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{{f5samples
{{f5samples
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|DRA_sample_Accession=CAGE@SAMD00005100
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|DRA_sample_Accession_RNASeq=RNA-Seq@SAMD00005100
|accession_numbers=CAGE;DRX008612;DRR009484;DRZ000909;DRZ002294;DRZ012259;DRZ013644
|accession_numbers_RNASeq=RNA-Seq;DRX057113;DRR062872;DRZ007948
|ancestors_in_anatomy_facet=UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=PATO:0000461
|has_quality=PATO:0000461
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|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/Universal%2520RNA%2520-%2520Human%2520Normal%2520Tissues%2520Biochain%252c%2520pool1.CNhs10612.10007-101B4.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/Universal%2520RNA%2520-%2520Human%2520Normal%2520Tissues%2520Biochain%252c%2520pool1.CNhs10612.10007-101B4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/Universal%2520RNA%2520-%2520Human%2520Normal%2520Tissues%2520Biochain%252c%2520pool1.CNhs10612.10007-101B4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/Universal%2520RNA%2520-%2520Human%2520Normal%2520Tissues%2520Biochain%252c%2520pool1.CNhs10612.10007-101B4.hg38.nobarcode.ctss.bed.gz
|id=FF:10007-101B4
|id=FF:10007-101B4
|is_a=FF:0000004;;FF:0000210
|is_a=FF:0000004;;FF:0000210
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|profile_rnaseq=
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|sample_category=tissues
Line 89: Line 98:
|top_motifs=HNF1A:6.206199919;HNF4A_NR2F1,2:6.20414706435;FOXA2:6.09055763221;RXR{A,B,G}_{NR1H2,PPAR}dimers:4.35633151755;FOX{F1,F2,J1}:3.92843373765;FOX{D1,D2}:3.31977493404;TBP:2.89587116945;STAT2,4,6:2.87827830829;NR6A1:2.61104828927;TFCP2:2.45213118036;AR:2.31726307156;FOXO1,3,4:2.30952220375;SP1:2.08228595159;HSF1,2:1.91479228087;FOX{I1,J2}:1.89653633008;MAZ:1.83486176725;TLX2:1.82864674351;EP300:1.77787295441;FOXQ1:1.67353246764;STAT1,3:1.53278318751;GATA6:1.43951661992;FOXD3:1.43442841718;HLF:1.41604847349;NKX3-2:1.41271324262;CUX2:1.4039393904;NFIL3:1.39795530052;TLX1..3_NFIC{dimer}:1.35438639345;PATZ1:1.28703090068;NR1H4:1.27902794072;HBP1_HMGB_SSRP1_UBTF:1.25711434342;BPTF:1.24237848461;NFATC1..3:1.22265944215;PPARG:1.20702472458;SNAI1..3:1.0773037029;MTF1:1.04945185303;ZNF423:1.03536070744;MED-1{core}:0.988707861868;ALX1:0.957048373755;SMAD1..7,9:0.934346920931;EVI1:0.906763236032;ZNF238:0.863563373772;HIC1:0.858758831155;XCPE1{core}:0.853095972767;MYOD1:0.837425696878;GFI1:0.813268949406;GZF1:0.786969665886;SREBF1,2:0.786290211119;PDX1:0.773449202459;ZEB1:0.765577123413;CEBPA,B_DDIT3:0.76471422366;GCM1,2:0.759952986442;IRF1,2:0.740328441745;TFAP2{A,C}:0.733259510289;ARID5B:0.73091190123;MYFfamily:0.720860149478;PAX6:0.714993384575;GTF2I:0.714504826258;IRF7:0.678451417334;PAX1,9:0.660722543802;SRF:0.652868230022;POU6F1:0.641749554664;TEAD1:0.615508179387;MTE{core}:0.61202400919;FOXP1:0.603932403409;TGIF1:0.587791554759;NFIX:0.566816024819;SOX5:0.563637087417;HMX1:0.537081120459;MAFB:0.467063429194;T:0.449396551819;ZNF148:0.419660648291;ATF6:0.418274235227;MYBL2:0.400351947632;TBX4,5:0.397654909358;RORA:0.389154344991;MZF1:0.38705883469;PAX5:0.386491832248;ESR1:0.370608804687;TOPORS:0.365400469527;ETS1,2:0.357764980915;ALX4:0.354933036861;IKZF1:0.336027063115;HOX{A6,A7,B6,B7}:0.320313825518;HOX{A4,D4}:0.273941124386;ADNP_IRX_SIX_ZHX:0.2649859136;FOXL1:0.259963663055;EBF1:0.249028878465;TFAP2B:0.247043101152;FOXP3:0.203244731384;TEF:0.183686526702;bHLH_family:0.180085785131;EGR1..3:0.164195277389;HAND1,2:0.157033888507;MEF2{A,B,C,D}:0.126204990714;ATF4:0.11594248023;FOXN1:0.110766831121;ZFP161:0.101107044412;EN1,2:0.0886744767314;GTF2A1,2:0.0804300936;TFAP4:0.0746772377719;ELF1,2,4:0.0741548056865;AIRE:0.0704529418348;NHLH1,2:0.0527800548926;RXR{A,B,G}:0.036974080387;FOXM1:0.0258613633751;GATA4:0.0121308602252;NR3C1:-0.00237916384674;POU2F1..3:-0.00319272630666;SPIB:-0.00562848295484;NFY{A,B,C}:-0.0241075085574;SPI1:-0.0295490333298;KLF4:-0.0386502765359;RREB1:-0.108979918157;SOX{8,9,10}:-0.114170599186;ATF2:-0.120223670554;VSX1,2:-0.134147627267;PRDM1:-0.139268390248;GFI1B:-0.166329088665;RBPJ:-0.186650661685;TAL1_TCF{3,4,12}:-0.207063360606;NANOG:-0.20884945012;LMO2:-0.212565232543;JUN:-0.220465112658;ZNF143:-0.240689494746;DMAP1_NCOR{1,2}_SMARC:-0.268287619058;DBP:-0.271049275012;NKX2-1,4:-0.307791406649;PBX1:-0.33699967835;ATF5_CREB3:-0.35386566571;NR5A1,2:-0.371412102262;TP53:-0.383265872571;SOX17:-0.394668248073;BREu{core}:-0.408894448624;PAX2:-0.429200003724;HES1:-0.440378806577;NFKB1_REL_RELA:-0.453145130536;HIF1A:-0.453505288386;NFE2L1:-0.469267219831;HMGA1,2:-0.485529427236;FOSL2:-0.501441981741;NRF1:-0.55732963045;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.565514630622;NFE2:-0.567524092563;IKZF2:-0.588580771301;ZIC1..3:-0.594505927595;RFX2..5_RFXANK_RFXAP:-0.605351774529;RXRA_VDR{dimer}:-0.61303782;ZBTB6:-0.644140656795;NFE2L2:-0.650262328207;RUNX1..3:-0.653924103954;UFEwm:-0.654297161754;REST:-0.666729927539;GLI1..3:-0.675581107531;LEF1_TCF7_TCF7L1,2:-0.680683621385;NANOG{mouse}:-0.685888079713;PRRX1,2:-0.739556405263;ZBTB16:-0.7694461573;RFX1:-0.777074167959;CDX1,2,4:-0.78770350635;HOX{A5,B5}:-0.818418359339;NKX2-2,8:-0.833083957806;FOS_FOS{B,L1}_JUN{B,D}:-0.835495367258;PITX1..3:-0.841651365648;SOX2:-0.842945494551;BACH2:-0.852960582369;ONECUT1,2:-0.865727443749;STAT5{A,B}:-0.898268802591;E2F1..5:-0.91784998529;AHR_ARNT_ARNT2:-0.922848577976;ESRRA:-0.985959105922;NKX2-3_NKX2-5:-1.00672063752;PAX4:-1.0098110346;CREB1:-1.02682169279;POU5F1:-1.10472620162;CDC5L:-1.11791076657;SPZ1:-1.13208459503;POU3F1..4:-1.14044767061;POU1F1:-1.20402043777;YY1:-1.22185149467;NKX3-1:-1.25683040956;MYB:-1.27317126127;XBP1:-1.30337681307;ZNF384:-1.33307324111;OCT4_SOX2{dimer}:-1.37195057208;TFDP1:-1.48652634875;PAX3,7:-1.50219543023;ELK1,4_GABP{A,B1}:-1.50296636772;CRX:-1.51430897529;HOXA9_MEIS1:-1.52906194524;LHX3,4:-1.66771450253;NKX6-1,2:-1.90951898978;PAX8:-2.35737439259
|top_motifs=HNF1A:6.206199919;HNF4A_NR2F1,2:6.20414706435;FOXA2:6.09055763221;RXR{A,B,G}_{NR1H2,PPAR}dimers:4.35633151755;FOX{F1,F2,J1}:3.92843373765;FOX{D1,D2}:3.31977493404;TBP:2.89587116945;STAT2,4,6:2.87827830829;NR6A1:2.61104828927;TFCP2:2.45213118036;AR:2.31726307156;FOXO1,3,4:2.30952220375;SP1:2.08228595159;HSF1,2:1.91479228087;FOX{I1,J2}:1.89653633008;MAZ:1.83486176725;TLX2:1.82864674351;EP300:1.77787295441;FOXQ1:1.67353246764;STAT1,3:1.53278318751;GATA6:1.43951661992;FOXD3:1.43442841718;HLF:1.41604847349;NKX3-2:1.41271324262;CUX2:1.4039393904;NFIL3:1.39795530052;TLX1..3_NFIC{dimer}:1.35438639345;PATZ1:1.28703090068;NR1H4:1.27902794072;HBP1_HMGB_SSRP1_UBTF:1.25711434342;BPTF:1.24237848461;NFATC1..3:1.22265944215;PPARG:1.20702472458;SNAI1..3:1.0773037029;MTF1:1.04945185303;ZNF423:1.03536070744;MED-1{core}:0.988707861868;ALX1:0.957048373755;SMAD1..7,9:0.934346920931;EVI1:0.906763236032;ZNF238:0.863563373772;HIC1:0.858758831155;XCPE1{core}:0.853095972767;MYOD1:0.837425696878;GFI1:0.813268949406;GZF1:0.786969665886;SREBF1,2:0.786290211119;PDX1:0.773449202459;ZEB1:0.765577123413;CEBPA,B_DDIT3:0.76471422366;GCM1,2:0.759952986442;IRF1,2:0.740328441745;TFAP2{A,C}:0.733259510289;ARID5B:0.73091190123;MYFfamily:0.720860149478;PAX6:0.714993384575;GTF2I:0.714504826258;IRF7:0.678451417334;PAX1,9:0.660722543802;SRF:0.652868230022;POU6F1:0.641749554664;TEAD1:0.615508179387;MTE{core}:0.61202400919;FOXP1:0.603932403409;TGIF1:0.587791554759;NFIX:0.566816024819;SOX5:0.563637087417;HMX1:0.537081120459;MAFB:0.467063429194;T:0.449396551819;ZNF148:0.419660648291;ATF6:0.418274235227;MYBL2:0.400351947632;TBX4,5:0.397654909358;RORA:0.389154344991;MZF1:0.38705883469;PAX5:0.386491832248;ESR1:0.370608804687;TOPORS:0.365400469527;ETS1,2:0.357764980915;ALX4:0.354933036861;IKZF1:0.336027063115;HOX{A6,A7,B6,B7}:0.320313825518;HOX{A4,D4}:0.273941124386;ADNP_IRX_SIX_ZHX:0.2649859136;FOXL1:0.259963663055;EBF1:0.249028878465;TFAP2B:0.247043101152;FOXP3:0.203244731384;TEF:0.183686526702;bHLH_family:0.180085785131;EGR1..3:0.164195277389;HAND1,2:0.157033888507;MEF2{A,B,C,D}:0.126204990714;ATF4:0.11594248023;FOXN1:0.110766831121;ZFP161:0.101107044412;EN1,2:0.0886744767314;GTF2A1,2:0.0804300936;TFAP4:0.0746772377719;ELF1,2,4:0.0741548056865;AIRE:0.0704529418348;NHLH1,2:0.0527800548926;RXR{A,B,G}:0.036974080387;FOXM1:0.0258613633751;GATA4:0.0121308602252;NR3C1:-0.00237916384674;POU2F1..3:-0.00319272630666;SPIB:-0.00562848295484;NFY{A,B,C}:-0.0241075085574;SPI1:-0.0295490333298;KLF4:-0.0386502765359;RREB1:-0.108979918157;SOX{8,9,10}:-0.114170599186;ATF2:-0.120223670554;VSX1,2:-0.134147627267;PRDM1:-0.139268390248;GFI1B:-0.166329088665;RBPJ:-0.186650661685;TAL1_TCF{3,4,12}:-0.207063360606;NANOG:-0.20884945012;LMO2:-0.212565232543;JUN:-0.220465112658;ZNF143:-0.240689494746;DMAP1_NCOR{1,2}_SMARC:-0.268287619058;DBP:-0.271049275012;NKX2-1,4:-0.307791406649;PBX1:-0.33699967835;ATF5_CREB3:-0.35386566571;NR5A1,2:-0.371412102262;TP53:-0.383265872571;SOX17:-0.394668248073;BREu{core}:-0.408894448624;PAX2:-0.429200003724;HES1:-0.440378806577;NFKB1_REL_RELA:-0.453145130536;HIF1A:-0.453505288386;NFE2L1:-0.469267219831;HMGA1,2:-0.485529427236;FOSL2:-0.501441981741;NRF1:-0.55732963045;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.565514630622;NFE2:-0.567524092563;IKZF2:-0.588580771301;ZIC1..3:-0.594505927595;RFX2..5_RFXANK_RFXAP:-0.605351774529;RXRA_VDR{dimer}:-0.61303782;ZBTB6:-0.644140656795;NFE2L2:-0.650262328207;RUNX1..3:-0.653924103954;UFEwm:-0.654297161754;REST:-0.666729927539;GLI1..3:-0.675581107531;LEF1_TCF7_TCF7L1,2:-0.680683621385;NANOG{mouse}:-0.685888079713;PRRX1,2:-0.739556405263;ZBTB16:-0.7694461573;RFX1:-0.777074167959;CDX1,2,4:-0.78770350635;HOX{A5,B5}:-0.818418359339;NKX2-2,8:-0.833083957806;FOS_FOS{B,L1}_JUN{B,D}:-0.835495367258;PITX1..3:-0.841651365648;SOX2:-0.842945494551;BACH2:-0.852960582369;ONECUT1,2:-0.865727443749;STAT5{A,B}:-0.898268802591;E2F1..5:-0.91784998529;AHR_ARNT_ARNT2:-0.922848577976;ESRRA:-0.985959105922;NKX2-3_NKX2-5:-1.00672063752;PAX4:-1.0098110346;CREB1:-1.02682169279;POU5F1:-1.10472620162;CDC5L:-1.11791076657;SPZ1:-1.13208459503;POU3F1..4:-1.14044767061;POU1F1:-1.20402043777;YY1:-1.22185149467;NKX3-1:-1.25683040956;MYB:-1.27317126127;XBP1:-1.30337681307;ZNF384:-1.33307324111;OCT4_SOX2{dimer}:-1.37195057208;TFDP1:-1.48652634875;PAX3,7:-1.50219543023;ELK1,4_GABP{A,B1}:-1.50296636772;CRX:-1.51430897529;HOXA9_MEIS1:-1.52906194524;LHX3,4:-1.66771450253;NKX6-1,2:-1.90951898978;PAX8:-2.35737439259
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10007-101B4;search_select_hide=table117:FF:10007-101B4
}}
}}

Latest revision as of 12:13, 3 June 2020

Name:Universal RNA - Human Normal Tissues Biochain, pool1
Species:Human (Homo sapiens)
Library ID:CNhs10612
Sample type:tissues
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stage34-76 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB208251
catalog numberCat:R4234565-1
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005100
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
CNhs10612 CAGE DRX008612 DRR009484
CollapseAccession ID Hg19

Library idBAMCTSS
CNhs10612 DRZ000909 DRZ002294
CollapseAccession ID Hg38

Library idBAMCTSS
CNhs10612 DRZ012259 DRZ013644
Download raw sequence, BAM & CTSS
CollapseHg19
FastaBAMCTSS
downloaddownloaddonwload
CollapseHg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
RNA-Seq  SAMD00005100
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
RDhi10055 RNA-Seq DRX057113 DRR062872
CollapseAccession ID Hg19

Library idBAMCTSS
RDhi10055 DRZ007948


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: CNhs10612



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: CNhs10612



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: CNhs10612


FANTOM5 (FF) ontology


Direct parent terms

has_quality relathionship
PATO:0000461

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

UBERON: Anatomy
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000004 (tissue 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