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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005439
|DRA_sample_Accession=CAGE@SAMD00005439
|accession_numbers=CAGE;DRX008045;DRR008917;DRZ000342;DRZ001727
|accession_numbers=CAGE;DRX008045;DRR008917;DRZ000342;DRZ001727;DRZ011692;DRZ013077
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000766,CL:0000081,CL:0000219,CL:0000738,CL:0000255,CL:0000094,CL:0000767
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000766,CL:0000081,CL:0000219,CL:0000738,CL:0000255,CL:0000094,CL:0000767
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|library_id=CNhs12546
|library_id=CNhs12546
|library_id_phase_based=2:CNhs12546
|library_id_phase_based=2:CNhs12546
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;12241
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;12241
|name=Basophils, donor1
|name=Basophils, donor1
|namespace=FANTOM5
|namespace=FANTOM5
Line 59: Line 63:
|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|refex=http://refex.dbcls.jp/genelist.php?lang=en&db=human&roku_valid=1&rk[]=&order_key=score
|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 97: Line 101:
|top_motifs=RUNX1..3:4.21575783649;ATF5_CREB3:3.69779579453;ETS1,2:3.65670332379;PAX2:3.61852322847;RORA:3.53943921668;SPIB:3.42978654309;NFKB1_REL_RELA:3.32387274331;CREB1:3.23673041271;NFIL3:3.23431794048;SPI1:3.2233103805;ATF4:3.13273070231;NFE2:3.08465508529;BACH2:3.06675242243;FOS_FOS{B,L1}_JUN{B,D}:2.86947807506;FOSL2:2.81454758208;EP300:2.80605574832;JUN:2.74497339738;FOX{F1,F2,J1}:2.69861036724;NANOG{mouse}:2.66378065212;NFE2L2:2.61236583708;ELF1,2,4:2.5047842114;RFX2..5_RFXANK_RFXAP:2.47060872985;FOX{D1,D2}:2.38601850077;CEBPA,B_DDIT3:2.36270839118;FOXO1,3,4:2.28351673006;HLF:2.26383202635;DMAP1_NCOR{1,2}_SMARC:2.23588721291;TGIF1:2.21914752344;FOXN1:2.16368898353;RFX1:2.09917611368;NFE2L1:1.89027283944;HMX1:1.86134851992;ATF6:1.6882144969;IRF1,2:1.6051585742;STAT2,4,6:1.58701527035;NFATC1..3:1.49739081121;BPTF:1.47897772528;SREBF1,2:1.45848823597;T:1.42352079;MAFB:1.39436833614;IRF7:1.3132189873;PAX3,7:1.2972273935;ATF2:1.24221185095;PPARG:1.14062657491;XBP1:1.01401168859;NKX2-1,4:0.983954111264;RXRA_VDR{dimer}:0.969602375297;FOXP3:0.891801889218;HBP1_HMGB_SSRP1_UBTF:0.88854976699;HIF1A:0.866172872035;TBX4,5:0.820196413646;SMAD1..7,9:0.742873460369;FOX{I1,J2}:0.736844345354;TLX2:0.733636248265;GLI1..3:0.707543457167;GATA6:0.679921784536;RBPJ:0.673413613135;HMGA1,2:0.662972341951;NANOG:0.620461213958;ESRRA:0.511785229587;HES1:0.411223846676;TFAP4:0.30163276289;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.27027724736;SRF:0.219936805208;MYB:0.189171460922;STAT5{A,B}:0.180612507564;TFCP2:0.134327159138;SOX2:0.128457781853;NR5A1,2:0.109386415455;BREu{core}:0.0711522688619;MEF2{A,B,C,D}:-0.00719524904109;ESR1:-0.0375248167593;PAX8:-0.0574841803767;EN1,2:-0.073587608417;DBP:-0.103838766024;NR1H4:-0.131776315182;HSF1,2:-0.134462418884;PDX1:-0.137109332718;HOX{A5,B5}:-0.153404368318;POU5F1:-0.178542263805;FOXA2:-0.22766449854;TBP:-0.25649020656;AHR_ARNT_ARNT2:-0.308539711621;MYFfamily:-0.34104911476;PAX6:-0.381570305853;EGR1..3:-0.388946176302;ALX4:-0.39801663325;ZNF148:-0.410733738371;NHLH1,2:-0.434928721703;POU2F1..3:-0.443701877982;GATA4:-0.486839463553;HOXA9_MEIS1:-0.489573266033;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.511497543804;ZNF238:-0.523570749281;TAL1_TCF{3,4,12}:-0.527808328056;NFIX:-0.577625554633;STAT1,3:-0.606355615702;PBX1:-0.612724871877;PATZ1:-0.61543031389;RXR{A,B,G}:-0.621062863875;CRX:-0.656952940324;VSX1,2:-0.662917090018;NFY{A,B,C}:-0.686176767883;MTE{core}:-0.721400109318;OCT4_SOX2{dimer}:-0.725289067037;MYOD1:-0.733211299058;LEF1_TCF7_TCF7L1,2:-0.736360986303;ELK1,4_GABP{A,B1}:-0.748697685529;PAX4:-0.770500442491;SPZ1:-0.797998448566;NR6A1:-0.81830211335;HNF4A_NR2F1,2:-0.832910867432;PAX5:-0.858677607487;MZF1:-0.868271499583;SP1:-0.909001904443;SOX5:-0.935907484808;FOXL1:-0.950459335898;ZEB1:-0.968528843233;PRRX1,2:-0.979977372009;TFAP2{A,C}:-0.981520875432;TFAP2B:-1.04359717013;SOX{8,9,10}:-1.04646541021;HNF1A:-1.0783660168;MED-1{core}:-1.08570679811;E2F1..5:-1.11846299555;TFDP1:-1.12596802842;REST:-1.14193710794;GCM1,2:-1.1566216709;IKZF1:-1.15971679684;ZFP161:-1.16827515115;SNAI1..3:-1.19110611437;RREB1:-1.21386551408;CDX1,2,4:-1.24634746803;PRDM1:-1.25953113324;MAZ:-1.29872663412;MTF1:-1.31818290064;EBF1:-1.32150076899;ZNF423:-1.34994250641;FOXD3:-1.38168884591;NR3C1:-1.38321574103;GZF1:-1.39040120629;IKZF2:-1.40103701661;HOX{A6,A7,B6,B7}:-1.43535826627;TP53:-1.45296038717;AR:-1.47023288814;FOXP1:-1.48248095731;LMO2:-1.52159650383;FOXM1:-1.53123860738;ZIC1..3:-1.54264709093;ZBTB6:-1.55543282261;GTF2I:-1.59418974775;TLX1..3_NFIC{dimer}:-1.60748834712;ZNF384:-1.62478623668;CUX2:-1.67203470095;XCPE1{core}:-1.68135066271;GTF2A1,2:-1.73447295122;PAX1,9:-1.73811066265;MYBL2:-1.74989044641;POU6F1:-1.76720703836;NKX2-2,8:-1.77785706088;HIC1:-1.78004303523;bHLH_family:-1.833615313;NKX2-3_NKX2-5:-1.85609861311;NKX3-1:-1.86686353938;TEAD1:-1.94911984373;KLF4:-1.9537093637;GFI1:-2.03863269678;FOXQ1:-2.0410707151;LHX3,4:-2.05432271145;ADNP_IRX_SIX_ZHX:-2.07519816418;HAND1,2:-2.20053751181;NRF1:-2.25522984359;PITX1..3:-2.30283429918;ZBTB16:-2.36000581482;GFI1B:-2.36009960536;POU1F1:-2.38906063519;ALX1:-2.40432990845;SOX17:-2.42560195282;NKX6-1,2:-2.42906304529;YY1:-2.4968046654;ZNF143:-2.56385147039;EVI1:-2.57491664199;CDC5L:-2.80297619677;NKX3-2:-2.87453752984;UFEwm:-2.8962959827;TOPORS:-2.93971331238;ARID5B:-2.95935256034;HOX{A4,D4}:-3.08809249976;AIRE:-3.15105574058;ONECUT1,2:-3.15462478093;TEF:-3.29397763921;POU3F1..4:-3.79328052392
|top_motifs=RUNX1..3:4.21575783649;ATF5_CREB3:3.69779579453;ETS1,2:3.65670332379;PAX2:3.61852322847;RORA:3.53943921668;SPIB:3.42978654309;NFKB1_REL_RELA:3.32387274331;CREB1:3.23673041271;NFIL3:3.23431794048;SPI1:3.2233103805;ATF4:3.13273070231;NFE2:3.08465508529;BACH2:3.06675242243;FOS_FOS{B,L1}_JUN{B,D}:2.86947807506;FOSL2:2.81454758208;EP300:2.80605574832;JUN:2.74497339738;FOX{F1,F2,J1}:2.69861036724;NANOG{mouse}:2.66378065212;NFE2L2:2.61236583708;ELF1,2,4:2.5047842114;RFX2..5_RFXANK_RFXAP:2.47060872985;FOX{D1,D2}:2.38601850077;CEBPA,B_DDIT3:2.36270839118;FOXO1,3,4:2.28351673006;HLF:2.26383202635;DMAP1_NCOR{1,2}_SMARC:2.23588721291;TGIF1:2.21914752344;FOXN1:2.16368898353;RFX1:2.09917611368;NFE2L1:1.89027283944;HMX1:1.86134851992;ATF6:1.6882144969;IRF1,2:1.6051585742;STAT2,4,6:1.58701527035;NFATC1..3:1.49739081121;BPTF:1.47897772528;SREBF1,2:1.45848823597;T:1.42352079;MAFB:1.39436833614;IRF7:1.3132189873;PAX3,7:1.2972273935;ATF2:1.24221185095;PPARG:1.14062657491;XBP1:1.01401168859;NKX2-1,4:0.983954111264;RXRA_VDR{dimer}:0.969602375297;FOXP3:0.891801889218;HBP1_HMGB_SSRP1_UBTF:0.88854976699;HIF1A:0.866172872035;TBX4,5:0.820196413646;SMAD1..7,9:0.742873460369;FOX{I1,J2}:0.736844345354;TLX2:0.733636248265;GLI1..3:0.707543457167;GATA6:0.679921784536;RBPJ:0.673413613135;HMGA1,2:0.662972341951;NANOG:0.620461213958;ESRRA:0.511785229587;HES1:0.411223846676;TFAP4:0.30163276289;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.27027724736;SRF:0.219936805208;MYB:0.189171460922;STAT5{A,B}:0.180612507564;TFCP2:0.134327159138;SOX2:0.128457781853;NR5A1,2:0.109386415455;BREu{core}:0.0711522688619;MEF2{A,B,C,D}:-0.00719524904109;ESR1:-0.0375248167593;PAX8:-0.0574841803767;EN1,2:-0.073587608417;DBP:-0.103838766024;NR1H4:-0.131776315182;HSF1,2:-0.134462418884;PDX1:-0.137109332718;HOX{A5,B5}:-0.153404368318;POU5F1:-0.178542263805;FOXA2:-0.22766449854;TBP:-0.25649020656;AHR_ARNT_ARNT2:-0.308539711621;MYFfamily:-0.34104911476;PAX6:-0.381570305853;EGR1..3:-0.388946176302;ALX4:-0.39801663325;ZNF148:-0.410733738371;NHLH1,2:-0.434928721703;POU2F1..3:-0.443701877982;GATA4:-0.486839463553;HOXA9_MEIS1:-0.489573266033;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.511497543804;ZNF238:-0.523570749281;TAL1_TCF{3,4,12}:-0.527808328056;NFIX:-0.577625554633;STAT1,3:-0.606355615702;PBX1:-0.612724871877;PATZ1:-0.61543031389;RXR{A,B,G}:-0.621062863875;CRX:-0.656952940324;VSX1,2:-0.662917090018;NFY{A,B,C}:-0.686176767883;MTE{core}:-0.721400109318;OCT4_SOX2{dimer}:-0.725289067037;MYOD1:-0.733211299058;LEF1_TCF7_TCF7L1,2:-0.736360986303;ELK1,4_GABP{A,B1}:-0.748697685529;PAX4:-0.770500442491;SPZ1:-0.797998448566;NR6A1:-0.81830211335;HNF4A_NR2F1,2:-0.832910867432;PAX5:-0.858677607487;MZF1:-0.868271499583;SP1:-0.909001904443;SOX5:-0.935907484808;FOXL1:-0.950459335898;ZEB1:-0.968528843233;PRRX1,2:-0.979977372009;TFAP2{A,C}:-0.981520875432;TFAP2B:-1.04359717013;SOX{8,9,10}:-1.04646541021;HNF1A:-1.0783660168;MED-1{core}:-1.08570679811;E2F1..5:-1.11846299555;TFDP1:-1.12596802842;REST:-1.14193710794;GCM1,2:-1.1566216709;IKZF1:-1.15971679684;ZFP161:-1.16827515115;SNAI1..3:-1.19110611437;RREB1:-1.21386551408;CDX1,2,4:-1.24634746803;PRDM1:-1.25953113324;MAZ:-1.29872663412;MTF1:-1.31818290064;EBF1:-1.32150076899;ZNF423:-1.34994250641;FOXD3:-1.38168884591;NR3C1:-1.38321574103;GZF1:-1.39040120629;IKZF2:-1.40103701661;HOX{A6,A7,B6,B7}:-1.43535826627;TP53:-1.45296038717;AR:-1.47023288814;FOXP1:-1.48248095731;LMO2:-1.52159650383;FOXM1:-1.53123860738;ZIC1..3:-1.54264709093;ZBTB6:-1.55543282261;GTF2I:-1.59418974775;TLX1..3_NFIC{dimer}:-1.60748834712;ZNF384:-1.62478623668;CUX2:-1.67203470095;XCPE1{core}:-1.68135066271;GTF2A1,2:-1.73447295122;PAX1,9:-1.73811066265;MYBL2:-1.74989044641;POU6F1:-1.76720703836;NKX2-2,8:-1.77785706088;HIC1:-1.78004303523;bHLH_family:-1.833615313;NKX2-3_NKX2-5:-1.85609861311;NKX3-1:-1.86686353938;TEAD1:-1.94911984373;KLF4:-1.9537093637;GFI1:-2.03863269678;FOXQ1:-2.0410707151;LHX3,4:-2.05432271145;ADNP_IRX_SIX_ZHX:-2.07519816418;HAND1,2:-2.20053751181;NRF1:-2.25522984359;PITX1..3:-2.30283429918;ZBTB16:-2.36000581482;GFI1B:-2.36009960536;POU1F1:-2.38906063519;ALX1:-2.40432990845;SOX17:-2.42560195282;NKX6-1,2:-2.42906304529;YY1:-2.4968046654;ZNF143:-2.56385147039;EVI1:-2.57491664199;CDC5L:-2.80297619677;NKX3-2:-2.87453752984;UFEwm:-2.8962959827;TOPORS:-2.93971331238;ARID5B:-2.95935256034;HOX{A4,D4}:-3.08809249976;AIRE:-3.15105574058;ONECUT1,2:-3.15462478093;TEF:-3.29397763921;POU3F1..4:-3.79328052392
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:12241-129G9;search_select_hide=table117:FF:12241-129G9
}}
}}

Latest revision as of 18:36, 4 June 2020

Name:Basophils, donor1
Species:Human (Homo sapiens)
Library ID:CNhs12546
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexNA
ageNA
cell typebasophil
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog number3H100-93-5
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005439
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12546 CAGE DRX008045 DRR008917
Accession ID Hg19

Library idBAMCTSS
CNhs12546 DRZ000342 DRZ001727
Accession ID Hg38

Library idBAMCTSS
CNhs12546 DRZ011692 DRZ013077
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
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Hg38
BAMCTSS
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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: CNhs12546



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: CNhs12546



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: CNhs12546


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000766 (myeloid leukocyte)
0000081 (blood cell)
0000219 (motile cell)
0000738 (leukocyte)
0000255 (eukaryotic cell)
0000094 (granulocyte)
0000767 (basophil)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000013 (human basophil sample)
0000212 (human basophil heparinase treated 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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

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