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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=BACH2:1.98459226229;GTF2A1,2:1.89796592157;NFE2L1:1.89613076671;HES1:1.88135096423;RFX1:1.50801497249;GLI1..3:1.49226670717;ZNF423:1.43099228348;TP53:1.41109980716;AR:1.39451649494;HMX1:1.38803393881;TFAP2{A,C}:1.38018791815;POU2F1..3:1.25899239333;FOXP3:1.16704823175;HOX{A5,B5}:1.13599248787;TFAP4:1.12449719032;NFE2L2:1.06992959091;NR1H4:1.05312601054;SPZ1:1.00760259382;HOXA9_MEIS1:0.969625871509;ZIC1..3:0.879335632675;TLX1..3_NFIC{dimer}:0.863458889146;RXR{A,B,G}:0.860940722506;VSX1,2:0.824842490265;ZNF148:0.818232626102;POU5F1:0.813618261787;TBX4,5:0.807772520666;ADNP_IRX_SIX_ZHX:0.792033258895;TEAD1:0.782034160003;LEF1_TCF7_TCF7L1,2:0.698097923226;MTF1:0.687427780038;GCM1,2:0.663835307367;EP300:0.66194404851;TFCP2:0.584937256288;SMAD1..7,9:0.577799229403;HIC1:0.540357212247;PAX5:0.521421061903;FOS_FOS{B,L1}_JUN{B,D}:0.51180134858;ZBTB6:0.500729004775;RFX2..5_RFXANK_RFXAP:0.49652239615;UFEwm:0.487457833252;ZNF384:0.47532423799;POU6F1:0.47114640791;PATZ1:0.441137996556;NR5A1,2:0.440109955657;POU3F1..4:0.431579918929;FOX{F1,F2,J1}:0.423723184946;ALX1:0.409336372437;ALX4:0.398555035716;RXRA_VDR{dimer}:0.37440477004;HSF1,2:0.373210419561;OCT4_SOX2{dimer}:0.350090574873;NKX3-1:0.342144206599;HOX{A4,D4}:0.328863571467;REST:0.321648741344;SOX2:0.31773643935;RREB1:0.293725063037;KLF4:0.287224978718;PBX1:0.284815852631;JUN:0.277799071817;T:0.260018348967;MTE{core}:0.253240252886;ATF6:0.242947314971;GZF1:0.23658100495;MAZ:0.234563681261;EBF1:0.208673989209;NR3C1:0.207797553706;SOX17:0.177350158352;PPARG:0.160024533941;ESR1:0.157736639321;RUNX1..3:0.154430532318;MYOD1:0.135520415979;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.129695295649;LHX3,4:0.108197386723;TAL1_TCF{3,4,12}:0.100018792931;HLF:0.096574599078;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.085705021041;HAND1,2:0.0837340705767;ESRRA:0.0591044461427;LMO2:0.0546976590279;SRF:0.048560887007;XCPE1{core}:0.0399872628662;NANOG:0.0314692866739;TFDP1:0.0210591250071;TOPORS:0.00940153845598;FOSL2:0.00425920597132;GATA4:0.0023951264299;STAT5{A,B}:-0.0139904695325;NFY{A,B,C}:-0.0258928831123;GTF2I:-0.0376872294787;CRX:-0.0381463236011;FOXO1,3,4:-0.0399659794376;HBP1_HMGB_SSRP1_UBTF:-0.0413295321361;RORA:-0.0479847561626;MYB:-0.0719617070125;TFAP2B:-0.0751613330969;SP1:-0.0853042598062;NFATC1..3:-0.108645433514;MED-1{core}:-0.109952119399;PAX6:-0.110574621149;NFKB1_REL_RELA:-0.118834825215;NFE2:-0.129928175754;NKX2-2,8:-0.13483523326;ONECUT1,2:-0.191892727566;TBP:-0.20049020469;STAT2,4,6:-0.20060602386;MYFfamily:-0.229948192059;SOX{8,9,10}:-0.232063336799;ZNF238:-0.237838982968;PDX1:-0.250567788759;RBPJ:-0.265685147478;NFIX:-0.268817621898;ZEB1:-0.281119561282;MZF1:-0.294075266561;HNF4A_NR2F1,2:-0.330914478491;NR6A1:-0.365711181966;IKZF1:-0.36975748213;SOX5:-0.372416070145;ZFP161:-0.388042762351;MYBL2:-0.420620025763;PRRX1,2:-0.435151291263;NHLH1,2:-0.457986821636;ATF4:-0.466580696014;CEBPA,B_DDIT3:-0.484117393828;GFI1:-0.48772984802;BREu{core}:-0.489475071096;HIF1A:-0.494675146106;MEF2{A,B,C,D}:-0.49639002761;DBP:-0.502731963682;EN1,2:-0.512010711938;NKX3-2:-0.52007967298;EGR1..3:-0.531039313433;HNF1A:-0.551379224758;AIRE:-0.553479237182;NFIL3:-0.556864986644;NANOG{mouse}:-0.565642321621;PAX2:-0.574818359602;ZBTB16:-0.580467541842;PAX1,9:-0.619454567622;GFI1B:-0.626674080618;FOX{D1,D2}:-0.650562429447;MAFB:-0.654118897382;PRDM1:-0.658077620667;ATF2:-0.663912743897;FOXL1:-0.685603512056;ETS1,2:-0.710782207213;PITX1..3:-0.713353538116;SNAI1..3:-0.723015087431;PAX8:-0.732582825108;ARID5B:-0.734032754201;CDX1,2,4:-0.748985140555;FOXQ1:-0.759132113413;SPIB:-0.763096106329;FOXA2:-0.77323150392;SREBF1,2:-0.782291825158;NKX2-1,4:-0.786155058191;NKX2-3_NKX2-5:-0.834076434575;CDC5L:-0.852695323295;FOXM1:-0.877489005911;GATA6:-0.890289804275;HMGA1,2:-0.904645135358;TGIF1:-0.910436622814;E2F1..5:-0.932857174489;PAX4:-0.939325272272;IRF7:-0.98198748683;CUX2:-0.994904768003;SPI1:-1.0012265309;DMAP1_NCOR{1,2}_SMARC:-1.01845961894;FOXN1:-1.03107507435;IKZF2:-1.06933082743;POU1F1:-1.11520108939;ELK1,4_GABP{A,B1}:-1.12633590747;IRF1,2:-1.15701470503;BPTF:-1.1784660831;NKX6-1,2:-1.22614306355;STAT1,3:-1.24497352507;FOXD3:-1.29417600559;CREB1:-1.31389930478;AHR_ARNT_ARNT2:-1.32945044025;ATF5_CREB3:-1.33045929832;ELF1,2,4:-1.35264598833;ZNF143:-1.36589086159;bHLH_family:-1.450721874;NRF1:-1.45224773597;EVI1:-1.51184474113;FOXP1:-1.7900708247;YY1:-1.84192784229;TLX2:-2.0437613517;TEF:-2.05748026701;FOX{I1,J2}:-2.50807716632
|top_motifs=BACH2:1.98459226229;GTF2A1,2:1.89796592157;NFE2L1:1.89613076671;HES1:1.88135096423;RFX1:1.50801497249;GLI1..3:1.49226670717;ZNF423:1.43099228348;TP53:1.41109980716;AR:1.39451649494;HMX1:1.38803393881;TFAP2{A,C}:1.38018791815;POU2F1..3:1.25899239333;FOXP3:1.16704823175;HOX{A5,B5}:1.13599248787;TFAP4:1.12449719032;NFE2L2:1.06992959091;NR1H4:1.05312601054;SPZ1:1.00760259382;HOXA9_MEIS1:0.969625871509;ZIC1..3:0.879335632675;TLX1..3_NFIC{dimer}:0.863458889146;RXR{A,B,G}:0.860940722506;VSX1,2:0.824842490265;ZNF148:0.818232626102;POU5F1:0.813618261787;TBX4,5:0.807772520666;ADNP_IRX_SIX_ZHX:0.792033258895;TEAD1:0.782034160003;LEF1_TCF7_TCF7L1,2:0.698097923226;MTF1:0.687427780038;GCM1,2:0.663835307367;EP300:0.66194404851;TFCP2:0.584937256288;SMAD1..7,9:0.577799229403;HIC1:0.540357212247;PAX5:0.521421061903;FOS_FOS{B,L1}_JUN{B,D}:0.51180134858;ZBTB6:0.500729004775;RFX2..5_RFXANK_RFXAP:0.49652239615;UFEwm:0.487457833252;ZNF384:0.47532423799;POU6F1:0.47114640791;PATZ1:0.441137996556;NR5A1,2:0.440109955657;POU3F1..4:0.431579918929;FOX{F1,F2,J1}:0.423723184946;ALX1:0.409336372437;ALX4:0.398555035716;RXRA_VDR{dimer}:0.37440477004;HSF1,2:0.373210419561;OCT4_SOX2{dimer}:0.350090574873;NKX3-1:0.342144206599;HOX{A4,D4}:0.328863571467;REST:0.321648741344;SOX2:0.31773643935;RREB1:0.293725063037;KLF4:0.287224978718;PBX1:0.284815852631;JUN:0.277799071817;T:0.260018348967;MTE{core}:0.253240252886;ATF6:0.242947314971;GZF1:0.23658100495;MAZ:0.234563681261;EBF1:0.208673989209;NR3C1:0.207797553706;SOX17:0.177350158352;PPARG:0.160024533941;ESR1:0.157736639321;RUNX1..3:0.154430532318;MYOD1:0.135520415979;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.129695295649;LHX3,4:0.108197386723;TAL1_TCF{3,4,12}:0.100018792931;HLF:0.096574599078;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.085705021041;HAND1,2:0.0837340705767;ESRRA:0.0591044461427;LMO2:0.0546976590279;SRF:0.048560887007;XCPE1{core}:0.0399872628662;NANOG:0.0314692866739;TFDP1:0.0210591250071;TOPORS:0.00940153845598;FOSL2:0.00425920597132;GATA4:0.0023951264299;STAT5{A,B}:-0.0139904695325;NFY{A,B,C}:-0.0258928831123;GTF2I:-0.0376872294787;CRX:-0.0381463236011;FOXO1,3,4:-0.0399659794376;HBP1_HMGB_SSRP1_UBTF:-0.0413295321361;RORA:-0.0479847561626;MYB:-0.0719617070125;TFAP2B:-0.0751613330969;SP1:-0.0853042598062;NFATC1..3:-0.108645433514;MED-1{core}:-0.109952119399;PAX6:-0.110574621149;NFKB1_REL_RELA:-0.118834825215;NFE2:-0.129928175754;NKX2-2,8:-0.13483523326;ONECUT1,2:-0.191892727566;TBP:-0.20049020469;STAT2,4,6:-0.20060602386;MYFfamily:-0.229948192059;SOX{8,9,10}:-0.232063336799;ZNF238:-0.237838982968;PDX1:-0.250567788759;RBPJ:-0.265685147478;NFIX:-0.268817621898;ZEB1:-0.281119561282;MZF1:-0.294075266561;HNF4A_NR2F1,2:-0.330914478491;NR6A1:-0.365711181966;IKZF1:-0.36975748213;SOX5:-0.372416070145;ZFP161:-0.388042762351;MYBL2:-0.420620025763;PRRX1,2:-0.435151291263;NHLH1,2:-0.457986821636;ATF4:-0.466580696014;CEBPA,B_DDIT3:-0.484117393828;GFI1:-0.48772984802;BREu{core}:-0.489475071096;HIF1A:-0.494675146106;MEF2{A,B,C,D}:-0.49639002761;DBP:-0.502731963682;EN1,2:-0.512010711938;NKX3-2:-0.52007967298;EGR1..3:-0.531039313433;HNF1A:-0.551379224758;AIRE:-0.553479237182;NFIL3:-0.556864986644;NANOG{mouse}:-0.565642321621;PAX2:-0.574818359602;ZBTB16:-0.580467541842;PAX1,9:-0.619454567622;GFI1B:-0.626674080618;FOX{D1,D2}:-0.650562429447;MAFB:-0.654118897382;PRDM1:-0.658077620667;ATF2:-0.663912743897;FOXL1:-0.685603512056;ETS1,2:-0.710782207213;PITX1..3:-0.713353538116;SNAI1..3:-0.723015087431;PAX8:-0.732582825108;ARID5B:-0.734032754201;CDX1,2,4:-0.748985140555;FOXQ1:-0.759132113413;SPIB:-0.763096106329;FOXA2:-0.77323150392;SREBF1,2:-0.782291825158;NKX2-1,4:-0.786155058191;NKX2-3_NKX2-5:-0.834076434575;CDC5L:-0.852695323295;FOXM1:-0.877489005911;GATA6:-0.890289804275;HMGA1,2:-0.904645135358;TGIF1:-0.910436622814;E2F1..5:-0.932857174489;PAX4:-0.939325272272;IRF7:-0.98198748683;CUX2:-0.994904768003;SPI1:-1.0012265309;DMAP1_NCOR{1,2}_SMARC:-1.01845961894;FOXN1:-1.03107507435;IKZF2:-1.06933082743;POU1F1:-1.11520108939;ELK1,4_GABP{A,B1}:-1.12633590747;IRF1,2:-1.15701470503;BPTF:-1.1784660831;NKX6-1,2:-1.22614306355;STAT1,3:-1.24497352507;FOXD3:-1.29417600559;CREB1:-1.31389930478;AHR_ARNT_ARNT2:-1.32945044025;ATF5_CREB3:-1.33045929832;ELF1,2,4:-1.35264598833;ZNF143:-1.36589086159;bHLH_family:-1.450721874;NRF1:-1.45224773597;EVI1:-1.51184474113;FOXP1:-1.7900708247;YY1:-1.84192784229;TLX2:-2.0437613517;TEF:-2.05748026701;FOX{I1,J2}:-2.50807716632
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000105
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 15:36, 7 March 2012


Name:Mouse Astrocytes, donor3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
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:4657
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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

CNhs12107

00
10
100
1000
10000.553
1001-0.0631
10020.168
10030.3
10040
1005-0.183
1006-0.00807
1007-0.466
10080
1009-0.19
101-0.555
10100
1011-0.0513
10120
10130.0718
10140
10150.00735
10160.365
10170
10180
10190
1020
10200.387
10210.179
1022-0.029
10230
1024-0.0899
10250
10260
10270
10280
1029-0.176
1030
10300
10310.514
10320.571
1033-0.0665
10340
10350
1036-0.183
10370
1038-0.298
10390.163
1040
10400.32
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: CNhs12107

Jaspar motifP-value
MA0002.20.0913
MA0003.10.198
MA0004.10.841
MA0006.10.442
MA0007.10.106
MA0009.10.87
MA0014.10.923
MA0017.10.58
MA0018.20.0242
MA0019.10.917
MA0024.10.00233
MA0025.10.238
MA0027.10.842
MA0028.15.28889e-4
MA0029.10.895
MA0030.10.558
MA0031.10.273
MA0035.20.376
MA0038.10.0936
MA0039.20.859
MA0040.10.309
MA0041.10.157
MA0042.10.587
MA0043.10.183
MA0046.14.37025e-4
MA0047.20.427
MA0048.10.624
MA0050.15.82335e-6
MA0051.11.82604e-4
MA0052.10.177
MA0055.10.553
MA0057.10.511
MA0058.10.94
MA0059.10.137
MA0060.10.487
MA0061.10.386
MA0062.23.92071e-9
MA0065.20.165
MA0066.10.235
MA0067.10.465
MA0068.10.644
MA0069.10.44
MA0070.10.696
MA0071.10.297
MA0072.10.764
MA0073.10.678
MA0074.10.194
MA0076.11.49376e-5
MA0077.10.0575
MA0078.10.0519
MA0079.20.643
MA0080.22.73016e-5
MA0081.10.0136
MA0083.10.885
MA0084.10.269
MA0087.10.45
MA0088.10.921
MA0090.10.00819
MA0091.10.954
MA0092.10.449
MA0093.10.979
MA0099.24.49846e-4
MA0100.10.796
MA0101.10.508
MA0102.20.0649
MA0103.10.98
MA0104.20.854
MA0105.10.13
MA0106.10.224
MA0107.10.335
MA0108.20.968
MA0111.10.27
MA0112.20.0378
MA0113.10.215
MA0114.10.875
MA0115.10.325
MA0116.10.0977
MA0117.10.221
MA0119.10.0352
MA0122.10.276
MA0124.10.833
MA0125.10.972
MA0131.10.19
MA0135.10.176
MA0136.12.47507e-7
MA0137.20.0428
MA0138.20.589
MA0139.10.644
MA0140.10.0207
MA0141.10.0252
MA0142.10.0374
MA0143.10.0491
MA0144.10.27
MA0145.10.152
MA0146.10.129
MA0147.10.563
MA0148.10.169
MA0149.10.198
MA0150.10.44
MA0152.10.46
MA0153.10.00832
MA0154.10.0941
MA0155.10.16
MA0156.12.62772e-11
MA0157.10.346
MA0159.10.159
MA0160.10.198
MA0162.10.122
MA0163.10.0421
MA0164.10.72
MA0258.10.0886
MA0259.10.483



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: CNhs12107

Novel motifP-value
10.652
100.852
1000.556
1010.72
1020.818
1030.944
1040.474
1051
1060.0202
1070.0856
1080.492
1090.0653
110.096
1100.563
1110.511
1120.851
1130.704
1140.171
1150.705
1160.0107
1170.512
1180.477
1190.799
120.914
1200.677
1210.761
1220.154
1230.347
1240.802
1250.68
1260.896
1270.631
1280.0594
1290.426
130.805
1300.491
1310.9
1320.00909
1330.108
1340.915
1350.0561
1360.816
1370.374
1380.912
1390.854
140.335
1400.203
1410.674
1420.47
1430.0529
1440.944
1450.407
1460.908
1470.86
1480.761
1490.324
150.706
1500.393
1510.634
1520.0476
1530.302
1540.565
1550.367
1560.133
1570.105
1580.154
1590.201
1600.734
1610.746
1620.13
1630.15
1640.102
1650.777
1660.399
1670.0495
1680.567
1690.161
170.35
180.228
190.159
20.195
200.795
210.115
220.137
230.0226
240.307
250.68
260.931
270.278
280.834
290.728
30.352
300.233
310.34
320.0348
330.78
340.117
350.688
360.986
370.157
380.389
390.238
40.288
400.367
410.197
420.346
430.273
440.103
450.306
460.916
470.394
480.695
490.612
50.623
500.259
510.798
520.125
530.982
540.876
550.205
560.219
570.07
580.612
590.0176
60.488
600.086
610.766
620.841
630.0187
640.172
650.055
660.613
670.297
680.728
690.251
70.971
700.0385
710.315
720.997
730.0776
740.892
750.879
760.292
770.00951
780.0711
790.992
80.0297
800.442
810.313
820.573
830.891
840.268
850.00419
860.972
870.0718
880.115
890.601
90.843
900.67
910.0863
920.856
930.456
940.736
950.04
960.823
970.967
980.0034
990.115



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: CNhs12107


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)

UBERON: Anatomy
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)

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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