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{{f5samples
{{f5samples
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|DRA_sample_Accession=CAGE@SAMD00004917
|accession_numbers=CAGE;DRX008113;DRR008985;DRZ000410;DRZ001795
|accession_numbers=CAGE;DRX008113;DRR008985;DRZ000410;DRZ001795;DRZ011760;DRZ013145
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000095,CL:0000243,CL:0000128,CL:0000126,CL:0000125,CL:0000255,CL:0000127,CL:0002603
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|fonse_treatment_closure=
|fonse_treatment_closure=
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|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebellum%252c%2520donor2.CNhs12081.11580-120F5.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebellum%252c%2520donor2.CNhs12081.11580-120F5.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebellum%252c%2520donor2.CNhs12081.11580-120F5.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebellum%252c%2520donor2.CNhs12081.11580-120F5.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebellum%252c%2520donor2.CNhs12081.11580-120F5.hg38.nobarcode.ctss.bed.gz
|id=FF:11580-120F5
|id=FF:11580-120F5
|is_a=EFO:0002091;;FF:0000195
|is_a=EFO:0002091;;FF:0000195
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|library_id=CNhs12081
|library_id=CNhs12081
|library_id_phase_based=2:CNhs12081
|library_id_phase_based=2:CNhs12081
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11580
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11580
|name=Astrocyte - cerebellum, donor2
|name=Astrocyte - cerebellum, donor2
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
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|top_motifs=ZIC1..3:1.86297544115;EBF1:1.80159451945;GTF2A1,2:1.6725788926;TFAP2{A,C}:1.64571854176;XCPE1{core}:1.51902160459;GZF1:1.3728093475;RXR{A,B,G}:1.26638888065;PBX1:1.23914219453;ZNF423:1.13429881838;TFAP4:1.0854478286;TFAP2B:1.08092906378;SP1:1.0452340403;GFI1:1.03898768192;ESR1:0.957396061101;ESRRA:0.915262927967;SOX{8,9,10}:0.910221939894;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.881708671774;ZNF148:0.881384119756;MZF1:0.855997514171;PAX1,9:0.84716680372;TEAD1:0.844689322218;RXRA_VDR{dimer}:0.83820766095;LEF1_TCF7_TCF7L1,2:0.835964780369;TLX1..3_NFIC{dimer}:0.803200449351;MTF1:0.797909941234;SPZ1:0.76168256711;POU2F1..3:0.712435231569;TFCP2:0.71198338702;RREB1:0.711510074663;NR6A1:0.691507779612;ZBTB6:0.684084269195;TAL1_TCF{3,4,12}:0.641022091794;HIC1:0.640057834274;LHX3,4:0.639130050119;GTF2I:0.614634891175;NR5A1,2:0.61451682199;PATZ1:0.592689471682;HES1:0.588301588258;NFY{A,B,C}:0.57970383367;E2F1..5:0.566237656946;TFDP1:0.561383023293;HMX1:0.547439879994;PAX5:0.547213050511;HOX{A5,B5}:0.541099992012;TP53:0.508526286497;MTE{core}:0.497702992561;MAZ:0.478320708491;KLF4:0.463895837972;SMAD1..7,9:0.45108939148;HNF4A_NR2F1,2:0.435427054837;GLI1..3:0.415625019226;NR3C1:0.406968704495;PPARG:0.385092800994;SRF:0.373323500315;POU5F1:0.365711183907;NKX2-3_NKX2-5:0.353641186414;SOX17:0.351385042419;ZNF143:0.348471820079;ONECUT1,2:0.337119935512;IKZF1:0.307117421398;bHLH_family:0.301336163962;UFEwm:0.298129691477;GFI1B:0.285133930374;TOPORS:0.281184520644;BREu{core}:0.278946275296;NHLH1,2:0.258862715182;NFE2L1:0.243338039739;EN1,2:0.224059796556;TBX4,5:0.220199027598;YY1:0.220056266371;TBP:0.21873974165;REST:0.209921965221;NR1H4:0.209574804663;MED-1{core}:0.190085271271;AR:0.188715493672;GCM1,2:0.185829108205;ZNF238:0.178568430977;ZFP161:0.152478887468;NKX2-2,8:0.144140252938;EGR1..3:0.137759645757;NFE2L2:0.117288969708;SOX2:0.10270291127;NFIX:0.0802531701907;NANOG:0.0609756125862;XBP1:0.0599185888989;BACH2:0.0359036285295;FOS_FOS{B,L1}_JUN{B,D}:0.0292315156519;OCT4_SOX2{dimer}:0.029046788739;SOX5:0.0240218548129;FOXL1:0.0142700113411;ZNF384:0.0134618512308;MEF2{A,B,C,D}:0.0127200201248;HNF1A:-0.0599702175604;MYB:-0.0663445889295;ALX4:-0.0708551254911;NRF1:-0.094079207839;NANOG{mouse}:-0.110271271211;PAX3,7:-0.113528381781;PRRX1,2:-0.127502976244;RUNX1..3:-0.163819541151;POU3F1..4:-0.166324284932;NKX6-1,2:-0.179570767657;FOSL2:-0.183047735539;FOXM1:-0.18881078083;ATF6:-0.212849046815;LMO2:-0.229372577761;MYBL2:-0.231169534256;CDC5L:-0.23656296474;NFE2:-0.245024604683;JUN:-0.245270033623;PAX8:-0.263652003142;EP300:-0.264476780918;HOX{A6,A7,B6,B7}:-0.290898024273;NFKB1_REL_RELA:-0.302509886125;RFX1:-0.305201839484;ELK1,4_GABP{A,B1}:-0.314421305981;PRDM1:-0.342795361373;SNAI1..3:-0.3469310073;STAT2,4,6:-0.354232470249;HOXA9_MEIS1:-0.358605703217;VSX1,2:-0.360283042729;NKX3-1:-0.3656425779;HAND1,2:-0.376226973158;ARID5B:-0.385886734772;CRX:-0.402060202169;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.412849976701;POU1F1:-0.41458449957;CUX2:-0.444543566985;GATA4:-0.458949402361;ETS1,2:-0.460176855686;HIF1A:-0.46326592571;MYOD1:-0.463806734454;DMAP1_NCOR{1,2}_SMARC:-0.463832061626;HOX{A4,D4}:-0.467839171719;GATA6:-0.475190133064;HSF1,2:-0.477179835956;NFATC1..3:-0.490168496541;DBP:-0.500747516651;T:-0.502369966002;MYFfamily:-0.521794691698;HLF:-0.541903727318;AHR_ARNT_ARNT2:-0.543801210519;SPIB:-0.563312846397;PAX2:-0.575018673686;RORA:-0.611536917453;FOXD3:-0.619464989063;STAT1,3:-0.632814573466;NKX3-2:-0.632838926458;ADNP_IRX_SIX_ZHX:-0.695557692637;SPI1:-0.702925316971;CEBPA,B_DDIT3:-0.753403475851;TGIF1:-0.769172129782;FOXP1:-0.770059100961;PAX6:-0.793731015077;POU6F1:-0.817779459289;FOXQ1:-0.832829535752;NFIL3:-0.833320804341;EVI1:-0.841688427073;PDX1:-0.888479273;PITX1..3:-0.889252442739;FOX{D1,D2}:-0.893149172005;IRF1,2:-0.909150012116;AIRE:-0.916729322539;ELF1,2,4:-0.947762655614;ZEB1:-0.948879115382;NKX2-1,4:-0.952913460216;RBPJ:-0.959969880788;MAFB:-0.961906197757;STAT5{A,B}:-1.0014350925;RFX2..5_RFXANK_RFXAP:-1.02006411438;TEF:-1.02457665267;IKZF2:-1.03131159381;CREB1:-1.03552208915;FOXP3:-1.05246328723;FOX{F1,F2,J1}:-1.05958219604;ATF4:-1.0625273881;HMGA1,2:-1.06640811535;ATF5_CREB3:-1.09398240404;PAX4:-1.10005707389;FOXO1,3,4:-1.1239848159;IRF7:-1.12603081269;FOXA2:-1.18304072957;FOX{I1,J2}:-1.23324912694;ATF2:-1.24991695542;BPTF:-1.29156939044;TLX2:-1.36356733774;HBP1_HMGB_SSRP1_UBTF:-1.40466323994;ALX1:-1.40725499644;CDX1,2,4:-1.44437994002;SREBF1,2:-1.45140234372;FOXN1:-1.6403364944;ZBTB16:-2.09043258883
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11580-120F5;search_select_hide=table117:FF:11580-120F5
}}
}}

Latest revision as of 18:10, 4 June 2020

Name:Astrocyte - cerebellum, donor2
Species:Human (Homo sapiens)
Library ID:CNhs12081
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6, 7, 8, 9, 10
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuecerebellum
dev stageNA
sexNA
ageNA
cell typeastrocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC1815
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004917
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12081 CAGE DRX008113 DRR008985
Accession ID Hg19

Library idBAMCTSS
CNhs12081 DRZ000410 DRZ001795
Accession ID Hg38

Library idBAMCTSS
CNhs12081 DRZ011760 DRZ013145
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0111
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.0749
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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: CNhs12081

Jaspar motifP-value
MA0002.20.287
MA0003.10.347
MA0004.10.657
MA0006.10.191
MA0007.10.236
MA0009.10.105
MA0014.10.608
MA0017.10.996
MA0018.20.139
MA0019.10.1
MA0024.10.0327
MA0025.10.959
MA0027.10.504
MA0028.10.126
MA0029.10.397
MA0030.10.265
MA0031.10.0688
MA0035.20.727
MA0038.10.00273
MA0039.20.545
MA0040.10.52
MA0041.10.182
MA0042.10.62
MA0043.10.0125
MA0046.10.0575
MA0047.20.156
MA0048.10.0863
MA0050.11.40205e-6
MA0051.15.9504e-4
MA0052.10.479
MA0055.10.0146
MA0057.10.851
MA0058.10.617
MA0059.10.55
MA0060.12.11617e-7
MA0061.10.0628
MA0062.24.84277e-4
MA0065.20.211
MA0066.10.97
MA0067.10.0121
MA0068.10.147
MA0069.10.758
MA0070.10.00107
MA0071.10.904
MA0072.10.985
MA0073.10.941
MA0074.10.618
MA0076.10.0736
MA0077.10.14
MA0078.10.933
MA0079.20.395
MA0080.21.3903e-8
MA0081.10.00401
MA0083.10.0151
MA0084.10.904
MA0087.10.886
MA0088.10.313
MA0090.10.00902
MA0091.10.868
MA0092.10.429
MA0093.10.679
MA0099.20.541
MA0100.10.722
MA0101.10.072
MA0102.23.16246e-5
MA0103.10.107
MA0104.20.145
MA0105.10.0405
MA0106.10.932
MA0107.10.0762
MA0108.21.03865e-5
MA0111.10.0771
MA0112.20.747
MA0113.10.365
MA0114.10.495
MA0115.10.974
MA0116.10.0654
MA0117.10.084
MA0119.10.495
MA0122.10.672
MA0124.10.616
MA0125.10.74
MA0131.10.772
MA0135.10.0147
MA0136.15.20072e-10
MA0137.20.0918
MA0138.20.574
MA0139.10.842
MA0140.10.571
MA0141.10.558
MA0142.10.707
MA0143.10.951
MA0144.10.227
MA0145.10.935
MA0146.10.114
MA0147.10.15
MA0148.10.165
MA0149.10.143
MA0150.10.0107
MA0152.10.966
MA0153.10.312
MA0154.10.711
MA0155.10.0861
MA0156.11.08181e-5
MA0157.10.194
MA0159.10.0585
MA0160.10.813
MA0162.10.116
MA0163.10.183
MA0164.10.699
MA0258.10.534
MA0259.10.317



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: CNhs12081

Novel motifP-value
10.034
100.0172
1000.808
1010.141
1020.411
1030.492
1040.494
1050.314
1060.871
1070.0729
1080.778
1090.864
110.942
1100.614
1110.0679
1120.0735
1130.419
1140.0571
1150.261
1160.382
1170.313
1180.608
1190.112
120.896
1200.338
1210.944
1220.77
1232.19386e-4
1240.739
1250.15
1260.566
1270.566
1280.872
1290.826
130.583
1300.0856
1310.268
1320.327
1330.998
1340.685
1350.74
1360.179
1370.0235
1380.178
1390.0447
140.775
1400.416
1410.364
1420.589
1430.679
1441
1450.742
1460.317
1470.635
1480.0364
1490.645
150.111
1500.178
1510.58
1520.217
1530.0253
1540.23
1550.205
1560.865
1570.642
1580.129
1590.777
160.814
1600.176
1610.907
1620.403
1630.632
1640.213
1650.0821
1660.977
1670.104
1680.56
1690.39
170.743
180.51
190.424
20.383
200.63
210.679
220.409
230.806
240.684
250.369
260.55
270.626
280.175
290.512
30.265
300.0463
310.829
321.50872e-4
330.965
340.299
350.147
360.0456
370.509
380.868
390.652
40.671
400.279
410.224
420.269
430.212
440.982
450.447
460.625
470.634
480.893
490.111
50.143
500.385
510.944
520.926
530.211
540.978
550.698
560.805
570.429
580.0587
590.121
60.417
600.452
610.234
620.0683
630.756
640.681
650.433
660.33
670.781
680.032
690.198
70.51
700.128
710.211
720.13
730.299
740.43
750.0234
760.0337
770.335
780.187
790.251
80.904
800.727
810.255
820.212
830.654
840.275
850.471
860.332
870.533
880.569
890.744
90.378
906.19139e-4
910.857
920.12
930.0727
940.383
950.962
960.164
970.828
980.697
990.0131



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: CNhs12081


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)
0002371 (somatic cell)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000128 (oligodendrocyte)
0000126 (macroglial cell)
0000125 (glial cell)
0000255 (eukaryotic cell)
0000127 (astrocyte)
0002603 (astrocyte of the cerebellum)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002037 (cerebellum)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002680 (regional part of metencephalon)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001895 (metencephalon)
0002028 (hindbrain)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000195 (human astrocyte of the cerebellum 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:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)

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