Personal tools

FF:1300-22B7: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005755
|DRA_sample_Accession=CAGE@SAMD00005755
|accession_numbers=CAGE;DRX009107;DRR009981;DRZ001406;DRZ002789
|accession_numbers=CAGE;DRX009107;DRR009981;DRZ001406;DRZ002789;DRZ012756;DRZ014139
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000473,UBERON:0000991,UBERON:0000479,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0003101,UBERON:0000079
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000473,UBERON:0000991,UBERON:0000479,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0003101,UBERON:0000079
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
Line 46: Line 46:
|library_id=CNhs11189
|library_id=CNhs11189
|library_id_phase_based=2:CNhs11189
|library_id_phase_based=2:CNhs11189
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1300
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1300
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N00.CNhs11189.1300-22B7.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N00.CNhs11189.1300-22B7.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N00.CNhs11189.1300-22B7.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N00.CNhs11189.1300-22B7.mm10.nobarcode.ctss.bed.gz
Line 93: Line 97:
|top_motifs=MYBL2:1.83856467801;ZNF384:1.75569699834;ZNF238:1.61188537824;TEF:1.47829107997;NKX6-1,2:1.40433202188;FOXP1:1.3828646081;HIF1A:1.37679725043;NANOG{mouse}:1.36144973788;ZBTB16:1.24971810844;NR6A1:1.22384299843;GATA4:1.15959685107;GLI1..3:1.15148813537;PITX1..3:1.13823839417;GFI1B:1.06143223015;SOX5:1.05164273125;NKX3-1:1.04364212147;TOPORS:1.04107858861;IKZF2:1.02388251127;ZNF423:0.964269866118;BPTF:0.960831763971;PATZ1:0.940336078374;ZIC1..3:0.9243426939;TFAP2{A,C}:0.907485744369;STAT1,3:0.885540080582;EVI1:0.880779458949;GCM1,2:0.870536659655;FOXD3:0.826828170954;EGR1..3:0.816095034744;RXR{A,B,G}:0.81311592953;HOX{A5,B5}:0.777981773931;SP1:0.776039418974;AIRE:0.757258245043;TEAD1:0.744233907976;EP300:0.744159440371;E2F1..5:0.736920495213;HMGA1,2:0.726948100447;NRF1:0.68858820965;XCPE1{core}:0.688389593433;IKZF1:0.663334492854;bHLH_family:0.620045668457;FOXP3:0.569510304698;TLX1..3_NFIC{dimer}:0.562085432936;PAX4:0.553662879019;CDC5L:0.540902417279;TFDP1:0.526836037313;CRX:0.524176071687;NR5A1,2:0.520375242723;FOXO1,3,4:0.482344729692;MTE{core}:0.466833125801;RREB1:0.458132009266;GFI1:0.436356263886;NFATC1..3:0.423748617503;FOXN1:0.41552733209;HBP1_HMGB_SSRP1_UBTF:0.414933973884;GTF2I:0.41329084293;POU1F1:0.378231254446;NR1H4:0.378156184273;NKX2-1,4:0.373166436375;DBP:0.358050453328;HOXA9_MEIS1:0.35187239878;NFIX:0.337075249137;MED-1{core}:0.329911349928;CREB1:0.324265116539;MZF1:0.320962349358;ZNF143:0.303587767493;TFAP2B:0.303095974476;ZFP161:0.3000307598;MAZ:0.266380627505;FOX{D1,D2}:0.25872283071;NFY{A,B,C}:0.256713834048;RBPJ:0.250080323399;SOX2:0.242400516752;TAL1_TCF{3,4,12}:0.223913049105;TFAP4:0.204132763945;BREu{core}:0.204108461688;HIC1:0.180720747512;ESR1:0.168975043778;CDX1,2,4:0.15731808635;KLF4:0.155777912202;UFEwm:0.142421720908;TFCP2:0.121987891521;ADNP_IRX_SIX_ZHX:0.110347746935;SOX17:0.0934591379749;FOXQ1:0.0662372770263;YY1:0.0613076673705;PAX6:0.0576261740348;MYB:0.0539140165853;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.0498081531163;ELK1,4_GABP{A,B1}:0.0438360354319;PRRX1,2:0.0179679076518;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.00761211823486;GATA6:0.00685961479099;POU6F1:-0.00420419486683;ALX4:-0.0110614029452;PRDM1:-0.0169052750056;HSF1,2:-0.0226188125262;MTF1:-0.0228195333424;RFX2..5_RFXANK_RFXAP:-0.0229707863017;MYFfamily:-0.0363403266531;AHR_ARNT_ARNT2:-0.0367234217186;ATF2:-0.0374740491983;SRF:-0.0448684244882;SPIB:-0.0874280200565;ARID5B:-0.099227289424;RFX1:-0.13571214668;AR:-0.140342545349;PAX5:-0.145892476658;CUX2:-0.154795136191;GZF1:-0.189216849566;IRF1,2:-0.191694705879;SOX{8,9,10}:-0.193709506381;NKX2-2,8:-0.194241597254;LEF1_TCF7_TCF7L1,2:-0.201232933797;GTF2A1,2:-0.219848369729;MEF2{A,B,C,D}:-0.227446715116;RUNX1..3:-0.242255614058;POU2F1..3:-0.272315462066;ATF4:-0.278058661739;NKX2-3_NKX2-5:-0.307823869088;SREBF1,2:-0.313928607751;PAX2:-0.317541417913;IRF7:-0.322862925492;HES1:-0.322951659367;FOXL1:-0.32438254047;ELF1,2,4:-0.334593577417;ESRRA:-0.335176352771;REST:-0.344000759215;RORA:-0.345746633612;EN1,2:-0.351409601624;ETS1,2:-0.390081681446;TBX4,5:-0.417793020642;POU3F1..4:-0.419516672879;HAND1,2:-0.427316466863;T:-0.431455029996;STAT5{A,B}:-0.445202864676;MAFB:-0.445695785331;BACH2:-0.450179404314;POU5F1:-0.453012806239;PBX1:-0.47398045799;OCT4_SOX2{dimer}:-0.475614370127;EBF1:-0.484451658333;NFKB1_REL_RELA:-0.508975477518;NFE2:-0.510380017604;SPZ1:-0.515208302992;ONECUT1,2:-0.520324267396;CEBPA,B_DDIT3:-0.529071638149;DMAP1_NCOR{1,2}_SMARC:-0.533125762475;HNF4A_NR2F1,2:-0.554743185737;PAX1,9:-0.561632643259;ATF6:-0.572821422251;NKX3-2:-0.5880172129;SPI1:-0.600979586327;ZBTB6:-0.616865238947;TP53:-0.638412616908;TBP:-0.645621823943;ZNF148:-0.64784639307;HNF1A:-0.66234402218;HLF:-0.699267733228;ALX1:-0.72640629786;SMAD1..7,9:-0.745081391465;NHLH1,2:-0.746255662925;FOXA2:-0.750873729341;NANOG:-0.756317305676;LMO2:-0.76288506774;RXRA_VDR{dimer}:-0.782193758719;HMX1:-0.791045851109;STAT2,4,6:-0.7910918524;NFIL3:-0.828824485477;TGIF1:-0.877297071;FOX{F1,F2,J1}:-0.887616975813;FOS_FOS{B,L1}_JUN{B,D}:-0.898709572061;LHX3,4:-0.918733600742;HOX{A4,D4}:-0.947257155715;VSX1,2:-0.965890087142;PAX8:-1.01806140589;JUN:-1.021527955;FOXM1:-1.04730428346;PDX1:-1.11521605634;NR3C1:-1.1273062244;NFE2L2:-1.16858432927;SNAI1..3:-1.21303273682;FOX{I1,J2}:-1.21571119036;MYOD1:-1.22269111325;TLX2:-1.30540445367;ATF5_CREB3:-1.3383360546;ZEB1:-1.42135827454;PPARG:-1.50718659645;FOSL2:-1.54150240423;NFE2L1:-1.66888812702
|top_motifs=MYBL2:1.83856467801;ZNF384:1.75569699834;ZNF238:1.61188537824;TEF:1.47829107997;NKX6-1,2:1.40433202188;FOXP1:1.3828646081;HIF1A:1.37679725043;NANOG{mouse}:1.36144973788;ZBTB16:1.24971810844;NR6A1:1.22384299843;GATA4:1.15959685107;GLI1..3:1.15148813537;PITX1..3:1.13823839417;GFI1B:1.06143223015;SOX5:1.05164273125;NKX3-1:1.04364212147;TOPORS:1.04107858861;IKZF2:1.02388251127;ZNF423:0.964269866118;BPTF:0.960831763971;PATZ1:0.940336078374;ZIC1..3:0.9243426939;TFAP2{A,C}:0.907485744369;STAT1,3:0.885540080582;EVI1:0.880779458949;GCM1,2:0.870536659655;FOXD3:0.826828170954;EGR1..3:0.816095034744;RXR{A,B,G}:0.81311592953;HOX{A5,B5}:0.777981773931;SP1:0.776039418974;AIRE:0.757258245043;TEAD1:0.744233907976;EP300:0.744159440371;E2F1..5:0.736920495213;HMGA1,2:0.726948100447;NRF1:0.68858820965;XCPE1{core}:0.688389593433;IKZF1:0.663334492854;bHLH_family:0.620045668457;FOXP3:0.569510304698;TLX1..3_NFIC{dimer}:0.562085432936;PAX4:0.553662879019;CDC5L:0.540902417279;TFDP1:0.526836037313;CRX:0.524176071687;NR5A1,2:0.520375242723;FOXO1,3,4:0.482344729692;MTE{core}:0.466833125801;RREB1:0.458132009266;GFI1:0.436356263886;NFATC1..3:0.423748617503;FOXN1:0.41552733209;HBP1_HMGB_SSRP1_UBTF:0.414933973884;GTF2I:0.41329084293;POU1F1:0.378231254446;NR1H4:0.378156184273;NKX2-1,4:0.373166436375;DBP:0.358050453328;HOXA9_MEIS1:0.35187239878;NFIX:0.337075249137;MED-1{core}:0.329911349928;CREB1:0.324265116539;MZF1:0.320962349358;ZNF143:0.303587767493;TFAP2B:0.303095974476;ZFP161:0.3000307598;MAZ:0.266380627505;FOX{D1,D2}:0.25872283071;NFY{A,B,C}:0.256713834048;RBPJ:0.250080323399;SOX2:0.242400516752;TAL1_TCF{3,4,12}:0.223913049105;TFAP4:0.204132763945;BREu{core}:0.204108461688;HIC1:0.180720747512;ESR1:0.168975043778;CDX1,2,4:0.15731808635;KLF4:0.155777912202;UFEwm:0.142421720908;TFCP2:0.121987891521;ADNP_IRX_SIX_ZHX:0.110347746935;SOX17:0.0934591379749;FOXQ1:0.0662372770263;YY1:0.0613076673705;PAX6:0.0576261740348;MYB:0.0539140165853;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.0498081531163;ELK1,4_GABP{A,B1}:0.0438360354319;PRRX1,2:0.0179679076518;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.00761211823486;GATA6:0.00685961479099;POU6F1:-0.00420419486683;ALX4:-0.0110614029452;PRDM1:-0.0169052750056;HSF1,2:-0.0226188125262;MTF1:-0.0228195333424;RFX2..5_RFXANK_RFXAP:-0.0229707863017;MYFfamily:-0.0363403266531;AHR_ARNT_ARNT2:-0.0367234217186;ATF2:-0.0374740491983;SRF:-0.0448684244882;SPIB:-0.0874280200565;ARID5B:-0.099227289424;RFX1:-0.13571214668;AR:-0.140342545349;PAX5:-0.145892476658;CUX2:-0.154795136191;GZF1:-0.189216849566;IRF1,2:-0.191694705879;SOX{8,9,10}:-0.193709506381;NKX2-2,8:-0.194241597254;LEF1_TCF7_TCF7L1,2:-0.201232933797;GTF2A1,2:-0.219848369729;MEF2{A,B,C,D}:-0.227446715116;RUNX1..3:-0.242255614058;POU2F1..3:-0.272315462066;ATF4:-0.278058661739;NKX2-3_NKX2-5:-0.307823869088;SREBF1,2:-0.313928607751;PAX2:-0.317541417913;IRF7:-0.322862925492;HES1:-0.322951659367;FOXL1:-0.32438254047;ELF1,2,4:-0.334593577417;ESRRA:-0.335176352771;REST:-0.344000759215;RORA:-0.345746633612;EN1,2:-0.351409601624;ETS1,2:-0.390081681446;TBX4,5:-0.417793020642;POU3F1..4:-0.419516672879;HAND1,2:-0.427316466863;T:-0.431455029996;STAT5{A,B}:-0.445202864676;MAFB:-0.445695785331;BACH2:-0.450179404314;POU5F1:-0.453012806239;PBX1:-0.47398045799;OCT4_SOX2{dimer}:-0.475614370127;EBF1:-0.484451658333;NFKB1_REL_RELA:-0.508975477518;NFE2:-0.510380017604;SPZ1:-0.515208302992;ONECUT1,2:-0.520324267396;CEBPA,B_DDIT3:-0.529071638149;DMAP1_NCOR{1,2}_SMARC:-0.533125762475;HNF4A_NR2F1,2:-0.554743185737;PAX1,9:-0.561632643259;ATF6:-0.572821422251;NKX3-2:-0.5880172129;SPI1:-0.600979586327;ZBTB6:-0.616865238947;TP53:-0.638412616908;TBP:-0.645621823943;ZNF148:-0.64784639307;HNF1A:-0.66234402218;HLF:-0.699267733228;ALX1:-0.72640629786;SMAD1..7,9:-0.745081391465;NHLH1,2:-0.746255662925;FOXA2:-0.750873729341;NANOG:-0.756317305676;LMO2:-0.76288506774;RXRA_VDR{dimer}:-0.782193758719;HMX1:-0.791045851109;STAT2,4,6:-0.7910918524;NFIL3:-0.828824485477;TGIF1:-0.877297071;FOX{F1,F2,J1}:-0.887616975813;FOS_FOS{B,L1}_JUN{B,D}:-0.898709572061;LHX3,4:-0.918733600742;HOX{A4,D4}:-0.947257155715;VSX1,2:-0.965890087142;PAX8:-1.01806140589;JUN:-1.021527955;FOXM1:-1.04730428346;PDX1:-1.11521605634;NR3C1:-1.1273062244;NFE2L2:-1.16858432927;SNAI1..3:-1.21303273682;FOX{I1,J2}:-1.21571119036;MYOD1:-1.22269111325;TLX2:-1.30540445367;ATF5_CREB3:-1.3383360546;ZEB1:-1.42135827454;PPARG:-1.50718659645;FOSL2:-1.54150240423;NFE2L1:-1.66888812702
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1300-22B7;search_select_hide=table117:1300-22B7
}}
}}

Latest revision as of 18:48, 4 June 2020


Name:testis, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11189
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuetestis
dev stage0 day neonate
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005755
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
CNhs11189 CAGE DRX009107 DRR009981
CollapseAccession ID Mm9

Library idBAMCTSS
CNhs11189 DRZ001406 DRZ002789
CollapseAccession ID Mm10

Library idBAMCTSS
CNhs11189 DRZ012756 DRZ014139
Download raw sequence, BAM & CTSS
CollapseMm9
FastaBAMCTSS
downloaddownloaddonwload
CollapseMm10
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

CNhs11189



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: CNhs11189



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: CNhs11189



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: CNhs11189


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000473 (testis)
0000991 (gonad)
0000479 (tissue)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011509 (mouse testis- neonate N00 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
UBERON:0009117 (indifferent gonad)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)