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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005256
|DRA_sample_Accession=CAGE@SAMD00005256
|accession_numbers=CAGE;DRX008025;DRR008897;DRZ000322;DRZ001707
|accession_numbers=CAGE;DRX008025;DRR008897;DRZ000322;DRZ001707;DRZ011672;DRZ013057
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000473,UBERON:0000991,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0003101,UBERON:0000079
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000473,UBERON:0000991,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0003101,UBERON:0000079
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255,CL:0000039,CL:0000586
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255,CL:0000039,CL:0000586
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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/testicular%2520germ%2520cell%2520embryonal%2520carcinoma%2520cell%2520line%253aNEC8.CNhs11726.10590-108D5.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/testicular%2520germ%2520cell%2520embryonal%2520carcinoma%2520cell%2520line%253aNEC8.CNhs11726.10590-108D5.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/testicular%2520germ%2520cell%2520embryonal%2520carcinoma%2520cell%2520line%253aNEC8.CNhs11726.10590-108D5.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/testicular%2520germ%2520cell%2520embryonal%2520carcinoma%2520cell%2520line%253aNEC8.CNhs11726.10590-108D5.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/testicular%2520germ%2520cell%2520embryonal%2520carcinoma%2520cell%2520line%253aNEC8.CNhs11726.10590-108D5.hg38.nobarcode.ctss.bed.gz
|id=FF:10590-108D5
|id=FF:10590-108D5
|is_a=CL:0000586;;DOID:3095;;EFO:0002091;;FF:0000210;;FF:0100297;;UBERON:0000473;;UBERON:0000922
|is_a=CL:0000586;;DOID:3095;;EFO:0002091;;FF:0000210;;FF:0100297;;UBERON:0000473;;UBERON:0000922
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|library_id=CNhs11726
|library_id=CNhs11726
|library_id_phase_based=2:CNhs11726
|library_id_phase_based=2:CNhs11726
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10590
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10590
|name=testicular germ cell embryonal carcinoma cell line:NEC8
|name=testicular germ cell embryonal carcinoma cell line:NEC8
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 90: Line 100:
|top_motifs=OCT4_SOX2{dimer}:3.34373330104;PITX1..3:2.71974093188;TOPORS:2.12276691599;ZNF384:1.72414536954;AIRE:1.66549826299;STAT5{A,B}:1.65868607104;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.53689595199;NFY{A,B,C}:1.45344252707;FOXM1:1.43051070941;E2F1..5:1.28392948162;MYB:1.19969720912;IKZF2:1.19962431619;NKX2-3_NKX2-5:1.17948168865;ZBTB16:1.15603420256;MYOD1:1.1296579711;FOXD3:1.12059680115;CDC5L:1.10189969198;bHLH_family:1.09722067104;CUX2:1.08905430543;SNAI1..3:1.06191743646;POU2F1..3:1.04993515461;ONECUT1,2:1.03586319445;T:1.02621416913;PBX1:0.928615613904;VSX1,2:0.884746978749;CDX1,2,4:0.870256209967;ZEB1:0.858364415601;NKX6-1,2:0.856546492406;EVI1:0.854658307467;HIF1A:0.851603208878;ALX1:0.84040328845;NRF1:0.833731497453;UFEwm:0.815284909136;STAT1,3:0.80241587672;SP1:0.790708151403;ZNF143:0.779247731491;HOX{A5,B5}:0.775887250703;NFIX:0.77364447298;TEF:0.721954115399;KLF4:0.688904551918;MTF1:0.677204638864;XCPE1{core}:0.674915118986;FOXQ1:0.661859596896;YY1:0.626230262582;GFI1:0.618043108586;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.609203720107;SOX{8,9,10}:0.599776815682;PAX8:0.497664920883;NR5A1,2:0.455116650684;PAX4:0.419812467792;FOXP1:0.398785188719;PAX1,9:0.357591598538;ESRRA:0.351644234883;ELK1,4_GABP{A,B1}:0.332942581052;POU1F1:0.301532664364;RORA:0.252185266244;FOXO1,3,4:0.227412230748;NR6A1:0.203059215776;FOXN1:0.190009022771;GZF1:0.187737284857;GATA4:0.147526406739;ZIC1..3:0.13296566337;PAX2:0.120035471926;HOX{A4,D4}:0.105071721306;NKX2-2,8:0.0835706714628;HNF4A_NR2F1,2:0.0760979166039;LEF1_TCF7_TCF7L1,2:0.0684418766736;TBP:0.0463936910375;NKX2-1,4:0.0413552825984;BPTF:0.0349345987341;ATF4:0.0347342335032;LHX3,4:0.0257808343703;ZNF148:0.00778279453425;LMO2:-0.0286354543454;RBPJ:-0.030165497496;EBF1:-0.0484414876319;GATA6:-0.0732409538182;TBX4,5:-0.0772631292856;ARID5B:-0.0869378926294;SOX17:-0.0918928861771;FOX{I1,J2}:-0.104732600002;FOX{F1,F2,J1}:-0.106735647764;HES1:-0.140286462088;SOX2:-0.157842555324;BREu{core}:-0.166129225469;TFDP1:-0.192655948045;ZFP161:-0.207804957073;NANOG:-0.209102537366;HSF1,2:-0.210187900334;PRRX1,2:-0.22198480395;IKZF1:-0.25146946973;HOX{A6,A7,B6,B7}:-0.257719495381;POU5F1:-0.264283379906;FOXA2:-0.268896094101;HNF1A:-0.304181114941;CRX:-0.31353959768;TLX2:-0.3165574065;ZBTB6:-0.378115440967;HAND1,2:-0.395435001327;RREB1:-0.399807009867;FOX{D1,D2}:-0.416451062799;REST:-0.41697105492;CREB1:-0.421161956034;EN1,2:-0.434209216779;PDX1:-0.454335052112;MYBL2:-0.459533863823;NFIL3:-0.478809620541;NFKB1_REL_RELA:-0.520478330828;RFX1:-0.53543108877;ATF5_CREB3:-0.540895939685;POU3F1..4:-0.545753222544;XBP1:-0.556927264506;AR:-0.567107095199;FOS_FOS{B,L1}_JUN{B,D}:-0.580764409333;POU6F1:-0.581016611201;TP53:-0.585287894619;PPARG:-0.585607830483;MTE{core}:-0.595808816062;PATZ1:-0.607162649629;ADNP_IRX_SIX_ZHX:-0.619131001714;BACH2:-0.620530126842;NFE2L2:-0.632883280321;ALX4:-0.651173784662;RFX2..5_RFXANK_RFXAP:-0.664928152864;AHR_ARNT_ARNT2:-0.665234005651;GFI1B:-0.682009070703;SPIB:-0.700852217493;NHLH1,2:-0.715364462583;SPI1:-0.720125940734;TEAD1:-0.720259610224;PRDM1:-0.727178001006;NKX3-1:-0.731167860935;NR3C1:-0.7332368391;MEF2{A,B,C,D}:-0.753265274969;FOXP3:-0.756727497218;MAZ:-0.761935845307;SOX5:-0.763235139549;GTF2I:-0.778648417839;MYFfamily:-0.781058756544;SREBF1,2:-0.791626273918;NFE2:-0.803088781546;PAX6:-0.804417357978;DMAP1_NCOR{1,2}_SMARC:-0.821070216806;MZF1:-0.836544780923;FOSL2:-0.83725720594;CEBPA,B_DDIT3:-0.860930909759;GCM1,2:-0.861740411183;NR1H4:-0.862902491465;HLF:-0.863446543095;SPZ1:-0.864100434171;ETS1,2:-0.864327361398;HBP1_HMGB_SSRP1_UBTF:-0.868537317526;PAX5:-0.876474150282;MED-1{core}:-0.883036881798;HMGA1,2:-0.887360677087;RUNX1..3:-0.888873792798;NKX3-2:-0.889972780999;FOXL1:-0.924128544031;ELF1,2,4:-0.987359601618;PAX3,7:-0.993272965012;RXR{A,B,G}:-1.02244975839;HMX1:-1.05385069626;NANOG{mouse}:-1.06009363047;HOXA9_MEIS1:-1.09316730767;IRF7:-1.11528582482;DBP:-1.12796060234;ZNF423:-1.13688058857;TFAP2B:-1.13827939321;ATF2:-1.15029059396;TFAP4:-1.19113051625;TGIF1:-1.21420370993;EGR1..3:-1.22198842648;NFE2L1:-1.23650471237;HIC1:-1.24700417336;JUN:-1.27974737876;TFCP2:-1.28426065345;TFAP2{A,C}:-1.35124078617;RXRA_VDR{dimer}:-1.36255621329;ZNF238:-1.37295128746;IRF1,2:-1.39802352708;TAL1_TCF{3,4,12}:-1.43226647016;STAT2,4,6:-1.48555639368;SRF:-1.4856624192;TLX1..3_NFIC{dimer}:-1.49709841797;GTF2A1,2:-1.62721346935;SMAD1..7,9:-1.63358182798;EP300:-1.67891929892;ATF6:-1.71860589245;NFATC1..3:-1.75190471818;ESR1:-1.89055572381;GLI1..3:-1.91183863978;MAFB:-2.17911623334
|top_motifs=OCT4_SOX2{dimer}:3.34373330104;PITX1..3:2.71974093188;TOPORS:2.12276691599;ZNF384:1.72414536954;AIRE:1.66549826299;STAT5{A,B}:1.65868607104;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.53689595199;NFY{A,B,C}:1.45344252707;FOXM1:1.43051070941;E2F1..5:1.28392948162;MYB:1.19969720912;IKZF2:1.19962431619;NKX2-3_NKX2-5:1.17948168865;ZBTB16:1.15603420256;MYOD1:1.1296579711;FOXD3:1.12059680115;CDC5L:1.10189969198;bHLH_family:1.09722067104;CUX2:1.08905430543;SNAI1..3:1.06191743646;POU2F1..3:1.04993515461;ONECUT1,2:1.03586319445;T:1.02621416913;PBX1:0.928615613904;VSX1,2:0.884746978749;CDX1,2,4:0.870256209967;ZEB1:0.858364415601;NKX6-1,2:0.856546492406;EVI1:0.854658307467;HIF1A:0.851603208878;ALX1:0.84040328845;NRF1:0.833731497453;UFEwm:0.815284909136;STAT1,3:0.80241587672;SP1:0.790708151403;ZNF143:0.779247731491;HOX{A5,B5}:0.775887250703;NFIX:0.77364447298;TEF:0.721954115399;KLF4:0.688904551918;MTF1:0.677204638864;XCPE1{core}:0.674915118986;FOXQ1:0.661859596896;YY1:0.626230262582;GFI1:0.618043108586;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.609203720107;SOX{8,9,10}:0.599776815682;PAX8:0.497664920883;NR5A1,2:0.455116650684;PAX4:0.419812467792;FOXP1:0.398785188719;PAX1,9:0.357591598538;ESRRA:0.351644234883;ELK1,4_GABP{A,B1}:0.332942581052;POU1F1:0.301532664364;RORA:0.252185266244;FOXO1,3,4:0.227412230748;NR6A1:0.203059215776;FOXN1:0.190009022771;GZF1:0.187737284857;GATA4:0.147526406739;ZIC1..3:0.13296566337;PAX2:0.120035471926;HOX{A4,D4}:0.105071721306;NKX2-2,8:0.0835706714628;HNF4A_NR2F1,2:0.0760979166039;LEF1_TCF7_TCF7L1,2:0.0684418766736;TBP:0.0463936910375;NKX2-1,4:0.0413552825984;BPTF:0.0349345987341;ATF4:0.0347342335032;LHX3,4:0.0257808343703;ZNF148:0.00778279453425;LMO2:-0.0286354543454;RBPJ:-0.030165497496;EBF1:-0.0484414876319;GATA6:-0.0732409538182;TBX4,5:-0.0772631292856;ARID5B:-0.0869378926294;SOX17:-0.0918928861771;FOX{I1,J2}:-0.104732600002;FOX{F1,F2,J1}:-0.106735647764;HES1:-0.140286462088;SOX2:-0.157842555324;BREu{core}:-0.166129225469;TFDP1:-0.192655948045;ZFP161:-0.207804957073;NANOG:-0.209102537366;HSF1,2:-0.210187900334;PRRX1,2:-0.22198480395;IKZF1:-0.25146946973;HOX{A6,A7,B6,B7}:-0.257719495381;POU5F1:-0.264283379906;FOXA2:-0.268896094101;HNF1A:-0.304181114941;CRX:-0.31353959768;TLX2:-0.3165574065;ZBTB6:-0.378115440967;HAND1,2:-0.395435001327;RREB1:-0.399807009867;FOX{D1,D2}:-0.416451062799;REST:-0.41697105492;CREB1:-0.421161956034;EN1,2:-0.434209216779;PDX1:-0.454335052112;MYBL2:-0.459533863823;NFIL3:-0.478809620541;NFKB1_REL_RELA:-0.520478330828;RFX1:-0.53543108877;ATF5_CREB3:-0.540895939685;POU3F1..4:-0.545753222544;XBP1:-0.556927264506;AR:-0.567107095199;FOS_FOS{B,L1}_JUN{B,D}:-0.580764409333;POU6F1:-0.581016611201;TP53:-0.585287894619;PPARG:-0.585607830483;MTE{core}:-0.595808816062;PATZ1:-0.607162649629;ADNP_IRX_SIX_ZHX:-0.619131001714;BACH2:-0.620530126842;NFE2L2:-0.632883280321;ALX4:-0.651173784662;RFX2..5_RFXANK_RFXAP:-0.664928152864;AHR_ARNT_ARNT2:-0.665234005651;GFI1B:-0.682009070703;SPIB:-0.700852217493;NHLH1,2:-0.715364462583;SPI1:-0.720125940734;TEAD1:-0.720259610224;PRDM1:-0.727178001006;NKX3-1:-0.731167860935;NR3C1:-0.7332368391;MEF2{A,B,C,D}:-0.753265274969;FOXP3:-0.756727497218;MAZ:-0.761935845307;SOX5:-0.763235139549;GTF2I:-0.778648417839;MYFfamily:-0.781058756544;SREBF1,2:-0.791626273918;NFE2:-0.803088781546;PAX6:-0.804417357978;DMAP1_NCOR{1,2}_SMARC:-0.821070216806;MZF1:-0.836544780923;FOSL2:-0.83725720594;CEBPA,B_DDIT3:-0.860930909759;GCM1,2:-0.861740411183;NR1H4:-0.862902491465;HLF:-0.863446543095;SPZ1:-0.864100434171;ETS1,2:-0.864327361398;HBP1_HMGB_SSRP1_UBTF:-0.868537317526;PAX5:-0.876474150282;MED-1{core}:-0.883036881798;HMGA1,2:-0.887360677087;RUNX1..3:-0.888873792798;NKX3-2:-0.889972780999;FOXL1:-0.924128544031;ELF1,2,4:-0.987359601618;PAX3,7:-0.993272965012;RXR{A,B,G}:-1.02244975839;HMX1:-1.05385069626;NANOG{mouse}:-1.06009363047;HOXA9_MEIS1:-1.09316730767;IRF7:-1.11528582482;DBP:-1.12796060234;ZNF423:-1.13688058857;TFAP2B:-1.13827939321;ATF2:-1.15029059396;TFAP4:-1.19113051625;TGIF1:-1.21420370993;EGR1..3:-1.22198842648;NFE2L1:-1.23650471237;HIC1:-1.24700417336;JUN:-1.27974737876;TFCP2:-1.28426065345;TFAP2{A,C}:-1.35124078617;RXRA_VDR{dimer}:-1.36255621329;ZNF238:-1.37295128746;IRF1,2:-1.39802352708;TAL1_TCF{3,4,12}:-1.43226647016;STAT2,4,6:-1.48555639368;SRF:-1.4856624192;TLX1..3_NFIC{dimer}:-1.49709841797;GTF2A1,2:-1.62721346935;SMAD1..7,9:-1.63358182798;EP300:-1.67891929892;ATF6:-1.71860589245;NFATC1..3:-1.75190471818;ESR1:-1.89055572381;GLI1..3:-1.91183863978;MAFB:-2.17911623334
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10590-108D5;search_select_hide=table117:FF:10590-108D5
}}
}}

Latest revision as of 14:30, 3 June 2020

Name:testicular germ cell embryonal carcinoma cell line:NEC8
Species:Human (Homo sapiens)
Library ID:CNhs11726
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuetestis
dev stageNA
sexmale
age24
cell typeunclassifiable
cell lineNEC8
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  SAMD00005256
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11726 CAGE DRX008025 DRR008897
Accession ID Hg19

Library idBAMCTSS
CNhs11726 DRZ000322 DRZ001707
Accession ID Hg38

Library idBAMCTSS
CNhs11726 DRZ011672 DRZ013057
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



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: CNhs11726



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: CNhs11726



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: CNhs11726


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)
0000039 (germ line cell)
0000586 (germ cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
3095 (germ cell and embryonal cancer)
305 (carcinoma)
2994 (germ cell cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000473 (testis)
0000991 (gonad)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)

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
UBERON:0009117 (indifferent gonad)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)

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