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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005154
|DRA_sample_Accession=CAGE@SAMD00005154
|accession_numbers=CAGE;DRX008003;DRR008875;DRZ000300;DRZ001685
|accession_numbers=CAGE;DRX008003;DRR008875;DRZ000300;DRZ001685;DRZ011650;DRZ013035
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/signet%2520ring%2520carcinoma%2520cell%2520line%253aNUGC-4.CNhs11270.10483-107A6.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/signet%2520ring%2520carcinoma%2520cell%2520line%253aNUGC-4.CNhs11270.10483-107A6.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/signet%2520ring%2520carcinoma%2520cell%2520line%253aNUGC-4.CNhs11270.10483-107A6.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/signet%2520ring%2520carcinoma%2520cell%2520line%253aNUGC-4.CNhs11270.10483-107A6.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/signet%2520ring%2520carcinoma%2520cell%2520line%253aNUGC-4.CNhs11270.10483-107A6.hg38.nobarcode.ctss.bed.gz
|id=FF:10483-107A6
|id=FF:10483-107A6
|is_a=DOID:3493;;EFO:0002091;;FF:0000210;;FF:0100297
|is_a=DOID:3493;;EFO:0002091;;FF:0000210;;FF:0100297
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|library_id=CNhs11270
|library_id=CNhs11270
|library_id_phase_based=2:CNhs11270
|library_id_phase_based=2:CNhs11270
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10483
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10483
|name=signet ring carcinoma cell line:NUGC-4
|name=signet ring carcinoma cell line:NUGC-4
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
|profile_rnaseq=
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|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 89: Line 99:
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|top_motifs=HNF4A_NR2F1,2:3.35518021202;HNF1A:2.83224406331;ZEB1:2.43951935814;SNAI1..3:2.33052860172;ADNP_IRX_SIX_ZHX:2.1580211538;FOX{F1,F2,J1}:2.06941365032;MYOD1:1.84089532293;LMO2:1.52455256578;NR5A1,2:1.39024639023;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.34638116537;VSX1,2:1.27838474329;RBPJ:1.23763180064;HOX{A5,B5}:1.02875623544;HOX{A6,A7,B6,B7}:1.0079022234;E2F1..5:0.974982595284;ZNF148:0.918132025395;FOXQ1:0.914984265607;NFE2L2:0.8611961989;ELK1,4_GABP{A,B1}:0.855029080854;T:0.807156264;STAT5{A,B}:0.794647170038;NKX3-2:0.788536019272;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.755788228552;GATA6:0.70100697363;TFCP2:0.687342328559;bHLH_family:0.669373845718;LEF1_TCF7_TCF7L1,2:0.663790294276;NANOG:0.627366724493;ESR1:0.608308358262;ESRRA:0.592125191407;NFY{A,B,C}:0.545959181841;PAX8:0.506223317502;XCPE1{core}:0.505745735538;RFX2..5_RFXANK_RFXAP:0.500496945622;YY1:0.440649291343;POU2F1..3:0.429846954293;PDX1:0.428686962789;ELF1,2,4:0.423015543231;TBX4,5:0.398563259235;NR6A1:0.395260690499;POU5F1:0.38351535444;MYB:0.381920616335;PITX1..3:0.356537898805;SOX2:0.321039021995;ATF5_CREB3:0.320926649827;CDC5L:0.314582068807;ZNF423:0.31378255987;NFE2:0.286528007286;HES1:0.28296614998;FOX{I1,J2}:0.280895514011;RXRA_VDR{dimer}:0.276522665203;NKX2-3_NKX2-5:0.274278309503;EBF1:0.250723400068;CUX2:0.238848486742;PBX1:0.230873087243;TP53:0.229766758368;FOXN1:0.219112925645;SOX5:0.171679475246;DBP:0.163383120475;FOXA2:0.160805597799;TEAD1:0.153093197282;IRF7:0.137721599542;IKZF1:0.130178364747;LHX3,4:0.1277971827;BACH2:0.124605028361;CDX1,2,4:0.107108181529;FOS_FOS{B,L1}_JUN{B,D}:0.0924345662643;CRX:0.092354281427;FOXL1:0.085656706444;SOX{8,9,10}:0.0503955260214;TLX1..3_NFIC{dimer}:0.0415836996556;FOX{D1,D2}:0.0414223304096;NKX6-1,2:0.0313082564354;FOSL2:0.0244955406995;NFIL3:0.0208069490417;ZBTB16:0.000358094370418;BREu{core}:-0.00703061078785;ATF4:-0.015445923431;GFI1:-0.0191183456143;FOXP1:-0.021574942089;TFDP1:-0.0249934626782;ONECUT1,2:-0.0331080067611;SP1:-0.0361272412881;FOXM1:-0.040670769313;PAX5:-0.0433144180286;BPTF:-0.0523265682797;NRF1:-0.0636146232847;POU6F1:-0.088209824991;MED-1{core}:-0.101237036471;MTF1:-0.11187423737;HIC1:-0.116048284742;FOXD3:-0.140940262846;HAND1,2:-0.166747424595;RORA:-0.185745566451;TBP:-0.204315766604;FOXO1,3,4:-0.214518646813;EP300:-0.216256446723;POU1F1:-0.248725343323;MAZ:-0.250628825891;MEF2{A,B,C,D}:-0.253256649392;AIRE:-0.264680548455;EN1,2:-0.276218062891;NFKB1_REL_RELA:-0.280730496319;ETS1,2:-0.280909682076;ZNF143:-0.290162596636;HLF:-0.316914586289;ARID5B:-0.319329877182;ATF2:-0.325960520894;TFAP2{A,C}:-0.330702877009;ZFP161:-0.344791849113;AR:-0.348102864124;PAX2:-0.352866126571;ALX1:-0.359973630047;SPI1:-0.362643891778;PPARG:-0.370939289045;SOX17:-0.375099143351;TOPORS:-0.380059477402;EGR1..3:-0.387455698272;TEF:-0.403732170751;NR1H4:-0.412092941577;RFX1:-0.414724347293;ALX4:-0.430993036255;PRRX1,2:-0.434694187767;OCT4_SOX2{dimer}:-0.456777203209;NKX2-1,4:-0.477910944266;ATF6:-0.481250181394;HOXA9_MEIS1:-0.48280059426;PAX6:-0.487748923336;DMAP1_NCOR{1,2}_SMARC:-0.492055740949;KLF4:-0.529057698992;IRF1,2:-0.529465140003;TFAP2B:-0.534567894834;EVI1:-0.535583703602;PAX4:-0.559886536637;CEBPA,B_DDIT3:-0.561504659748;RREB1:-0.567778153611;JUN:-0.573378075191;ZBTB6:-0.581067097924;SREBF1,2:-0.583960320672;SPIB:-0.589673735308;FOXP3:-0.592679251432;GLI1..3:-0.598166691284;GFI1B:-0.626741175063;GTF2I:-0.650096393099;HSF1,2:-0.660509887303;HMX1:-0.695940954684;PATZ1:-0.697207770989;NR3C1:-0.719786364343;UFEwm:-0.726392587823;RUNX1..3:-0.744138488042;REST:-0.753290486885;PAX3,7:-0.75575924602;MYFfamily:-0.775625557837;NHLH1,2:-0.785567737157;CREB1:-0.802670980992;ZIC1..3:-0.813464251657;STAT2,4,6:-0.814493513349;TAL1_TCF{3,4,12}:-0.817037057199;AHR_ARNT_ARNT2:-0.819146884572;POU3F1..4:-0.836240608025;XBP1:-0.860552624282;HOX{A4,D4}:-0.895624990432;SPZ1:-0.917170488046;IKZF2:-0.917819602492;STAT1,3:-0.94660727406;MTE{core}:-1.02354250915;NKX2-2,8:-1.02853564258;MYBL2:-1.04335709222;MAFB:-1.05390455292;HMGA1,2:-1.08779097478;TGIF1:-1.09724605002;GTF2A1,2:-1.19316359914;MZF1:-1.21199062931;TFAP4:-1.22893876484;HBP1_HMGB_SSRP1_UBTF:-1.23286906799;SRF:-1.26435069296;ZNF238:-1.28746916534;TLX2:-1.31854709487;NFIX:-1.32772152361;GCM1,2:-1.34626313543;PRDM1:-1.39168064047;GZF1:-1.41990780711;ZNF384:-1.42556930831;HIF1A:-1.44565234037;RXR{A,B,G}:-1.44626438484;NANOG{mouse}:-1.49112136342;NFATC1..3:-1.54704922807;SMAD1..7,9:-1.57241520968;PAX1,9:-1.65035542365;NFE2L1:-1.67718572849;NKX3-1:-1.73843949205;GATA4:-1.89824741523
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10483-107A6;search_select_hide=table117:FF:10483-107A6
}}
}}

Latest revision as of 14:26, 3 June 2020

Name:signet ring carcinoma cell line:NUGC-4
Species:Human (Homo sapiens)
Library ID:CNhs11270
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuestomach
dev stageNA
sexunknown
ageNA
cell typeunclassifiable
cell lineNUGC-4
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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  SAMD00005154
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11270 CAGE DRX008003 DRR008875
Accession ID Hg19

Library idBAMCTSS
CNhs11270 DRZ000300 DRZ001685
Accession ID Hg38

Library idBAMCTSS
CNhs11270 DRZ011650 DRZ013035
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
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
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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: CNhs11270

Jaspar motifP-value
MA0002.20.0892
MA0003.10.554
MA0004.10.38
MA0006.10.245
MA0007.10.11
MA0009.10.0124
MA0014.10.189
MA0017.11.54316e-14
MA0018.20.465
MA0019.10.971
MA0024.10.006
MA0025.10.935
MA0027.10.158
MA0028.18.89294e-4
MA0029.10.25
MA0030.10.0264
MA0031.10.0843
MA0035.27.11828e-4
MA0038.10.181
MA0039.20.00575
MA0040.10.0886
MA0041.10.618
MA0042.10.218
MA0043.10.636
MA0046.13.76191e-65
MA0047.24.24887e-7
MA0048.10.777
MA0050.10.407
MA0051.10.455
MA0052.10.492
MA0055.10.05
MA0057.10.642
MA0058.10.286
MA0059.10.0507
MA0060.10.0232
MA0061.10.268
MA0062.22.70212e-4
MA0065.21.3356e-6
MA0066.10.87
MA0067.10.0665
MA0068.10.0443
MA0069.10.693
MA0070.10.366
MA0071.10.775
MA0072.10.584
MA0073.10.939
MA0074.10.572
MA0076.10.0232
MA0077.10.314
MA0078.10.574
MA0079.20.827
MA0080.20.742
MA0081.10.107
MA0083.10.0703
MA0084.10.485
MA0087.10.132
MA0088.10.742
MA0090.10.607
MA0091.10.213
MA0092.10.774
MA0093.10.29
MA0099.20.00122
MA0100.10.938
MA0101.10.109
MA0102.20.796
MA0103.11.94477e-9
MA0104.20.0703
MA0105.10.32
MA0106.10.163
MA0107.10.11
MA0108.20.61
MA0111.10.836
MA0112.27.32419e-4
MA0113.10.23
MA0114.16.86345e-21
MA0115.14.19343e-6
MA0116.10.472
MA0117.10.375
MA0119.10.109
MA0122.10.776
MA0124.10.236
MA0125.10.0128
MA0131.10.752
MA0135.10.521
MA0136.10.596
MA0137.20.219
MA0138.20.487
MA0139.10.0373
MA0140.10.163
MA0141.11.50743e-4
MA0142.10.803
MA0143.10.833
MA0144.10.311
MA0145.10.00774
MA0146.10.0898
MA0147.10.0397
MA0148.15.54391e-8
MA0149.10.156
MA0150.10.138
MA0152.10.461
MA0153.12.45286e-29
MA0154.10.375
MA0155.10.382
MA0156.10.229
MA0157.10.628
MA0159.10.18
MA0160.10.0053
MA0162.10.691
MA0163.10.835
MA0164.10.0761
MA0258.10.0391
MA0259.10.869



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: CNhs11270

Novel motifP-value
10.136
100.269
1000.46
1010.199
1020.591
1030.73
1040.606
1050.251
1060.31
1070.239
1080.652
1090.00899
110.634
1100.446
1110.915
1120.925
1130.759
1140.823
1150.834
1160.537
1170.0891
1180.294
1190.17
120.518
1200.0922
1210.404
1220.132
1230.548
1240.398
1250.0899
1260.381
1270.529
1280.51
1290.0435
130.00618
1300.943
1310.126
1320.519
1330.0139
1340.0392
1350.0137
1360.00241
1370.0797
1380.931
1390.0906
140.919
1400.907
1410.794
1420.993
1430.0125
1440.315
1450.781
1460.0961
1470.703
1480.157
1490.949
150.152
1500.636
1510.288
1520.279
1530.323
1540.512
1550.209
1560.335
1570.391
1580.905
1590.943
160.146
1600.743
1610.357
1620.652
1630.751
1640.361
1650.994
1660.842
1670.397
1680.856
1690.012
170.372
180.101
190.816
20.732
200.488
210.27
220.596
230.641
240.0717
250.61
260.00379
270.695
280.43
290.154
30.78
300.534
310.767
320.524
330.386
340.549
350.691
360.267
370.539
380.299
390.419
40.445
400.0787
410.151
420.528
430.787
440.473
450.537
460.657
470.279
480.488
490.773
50.636
500.359
510.809
520.532
530.829
540.713
550.825
560.481
570.428
580.523
590.551
60.295
600.362
610.105
620.916
630.131
640.496
650.895
660.138
670.354
680.115
690.116
70.049
700.909
710.293
720.634
730.193
740.945
750.137
760.819
770.0536
782.92064e-5
790.4
80.389
800.467
810.127
820.511
830.424
840.486
850.901
860.857
870.0518
880.843
890.238
90.99
900.885
910.0101
920.48
930.615
940.079
950.0847
960.388
970.713
980.488
990.403



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: CNhs11270


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

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
305 (carcinoma)
299 (adenocarcinoma)
3493 (signet ring cell adenocarcinoma)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial 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
NA

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