Personal tools

FF:11713-123C3: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:11713-123C3 |name=Mouse Granule cells, donor1 |sample_id=11713 |rna_tube_id=123C3 |rna_box=123 |rna_position=C3 |sample_cell_lot=N/A |sample_cell_ca...")
 
No edit summary
Line 40: Line 40:
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|sample_description=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 66:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=LHX3,4:2.90925500971;POU6F1:2.75967368021;TFDP1:2.63599158536;BREu{core}:2.45865885917;ZFP161:2.41909167869;SOX{8,9,10}:2.36075167057;SOX2:2.31618523213;MED-1{core}:2.26903453171;ADNP_IRX_SIX_ZHX:2.21106929333;OCT4_SOX2{dimer}:2.1578716618;MTE{core}:2.1272512181;PAX6:2.12105601181;MZF1:2.04984977794;AHR_ARNT_ARNT2:1.99050492084;VSX1,2:1.9823081991;LEF1_TCF7_TCF7L1,2:1.98038304309;TFAP2B:1.92844098192;ZBTB6:1.91928469863;RREB1:1.71860287007;SOX17:1.69987573316;FOXD3:1.69852417848;HIC1:1.69486708851;REST:1.66098971227;POU5F1:1.65850402332;EGR1..3:1.65757084157;NRF1:1.64765325928;ONECUT1,2:1.64371216785;HMX1:1.58793188998;ALX1:1.53861572837;FOXQ1:1.51281781883;ZIC1..3:1.5030426356;KLF4:1.48010122812;PRDM1:1.47188336455;PATZ1:1.44149453614;POU3F1..4:1.41862815462;RFX1:1.41440774782;SMAD1..7,9:1.34425386466;LMO2:1.31815431408;NKX6-1,2:1.28906516613;NANOG:1.28203649164;ATF2:1.27141518736;POU2F1..3:1.26792458057;NHLH1,2:1.23935770108;PRRX1,2:1.2317198947;UFEwm:1.16728263909;NANOG{mouse}:1.1096798367;TGIF1:1.07294817208;ZNF143:1.0638246594;GTF2I:1.04818335351;GFI1B:1.04334874978;HOXA9_MEIS1:1.0148727593;YY1:0.99923891668;ZNF423:0.979577782128;JUN:0.931679042449;NFE2L1:0.931533714829;EN1,2:0.866563798061;DBP:0.851991477639;RFX2..5_RFXANK_RFXAP:0.847728221707;MYFfamily:0.842551852891;CDX1,2,4:0.834068860946;PAX5:0.785235541487;PAX8:0.696591313057;MTF1:0.681631497913;HOX{A5,B5}:0.675450256313;HOX{A4,D4}:0.671277404657;CUX2:0.646896222005;BPTF:0.629316393414;MAZ:0.627594402993;NR5A1,2:0.615146396318;NKX2-1,4:0.614298361416;FOX{I1,J2}:0.55947454945;CREB1:0.554910699937;ELK1,4_GABP{A,B1}:0.520641272012;RORA:0.512218959007;RBPJ:0.489282562203;NFY{A,B,C}:0.482197874356;HBP1_HMGB_SSRP1_UBTF:0.480653281024;EP300:0.467809552193;PAX4:0.434539291827;PBX1:0.381685854996;GTF2A1,2:0.369895219203;ATF5_CREB3:0.356384828421;HES1:0.35009940006;FOXL1:0.288600445527;SOX5:0.287448691904;FOXM1:0.286749267075;TFAP2{A,C}:0.252077729756;MAFB:0.249636191351;ZNF384:0.246767170172;NKX3-1:0.243869321499;NKX3-2:0.231674414459;RXR{A,B,G}:0.20578595325;HMGA1,2:0.197336459209;PAX2:0.190048498838;HIF1A:0.189242946795;STAT5{A,B}:0.146231813787;TBX4,5:0.131594904535;NKX2-3_NKX2-5:0.124389722953;HAND1,2:0.12043566676;GATA4:0.118326155843;ATF4:0.085074342631;TEF:0.0766515658127;ARID5B:0.0738924848593;FOXP3:0.0547919537458;FOX{F1,F2,J1}:0.040804598907;NR3C1:0.0341709111473;ZBTB16:0.0170490713437;CRX:0.00232237972291;SP1:-0.00381307087567;CDC5L:-0.0140622876239;PPARG:-0.0503833709406;HSF1,2:-0.0925373592086;FOXN1:-0.111133995473;GZF1:-0.124355817296;NFIL3:-0.132859992253;TFAP4:-0.142376829842;NFIX:-0.183660431505;ATF6:-0.184251974428;POU1F1:-0.193251564576;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.202465933671;ZEB1:-0.203996336546;ESR1:-0.205579922698;MYB:-0.20787887452;bHLH_family:-0.219164488887;GFI1:-0.246893818626;SPZ1:-0.248863801289;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.256522308035;PAX1,9:-0.327862555365;TAL1_TCF{3,4,12}:-0.355051966133;EVI1:-0.40185925796;MYOD1:-0.415833279207;IKZF2:-0.419381402838;PITX1..3:-0.423264902036;ALX4:-0.433444894047;GCM1,2:-0.438430254743;XCPE1{core}:-0.45759395871;ESRRA:-0.467961088169;STAT1,3:-0.46833275588;ZNF238:-0.516531183527;TOPORS:-0.521850699147;AIRE:-0.529597715087;SNAI1..3:-0.552378599586;RUNX1..3:-0.554304639766;NR1H4:-0.57641593184;HNF4A_NR2F1,2:-0.596028416998;IKZF1:-0.607794323291;GATA6:-0.623108818558;TLX1..3_NFIC{dimer}:-0.635576047179;TP53:-0.636133296417;SPI1:-0.645326754988;NFKB1_REL_RELA:-0.672785290435;HNF1A:-0.694529531682;SREBF1,2:-0.705399046414;MEF2{A,B,C,D}:-0.724509969726;E2F1..5:-0.736125002435;FOXA2:-0.832055767252;FOXP1:-0.832901880068;ZNF148:-0.851588048125;TBP:-0.852787039212;GLI1..3:-0.868006919721;T:-0.884750374292;AR:-0.90980033128;NFE2L2:-0.937353817904;HLF:-0.957351048249;ELF1,2,4:-0.986088438964;SPIB:-0.992190187455;TLX2:-1.05989256189;EBF1:-1.08132825393;TFCP2:-1.09055515507;FOSL2:-1.09175227849;MYBL2:-1.09433779954;CEBPA,B_DDIT3:-1.13242728097;TEAD1:-1.15286629112;ETS1,2:-1.19315544476;BACH2:-1.19322571242;FOS_FOS{B,L1}_JUN{B,D}:-1.21827800607;FOXO1,3,4:-1.22016545382;NFE2:-1.28168145381;PDX1:-1.30153290701;NFATC1..3:-1.38206564548;DMAP1_NCOR{1,2}_SMARC:-1.3862814337;RXRA_VDR{dimer}:-1.41013229341;FOX{D1,D2}:-1.47260703796;SRF:-1.65004207258;IRF7:-1.66891131064;NKX2-2,8:-1.69840024069;NR6A1:-1.74207008796;IRF1,2:-1.75747311891;STAT2,4,6:-1.94272168275
}}
}}

Revision as of 15:17, 15 February 2012


Name:Mouse Granule cells, donor1
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 typeneuron, granule 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-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

CNhs12131

00
10.378
100
1000.48
10000
1001-0.0749
10020.0437
10030.0404
10040
1005-0.191
10060.305
10070.0237
10080
1009-0.19
101-0.199
10100
10110.183
10120.08
1013-0.117
10140
10150.383
10160.299
10170
10180
10190
1020
10200.583
10210.0313
1022-0.0704
10230
1024-0.14
10250
10260
10270.294
10280
1029-0.176
103-0.0887
10300
1031-0.547
10320.0302
10330
10340
10350
1036-0.217
10370
10380.0857
1039-0.196
1040
1040-0.171
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: CNhs12131

Jaspar motifP-value
MA0002.20.00191
MA0003.10.185
MA0004.10.618
MA0006.10.095
MA0007.10.19
MA0009.10.888
MA0014.10.484
MA0017.16.46573e-5
MA0018.20.00735
MA0019.10.412
MA0024.10.59
MA0025.10.824
MA0027.10.423
MA0028.10.504
MA0029.10.86
MA0030.10.66
MA0031.10.0945
MA0035.20.177
MA0038.10.227
MA0039.20.0267
MA0040.10.807
MA0041.10.189
MA0042.10.53
MA0043.10.0677
MA0046.16.16299e-7
MA0047.20.00219
MA0048.10.379
MA0050.12.79392e-9
MA0051.12.05134e-4
MA0052.10.0442
MA0055.10.469
MA0057.10.118
MA0058.10.584
MA0059.10.365
MA0060.19.34294e-5
MA0061.10.0529
MA0062.20.14
MA0065.23.57478e-5
MA0066.10.139
MA0067.10.75
MA0068.10.895
MA0069.10.108
MA0070.10.139
MA0071.10.223
MA0072.10.203
MA0073.10.939
MA0074.10.419
MA0076.10.807
MA0077.10.00377
MA0078.10.0509
MA0079.20.558
MA0080.22.6858e-10
MA0081.10.341
MA0083.10.00384
MA0084.10.409
MA0087.10.332
MA0088.10.158
MA0090.10.0285
MA0091.10.23
MA0092.10.183
MA0093.10.628
MA0099.22.81048e-4
MA0100.10.805
MA0101.10.098
MA0102.20.942
MA0103.10.149
MA0104.20.687
MA0105.10.0304
MA0106.10.0942
MA0107.10.0701
MA0108.20.241
MA0111.10.981
MA0112.21.18615e-4
MA0113.10.221
MA0114.11.48614e-4
MA0115.10.00957
MA0116.10.055
MA0117.10.766
MA0119.10.0643
MA0122.10.465
MA0124.10.825
MA0125.10.207
MA0131.10.815
MA0135.10.0852
MA0136.16.99451e-8
MA0137.20.0182
MA0138.20.237
MA0139.10.258
MA0140.10.00344
MA0141.10.0151
MA0142.10.02
MA0143.10.00992
MA0144.10.0224
MA0145.10.0509
MA0146.10.0576
MA0147.10.758
MA0148.12.24275e-5
MA0149.10.069
MA0150.10.0381
MA0152.10.0516
MA0153.11.91811e-6
MA0154.10.0109
MA0155.10.665
MA0156.12.42299e-5
MA0157.10.0336
MA0159.10.00276
MA0160.10.111
MA0162.10.306
MA0163.10.00254
MA0164.10.759
MA0258.10.0127
MA0259.10.634



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: CNhs12131

Novel motifP-value
10.129
100.0842
1000.74
1010.8
1020.915
1030.0804
1040.942
1050.168
1060.0118
1070.0427
1080.391
1090.00513
110.0954
1100.0876
1110.0654
1120.00305
1130.979
1140.189
1150.57
1160.6
1170.0433
1180.405
1190.0953
120.602
1200.895
1210.422
1220.681
1230.192
1240.787
1250.389
1260.22
1270.139
1280.0256
1290.214
131.93392e-5
1300.379
1310.499
1320.916
1330.374
1340.36
1350.704
1360.276
1370.212
1380.612
1390.109
140.622
1400.0952
1410.135
1420.0315
1430.528
1440.992
1450.00844
1460.434
1470.892
1480.492
1490.124
150.138
1500.165
1510.405
1520.047
1530.576
1540.613
1550.8
1560.00677
1570.188
1580.154
1590.059
1600.272
1610.336
1620.744
1630.445
1640.0188
1650.0377
1660.655
1670.956
1680.603
1690.00365
170.0197
180.751
190.0548
20.86
200.44
210.488
220.111
230.25
240.0351
250.721
264.49515e-4
270.87
280.398
290.105
30.0646
300.757
310.906
320.459
330.16
340.578
350.607
360.316
370.0115
380.323
390.213
40.546
400.287
410.929
420.201
430.12
440.759
450.59
460.11
470.229
480.114
490.136
50.142
500.258
510.62
520.128
530.63
540.681
550.962
560.353
570.582
580.213
590.079
60.612
600.0145
610.158
620.111
630.0981
640.88
650.261
660.712
670.688
680.209
690.527
70.0201
700.014
710.0136
720.354
730.0227
740.235
750.107
760.637
770.211
780.0313
790.424
80.119
800.995
810.502
820.0967
830.271
840.766
850.0568
860.262
870.314
880.326
890.277
90.287
900.134
910.289
920.2
930.0409
940.8
950.0439
960.256
970.884
980.659
990.235



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: CNhs12131


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000117 (CNS neuron (sensu Vertebrata))
0000120 (granule cell)
0000133 (neurectodermal cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000337 (neuroblast (sensu Vertebrata))
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000723 (somatic stem cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic 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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11713-123C3&oldid=413679"