Personal tools

FF:11736-123E8: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 97: Line 97:
|top_motifs=ZNF423:3.45005045587;GTF2A1,2:3.35580476845;EBF1:3.23772402366;TFAP2{A,C}:2.52171136418;RFX1:2.27406682305;TFCP2:2.27229481451;ESR1:2.26462131523;HMX1:2.2046794543;HES1:2.05396489308;ZIC1..3:1.89596361568;TP53:1.80457456429;TFAP4:1.73960427643;NR1H4:1.73615239877;MTF1:1.69519893147;RXR{A,B,G}:1.65946055349;EP300:1.64789723742;HAND1,2:1.60120595501;ZNF148:1.53847056328;ZBTB6:1.48310391722;BACH2:1.36274350375;RFX2..5_RFXANK_RFXAP:1.33596546819;POU2F1..3:1.32194067009;UFEwm:1.27284227081;PATZ1:1.2405365896;TLX1..3_NFIC{dimer}:1.20628659986;PAX5:1.17012309051;MYOD1:1.15695270894;NFE2L1:1.13175693606;RREB1:1.11080599922;MTE{core}:1.08333873098;GLI1..3:1.06433064083;TFAP2B:1.01583236086;IKZF1:1.00416210916;SP1:0.975400810093;HOXA9_MEIS1:0.968016181847;HIC1:0.955720335694;RXRA_VDR{dimer}:0.913887987243;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.884634581826;MAZ:0.881980465262;SMAD1..7,9:0.850167768834;REST:0.798871190023;FOXM1:0.786800092277;GTF2I:0.774316661349;ATF6:0.760886620488;POU5F1:0.726957435225;LMO2:0.703524818497;KLF4:0.686353925619;FOXO1,3,4:0.678310741858;VSX1,2:0.667128505023;XCPE1{core}:0.631906816415;TEAD1:0.628560612839;MED-1{core}:0.612204300908;NHLH1,2:0.579794763895;GCM1,2:0.57826768965;RUNX1..3:0.469448429323;GATA4:0.468101780297;HOX{A5,B5}:0.461179557057;SOX2:0.446294567695;SPIB:0.442797485771;MZF1:0.432683262308;FOS_FOS{B,L1}_JUN{B,D}:0.401323748042;NKX3-2:0.399683158877;FOXN1:0.389094707394;EGR1..3:0.388544619865;STAT2,4,6:0.387712529081;TOPORS:0.382170896371;TBX4,5:0.358058330678;SPZ1:0.347377753834;ZNF384:0.344560469254;ZFP161:0.31991980923;ATF4:0.318942328072;TFDP1:0.294511004969;NFE2L2:0.291620260245;NFIL3:0.267078089668;MYFfamily:0.266601935529;OCT4_SOX2{dimer}:0.257670408666;PRDM1:0.232061596259;NR5A1,2:0.199369030263;HIF1A:0.179670773385;FOX{F1,F2,J1}:0.177526842617;PAX1,9:0.176373818928;BREu{core}:0.156371057354;JUN:0.131333082525;ZNF238:0.122560967904;FOXP3:0.11493817222;MYBL2:0.0759503789398;NFKB1_REL_RELA:0.0579060935796;FOXL1:-0.03190014359;SPI1:-0.0527332856699;AR:-0.116041383833;IRF7:-0.138100048148;NR6A1:-0.141438690242;HBP1_HMGB_SSRP1_UBTF:-0.160854213368;LEF1_TCF7_TCF7L1,2:-0.180897564583;SOX5:-0.198981215665;HLF:-0.200126173553;NANOG{mouse}:-0.205083547036;RORA:-0.206930085559;TBP:-0.229402442241;NKX2-2,8:-0.25975200435;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.260592513257;SOX17:-0.267032040198;POU3F1..4:-0.267371158343;IRF1,2:-0.271243749685;HSF1,2:-0.276140875938;FOSL2:-0.287992044254;GFI1:-0.33405795384;MYB:-0.341466456814;ETS1,2:-0.344977894848;HNF4A_NR2F1,2:-0.373850748452;SRF:-0.373953676507;RBPJ:-0.377125565404;POU6F1:-0.379773989012;HOX{A4,D4}:-0.389792913086;ESRRA:-0.391136314142;ALX4:-0.393496631257;NFY{A,B,C}:-0.414997735667;NKX3-1:-0.430385385133;SREBF1,2:-0.455615691219;EN1,2:-0.470957985285;GZF1:-0.485274261545;ADNP_IRX_SIX_ZHX:-0.490691622598;SOX{8,9,10}:-0.50167098639;ONECUT1,2:-0.504516300559;CDC5L:-0.508586575056;PAX6:-0.527285653931;ZEB1:-0.529726360936;ARID5B:-0.540053656035;MEF2{A,B,C,D}:-0.573152420724;ATF2:-0.5837980028;PAX2:-0.585978933792;MAFB:-0.593120304628;NR3C1:-0.594819008473;FOX{D1,D2}:-0.598779915097;DMAP1_NCOR{1,2}_SMARC:-0.602162302018;HMGA1,2:-0.608929372586;TAL1_TCF{3,4,12}:-0.640175197482;PAX4:-0.641584854956;ZNF143:-0.657669361767;HNF1A:-0.699250953611;PAX8:-0.701111586314;STAT1,3:-0.709920586014;DBP:-0.711153654175;NANOG:-0.723886770214;STAT5{A,B}:-0.735365788104;CREB1:-0.752677331938;TLX2:-0.759329073983;GFI1B:-0.770253713078;NKX2-3_NKX2-5:-0.787486671337;SNAI1..3:-0.792248229282;PPARG:-0.854715403914;IKZF2:-0.869920568862;LHX3,4:-0.879956195167;NRF1:-0.901710404141;ELK1,4_GABP{A,B1}:-0.903477812884;CUX2:-0.917905369501;CRX:-0.917912036557;PBX1:-0.948402483908;CEBPA,B_DDIT3:-0.991954578246;ALX1:-0.998087868878;ELF1,2,4:-1.05830639132;PRRX1,2:-1.13244590164;NFE2:-1.15784180504;NFATC1..3:-1.1592564503;T:-1.19881493989;E2F1..5:-1.20072598172;BPTF:-1.20697312809;ZBTB16:-1.23076615696;ATF5_CREB3:-1.24659361091;GATA6:-1.30847056115;bHLH_family:-1.36280650333;AHR_ARNT_ARNT2:-1.40008652395;NFIX:-1.4073662254;NKX2-1,4:-1.41613167451;YY1:-1.44102090382;NKX6-1,2:-1.56789526174;TGIF1:-1.57301088846;PITX1..3:-1.59470631149;FOXA2:-1.66809055955;FOX{I1,J2}:-1.70980180945;EVI1:-1.81158765122;POU1F1:-1.81275209114;PDX1:-1.81906902842;FOXP1:-1.83986204308;FOXQ1:-1.96360515583;TEF:-2.01500127769;FOXD3:-2.11184933752;CDX1,2,4:-2.74663059449;AIRE:-2.82541848388
|top_motifs=ZNF423:3.45005045587;GTF2A1,2:3.35580476845;EBF1:3.23772402366;TFAP2{A,C}:2.52171136418;RFX1:2.27406682305;TFCP2:2.27229481451;ESR1:2.26462131523;HMX1:2.2046794543;HES1:2.05396489308;ZIC1..3:1.89596361568;TP53:1.80457456429;TFAP4:1.73960427643;NR1H4:1.73615239877;MTF1:1.69519893147;RXR{A,B,G}:1.65946055349;EP300:1.64789723742;HAND1,2:1.60120595501;ZNF148:1.53847056328;ZBTB6:1.48310391722;BACH2:1.36274350375;RFX2..5_RFXANK_RFXAP:1.33596546819;POU2F1..3:1.32194067009;UFEwm:1.27284227081;PATZ1:1.2405365896;TLX1..3_NFIC{dimer}:1.20628659986;PAX5:1.17012309051;MYOD1:1.15695270894;NFE2L1:1.13175693606;RREB1:1.11080599922;MTE{core}:1.08333873098;GLI1..3:1.06433064083;TFAP2B:1.01583236086;IKZF1:1.00416210916;SP1:0.975400810093;HOXA9_MEIS1:0.968016181847;HIC1:0.955720335694;RXRA_VDR{dimer}:0.913887987243;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.884634581826;MAZ:0.881980465262;SMAD1..7,9:0.850167768834;REST:0.798871190023;FOXM1:0.786800092277;GTF2I:0.774316661349;ATF6:0.760886620488;POU5F1:0.726957435225;LMO2:0.703524818497;KLF4:0.686353925619;FOXO1,3,4:0.678310741858;VSX1,2:0.667128505023;XCPE1{core}:0.631906816415;TEAD1:0.628560612839;MED-1{core}:0.612204300908;NHLH1,2:0.579794763895;GCM1,2:0.57826768965;RUNX1..3:0.469448429323;GATA4:0.468101780297;HOX{A5,B5}:0.461179557057;SOX2:0.446294567695;SPIB:0.442797485771;MZF1:0.432683262308;FOS_FOS{B,L1}_JUN{B,D}:0.401323748042;NKX3-2:0.399683158877;FOXN1:0.389094707394;EGR1..3:0.388544619865;STAT2,4,6:0.387712529081;TOPORS:0.382170896371;TBX4,5:0.358058330678;SPZ1:0.347377753834;ZNF384:0.344560469254;ZFP161:0.31991980923;ATF4:0.318942328072;TFDP1:0.294511004969;NFE2L2:0.291620260245;NFIL3:0.267078089668;MYFfamily:0.266601935529;OCT4_SOX2{dimer}:0.257670408666;PRDM1:0.232061596259;NR5A1,2:0.199369030263;HIF1A:0.179670773385;FOX{F1,F2,J1}:0.177526842617;PAX1,9:0.176373818928;BREu{core}:0.156371057354;JUN:0.131333082525;ZNF238:0.122560967904;FOXP3:0.11493817222;MYBL2:0.0759503789398;NFKB1_REL_RELA:0.0579060935796;FOXL1:-0.03190014359;SPI1:-0.0527332856699;AR:-0.116041383833;IRF7:-0.138100048148;NR6A1:-0.141438690242;HBP1_HMGB_SSRP1_UBTF:-0.160854213368;LEF1_TCF7_TCF7L1,2:-0.180897564583;SOX5:-0.198981215665;HLF:-0.200126173553;NANOG{mouse}:-0.205083547036;RORA:-0.206930085559;TBP:-0.229402442241;NKX2-2,8:-0.25975200435;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.260592513257;SOX17:-0.267032040198;POU3F1..4:-0.267371158343;IRF1,2:-0.271243749685;HSF1,2:-0.276140875938;FOSL2:-0.287992044254;GFI1:-0.33405795384;MYB:-0.341466456814;ETS1,2:-0.344977894848;HNF4A_NR2F1,2:-0.373850748452;SRF:-0.373953676507;RBPJ:-0.377125565404;POU6F1:-0.379773989012;HOX{A4,D4}:-0.389792913086;ESRRA:-0.391136314142;ALX4:-0.393496631257;NFY{A,B,C}:-0.414997735667;NKX3-1:-0.430385385133;SREBF1,2:-0.455615691219;EN1,2:-0.470957985285;GZF1:-0.485274261545;ADNP_IRX_SIX_ZHX:-0.490691622598;SOX{8,9,10}:-0.50167098639;ONECUT1,2:-0.504516300559;CDC5L:-0.508586575056;PAX6:-0.527285653931;ZEB1:-0.529726360936;ARID5B:-0.540053656035;MEF2{A,B,C,D}:-0.573152420724;ATF2:-0.5837980028;PAX2:-0.585978933792;MAFB:-0.593120304628;NR3C1:-0.594819008473;FOX{D1,D2}:-0.598779915097;DMAP1_NCOR{1,2}_SMARC:-0.602162302018;HMGA1,2:-0.608929372586;TAL1_TCF{3,4,12}:-0.640175197482;PAX4:-0.641584854956;ZNF143:-0.657669361767;HNF1A:-0.699250953611;PAX8:-0.701111586314;STAT1,3:-0.709920586014;DBP:-0.711153654175;NANOG:-0.723886770214;STAT5{A,B}:-0.735365788104;CREB1:-0.752677331938;TLX2:-0.759329073983;GFI1B:-0.770253713078;NKX2-3_NKX2-5:-0.787486671337;SNAI1..3:-0.792248229282;PPARG:-0.854715403914;IKZF2:-0.869920568862;LHX3,4:-0.879956195167;NRF1:-0.901710404141;ELK1,4_GABP{A,B1}:-0.903477812884;CUX2:-0.917905369501;CRX:-0.917912036557;PBX1:-0.948402483908;CEBPA,B_DDIT3:-0.991954578246;ALX1:-0.998087868878;ELF1,2,4:-1.05830639132;PRRX1,2:-1.13244590164;NFE2:-1.15784180504;NFATC1..3:-1.1592564503;T:-1.19881493989;E2F1..5:-1.20072598172;BPTF:-1.20697312809;ZBTB16:-1.23076615696;ATF5_CREB3:-1.24659361091;GATA6:-1.30847056115;bHLH_family:-1.36280650333;AHR_ARNT_ARNT2:-1.40008652395;NFIX:-1.4073662254;NKX2-1,4:-1.41613167451;YY1:-1.44102090382;NKX6-1,2:-1.56789526174;TGIF1:-1.57301088846;PITX1..3:-1.59470631149;FOXA2:-1.66809055955;FOX{I1,J2}:-1.70980180945;EVI1:-1.81158765122;POU1F1:-1.81275209114;PDX1:-1.81906902842;FOXP1:-1.83986204308;FOXQ1:-1.96360515583;TEF:-2.01500127769;FOXD3:-2.11184933752;CDX1,2,4:-2.74663059449;AIRE:-2.82541848388
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11736-123E8;search_select_hide=table117:11736-123E8
}}
}}

Latest revision as of 18:16, 4 June 2020


Name:Mouse Microglia, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12634
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexNA
ageNA
cell typemicroglial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMG2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005410
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
CNhs12634 CAGE DRX008829 DRR009701
CollapseAccession ID Mm9

Library idBAMCTSS
CNhs12634 DRZ001126 DRZ002511
CollapseAccession ID Mm10

Library idBAMCTSS
CNhs12634 DRZ012476 DRZ013861
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

CNhs12634



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: CNhs12634



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: CNhs12634



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: CNhs12634


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)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000878 (central nervous system macrophage)
0000219 (motile cell)
0000325 (stuff accumulating cell)
0000473 (defensive cell)
0000234 (phagocyte)
0000125 (glial cell)
0000738 (leukocyte)
0000255 (eukaryotic cell)
0000235 (macrophage)
0000864 (tissue-resident macrophage)
0000129 (microglial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000113 (mouse microglial cell 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:0000133 (neurectodermal cell)
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)