10.916
MA0153.10.371
MA0154.10.00443
MA0155.10.221
MA0156.10.0976
MA0157.10.365
MA0159.10.0607
MA0160.10.147
MA0162.10.203
MA0163.16.36912e-6
MA0164.10.52
MA0258.10.00657
MA0259.10.563



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: CNhs11885

Novel motifP-value
10.166
100.194
1000.989
1010.288
1020.504
1030.0632
1040.583
1050.615
1060.0168
1070.131
1080.909
1090.223
110.13
1100.229
1110.274
1120.0495
1130.299
1140.0139
1150.624
1160.591
1170.152
1180.454
1190.19
120.963
1200.637
1210.876
1220.52
1230.511
1240.367
1250.627
1260.525
1270.148
1280.136
1290.563
130.101
1300.812
1310.387
1320.623
1330.0249
1340.751
1350.00171
1360.197
1370.28
1380.171
1390.0558
140.617
1400.187
1410.76
1420.631
1430.0128
1440.516
1450.175
1460.669
1470.692
1480.118
1490.0183
150.188
1500.576
1510.289
1520.116
1530.245
1540.684
1550.628
1560.767
1570.674
1580.561
1590.617
160.253
1600.12
1610.199
1620.97
1630.663
1640.343
1650.462
1660.168
1670.86
1680.0792
1690.00453
170.158
180.101
190.0843
20.5
200.592
210.186
220.0999
230.00964
240.122
250.77
260.208
270.276
280.807
290.342
30.0518
300.646
310.635
320.0217
330.549
340.264
350.173
360.134
370.113
380.193
390.226
40.887
400.416
410.519
420.184
430.0997
440.354
450.444
460.172
470.373
480.287
490.171
50.13
500.388
510.141
520.226
530.375
540.215
550.0476
560.507
570.292
580.243
590.0328
60.445
600.0233
610.382
620.0772
630.0717
640.602
650.0429
660.163
670.862
680.571
690.743
70.296
700.00444
710.104
720.189
730.152
740.133
750.15
760.709
770.126
780.358
790.117
80.155
800.0428
810.178
820.00936
830.254
840.835
850.00344
860.305
870.518
880.702
890.132
90.15
900.0373
910.18
920.0886
930.0928
940.175
950.457
960.0766
970.742
980.4
990.493



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: CNhs11885


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

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
193 (reproductive organ cancer)
120 (female reproductive organ cancer)
4362 (cervical cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000002 (uterine cervix)
0000995 (uterus)
0003134 (female reproductive organ)
0001560 (neck of organ)
0005156 (reproductive structure)
0000064 (organ part)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003133 (reproductive organ)
0003975 (internal female genitalia)
0004175 (internal genitalia)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0000474 (female reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0101967 (cervical cancer cell line sample)

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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

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