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{{f5samples
{{f5samples
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|DRA_sample_Accession=CAGE@SAMD00005512
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005512
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Line 66: Line 68:
|profile_rnaseq=
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Line 81: Line 83:
|rna_tube_id=116B9
|rna_tube_id=116B9
|rna_weight_ug=10
|rna_weight_ug=10
|rnaseq_library_id=SRhi10008.TTAGGC
|sample_age=47
|sample_age=47
|sample_category=primary cells
|sample_category=primary cells
Line 104: Line 107:
|top_motifs=NFKB1_REL_RELA:5.20111330288;FOS_FOS{B,L1}_JUN{B,D}:4.99137822902;BACH2:4.98649943902;PAX3,7:4.93922810447;FOSL2:4.73122190829;PAX2:4.60488025566;NFE2:4.6032202759;NFIL3:4.43052605432;RUNX1..3:3.60977922241;CEBPA,B_DDIT3:3.5862094667;SPIB:3.58334586612;HLF:3.47788293066;ETS1,2:3.45762786239;CREB1:3.43269567831;ATF5_CREB3:3.35067726582;SPI1:3.34858486843;NFE2L2:3.32086707986;ATF4:3.02797519793;DMAP1_NCOR{1,2}_SMARC:2.89504832739;NFATC1..3:2.8889377524;TGIF1:2.81461366407;HMGA1,2:2.67205762209;IRF1,2:2.59656277515;FOXP3:2.55898322006;JUN:2.54321098973;RXRA_VDR{dimer}:2.47942754302;FOXN1:2.33868253909;STAT2,4,6:2.27401737425;IRF7:2.24850842036;PAX8:2.1730366823;FOXO1,3,4:2.02035586908;ATF2:1.90509779592;BPTF:1.69587965645;ELF1,2,4:1.66903046797;NANOG{mouse}:1.65148663307;NFE2L1:1.60609359846;MAFB:1.57781336507;SREBF1,2:1.54308457117;FOX{D1,D2}:1.50113502462;RFX2..5_RFXANK_RFXAP:1.49879035635;ATF6:1.4449086637;RORA:1.43700389136;HOXA9_MEIS1:1.29041009157;FOXP1:1.09904417529;HSF1,2:1.0791149432;EP300:0.981875143626;NANOG:0.917020382605;NKX2-1,4:0.892073137455;HIF1A:0.890544635324;T:0.816095716153;PDX1:0.530547355441;RBPJ:0.519768281484;HMX1:0.502087562498;HBP1_HMGB_SSRP1_UBTF:0.467256631114;PITX1..3:0.379446414851;ALX4:0.376655829428;GLI1..3:0.306565021745;HOX{A5,B5}:0.282547601332;XBP1:0.278226197189;EGR1..3:0.25087619499;MEF2{A,B,C,D}:0.215555009195;SMAD1..7,9:0.195303985216;SOX2:0.133459604334;SRF:0.0977872613699;TBX4,5:0.020315704756;BREu{core}:-0.0442718870034;RXR{A,B,G}:-0.0571184001155;POU2F1..3:-0.112922929075;GATA4:-0.214787493221;ZBTB16:-0.226706865266;IKZF1:-0.232214069807;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.249067841013;NR3C1:-0.253688595469;POU5F1:-0.255557627988;STAT5{A,B}:-0.345450755453;AHR_ARNT_ARNT2:-0.38544295757;VSX1,2:-0.461334745888;STAT1,3:-0.490741339471;CDX1,2,4:-0.493493206317;FOXL1:-0.497961599052;ZNF238:-0.531306360694;TFDP1:-0.541616203946;NKX3-1:-0.542656794189;EN1,2:-0.547844710922;TFCP2:-0.576378241828;MYB:-0.584239591876;FOX{F1,F2,J1}:-0.594788965925;MTE{core}:-0.610608995621;ZNF384:-0.625487346407;TBP:-0.674703098221;TLX2:-0.713643464548;IKZF2:-0.725109124405;TEF:-0.747428355844;RFX1:-0.7661834585;TFAP2{A,C}:-0.815304944304;OCT4_SOX2{dimer}:-0.844223370341;NR1H4:-0.866553630201;TFAP2B:-0.878312344752;GATA6:-0.881280695729;NHLH1,2:-0.896936766948;ESR1:-0.898690376804;ZFP161:-0.913944685913;MED-1{core}:-0.942664469025;ESRRA:-0.985409656699;SP1:-1.00485954731;PRRX1,2:-1.0207917951;FOXA2:-1.03490910287;FOX{I1,J2}:-1.03719876129;MZF1:-1.04971539974;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.07774871136;NKX2-3_NKX2-5:-1.08616133908;PAX6:-1.1122350698;PPARG:-1.13942942341;TAL1_TCF{3,4,12}:-1.17927158884;GCM1,2:-1.19186325444;TFAP4:-1.22329438424;PRDM1:-1.22850651564;NKX6-1,2:-1.23284162358;E2F1..5:-1.25879029475;PATZ1:-1.25978569145;CRX:-1.26091761069;MYFfamily:-1.29740209201;DBP:-1.31126465691;NR5A1,2:-1.31560492323;FOXM1:-1.3195428124;ADNP_IRX_SIX_ZHX:-1.32740426228;HNF1A:-1.33247001416;HNF4A_NR2F1,2:-1.39003812445;PAX1,9:-1.40302676351;HES1:-1.41653110666;NR6A1:-1.42594776006;SOX5:-1.42720658199;POU3F1..4:-1.43984329647;CUX2:-1.47495498032;PAX4:-1.51336833771;REST:-1.51532624724;MAZ:-1.53056777399;MYBL2:-1.5386407075;HIC1:-1.58482042566;SOX{8,9,10}:-1.59390892506;MTF1:-1.62116176555;GTF2A1,2:-1.63658389727;TP53:-1.67719676783;TEAD1:-1.68285507803;HOX{A4,D4}:-1.69985111178;ALX1:-1.7356453207;ZNF148:-1.73910992226;NFY{A,B,C}:-1.75049026623;GTF2I:-1.79386042912;ZEB1:-1.81424862702;HOX{A6,A7,B6,B7}:-1.93585777892;TLX1..3_NFIC{dimer}:-1.96563778025;RREB1:-1.97019901905;PAX5:-1.97893400361;PBX1:-1.9970570535;EBF1:-2.01757283439;LEF1_TCF7_TCF7L1,2:-2.04499355901;TOPORS:-2.05375463138;XCPE1{core}:-2.12699586933;ELK1,4_GABP{A,B1}:-2.13912557194;MYOD1:-2.15956650476;GFI1B:-2.19749782695;ZIC1..3:-2.28646041987;SNAI1..3:-2.31298077321;CDC5L:-2.35569223639;LHX3,4:-2.37253882826;SPZ1:-2.3783742361;SOX17:-2.41303765227;NRF1:-2.41383141429;FOXD3:-2.42992958983;AIRE:-2.43570392888;GZF1:-2.44190599247;POU6F1:-2.44267519311;ZBTB6:-2.51405207452;GFI1:-2.60346815896;NFIX:-2.64726535853;FOXQ1:-2.6554117954;ZNF423:-2.73944548611;bHLH_family:-2.87391455435;NKX2-2,8:-2.9034588115;AR:-2.90586158698;LMO2:-2.95524511272;KLF4:-3.02283021346;EVI1:-3.30326000345;ZNF143:-3.40469476102;ARID5B:-3.65006977373;ONECUT1,2:-3.67438967688;UFEwm:-3.72056476276;YY1:-3.73929141443;POU1F1:-3.79807180336;NKX3-2:-3.84707494243;HAND1,2:-4.76387766823
|top_motifs=NFKB1_REL_RELA:5.20111330288;FOS_FOS{B,L1}_JUN{B,D}:4.99137822902;BACH2:4.98649943902;PAX3,7:4.93922810447;FOSL2:4.73122190829;PAX2:4.60488025566;NFE2:4.6032202759;NFIL3:4.43052605432;RUNX1..3:3.60977922241;CEBPA,B_DDIT3:3.5862094667;SPIB:3.58334586612;HLF:3.47788293066;ETS1,2:3.45762786239;CREB1:3.43269567831;ATF5_CREB3:3.35067726582;SPI1:3.34858486843;NFE2L2:3.32086707986;ATF4:3.02797519793;DMAP1_NCOR{1,2}_SMARC:2.89504832739;NFATC1..3:2.8889377524;TGIF1:2.81461366407;HMGA1,2:2.67205762209;IRF1,2:2.59656277515;FOXP3:2.55898322006;JUN:2.54321098973;RXRA_VDR{dimer}:2.47942754302;FOXN1:2.33868253909;STAT2,4,6:2.27401737425;IRF7:2.24850842036;PAX8:2.1730366823;FOXO1,3,4:2.02035586908;ATF2:1.90509779592;BPTF:1.69587965645;ELF1,2,4:1.66903046797;NANOG{mouse}:1.65148663307;NFE2L1:1.60609359846;MAFB:1.57781336507;SREBF1,2:1.54308457117;FOX{D1,D2}:1.50113502462;RFX2..5_RFXANK_RFXAP:1.49879035635;ATF6:1.4449086637;RORA:1.43700389136;HOXA9_MEIS1:1.29041009157;FOXP1:1.09904417529;HSF1,2:1.0791149432;EP300:0.981875143626;NANOG:0.917020382605;NKX2-1,4:0.892073137455;HIF1A:0.890544635324;T:0.816095716153;PDX1:0.530547355441;RBPJ:0.519768281484;HMX1:0.502087562498;HBP1_HMGB_SSRP1_UBTF:0.467256631114;PITX1..3:0.379446414851;ALX4:0.376655829428;GLI1..3:0.306565021745;HOX{A5,B5}:0.282547601332;XBP1:0.278226197189;EGR1..3:0.25087619499;MEF2{A,B,C,D}:0.215555009195;SMAD1..7,9:0.195303985216;SOX2:0.133459604334;SRF:0.0977872613699;TBX4,5:0.020315704756;BREu{core}:-0.0442718870034;RXR{A,B,G}:-0.0571184001155;POU2F1..3:-0.112922929075;GATA4:-0.214787493221;ZBTB16:-0.226706865266;IKZF1:-0.232214069807;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.249067841013;NR3C1:-0.253688595469;POU5F1:-0.255557627988;STAT5{A,B}:-0.345450755453;AHR_ARNT_ARNT2:-0.38544295757;VSX1,2:-0.461334745888;STAT1,3:-0.490741339471;CDX1,2,4:-0.493493206317;FOXL1:-0.497961599052;ZNF238:-0.531306360694;TFDP1:-0.541616203946;NKX3-1:-0.542656794189;EN1,2:-0.547844710922;TFCP2:-0.576378241828;MYB:-0.584239591876;FOX{F1,F2,J1}:-0.594788965925;MTE{core}:-0.610608995621;ZNF384:-0.625487346407;TBP:-0.674703098221;TLX2:-0.713643464548;IKZF2:-0.725109124405;TEF:-0.747428355844;RFX1:-0.7661834585;TFAP2{A,C}:-0.815304944304;OCT4_SOX2{dimer}:-0.844223370341;NR1H4:-0.866553630201;TFAP2B:-0.878312344752;GATA6:-0.881280695729;NHLH1,2:-0.896936766948;ESR1:-0.898690376804;ZFP161:-0.913944685913;MED-1{core}:-0.942664469025;ESRRA:-0.985409656699;SP1:-1.00485954731;PRRX1,2:-1.0207917951;FOXA2:-1.03490910287;FOX{I1,J2}:-1.03719876129;MZF1:-1.04971539974;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.07774871136;NKX2-3_NKX2-5:-1.08616133908;PAX6:-1.1122350698;PPARG:-1.13942942341;TAL1_TCF{3,4,12}:-1.17927158884;GCM1,2:-1.19186325444;TFAP4:-1.22329438424;PRDM1:-1.22850651564;NKX6-1,2:-1.23284162358;E2F1..5:-1.25879029475;PATZ1:-1.25978569145;CRX:-1.26091761069;MYFfamily:-1.29740209201;DBP:-1.31126465691;NR5A1,2:-1.31560492323;FOXM1:-1.3195428124;ADNP_IRX_SIX_ZHX:-1.32740426228;HNF1A:-1.33247001416;HNF4A_NR2F1,2:-1.39003812445;PAX1,9:-1.40302676351;HES1:-1.41653110666;NR6A1:-1.42594776006;SOX5:-1.42720658199;POU3F1..4:-1.43984329647;CUX2:-1.47495498032;PAX4:-1.51336833771;REST:-1.51532624724;MAZ:-1.53056777399;MYBL2:-1.5386407075;HIC1:-1.58482042566;SOX{8,9,10}:-1.59390892506;MTF1:-1.62116176555;GTF2A1,2:-1.63658389727;TP53:-1.67719676783;TEAD1:-1.68285507803;HOX{A4,D4}:-1.69985111178;ALX1:-1.7356453207;ZNF148:-1.73910992226;NFY{A,B,C}:-1.75049026623;GTF2I:-1.79386042912;ZEB1:-1.81424862702;HOX{A6,A7,B6,B7}:-1.93585777892;TLX1..3_NFIC{dimer}:-1.96563778025;RREB1:-1.97019901905;PAX5:-1.97893400361;PBX1:-1.9970570535;EBF1:-2.01757283439;LEF1_TCF7_TCF7L1,2:-2.04499355901;TOPORS:-2.05375463138;XCPE1{core}:-2.12699586933;ELK1,4_GABP{A,B1}:-2.13912557194;MYOD1:-2.15956650476;GFI1B:-2.19749782695;ZIC1..3:-2.28646041987;SNAI1..3:-2.31298077321;CDC5L:-2.35569223639;LHX3,4:-2.37253882826;SPZ1:-2.3783742361;SOX17:-2.41303765227;NRF1:-2.41383141429;FOXD3:-2.42992958983;AIRE:-2.43570392888;GZF1:-2.44190599247;POU6F1:-2.44267519311;ZBTB6:-2.51405207452;GFI1:-2.60346815896;NFIX:-2.64726535853;FOXQ1:-2.6554117954;ZNF423:-2.73944548611;bHLH_family:-2.87391455435;NKX2-2,8:-2.9034588115;AR:-2.90586158698;LMO2:-2.95524511272;KLF4:-3.02283021346;EVI1:-3.30326000345;ZNF143:-3.40469476102;ARID5B:-3.65006977373;ONECUT1,2:-3.67438967688;UFEwm:-3.72056476276;YY1:-3.73929141443;POU1F1:-3.79807180336;NKX3-2:-3.84707494243;HAND1,2:-4.76387766823
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11224-116B9;search_select_hide=table117:FF:11224-116B9
}}
}}

Latest revision as of 16:25, 3 June 2020

Name:CD14+ Monocytes, donor1
Species:Human (Homo sapiens)
Library ID:CNhs10852
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueblood
dev stage47 years old adult
sexmale
age47
cell typemonocyte
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberMon725
catalog number3H100-30-10
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005512
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10852 CAGE DRX008126 DRR008998
Accession ID Hg19

Library idBAMCTSS
CNhs10852 DRZ000423 DRZ001808
Accession ID Hg38

Library idBAMCTSS
CNhs10852 DRZ011773 DRZ013158
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload
HumanCAGEScan Download raw sequence, BAM & CTSS

Library id3prime-FASTQ5prime-FASTQBAMCTSS
NCig10040downloaddownloaddownloaddownload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005512
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10008.TTAGGC sRNA-Seq DRX037109 DRR041475
Accession ID Hg19

Library idBAMCTSS
SRhi10008.TTAGGC DRZ007117


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: CNhs10852



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: CNhs10852



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: CNhs10852


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)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0000255 (eukaryotic cell)
0000576 (monocyte)
0002393 (intermediate monocyte)
0002397 (CD14-positive, CD16-positive monocyte)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000024 (human CD14-positive monocyte 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)
CL:0002057 (CD14-positive, CD16-negative classical monocyte)