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|CNhs11248=
|CNhs11248=
|DRA_sample_Accession=CAGE@SAMD00005163
|DRA_sample_Accession=CAGE@SAMD00005163
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|accession_numbers=CAGE;DRX007897;DRR008769;DRZ000194;DRZ001579;DRZ011544;DRZ012929!CAGE;DRX007898;DRR008770;DRZ000195;DRZ001580;DRZ011545;DRZ012930
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|fonse_treatment_closure=
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|has_quality=
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|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/glioblastoma%2520cell%2520line%253aA172%252c%2520tech_rep2.CNhs11248.10444-106F3.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/glioblastoma%2520cell%2520line%253aA172%252c%2520tech_rep2.CNhs11248.10444-106F3.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/glioblastoma%2520cell%2520line%253aA172%252c%2520tech_rep2.CNhs11248.10444-106F3.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/glioblastoma%2520cell%2520line%253aA172%252c%2520tech_rep2.CNhs11248.10444-106F3.hg38.nobarcode.ctss.bed.gz
|id=FF:10444-106F3
|id=FF:10444-106F3
|is_a=EFO:0002091;;FF:0000210;;FF:0100016
|is_a=EFO:0002091;;FF:0000210;;FF:0100016
|is_obsolete=
|is_obsolete=
|library_id=CNhs11248
|library_id=CNhs11248!CNhs11185
|library_id_phase_based=2:CNhs11248
|library_id_phase_based=2:CNhs11248
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10444
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10444
|name=glioblastoma cell line:A172
|name=glioblastoma cell line:A172
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
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Line 92: Line 102:
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|top_motifs=HOXA9_MEIS1:2.0308510814;TFDP1:1.44560807399;ZNF384:1.36614042134;POU3F1..4:1.25559179789;GFI1:1.09541412181;EN1,2:1.07886127724;E2F1..5:0.967869148778;ADNP_IRX_SIX_ZHX:0.952054189441;PRRX1,2:0.931765634854;ZIC1..3:0.922927369268;PITX1..3:0.888587914613;XCPE1{core}:0.881394195531;NKX3-1:0.868990008005;TLX1..3_NFIC{dimer}:0.802716541321;NRF1:0.7910783973;ZNF143:0.768209080049;NR3C1:0.754449678431;FOXD3:0.751589364447;ARID5B:0.715545644575;NKX6-1,2:0.660975253586;TEAD1:0.65553060343;NFY{A,B,C}:0.650179334209;SOX2:0.609913936407;PDX1:0.609425933543;NKX2-3_NKX2-5:0.594701126518;STAT5{A,B}:0.593419573554;RXRA_VDR{dimer}:0.590701989259;ZNF238:0.568399161521;EGR1..3:0.564417093265;HBP1_HMGB_SSRP1_UBTF:0.549603889316;SOX17:0.542425314538;MZF1:0.541425590102;PAX8:0.535867777999;AIRE:0.531134701026;GTF2A1,2:0.519452463096;PAX4:0.511173887506;GTF2I:0.495718733122;ZNF148:0.489063498472;FOXP1:0.483187887044;ELK1,4_GABP{A,B1}:0.461008643907;RFX1:0.453804666063;NFE2:0.438699540418;ALX4:0.435261396517;TLX2:0.422536756978;FOXM1:0.411709208258;OCT4_SOX2{dimer}:0.409684461156;NFE2L2:0.405630186171;EBF1:0.396847707841;ONECUT1,2:0.396174585578;BACH2:0.38565888224;GFI1B:0.37001753252;EVI1:0.34819202133;TP53:0.343779734831;ZBTB6:0.333979081191;CUX2:0.332363152851;TFAP2{A,C}:0.331354913544;TAL1_TCF{3,4,12}:0.318217691099;MYBL2:0.316271498654;NR1H4:0.310933755309;PBX1:0.310745004025;TFAP2B:0.257119779175;POU2F1..3:0.246612876637;PATZ1:0.246514686035;HIC1:0.245112576757;FOS_FOS{B,L1}_JUN{B,D}:0.228858462175;HOX{A5,B5}:0.21348235133;HSF1,2:0.206959074936;LEF1_TCF7_TCF7L1,2:0.199174380805;SP1:0.192825354775;CRX:0.185901023484;RREB1:0.181220641838;NANOG:0.180211535044;STAT1,3:0.175744416685;KLF4:0.164338893035;CDC5L:0.148642986637;PRDM1:0.140617159071;PAX5:0.130611199099;NFIX:0.125199881823;IKZF1:0.120197503694;HOX{A6,A7,B6,B7}:0.11363439129;RBPJ:0.1093573636;bHLH_family:0.108706916478;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.103776825436;TEF:0.1000939963;POU5F1:0.085957420229;LHX3,4:0.0812181152581;MYB:0.0728936171304;FOXQ1:0.0677384756117;FOSL2:0.0644909283157;EP300:0.0635807305397;FOX{I1,J2}:0.0556109948412;TBX4,5:0.0496294956253;GCM1,2:0.0252935781697;YY1:0.00785358288823;GATA4:-0.0144103114764;MEF2{A,B,C,D}:-0.0150541943603;MAZ:-0.0153335901001;CDX1,2,4:-0.0170800475802;ZFP161:-0.0191598101563;FOX{F1,F2,J1}:-0.033116065773;RXR{A,B,G}:-0.0635582853244;MTE{core}:-0.0734782786996;FOXA2:-0.0847933466878;POU1F1:-0.0961003282527;MYOD1:-0.0967704082586;NKX3-2:-0.112012812012;HNF1A:-0.118257621388;BREu{core}:-0.125436066833;PAX1,9:-0.131211589904;IRF1,2:-0.132238232741;PPARG:-0.132910553981;ELF1,2,4:-0.133399763355;IRF7:-0.140218263089;IKZF2:-0.142101911517;MED-1{core}:-0.157008827783;STAT2,4,6:-0.158073854574;NFATC1..3:-0.15962008775;DBP:-0.180337332654;SMAD1..7,9:-0.182834495893;RUNX1..3:-0.192969036119;TOPORS:-0.192987222319;NR6A1:-0.193243903967;TFCP2:-0.196320218433;DMAP1_NCOR{1,2}_SMARC:-0.20864539805;SREBF1,2:-0.213257344232;HLF:-0.216669229126;SOX{8,9,10}:-0.228112327822;ZBTB16:-0.232189307755;MYFfamily:-0.246464780575;GATA6:-0.247218309394;HOX{A4,D4}:-0.251881268046;HNF4A_NR2F1,2:-0.261781049149;PAX3,7:-0.263409909553;UFEwm:-0.265190863809;RORA:-0.271571748854;SRF:-0.277683006477;NFKB1_REL_RELA:-0.278765054559;ATF2:-0.281229261349;LMO2:-0.292335370856;ETS1,2:-0.299320028685;RFX2..5_RFXANK_RFXAP:-0.303726459801;PAX6:-0.31372852823;XBP1:-0.327174131894;FOXO1,3,4:-0.349288712364;FOXN1:-0.358508783565;SNAI1..3:-0.387231895152;REST:-0.40319522783;CEBPA,B_DDIT3:-0.405816071365;CREB1:-0.413296228401;GZF1:-0.419899109939;SPIB:-0.422731285586;VSX1,2:-0.42318298893;HMGA1,2:-0.45578221579;JUN:-0.464680084453;FOXP3:-0.492596705842;TGIF1:-0.496466722919;ATF5_CREB3:-0.504491830844;ALX1:-0.52129987078;TFAP4:-0.52503641612;SPI1:-0.529304045129;NR5A1,2:-0.586895590424;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.595174465073;ESRRA:-0.596713503804;NKX2-2,8:-0.59766547025;ATF4:-0.603733081887;SOX5:-0.6154507639;NFIL3:-0.616672524116;POU6F1:-0.621474689629;FOX{D1,D2}:-0.624958182379;NFE2L1:-0.658373806944;HAND1,2:-0.660697170104;BPTF:-0.666705976034;FOXL1:-0.706653019182;T:-0.712345062373;SPZ1:-0.715503908595;AHR_ARNT_ARNT2:-0.74944265521;ZNF423:-0.749966252093;HES1:-0.758936245558;NHLH1,2:-0.759679488131;NKX2-1,4:-0.787933336538;PAX2:-0.796134735369;HMX1:-0.842171053837;ZEB1:-0.920020065438;MAFB:-0.949567198456;GLI1..3:-0.973031800126;NANOG{mouse}:-0.974287181741;ATF6:-1.00971840022;MTF1:-1.01441224337;TBP:-1.02453780208;AR:-1.17451334092;ESR1:-1.23409759281;HIF1A:-1.44653644786HOXA9_MEIS1:1.56891988048;ZNF384:1.50429374809;TFDP1:1.48315412703;POU3F1..4:1.28353871852;FOXD3:1.15739213951;GFI1:1.09682925119;ZIC1..3:1.00548160803;PRRX1,2:0.987949829276;XCPE1{core}:0.946020048246;ADNP_IRX_SIX_ZHX:0.916756218003;E2F1..5:0.912049446247;NKX2-3_NKX2-5:0.897542744393;NKX6-1,2:0.869410711027;NR3C1:0.861893142482;ZNF143:0.838769432062;EN1,2:0.833327232514;NRF1:0.817646622573;PITX1..3:0.80014656972;EVI1:0.782884243858;TLX1..3_NFIC{dimer}:0.760301678428;PAX4:0.727914137584;ARID5B:0.726601756758;STAT5{A,B}:0.724040308376;NFY{A,B,C}:0.708599381552;NKX3-1:0.704302365479;TEAD1:0.682307687602;FOXM1:0.668689159644;HBP1_HMGB_SSRP1_UBTF:0.650089253339;OCT4_SOX2{dimer}:0.554838880731;EGR1..3:0.543722264576;ALX4:0.54301582737;SOX2:0.537297085458;SOX17:0.529742096863;ELK1,4_GABP{A,B1}:0.524237296128;AIRE:0.4922945392;MZF1:0.467499332397;RFX1:0.464430303252;ZNF148:0.456877837395;GTF2I:0.439649537783;GTF2A1,2:0.433937649855;TLX2:0.430857691968;HOX{A6,A7,B6,B7}:0.423264982165;GFI1B:0.409704372625;PDX1:0.403395697911;ONECUT1,2:0.403311650471;MYBL2:0.40138079277;TEF:0.395779604734;TFAP2{A,C}:0.395212660146;TAL1_TCF{3,4,12}:0.392795959431;ZNF238:0.387396615103;NFE2:0.375837715522;HOX{A5,B5}:0.365501924496;NFIX:0.364927391797;BACH2:0.353355051367;NFE2L2:0.347210665671;FOXQ1:0.346445790501;PBX1:0.343020842105;IKZF2:0.334434171323;LHX3,4:0.300315595916;KLF4:0.294401232163;SP1:0.29234147276;GATA4:0.29126086062;EBF1:0.289518596668;TP53:0.284037939544;RBPJ:0.279940551118;HIC1:0.26694633634;RXRA_VDR{dimer}:0.256985529281;TFAP2B:0.252086297802;HSF1,2:0.241762064107;CDX1,2,4:0.224294686574;PRDM1:0.223697517975;CUX2:0.220153261232;PAX8:0.215699228713;STAT1,3:0.208315610608;FOS_FOS{B,L1}_JUN{B,D}:0.199582572243;LEF1_TCF7_TCF7L1,2:0.173709422215;FOX{F1,F2,J1}:0.172074405678;PATZ1:0.171400607961;CRX:0.156051289983;POU2F1..3:0.135119918285;ZBTB6:0.126281320493;RREB1:0.115636995867;FOXP1:0.107248936749;ZFP161:0.0962191048444;NR1H4:0.0898864719947;DBP:0.076687927317;HMGA1,2:0.0702330893517;POU5F1:0.0700515352699;PPARG:0.0644075938692;GCM1,2:0.054776104111;FOX{I1,J2}:0.0529976597621;MEF2{A,B,C,D}:0.0324850790642;MYB:0.0279756868478;FOXA2:0.0226085639019;NANOG:0.0210490830619;bHLH_family:0.0169237731466;PAX5:0.0165510444121;ZBTB16:0.00969705596414;FOSL2:0.000419134560721;CDC5L:-0.003791170842;PAX6:-0.016037677669;MAZ:-0.0291300535691;PAX3,7:-0.036916662813;IRF7:-0.0547088789851;POU1F1:-0.0573929669937;HNF1A:-0.0612811437156;MED-1{core}:-0.0621975045573;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.0654864281347;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0744799394941;MTE{core}:-0.0835281754505;YY1:-0.096011907499;IRF1,2:-0.0965854553695;NFATC1..3:-0.131682678989;RXR{A,B,G}:-0.140749958487;BREu{core}:-0.169341066623;RUNX1..3:-0.174194242764;EP300:-0.179671100097;DMAP1_NCOR{1,2}_SMARC:-0.179753538878;ELF1,2,4:-0.182568858764;PAX1,9:-0.187757660664;STAT2,4,6:-0.204777133229;NKX3-2:-0.210036102811;FOXO1,3,4:-0.217311066637;HOX{A4,D4}:-0.217843938571;BPTF:-0.218574937013;TFCP2:-0.223777731752;FOXN1:-0.224914110654;HNF4A_NR2F1,2:-0.226866237077;SMAD1..7,9:-0.228302755109;UFEwm:-0.242797136038;IKZF1:-0.243773743414;SOX{8,9,10}:-0.247985797887;HLF:-0.251087879993;GATA6:-0.252600918913;SRF:-0.267698329311;MYFfamily:-0.278950239244;LMO2:-0.28492400918;MYOD1:-0.295078764939;SREBF1,2:-0.295376442915;NFKB1_REL_RELA:-0.298840253187;VSX1,2:-0.319010117347;TBX4,5:-0.3195608387;POU6F1:-0.323295326704;RORA:-0.326324102292;T:-0.337013705788;ETS1,2:-0.341808504568;NR6A1:-0.346700623035;XBP1:-0.347971395184;SNAI1..3:-0.381954753957;CEBPA,B_DDIT3:-0.384772828434;SOX5:-0.386033407687;ATF2:-0.417313391185;TGIF1:-0.43231836085;SPIB:-0.435029987979;FOXP3:-0.445680947049;REST:-0.450385534166;FOXL1:-0.463835183603;SPI1:-0.491033514912;ATF4:-0.491639242431;GZF1:-0.504421677372;ATF5_CREB3:-0.512056098113;TOPORS:-0.523925803734;JUN:-0.539785820423;TFAP4:-0.546592761034;RFX2..5_RFXANK_RFXAP:-0.563323257556;NKX2-1,4:-0.584514308746;NFIL3:-0.587545586975;CREB1:-0.598143438596;ESRRA:-0.646185228617;ZNF423:-0.68744848675;ALX1:-0.699007194503;SPZ1:-0.699294522183;GLI1..3:-0.710422105591;PAX2:-0.713463081882;HAND1,2:-0.714351002054;NR5A1,2:-0.718276199324;NFE2L1:-0.726355184719;NHLH1,2:-0.740298406838;FOX{D1,D2}:-0.806806231106;AHR_ARNT_ARNT2:-0.807773028169;HES1:-0.843751799549;MTF1:-0.857129175993;NKX2-2,8:-0.871206911279;HMX1:-0.871478569741;ZEB1:-0.890338797116;ATF6:-1.00401389868;MAFB:-1.06034076665;TBP:-1.07851206176;AR:-1.09445392476;NANOG{mouse}:-1.10226740796;ESR1:-1.20572312277;HIF1A:-1.34887487836
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10444-106F3;search_select_hide=table117:FF:10444-106F3
}}
}}

Latest revision as of 14:02, 3 June 2020

Name:glioblastoma cell line:A172
Species:Human (Homo sapiens)
Library ID:CNhs11248,CNhs11185
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexunknown
ageunknown
cell typeglioblast
cell lineA172
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  SAMD00005163
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
CNhs11248 CAGE DRX007897 DRR008769
CNhs11185 CAGE DRX007898 DRR008770
CollapseAccession ID Hg19

Library idBAMCTSS
CNhs11248 DRZ000194 DRZ001579
CNhs11185 DRZ000195 DRZ001580
CollapseAccession ID Hg38

Library idBAMCTSS
CNhs11248 DRZ011544 DRZ012929
CNhs11185 DRZ011545 DRZ012930
Download raw sequence, BAM & CTSS
CollapseHg19
FastaBAMCTSS
downloaddownloaddonwload
CollapseHg38
BAMCTSS
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HumanCAGEScan Download raw sequence, BAM & CTSS

Library id3prime-FASTQ5prime-FASTQBAMCTSS
NCig10059downloaddownloaddownloaddownload


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: CNhs11248


library id: CNhs11185



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: CNhs11248


library id: CNhs11185



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: CNhs11248
library id: CNhs11185


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)
0002371 (somatic cell)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000125 (glial cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
3093 (nervous system cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0101530 (glioblastoma cell line sample)
0100711 (glioma cell line sample)
0100255 (brain cell line sample)
0100690 (brain cancer cell line sample)
0101531 (glial cell line sample)
0100016 (A-172 cell 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
CL:0000133 (neurectodermal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006238 (future brain)
UBERON:0010316 (germ layer / neural crest)

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