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{{f5samples
{{f5samples
|id=FF:11709-123B8
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000349,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0000956,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001869,UBERON:0001890,UBERON:0001893,UBERON:0001954,UBERON:0002050,UBERON:0002346,UBERON:0002421,UBERON:0002532,UBERON:0002600,UBERON:0002616,UBERON:0002619,UBERON:0002780,UBERON:0002791,UBERON:0003022,UBERON:0003056,UBERON:0003075,UBERON:0003080,UBERON:0004121,UBERON:0005068,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007135,UBERON:0007284
|name=Mouse Astrocytes - hippocampus, donor1
|sample_id=11709
|rna_tube_id=123B8
|rna_box=123
|rna_position=B8
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=Sciencell/3H
|rna_lot_number=lot:5772
|rna_catalog_number=custom
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_dev_stage=
|sample_tissue=hippocampus
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=9.5
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=astrocyte
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=10
|rna_concentration=0.954
|sample_note=
|profile_hcage=CNhs12129,LSID839,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000030,CL:0000055,CL:0000095,CL:0000123,CL:0000125,CL:0000126,CL:0000127,CL:0000128,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000243,CL:0000255,CL:0000333,CL:0000339,CL:0000548,CL:0002319,CL:0002321,CL:0002371,CL:0002453,CL:0002604
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000030,CL:0000055,CL:0000095,CL:0000123,CL:0000125,CL:0000126,CL:0000127,CL:0000128,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000243,CL:0000255,CL:0000333,CL:0000339,CL:0000548,CL:0002319,CL:0002321,CL:0002371,CL:0002453,CL:0002604
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000349,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0000956,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001869,UBERON:0001890,UBERON:0001893,UBERON:0001954,UBERON:0002050,UBERON:0002346,UBERON:0002421,UBERON:0002532,UBERON:0002600,UBERON:0002616,UBERON:0002619,UBERON:0002780,UBERON:0002791,UBERON:0003022,UBERON:0003056,UBERON:0003075,UBERON:0003080,UBERON:0004121,UBERON:0005068,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007135,UBERON:0007284
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11709-123B8
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000197
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000197
|name=Mouse Astrocytes - hippocampus, donor1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12129,LSID839,release011,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=123
|rna_catalog_number=custom
|rna_concentration=0.954
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=lot:5772
|rna_od260/230=
|rna_od260/280=
|rna_position=B8
|rna_rin=9.5
|rna_sample_type=total RNA
|rna_tube_id=123B8
|rna_weight_ug=10
|sample_age=
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=astrocyte
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Sciencell/3H
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11709
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=hippocampus
|top_motifs=GTF2A1,2:2.88769751346;BACH2:2.44222230751;TFAP2{A,C}:1.95698822168;HES1:1.92657702048;TP53:1.87313609098;HMX1:1.81497064995;EP300:1.76451091384;ZNF423:1.7353852529;TEAD1:1.72729935111;TLX1..3_NFIC{dimer}:1.66096677701;AR:1.6546167074;NFE2L2:1.60955284293;NR1H4:1.53366557087;ESR1:1.52780239961;PAX5:1.44118562995;RXRA_VDR{dimer}:1.41720144338;MTE{core}:1.37519198355;NFE2L1:1.36428390889;TFCP2:1.3387745021;ZNF148:1.33388616577;FOXP3:1.31091340713;TFAP4:1.3003101212;MTF1:1.2997378499;RFX1:1.26976559425;RXR{A,B,G}:1.19067872522;HAND1,2:1.1844186827;FOS_FOS{B,L1}_JUN{B,D}:1.08086692903;ZBTB6:1.0798191562;GCM1,2:1.07950261259;XCPE1{core}:1.0600980348;FOXN1:0.967996954842;ALX4:0.887931577874;ATF6:0.881723222718;VSX1,2:0.802892840984;SP1:0.801707044539;ZIC1..3:0.799683606299;HOXA9_MEIS1:0.794491581139;POU2F1..3:0.764090045424;GLI1..3:0.758631470617;EBF1:0.755975591356;PATZ1:0.73156715879;ATF4:0.726606015771;UFEwm:0.721676603523;FOX{F1,F2,J1}:0.717852084282;GZF1:0.705527939548;TBX4,5:0.670382537047;HIC1:0.633484597482;MAZ:0.563409567562;TFAP2B:0.56005583497;ZNF238:0.549833077434;PAX6:0.528550723005;RREB1:0.523283302251;CRX:0.500307217336;HOX{A4,D4}:0.495312716989;FOSL2:0.453091348991;HSF1,2:0.427546003311;HOX{A5,B5}:0.427268052724;ARID5B:0.418089341233;ADNP_IRX_SIX_ZHX:0.416887208283;HBP1_HMGB_SSRP1_UBTF:0.383319553646;RFX2..5_RFXANK_RFXAP:0.374097859025;HIF1A:0.373279435828;MYOD1:0.359054516982;SMAD1..7,9:0.328857160981;GTF2I:0.306416958558;EGR1..3:0.284300938467;T:0.273871936552;NKX3-1:0.254408194162;REST:0.252865684019;STAT2,4,6:0.220800793068;IKZF1:0.217256639841;KLF4:0.164002130744;LEF1_TCF7_TCF7L1,2:0.162225582186;MED-1{core}:0.153074462345;NFIL3:0.150610663647;NFE2:0.142854085237;SPZ1:0.128853292981;EN1,2:0.117158469629;JUN:0.116404385085;NR5A1,2:0.101795276094;MYFfamily:0.0917730172524;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.0880303675132;HLF:0.074252128564;NFIX:0.061588358389;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0530427697512;RUNX1..3:0.0146710598995;ZFP161:0.00943202747982;FOX{D1,D2}:-0.00178049755218;SRF:-0.0194258130896;FOXM1:-0.0327377291897;NR3C1:-0.0553906091376;OCT4_SOX2{dimer}:-0.0747563137751;SOX2:-0.0869480233571;PDX1:-0.089409369042;NKX2-3_NKX2-5:-0.0929697400751;RORA:-0.0930366963767;POU5F1:-0.093682971214;SOX17:-0.12544631084;ONECUT1,2:-0.14736670675;ESRRA:-0.149456241891;ZEB1:-0.164373656122;PBX1:-0.196845661753;PAX8:-0.205693176965;MZF1:-0.209210755053;GATA4:-0.235915063709;NR6A1:-0.247982854237;PPARG:-0.258425673669;ATF2:-0.263237511517;MYB:-0.267354800394;CDC5L:-0.282832322952;TBP:-0.283918609817;NFATC1..3:-0.288528554737;NFKB1_REL_RELA:-0.292921273053;GFI1B:-0.328745898441;NKX2-2,8:-0.336699530397;NHLH1,2:-0.353126603648;ALX1:-0.356315721027;NKX3-2:-0.36758187725;STAT5{A,B}:-0.374109028913;HNF4A_NR2F1,2:-0.383733872658;ZNF384:-0.39609895757;NFY{A,B,C}:-0.40061264784;TOPORS:-0.409348917409;FOXO1,3,4:-0.42203712126;LHX3,4:-0.429727030838;PAX1,9:-0.437078407253;SOX5:-0.437530406468;BREu{core}:-0.444700980335;IRF1,2:-0.44588778487;NKX2-1,4:-0.452402581235;LMO2:-0.466023519438;MEF2{A,B,C,D}:-0.467385294356;CEBPA,B_DDIT3:-0.499972041179;ELK1,4_GABP{A,B1}:-0.501145130194;PRDM1:-0.550461494726;ELF1,2,4:-0.569143777043;TAL1_TCF{3,4,12}:-0.572196015083;HNF1A:-0.579388275728;POU1F1:-0.580965095964;PAX2:-0.600847790776;NANOG{mouse}:-0.603007928012;RBPJ:-0.620615668156;SPIB:-0.637624788172;SNAI1..3:-0.64698090241;IRF7:-0.666188658718;GFI1:-0.667630749473;TFDP1:-0.669472701313;bHLH_family:-0.672677604577;SREBF1,2:-0.684714183826;CREB1:-0.703011549238;PRRX1,2:-0.708719639723;YY1:-0.728865523133;POU3F1..4:-0.760723783267;NANOG:-0.764572074642;FOXL1:-0.779474859321;ETS1,2:-0.787638743917;FOXA2:-0.794101259489;TGIF1:-0.80576845789;IKZF2:-0.813577822414;ZBTB16:-0.816633265432;STAT1,3:-0.827486240579;CUX2:-0.853857791993;ATF5_CREB3:-0.874130182364;SPI1:-0.911101889671;MYBL2:-0.929407984076;HMGA1,2:-0.940944361412;POU6F1:-0.957225751607;ZNF143:-0.967437193311;SOX{8,9,10}:-1.02055638478;GATA6:-1.04562120505;MAFB:-1.0559527998;NRF1:-1.14494948077;AIRE:-1.16763716881;PITX1..3:-1.18830467879;TEF:-1.21276658072;FOXD3:-1.22848882786;DMAP1_NCOR{1,2}_SMARC:-1.29258292872;BPTF:-1.30186279573;DBP:-1.31384167854;E2F1..5:-1.32906798098;PAX4:-1.3395541847;AHR_ARNT_ARNT2:-1.42135770354;CDX1,2,4:-1.44617086515;FOX{I1,J2}:-1.55804523515;TLX2:-1.55914738059;EVI1:-1.61490393694;NKX6-1,2:-1.65096311527;FOXP1:-1.91334847264;FOXQ1:-2.35802267776
}}
}}

Revision as of 15:00, 21 March 2012


Name:Mouse Astrocytes - hippocampus, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuehippocampus
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 numberlot:5772
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs12129

00
10
100
1000
10000.598
1001-0.0668
10020.268
10030.502
10040
10050
10060.247
1007-0.368
10080
10090.281
101-0.477
10100
10110.0299
10120
10130.172
1014-0.0083
10150.132
10160.317
10170
10180
10190
1020
10200.404
10210.0871
10220.0862
10230
10240.0941
1025-0.0611
10260
10270.0383
10280
1029-0.176
1030.181
10300
10310.146
10320.583
1033-0.00544
10340
10350
1036-0.223
10370
10380.0889
10390.0561
1040
10400.563
10410



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 no result for this sample


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: CNhs12129

Jaspar motifP-value
MA0002.20.707
MA0003.10.243
MA0004.10.89
MA0006.10.285
MA0007.10.078
MA0009.10.601
MA0014.10.543
MA0017.10.13
MA0018.20.369
MA0019.10.382
MA0024.18.68507e-6
MA0025.10.821
MA0027.10.377
MA0028.10.0184
MA0029.10.959
MA0030.10.736
MA0031.10.812
MA0035.20.03
MA0038.10.157
MA0039.20.226
MA0040.10.659
MA0041.10.171
MA0042.10.584
MA0043.10.758
MA0046.14.33986e-4
MA0047.20.596
MA0048.10.649
MA0050.10.139
MA0051.10.708
MA0052.10.453
MA0055.10.272
MA0057.10.854
MA0058.10.936
MA0059.10.874
MA0060.10.444
MA0061.10.973
MA0062.22.09459e-6
MA0065.20.932
MA0066.10.92
MA0067.10.489
MA0068.10.326
MA0069.10.0526
MA0070.10.526
MA0071.10.535
MA0072.10.634
MA0073.10.815
MA0074.10.618
MA0076.10.00269
MA0077.10.515
MA0078.10.836
MA0079.20.0117
MA0080.28.33241e-6
MA0081.10.0944
MA0083.10.734
MA0084.10.131
MA0087.10.201
MA0088.10.812
MA0090.13.69544e-5
MA0091.10.0739
MA0092.10.506
MA0093.10.901
MA0099.22.68476e-4
MA0100.10.778
MA0101.10.175
MA0102.20.247
MA0103.10.0892
MA0104.20.489
MA0105.10.699
MA0106.10.101
MA0107.10.102
MA0108.20.741
MA0111.10.848
MA0112.20.2
MA0113.10.309
MA0114.10.0487
MA0115.10.125
MA0116.10.982
MA0117.10.609
MA0119.10.0832
MA0122.10.765
MA0124.10.497
MA0125.10.922
MA0131.10.0365
MA0135.10.27
MA0136.15.13925e-7
MA0137.20.545
MA0138.20.787
MA0139.10.816
MA0140.15.23638e-5
MA0141.10.899
MA0142.10.93
MA0143.10.54
MA0144.10.788
MA0145.10.0249
MA0146.10.0242
MA0147.10.504
MA0148.10.206
MA0149.10.766
MA0150.10.76
MA0152.10.346
MA0153.10.00105
MA0154.10.722
MA0155.10.221
MA0156.16.54047e-10
MA0157.10.8
MA0159.10.523
MA0160.10.577
MA0162.10.155
MA0163.10.821
MA0164.10.84
MA0258.10.803
MA0259.10.184



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: CNhs12129

Novel motifP-value
10.33
100.315
1000.674
1010.975
1020.43
1030.103
1040.822
1050.694
1060.0181
1070.394
1080.488
1090.0211
110.242
1100.913
1110.555
1120.59
1130.412
1140.528
1150.853
1160.153
1170.252
1180.152
1190.69
120.861
1200.648
1210.617
1220.564
1230.962
1240.718
1250.766
1260.303
1270.71
1280.214
1290.296
130.324
1300.764
1310.93
1320.0389
1330.408
1340.756
1350.235
1360.0475
1370.216
1380.875
1390.901
140.246
1400.0145
1410.903
1420.12
1430.245
1440.77
1450.676
1460.688
1470.896
1480.627
1490.536
150.936
1500.198
1510.826
1520.00401
1530.052
1540.295
1550.299
1560.0156
1570.436
1580.0231
1590.139
1600.371
1610.747
1620.586
1630.353
1640.00691
1650.809
1660.804
1670.0316
1680.434
1690.142
170.317
180.984
190.27
20.0763
200.794
210.325
220.0645
230.0711
240.236
250.214
260.396
270.738
280.648
290.548
30.884
300.194
310.33
320.00984
330.774
340.15
350.493
360.129
370.148
380.528
390.262
40.778
400.871
410.819
420.951
430.734
440.209
450.228
460.222
470.656
480.737
490.171
50.176
500.12
510.462
520.0627
530.814
540.511
550.477
560.406
570.56
580.124
590.079
60.798
600.099
610.705
620.435
630.0454
640.386
650.0583
660.313
670.963
680.713
690.257
70.223
700.0814
710.583
720.708
730.00507
740.186
750.642
760.114
770.00442
780.0129
790.883
80.645
800.327
810.936
820.903
830.8
840.202
850.0499
860.946
878.85116e-4
880.421
890.75
90.574
900.487
910.561
920.768
930.148
940.0428
950.0276
960.14
970.832
980.105
990.281



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: CNhs12129


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)
0000030 (glioblast)
0000055 (non-terminally differentiated cell)
0000095 (neuron associated cell)
0000123 (neuron associated cell (sensu Vertebrata))
0000125 (glial cell)
0000126 (macroglial cell)
0000127 (astrocyte)
0000128 (oligodendrocyte)
0000133 (neurectodermal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000243 (glial cell (sensu Vertebrata))
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000339 (glioblast (sensu Vertebrata))
0000548 (animal cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002453 (oligodendrocyte precursor cell)
0002604 (astrocyte of the hippocampus)

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000349 (limbic system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001890 (forebrain)
0001893 (telencephalon)
0001954 (Ammon's horn)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002421 (hippocampal formation)
0002532 (epiblast (generic))
0002600 (limbic lobe)
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003022 (lobe parts of cerebral cortex)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

FF: FANTOM5
NA

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
NA

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