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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004678
|DRA_sample_Accession=CAGE@SAMD00004678
|accession_numbers=CAGE;DRX008788;DRR009660;DRZ001085;DRZ002470
|accession_numbers=CAGE;DRX008788;DRR009660;DRZ001085;DRZ002470;DRZ012435;DRZ013820
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000483,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0005911,UBERON:0004923,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0000490,UBERON:0001262,UBERON:0004786,UBERON:0000485,UBERON:0003350,UBERON:0003929,UBERON:0004808,UBERON:0001277,UBERON:0010317,UBERON:0001555,UBERON:0005409
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000483,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0005911,UBERON:0004923,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0000490,UBERON:0001262,UBERON:0004786,UBERON:0000485,UBERON:0003350,UBERON:0003929,UBERON:0004808,UBERON:0001277,UBERON:0010317,UBERON:0001555,UBERON:0005409
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000075,CL:0000066,CL:0002371,CL:0002563,CL:0000255,CL:0000239,CL:0000677,CL:0000212,CL:0002076,CL:0002251,CL:0000584
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000075,CL:0000066,CL:0002371,CL:0002563,CL:0000255,CL:0000239,CL:0000677,CL:0000212,CL:0002076,CL:0002251,CL:0000584
Line 48: Line 48:
|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11849
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11849
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11849
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11849
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%2520enterocyte%252c%2520pool2.CNhs13197.11849-124I4.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%2520enterocyte%252c%2520pool2.CNhs13197.11849-124I4.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%2520enterocyte%252c%2520pool2.CNhs13197.11849-124I4.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%2520enterocyte%252c%2520pool2.CNhs13197.11849-124I4.mm10.nobarcode.ctss.bed.gz
Line 97: Line 97:
|top_motifs=HNF4A_NR2F1,2:3.18450366489;ESRRA:2.63315509929;ZEB1:2.5915728042;FOXN1:2.35072647535;PAX2:2.31193040361;RXR{A,B,G}_{NR1H2,PPAR}dimers:2.2694092643;ATF4:2.19997604008;SNAI1..3:2.08612881781;FOXM1:2.08504951106;PDX1:1.99052891189;TBX4,5:1.87606945968;ATF5_CREB3:1.80657359091;HNF1A:1.76360033291;PPARG:1.73810790227;SP1:1.7106315154;NR6A1:1.70614392642;NFIX:1.65973758591;CREB1:1.61336416687;NR5A1,2:1.54149969552;FOSL2:1.5366103188;GTF2A1,2:1.31596141512;bHLH_family:1.25734734857;PAX8:1.19920494356;FOS_FOS{B,L1}_JUN{B,D}:1.16304348973;FOX{D1,D2}:1.11321842664;AR:1.09771252655;IRF1,2:1.08364495761;DMAP1_NCOR{1,2}_SMARC:0.987062702842;FOX{I1,J2}:0.976635010608;ARID5B:0.973905034181;NR1H4:0.941161560913;ATF6:0.932484589146;SREBF1,2:0.911023756656;LMO2:0.894802301168;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.850595721215;ELK1,4_GABP{A,B1}:0.77890908481;ADNP_IRX_SIX_ZHX:0.768123340169;TP53:0.757808038963;NFKB1_REL_RELA:0.667918494307;CDX1,2,4:0.664731958916;RORA:0.592583231147;HES1:0.581537799635;STAT2,4,6:0.55726987869;XCPE1{core}:0.543415823617;ZBTB6:0.540668746629;MYOD1:0.487470733578;BACH2:0.486059886969;STAT5{A,B}:0.476018120943;POU3F1..4:0.412194516918;NFY{A,B,C}:0.406074085191;T:0.398472041688;TLX1..3_NFIC{dimer}:0.371769085416;FOXO1,3,4:0.335196336948;HBP1_HMGB_SSRP1_UBTF:0.324224144156;LHX3,4:0.26254740877;VSX1,2:0.24687728167;NKX6-1,2:0.235917642425;ESR1:0.222932919282;FOXQ1:0.158151131303;RXRA_VDR{dimer}:0.152306475356;JUN:0.097642515962;RXR{A,B,G}:0.0498143068808;HOXA9_MEIS1:0.0473353166615;GATA6:0.0349490218568;FOXL1:0.0296113359074;HIF1A:0.0193947486164;ONECUT1,2:0.00920758182076;MAFB:0.00562793218861;TBP:-0.0230585015688;ETS1,2:-0.0336523896733;HOX{A4,D4}:-0.11670309712;SPI1:-0.131620942228;HLF:-0.140478524703;IRF7:-0.147019816432;SRF:-0.15097897778;MYB:-0.177151729458;TFAP2B:-0.18706808367;LEF1_TCF7_TCF7L1,2:-0.23486550153;ZNF148:-0.235055155513;FOXA2:-0.278504728127;MED-1{core}:-0.2952941584;ALX4:-0.309163853555;TLX2:-0.345000326422;ZFP161:-0.351488802695;PBX1:-0.352773491306;ELF1,2,4:-0.357709319077;PAX5:-0.377383562149;POU2F1..3:-0.385775028724;NFE2L1:-0.408221270398;YY1:-0.447131651829;STAT1,3:-0.449192681184;RUNX1..3:-0.474538534456;CUX2:-0.474928653757;MTE{core}:-0.476384797208;ZNF143:-0.481337034975;NKX3-2:-0.493444499455;EGR1..3:-0.495543884381;EBF1:-0.496949013145;BPTF:-0.528346344921;HOX{A5,B5}:-0.550371192478;REST:-0.557803551311;PITX1..3:-0.572597858413;OCT4_SOX2{dimer}:-0.589462811422;RFX2..5_RFXANK_RFXAP:-0.596847709287;NFE2:-0.601903521066;CEBPA,B_DDIT3:-0.633483051863;SOX17:-0.642232168175;MEF2{A,B,C,D}:-0.671050931553;FOXP3:-0.672995705469;POU6F1:-0.694499745676;HIC1:-0.726094494638;MYBL2:-0.731135455684;NKX2-1,4:-0.732300136603;CRX:-0.737241446346;NFIL3:-0.742849619247;NFE2L2:-0.751071873094;FOX{F1,F2,J1}:-0.756170393968;SPZ1:-0.756775416516;TEAD1:-0.764670643205;EVI1:-0.76511590296;NANOG{mouse}:-0.772230484201;PRRX1,2:-0.799033454987;NRF1:-0.80816968514;NANOG:-0.812581356039;TGIF1:-0.831741103716;GFI1B:-0.869562099527;CDC5L:-0.880734690854;TFCP2:-0.8902362321;TFAP2{A,C}:-0.907264770813;GZF1:-0.90741726609;AHR_ARNT_ARNT2:-0.914738101119;RFX1:-0.932714015406;TAL1_TCF{3,4,12}:-0.955647912767;PAX6:-0.961014229527;GFI1:-0.979731724598;SOX5:-0.992200847022;MAZ:-1.01568638278;SPIB:-1.03563996631;AIRE:-1.03810906157;SOX{8,9,10}:-1.0392227123;NHLH1,2:-1.08859144326;ZBTB16:-1.09540639408;DBP:-1.0971064505;TFAP4:-1.1214538441;MYFfamily:-1.12535882687;BREu{core}:-1.16839597469;E2F1..5:-1.23962343998;GTF2I:-1.25899208953;GLI1..3:-1.27535714442;NKX2-3_NKX2-5:-1.28837974059;MTF1:-1.29024708927;ATF2:-1.39335287845;NKX2-2,8:-1.40664512644;TOPORS:-1.41579765881;MZF1:-1.41602140339;SOX2:-1.45451974676;PATZ1:-1.46325125217;SMAD1..7,9:-1.4734969991;ZNF238:-1.50203859286;ZNF423:-1.50208761701;EP300:-1.52843280218;UFEwm:-1.58326447902;ZIC1..3:-1.58974306797;GCM1,2:-1.59124258588;IKZF1:-1.61869932744;RBPJ:-1.66569959119;FOXD3:-1.66683557706;FOXP1:-1.66861180694;HMGA1,2:-1.69730392743;TFDP1:-1.70702373914;PAX4:-1.71631345563;HAND1,2:-1.7760072225;GATA4:-1.78549595541;ALX1:-1.78910818085;RREB1:-1.95845474319;ZNF384:-1.95940070733;HSF1,2:-1.9786064468;PAX1,9:-2.03151142005;KLF4:-2.06425937;PRDM1:-2.10900950129;EN1,2:-2.15185662114;POU5F1:-2.17684403653;POU1F1:-2.24975786976;NFATC1..3:-2.45770914257;HMX1:-2.51219909667;NR3C1:-2.56644264917;IKZF2:-2.58992871991;NKX3-1:-2.81206837096;TEF:-3.11803633876
|top_motifs=HNF4A_NR2F1,2:3.18450366489;ESRRA:2.63315509929;ZEB1:2.5915728042;FOXN1:2.35072647535;PAX2:2.31193040361;RXR{A,B,G}_{NR1H2,PPAR}dimers:2.2694092643;ATF4:2.19997604008;SNAI1..3:2.08612881781;FOXM1:2.08504951106;PDX1:1.99052891189;TBX4,5:1.87606945968;ATF5_CREB3:1.80657359091;HNF1A:1.76360033291;PPARG:1.73810790227;SP1:1.7106315154;NR6A1:1.70614392642;NFIX:1.65973758591;CREB1:1.61336416687;NR5A1,2:1.54149969552;FOSL2:1.5366103188;GTF2A1,2:1.31596141512;bHLH_family:1.25734734857;PAX8:1.19920494356;FOS_FOS{B,L1}_JUN{B,D}:1.16304348973;FOX{D1,D2}:1.11321842664;AR:1.09771252655;IRF1,2:1.08364495761;DMAP1_NCOR{1,2}_SMARC:0.987062702842;FOX{I1,J2}:0.976635010608;ARID5B:0.973905034181;NR1H4:0.941161560913;ATF6:0.932484589146;SREBF1,2:0.911023756656;LMO2:0.894802301168;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.850595721215;ELK1,4_GABP{A,B1}:0.77890908481;ADNP_IRX_SIX_ZHX:0.768123340169;TP53:0.757808038963;NFKB1_REL_RELA:0.667918494307;CDX1,2,4:0.664731958916;RORA:0.592583231147;HES1:0.581537799635;STAT2,4,6:0.55726987869;XCPE1{core}:0.543415823617;ZBTB6:0.540668746629;MYOD1:0.487470733578;BACH2:0.486059886969;STAT5{A,B}:0.476018120943;POU3F1..4:0.412194516918;NFY{A,B,C}:0.406074085191;T:0.398472041688;TLX1..3_NFIC{dimer}:0.371769085416;FOXO1,3,4:0.335196336948;HBP1_HMGB_SSRP1_UBTF:0.324224144156;LHX3,4:0.26254740877;VSX1,2:0.24687728167;NKX6-1,2:0.235917642425;ESR1:0.222932919282;FOXQ1:0.158151131303;RXRA_VDR{dimer}:0.152306475356;JUN:0.097642515962;RXR{A,B,G}:0.0498143068808;HOXA9_MEIS1:0.0473353166615;GATA6:0.0349490218568;FOXL1:0.0296113359074;HIF1A:0.0193947486164;ONECUT1,2:0.00920758182076;MAFB:0.00562793218861;TBP:-0.0230585015688;ETS1,2:-0.0336523896733;HOX{A4,D4}:-0.11670309712;SPI1:-0.131620942228;HLF:-0.140478524703;IRF7:-0.147019816432;SRF:-0.15097897778;MYB:-0.177151729458;TFAP2B:-0.18706808367;LEF1_TCF7_TCF7L1,2:-0.23486550153;ZNF148:-0.235055155513;FOXA2:-0.278504728127;MED-1{core}:-0.2952941584;ALX4:-0.309163853555;TLX2:-0.345000326422;ZFP161:-0.351488802695;PBX1:-0.352773491306;ELF1,2,4:-0.357709319077;PAX5:-0.377383562149;POU2F1..3:-0.385775028724;NFE2L1:-0.408221270398;YY1:-0.447131651829;STAT1,3:-0.449192681184;RUNX1..3:-0.474538534456;CUX2:-0.474928653757;MTE{core}:-0.476384797208;ZNF143:-0.481337034975;NKX3-2:-0.493444499455;EGR1..3:-0.495543884381;EBF1:-0.496949013145;BPTF:-0.528346344921;HOX{A5,B5}:-0.550371192478;REST:-0.557803551311;PITX1..3:-0.572597858413;OCT4_SOX2{dimer}:-0.589462811422;RFX2..5_RFXANK_RFXAP:-0.596847709287;NFE2:-0.601903521066;CEBPA,B_DDIT3:-0.633483051863;SOX17:-0.642232168175;MEF2{A,B,C,D}:-0.671050931553;FOXP3:-0.672995705469;POU6F1:-0.694499745676;HIC1:-0.726094494638;MYBL2:-0.731135455684;NKX2-1,4:-0.732300136603;CRX:-0.737241446346;NFIL3:-0.742849619247;NFE2L2:-0.751071873094;FOX{F1,F2,J1}:-0.756170393968;SPZ1:-0.756775416516;TEAD1:-0.764670643205;EVI1:-0.76511590296;NANOG{mouse}:-0.772230484201;PRRX1,2:-0.799033454987;NRF1:-0.80816968514;NANOG:-0.812581356039;TGIF1:-0.831741103716;GFI1B:-0.869562099527;CDC5L:-0.880734690854;TFCP2:-0.8902362321;TFAP2{A,C}:-0.907264770813;GZF1:-0.90741726609;AHR_ARNT_ARNT2:-0.914738101119;RFX1:-0.932714015406;TAL1_TCF{3,4,12}:-0.955647912767;PAX6:-0.961014229527;GFI1:-0.979731724598;SOX5:-0.992200847022;MAZ:-1.01568638278;SPIB:-1.03563996631;AIRE:-1.03810906157;SOX{8,9,10}:-1.0392227123;NHLH1,2:-1.08859144326;ZBTB16:-1.09540639408;DBP:-1.0971064505;TFAP4:-1.1214538441;MYFfamily:-1.12535882687;BREu{core}:-1.16839597469;E2F1..5:-1.23962343998;GTF2I:-1.25899208953;GLI1..3:-1.27535714442;NKX2-3_NKX2-5:-1.28837974059;MTF1:-1.29024708927;ATF2:-1.39335287845;NKX2-2,8:-1.40664512644;TOPORS:-1.41579765881;MZF1:-1.41602140339;SOX2:-1.45451974676;PATZ1:-1.46325125217;SMAD1..7,9:-1.4734969991;ZNF238:-1.50203859286;ZNF423:-1.50208761701;EP300:-1.52843280218;UFEwm:-1.58326447902;ZIC1..3:-1.58974306797;GCM1,2:-1.59124258588;IKZF1:-1.61869932744;RBPJ:-1.66569959119;FOXD3:-1.66683557706;FOXP1:-1.66861180694;HMGA1,2:-1.69730392743;TFDP1:-1.70702373914;PAX4:-1.71631345563;HAND1,2:-1.7760072225;GATA4:-1.78549595541;ALX1:-1.78910818085;RREB1:-1.95845474319;ZNF384:-1.95940070733;HSF1,2:-1.9786064468;PAX1,9:-2.03151142005;KLF4:-2.06425937;PRDM1:-2.10900950129;EN1,2:-2.15185662114;POU5F1:-2.17684403653;POU1F1:-2.24975786976;NFATC1..3:-2.45770914257;HMX1:-2.51219909667;NR3C1:-2.56644264917;IKZF2:-2.58992871991;NKX3-1:-2.81206837096;TEF:-3.11803633876
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11849-124I4;search_select_hide=table117:11849-124I4
}}
}}

Latest revision as of 18:23, 4 June 2020


Name:CD326+ enterocyte, pool2
Species:Mouse (Mus musculus)
Library ID:CNhs13197
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainBalb/c
tissueileum
dev stageadult
sexmale
ageNA
cell typeenterocyte
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberCont_Ep+_b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004678
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13197 CAGE DRX008788 DRR009660
Accession ID Mm9

Library idBAMCTSS
CNhs13197 DRZ001085 DRZ002470
Accession ID Mm10

Library idBAMCTSS
CNhs13197 DRZ012435 DRZ013820
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs13197



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: CNhs13197



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: CNhs13197



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: CNhs13197


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)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0000239 (brush border epithelial cell)
0000677 (gut absorptive cell)
0000212 (absorptive cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0000584 (enterocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000160 (intestine)
0000483 (epithelium)
0001242 (intestinal mucosa)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0005911 (endo-epithelium)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0000485 (simple columnar epithelium)
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004808 (gastrointestinal system epithelium)
0001277 (intestinal epithelium)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0011149 (mouse CD326-positive enterocyte 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:0000223 (endodermal cell)