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{{f5samples
{{f5samples
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|DRA_sample_Accession=CAGE@SAMD00005906
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|HumanCAGEScanFiles=NCig10046;http://fantom.gsc.riken.jp/5/datafiles/phase2.3/basic/human.primary_cell.CAGEScan/Pancreatic%2520stromal%2520cells%252c%2520donor1.NCig10046.11249-116E7.hg19.GCTATA.3prime.fq.gz;http://fantom.gsc.riken.jp/5/datafiles/phase2.3/basic/human.primary_cell.CAGEScan/Pancreatic%2520stromal%2520cells%252c%2520donor1.NCig10046.11249-116E7.hg19.GCTATA.5prime.fq.gz;http://fantom.gsc.riken.jp/5/datafiles/phase2.3/basic/human.primary_cell.CAGEScan/Pancreatic%2520stromal%2520cells%252c%2520donor1.NCig10046.11249-116E7.hg19.GCTATA.bam;http://fantom.gsc.riken.jp/5/datafiles/phase2.3/basic/human.primary_cell.CAGEScan/Pancreatic%2520stromal%2520cells%252c%2520donor1.NCig10046.11249-116E7.hg19.GCTATA.pairs.bed.gz
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|library_id=CNhs10877
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|microRNAs=
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|name=Pancreatic stromal cells, donor1
|name=Pancreatic stromal cells, donor1
|namespace=FANTOM5
|namespace=FANTOM5
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|sample_category=primary cells
Line 98: Line 107:
|top_motifs=ZNF238:2.14110736379;GZF1:1.55302192738;NKX2-2,8:1.51476974551;ALX4:1.27574559062;TFAP4:1.19401129772;UFEwm:1.13573199018;NKX6-1,2:1.13414504642;RXR{A,B,G}:1.12090533091;HOX{A4,D4}:1.10385104389;HAND1,2:1.06711420311;TP53:1.00141525195;PAX1,9:0.967216245342;YY1:0.953555300585;EN1,2:0.923132152645;GFI1:0.920155952869;LHX3,4:0.908189134647;HSF1,2:0.89222429075;TAL1_TCF{3,4,12}:0.881987699111;TEAD1:0.864765591767;SPZ1:0.830976516144;KLF4:0.827976970761;MZF1:0.773204479546;GTF2I:0.772216833699;GFI1B:0.740902313156;ESR1:0.71522424007;GATA4:0.703939178338;NKX3-2:0.700244434974;NFATC1..3:0.689172002973;MYBL2:0.683440722776;PRDM1:0.672498548156;FOXL1:0.666368036749;CDC5L:0.66103971174;ARID5B:0.658436021649;PDX1:0.65343790442;STAT1,3:0.585038041967;MYB:0.577624924755;TFCP2:0.567235299077;HES1:0.565072879156;TBX4,5:0.543803334954;EVI1:0.542293449763;TOPORS:0.513034256386;EBF1:0.512193289864;FOXO1,3,4:0.50905699096;ZIC1..3:0.50134071588;HMGA1,2:0.485703281079;POU3F1..4:0.47882073552;SREBF1,2:0.472090892002;PATZ1:0.458456455938;GTF2A1,2:0.456747292257;TLX1..3_NFIC{dimer}:0.455860572337;MAZ:0.438947499657;TFDP1:0.437521997921;NR3C1:0.430135583324;XBP1:0.429078913763;SOX17:0.409201983466;FOX{I1,J2}:0.405850509049;ZNF384:0.40292069646;FOXD3:0.397114813487;DMAP1_NCOR{1,2}_SMARC:0.396957617351;HBP1_HMGB_SSRP1_UBTF:0.376614007798;SRF:0.3718383519;NFIX:0.362471140749;ZNF423:0.343516815025;ZBTB6:0.331054209448;TEF:0.322719794479;NANOG{mouse}:0.317409387366;FOXQ1:0.304280352743;NFE2L2:0.299491517931;TLX2:0.29553222027;TFAP2{A,C}:0.28260985029;IRF1,2:0.276048892695;bHLH_family:0.248756902475;ZNF143:0.23004636995;NKX2-3_NKX2-5:0.228229370596;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.220972842139;RREB1:0.210321453764;ATF6:0.206235623192;POU5F1:0.195749039745;AHR_ARNT_ARNT2:0.192458568459;NRF1:0.192187561445;E2F1..5:0.191116892867;MYFfamily:0.176706001875;FOXM1:0.170133111803;NKX3-1:0.160312701375;GCM1,2:0.146390371868;HLF:0.144255135269;ELK1,4_GABP{A,B1}:0.142930321808;STAT5{A,B}:0.137591956875;SP1:0.135667309411;NR1H4:0.125559611241;HNF4A_NR2F1,2:0.120220036709;HMX1:0.114605229731;AIRE:0.110380206056;HOX{A5,B5}:0.0889327155707;BACH2:0.0844685539354;PAX5:0.0725837614139;HNF1A:0.0673254591939;LEF1_TCF7_TCF7L1,2:0.066015788539;MTE{core}:0.0653479682656;RFX1:0.0593856750466;ZNF148:0.044007959303;PAX4:0.0412303127143;PAX8:0.0394431606672;SMAD1..7,9:0.0302824665445;ESRRA:0.0244849270532;NFE2L1:0.0140383820342;FOS_FOS{B,L1}_JUN{B,D}:0.0123216106225;HOX{A6,A7,B6,B7}:-0.00257679816896;GLI1..3:-0.00406608214916;RXRA_VDR{dimer}:-0.00461690021376;IKZF1:-0.00788179499416;MTF1:-0.0197547804529;NFY{A,B,C}:-0.0201336993561;HIC1:-0.0258862165993;NHLH1,2:-0.0369799321552;ALX1:-0.0428602156547;TFAP2B:-0.0442531648831;NR6A1:-0.0477654818367;MAFB:-0.0698529223647;T:-0.0748810085053;TBP:-0.0809880029576;TGIF1:-0.109097415241;ADNP_IRX_SIX_ZHX:-0.11038993327;NFE2:-0.12809768582;PRRX1,2:-0.131014153235;FOXP1:-0.156586416274;REST:-0.163335835994;XCPE1{core}:-0.178085694931;RBPJ:-0.17995003701;EGR1..3:-0.185630556192;HOXA9_MEIS1:-0.216756482172;DBP:-0.220363275731;FOSL2:-0.222739085047;RUNX1..3:-0.239829109376;CEBPA,B_DDIT3:-0.263283434238;STAT2,4,6:-0.281364708664;POU2F1..3:-0.28372456246;NKX2-1,4:-0.291084490977;RFX2..5_RFXANK_RFXAP:-0.296349326204;MED-1{core}:-0.313516811217;NFKB1_REL_RELA:-0.321690142349;PAX3,7:-0.325007808219;PBX1:-0.356509103438;ZFP161:-0.362957132899;IRF7:-0.390618326973;CREB1:-0.401302052365;ELF1,2,4:-0.405180504925;CRX:-0.407412546613;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.41678434138;MEF2{A,B,C,D}:-0.421839385013;BPTF:-0.428427336885;CDX1,2,4:-0.448337489734;SPI1:-0.448829626166;ONECUT1,2:-0.452823556285;FOXN1:-0.465927912159;FOX{D1,D2}:-0.473683797753;BREu{core}:-0.501425259409;HIF1A:-0.510834549759;SPIB:-0.520958756504;ZBTB16:-0.530204284816;PAX2:-0.530870841443;JUN:-0.532025072624;ATF5_CREB3:-0.546720839067;ATF4:-0.567938911817;CUX2:-0.585799649;ETS1,2:-0.617297947178;PITX1..3:-0.620386915663;OCT4_SOX2{dimer}:-0.654519925508;LMO2:-0.658766195302;NFIL3:-0.660386465234;FOXA2:-0.664342835218;PPARG:-0.70197628389;SNAI1..3:-0.719359573716;SOX5:-0.754159409432;AR:-0.779588194765;IKZF2:-0.804029810365;ATF2:-0.812451068194;NR5A1,2:-0.82083052466;EP300:-0.860253647131;POU1F1:-0.878917886497;GATA6:-0.879865057221;PAX6:-0.905842288081;SOX2:-0.917244530833;VSX1,2:-0.92265492149;ZEB1:-1.01218802404;FOXP3:-1.01367684831;POU6F1:-1.04462708209;MYOD1:-1.09138114776;SOX{8,9,10}:-1.13046628727;RORA:-1.20555634234;NANOG:-1.25325672126;FOX{F1,F2,J1}:-1.51067432229
|top_motifs=ZNF238:2.14110736379;GZF1:1.55302192738;NKX2-2,8:1.51476974551;ALX4:1.27574559062;TFAP4:1.19401129772;UFEwm:1.13573199018;NKX6-1,2:1.13414504642;RXR{A,B,G}:1.12090533091;HOX{A4,D4}:1.10385104389;HAND1,2:1.06711420311;TP53:1.00141525195;PAX1,9:0.967216245342;YY1:0.953555300585;EN1,2:0.923132152645;GFI1:0.920155952869;LHX3,4:0.908189134647;HSF1,2:0.89222429075;TAL1_TCF{3,4,12}:0.881987699111;TEAD1:0.864765591767;SPZ1:0.830976516144;KLF4:0.827976970761;MZF1:0.773204479546;GTF2I:0.772216833699;GFI1B:0.740902313156;ESR1:0.71522424007;GATA4:0.703939178338;NKX3-2:0.700244434974;NFATC1..3:0.689172002973;MYBL2:0.683440722776;PRDM1:0.672498548156;FOXL1:0.666368036749;CDC5L:0.66103971174;ARID5B:0.658436021649;PDX1:0.65343790442;STAT1,3:0.585038041967;MYB:0.577624924755;TFCP2:0.567235299077;HES1:0.565072879156;TBX4,5:0.543803334954;EVI1:0.542293449763;TOPORS:0.513034256386;EBF1:0.512193289864;FOXO1,3,4:0.50905699096;ZIC1..3:0.50134071588;HMGA1,2:0.485703281079;POU3F1..4:0.47882073552;SREBF1,2:0.472090892002;PATZ1:0.458456455938;GTF2A1,2:0.456747292257;TLX1..3_NFIC{dimer}:0.455860572337;MAZ:0.438947499657;TFDP1:0.437521997921;NR3C1:0.430135583324;XBP1:0.429078913763;SOX17:0.409201983466;FOX{I1,J2}:0.405850509049;ZNF384:0.40292069646;FOXD3:0.397114813487;DMAP1_NCOR{1,2}_SMARC:0.396957617351;HBP1_HMGB_SSRP1_UBTF:0.376614007798;SRF:0.3718383519;NFIX:0.362471140749;ZNF423:0.343516815025;ZBTB6:0.331054209448;TEF:0.322719794479;NANOG{mouse}:0.317409387366;FOXQ1:0.304280352743;NFE2L2:0.299491517931;TLX2:0.29553222027;TFAP2{A,C}:0.28260985029;IRF1,2:0.276048892695;bHLH_family:0.248756902475;ZNF143:0.23004636995;NKX2-3_NKX2-5:0.228229370596;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.220972842139;RREB1:0.210321453764;ATF6:0.206235623192;POU5F1:0.195749039745;AHR_ARNT_ARNT2:0.192458568459;NRF1:0.192187561445;E2F1..5:0.191116892867;MYFfamily:0.176706001875;FOXM1:0.170133111803;NKX3-1:0.160312701375;GCM1,2:0.146390371868;HLF:0.144255135269;ELK1,4_GABP{A,B1}:0.142930321808;STAT5{A,B}:0.137591956875;SP1:0.135667309411;NR1H4:0.125559611241;HNF4A_NR2F1,2:0.120220036709;HMX1:0.114605229731;AIRE:0.110380206056;HOX{A5,B5}:0.0889327155707;BACH2:0.0844685539354;PAX5:0.0725837614139;HNF1A:0.0673254591939;LEF1_TCF7_TCF7L1,2:0.066015788539;MTE{core}:0.0653479682656;RFX1:0.0593856750466;ZNF148:0.044007959303;PAX4:0.0412303127143;PAX8:0.0394431606672;SMAD1..7,9:0.0302824665445;ESRRA:0.0244849270532;NFE2L1:0.0140383820342;FOS_FOS{B,L1}_JUN{B,D}:0.0123216106225;HOX{A6,A7,B6,B7}:-0.00257679816896;GLI1..3:-0.00406608214916;RXRA_VDR{dimer}:-0.00461690021376;IKZF1:-0.00788179499416;MTF1:-0.0197547804529;NFY{A,B,C}:-0.0201336993561;HIC1:-0.0258862165993;NHLH1,2:-0.0369799321552;ALX1:-0.0428602156547;TFAP2B:-0.0442531648831;NR6A1:-0.0477654818367;MAFB:-0.0698529223647;T:-0.0748810085053;TBP:-0.0809880029576;TGIF1:-0.109097415241;ADNP_IRX_SIX_ZHX:-0.11038993327;NFE2:-0.12809768582;PRRX1,2:-0.131014153235;FOXP1:-0.156586416274;REST:-0.163335835994;XCPE1{core}:-0.178085694931;RBPJ:-0.17995003701;EGR1..3:-0.185630556192;HOXA9_MEIS1:-0.216756482172;DBP:-0.220363275731;FOSL2:-0.222739085047;RUNX1..3:-0.239829109376;CEBPA,B_DDIT3:-0.263283434238;STAT2,4,6:-0.281364708664;POU2F1..3:-0.28372456246;NKX2-1,4:-0.291084490977;RFX2..5_RFXANK_RFXAP:-0.296349326204;MED-1{core}:-0.313516811217;NFKB1_REL_RELA:-0.321690142349;PAX3,7:-0.325007808219;PBX1:-0.356509103438;ZFP161:-0.362957132899;IRF7:-0.390618326973;CREB1:-0.401302052365;ELF1,2,4:-0.405180504925;CRX:-0.407412546613;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.41678434138;MEF2{A,B,C,D}:-0.421839385013;BPTF:-0.428427336885;CDX1,2,4:-0.448337489734;SPI1:-0.448829626166;ONECUT1,2:-0.452823556285;FOXN1:-0.465927912159;FOX{D1,D2}:-0.473683797753;BREu{core}:-0.501425259409;HIF1A:-0.510834549759;SPIB:-0.520958756504;ZBTB16:-0.530204284816;PAX2:-0.530870841443;JUN:-0.532025072624;ATF5_CREB3:-0.546720839067;ATF4:-0.567938911817;CUX2:-0.585799649;ETS1,2:-0.617297947178;PITX1..3:-0.620386915663;OCT4_SOX2{dimer}:-0.654519925508;LMO2:-0.658766195302;NFIL3:-0.660386465234;FOXA2:-0.664342835218;PPARG:-0.70197628389;SNAI1..3:-0.719359573716;SOX5:-0.754159409432;AR:-0.779588194765;IKZF2:-0.804029810365;ATF2:-0.812451068194;NR5A1,2:-0.82083052466;EP300:-0.860253647131;POU1F1:-0.878917886497;GATA6:-0.879865057221;PAX6:-0.905842288081;SOX2:-0.917244530833;VSX1,2:-0.92265492149;ZEB1:-1.01218802404;FOXP3:-1.01367684831;POU6F1:-1.04462708209;MYOD1:-1.09138114776;SOX{8,9,10}:-1.13046628727;RORA:-1.20555634234;NANOG:-1.25325672126;FOX{F1,F2,J1}:-1.51067432229
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11249-116E7;search_select_hide=table117:FF:11249-116E7
}}
}}

Latest revision as of 16:27, 3 June 2020

Name:Pancreatic stromal cells, donor1
Species:Human (Homo sapiens)
Library ID:CNhs10877
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuepancreas
dev stage39 years old adult
sexmale
age39
cell typepancreatic stromal cell
cell lineNA
companyCell systems
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005906
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
CNhs10877 CAGE DRX008395 DRR009267
CollapseAccession ID Hg19

Library idBAMCTSS
CNhs10877 DRZ000692 DRZ002077
CollapseAccession ID Hg38

Library idBAMCTSS
CNhs10877 DRZ012042 DRZ013427
Download raw sequence, BAM & CTSS
CollapseHg19
FastaBAMCTSS
downloaddownloaddonwload
CollapseHg38
BAMCTSS
downloaddonwload
HumanCAGEScan Download raw sequence, BAM & CTSS

Library id3prime-FASTQ5prime-FASTQBAMCTSS
NCig10046downloaddownloaddownloaddownload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005906
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
SRhi10003.ACTTGA sRNA-Seq DRX037017 DRR041383
CollapseAccession ID Hg19

Library idBAMCTSS
SRhi10003.ACTTGA DRZ007025


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: CNhs10877



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: CNhs10877



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: CNhs10877


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)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000499 (stromal cell)
0000255 (eukaryotic cell)
0002574 (stromal cell of pancreas)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001264 (pancreas)
0002100 (trunk)
0002384 (connective tissue)
0000479 (tissue)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002323 (body cavity)
0005177 (trunk region element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000042 (pancreatic stromal cell)
0000146 (human stromal cell of pancreas 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:0000134 (mesenchymal cell)