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|top_motifs=HES1:2.17829646799;GLI1..3:1.93671341292;TP53:1.93327275655;ATF6:1.70124808789;BACH2:1.65847612538;HOX{A5,B5}:1.63886828647;ESR1:1.53248934913;ZNF423:1.46621846594;EP300:1.39977541295;GCM1,2:1.19827478212;HOXA9_MEIS1:1.19647793969;HAND1,2:1.1379549587;FOSL2:1.06650950964;TFAP2{A,C}:1.04559529532;ALX4:0.995308620684;ZIC1..3:0.974910625134;TFCP2:0.973487816277;GTF2A1,2:0.952688528722;ZNF238:0.936524588696;AR:0.869328605163;TEAD1:0.862409088039;TLX1..3_NFIC{dimer}:0.809827386722;POU2F1..3:0.782907765612;ZNF148:0.782528334778;PDX1:0.733138783183;NR1H4:0.711345364599;PPARG:0.702366695278;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.69443115631;FOS_FOS{B,L1}_JUN{B,D}:0.664390289432;UFEwm:0.652454938781;PAX2:0.614238620512;NFE2L2:0.605926995615;EBF1:0.58948982466;MTE{core}:0.526052957341;HMX1:0.520174533641;TFAP4:0.483237805709;RXRA_VDR{dimer}:0.479488049509;GZF1:0.445391279902;ZNF384:0.442986600102;SRF:0.442135504901;RREB1:0.431512670446;TAL1_TCF{3,4,12}:0.404296362957;NFATC1..3:0.400965649717;HSF1,2:0.379552387183;POU3F1..4:0.354030198258;TOPORS:0.334362727382;XCPE1{core}:0.324118152935;GATA4:0.297282447728;HIC1:0.29111495282;IRF7:0.266924181157;ALX1:0.242096719384;HBP1_HMGB_SSRP1_UBTF:0.236240402254;FOX{F1,F2,J1}:0.192857617368;VSX1,2:0.191573554459;GTF2I:0.168539948134;IKZF1:0.162623805516;LHX3,4:0.155194420509;RUNX1..3:0.150840195352;PATZ1:0.149851336342;MTF1:0.140856434512;STAT1,3:0.138897314642;STAT2,4,6:0.132272130016;MAZ:0.118015471828;NFE2L1:0.112882829015;LEF1_TCF7_TCF7L1,2:0.0990768827593;FOXO1,3,4:0.0927771269335;RFX1:0.0865988871079;REST:0.0518933614496;SOX5:0.0493092954782;NFE2:0.0483196392321;TBP:0.046100227765;JUN:0.0408035823026;SOX17:0.0385574840466;ADNP_IRX_SIX_ZHX:0.0315436173472;HMGA1,2:0.0313603152381;FOXP3:0.030596714243;TBX4,5:0.0293130296335;SP1:0.00501212482798;NFKB1_REL_RELA:-0.00345618975065;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.00415875812694;IRF1,2:-0.0176803336698;KLF4:-0.0179791903317;HOX{A4,D4}:-0.067539938393;NKX3-1:-0.0679686027095;HLF:-0.0695481183641;NKX2-3_NKX2-5:-0.0908677586919;CRX:-0.106060784973;PAX5:-0.11338625048;ONECUT1,2:-0.113588555894;NR6A1:-0.13961118097;SMAD1..7,9:-0.143233746915;ZBTB6:-0.147830758922;CDC5L:-0.148297869907;NR5A1,2:-0.161561260005;RORA:-0.18514317017;MYB:-0.197760205588;PRRX1,2:-0.226076991099;NFIL3:-0.226177400598;TFAP2B:-0.239174126662;HNF4A_NR2F1,2:-0.254953721756;GFI1B:-0.259998425171;RXR{A,B,G}:-0.27180858157;ESRRA:-0.276767116729;TLX2:-0.279085617475;DMAP1_NCOR{1,2}_SMARC:-0.291447408342;CEBPA,B_DDIT3:-0.303035733576;SPIB:-0.304271333424;ZBTB16:-0.306383417518;NKX2-2,8:-0.32564995054;ETS1,2:-0.342970892622;NFY{A,B,C}:-0.347564027342;MED-1{core}:-0.347882238236;EGR1..3:-0.35831759938;EN1,2:-0.376861290231;T:-0.387935031975;SREBF1,2:-0.396888322259;FOX{D1,D2}:-0.416180808272;FOXM1:-0.434916536579;HIF1A:-0.437973571711;TFDP1:-0.452608499205;MYBL2:-0.456425040442;MYFfamily:-0.457710499304;PAX8:-0.461280889387;NR3C1:-0.461764680304;NHLH1,2:-0.468139940199;SOX{8,9,10}:-0.483135740787;HNF1A:-0.490766172218;SOX2:-0.493049082413;POU5F1:-0.511344937522;FOXL1:-0.518757185198;MAFB:-0.519353689517;MZF1:-0.519976861843;ELF1,2,4:-0.52899470176;MEF2{A,B,C,D}:-0.532053608564;STAT5{A,B}:-0.533136238488;SPZ1:-0.555575469636;ATF4:-0.596489698032;DBP:-0.598955703016;FOXA2:-0.609080371877;PAX1,9:-0.615197930226;E2F1..5:-0.652301260566;NANOG:-0.670002851062;POU1F1:-0.688128963568;ZFP161:-0.694484303957;ELK1,4_GABP{A,B1}:-0.729364275842;BREu{core}:-0.773715181836;ZEB1:-0.777346811291;PAX4:-0.778449990219;SPI1:-0.78741312886;NANOG{mouse}:-0.795894020623;POU6F1:-0.801119433903;TEF:-0.809762169733;ATF2:-0.858724061845;OCT4_SOX2{dimer}:-0.862662146341;AIRE:-0.868710296059;GATA6:-0.888640066266;NFIX:-0.901997362513;RFX2..5_RFXANK_RFXAP:-0.905675893748;GFI1:-0.953730807637;NKX2-1,4:-0.979934029133;MYOD1:-0.987543364143;PRDM1:-0.988591258125;IKZF2:-0.994301716039;SNAI1..3:-1.00911766924;YY1:-1.02078052502;AHR_ARNT_ARNT2:-1.02407254323;bHLH_family:-1.02931495272;ARID5B:-1.04824579475;CREB1:-1.05020412842;CUX2:-1.07692782663;TGIF1:-1.11640065008;LMO2:-1.19001966419;PAX6:-1.20355109009;ATF5_CREB3:-1.23615696982;CDX1,2,4:-1.24756173981;NRF1:-1.33657636854;PITX1..3:-1.35895460394;RBPJ:-1.38105871422;EVI1:-1.41271077404;NKX6-1,2:-1.50250421714;PBX1:-1.52099125947;ZNF143:-1.65267069228;FOXN1:-1.69481661651;FOXP1:-1.70303884758;NKX3-2:-1.84976387377;BPTF:-2.12230353773;FOXQ1:-2.1838760723;FOX{I1,J2}:-2.31077768653;FOXD3:-2.39583987859
 
}}
 
}}

Revision as of 06:17, 15 February 2012


Name:Mouse Meningeal cells, donor3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemeninges
dev stageNA
sexNA
ageNA
cell typemeningeal cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAM5771
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.
Analyst:NA

link to dataset.
data

CNhs12109

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0749
1002 0.157
1003 0.101
1004 0
1005 0
1006 --0.143
1007 --0.228
1008 0
1009 --0.0572
101 --0.475
1010 0
1011 --0.3
1012 0
1013 0.0596
1014 --0.0851
1015 0.114
1016 0.265
1017 0
1018 0
1019 0
102 0
1020 0.444
1021 0.444
1022 --0.124
1023 0
1024 --0.307
1025 --0.0233
1026 0
1027 --0.048
1028 0
1029 --0.176
103 0.444
1030 0
1031 1.094
1032 --0.177
1033 --0.0665
1034 0
1035 0
1036 --0.183
1037 0
1038 --0.0779
1039 --0.072
104 0
1040 0.513
1041 0



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data
no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs12109

Jaspar motif P-value
MA0002.2 0.0221
MA0003.1 0.277
MA0004.1 0.289
MA0006.1 0.45
MA0007.1 0.113
MA0009.1 0.586
MA0014.1 0.453
MA0017.1 0.781
MA0018.2 0.00341
MA0019.1 0.643
MA0024.1 0.00334
MA0025.1 0.188
MA0027.1 0.742
MA0028.1 0.0689
MA0029.1 0.673
MA0030.1 0.253
MA0031.1 0.667
MA0035.2 0.301
MA0038.1 0.0102
MA0039.2 0.342
MA0040.1 0.385
MA0041.1 0.296
MA0042.1 0.681
MA0043.1 0.0144
MA0046.1 6.44568e-5
MA0047.2 0.193
MA0048.1 0.261
MA0050.1 0.365
MA0051.1 0.873
MA0052.1 0.0308
MA0055.1 0.0927
MA0057.1 0.142
MA0058.1 0.216
MA0059.1 0.164
MA0060.1 0.0124
MA0061.1 0.141
MA0062.2 7.4938e-4
MA0065.2 0.312
MA0066.1 0.0676
MA0067.1 0.284
MA0068.1 0.816
MA0069.1 0.7
MA0070.1 0.824
MA0071.1 0.552
MA0072.1 0.147
MA0073.1 0.689
MA0074.1 0.0875
MA0076.1 0.00456
MA0077.1 0.0337
MA0078.1 0.165
MA0079.2 0.474
MA0080.2 0.00453
MA0081.1 0.112
MA0083.1 0.00561
MA0084.1 0.747
MA0087.1 0.617
MA0088.1 0.464
MA0090.1 0.00146
MA0091.1 0.744
MA0092.1 0.0168
MA0093.1 0.353
MA0099.2 3.22535e-6
MA0100.1 0.561
MA0101.1 0.44
MA0102.2 0.0378
MA0103.1 0.0947
MA0104.2 0.808
MA0105.1 0.0619
MA0106.1 0.00236
MA0107.1 0.88
MA0108.2 0.587
MA0111.1 0.567
MA0112.2 0.00439
MA0113.1 0.324
MA0114.1 0.798
MA0115.1 0.619
MA0116.1 0.0147
MA0117.1 0.345
MA0119.1 0.0861
MA0122.1 0.809
MA0124.1 0.285
MA0125.1 0.257
MA0131.1 0.225
MA0135.1 0.92
MA0136.1 0.00709
MA0137.2 0.524
MA0138.2 0.0389
MA0139.1 0.228
MA0140.1 0.0271
MA0141.1 0.105
MA0142.1 0.811
MA0143.1 0.603
MA0144.1 0.777
MA0145.1 0.0516
MA0146.1 0.0103
MA0147.1 0.742
MA0148.1 0.144
MA0149.1 0.181
MA0150.1 0.498
MA0152.1 0.235
MA0153.1 0.00644
MA0154.1 0.0886
MA0155.1 0.273
MA0156.1 3.23238e-5
MA0157.1 0.757
MA0159.1 0.221
MA0160.1 0.303
MA0162.1 0.126
MA0163.1 0.00397
MA0164.1 0.918
MA0258.1 0.0136
MA0259.1 0.817



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs12109

Novel motif P-value
1 0.284
10 0.309
100 0.927
101 0.982
102 0.417
103 0.259
104 0.982
105 0.59
106 0.00924
107 0.426
108 0.497
109 0.00376
11 0.0187
110 0.303
111 0.535
112 0.201
113 0.774
114 0.234
115 0.834
116 0.0164
117 0.373
118 0.629
119 0.0127
12 0.77
120 0.871
121 0.664
122 0.201
123 0.634
124 0.195
125 0.169
126 0.78
127 0.0858
128 0.0798
129 0.53
13 0.337
130 0.288
131 0.266
132 0.244
133 0.905
134 0.429
135 0.474
136 0.492
137 0.454
138 0.323
139 0.535
14 0.872
140 0.963
141 0.392
142 0.399
143 0.0169
144 0.473
145 0.0248
146 0.93
147 0.404
148 0.627
149 0.029
15 0.631
150 0.193
151 0.704
152 0.0431
153 0.333
154 0.423
155 0.177
156 0.0534
157 0.258
158 0.356
159 0.262
160 0.382
161 0.168
162 0.291
163 0.432
164 0.836
165 0.907
166 0.324
167 0.103
168 0.545
169 0.0403
17 0.188
18 0.103
19 0.0965
2 0.19
20 0.853
21 0.132
22 0.0339
23 0.0619
24 0.0564
25 0.357
26 0.0709
27 0.581
28 0.945
29 0.261
3 0.19
30 0.338
31 0.479
32 0.0613
33 0.734
34 0.156
35 0.903
36 0.546
37 0.0531
38 0.178
39 0.272
4 0.174
40 0.18
41 0.52
42 0.189
43 0.073
44 0.04
45 0.388
46 0.0822
47 0.0489
48 0.398
49 0.263
5 0.909
50 0.158
51 0.997
52 0.103
53 0.989
54 0.647
55 0.201
56 0.302
57 0.162
58 0.76
59 0.014
6 0.771
60 0.072
61 0.973
62 0.453
63 0.0835
64 0.162
65 0.0154
66 0.307
67 0.766
68 0.942
69 0.14
7 0.927
70 0.0388
71 0.151
72 0.636
73 0.016
74 0.883
75 0.176
76 0.929
77 0.00931
78 0.329
79 0.698
8 0.109
80 0.574
81 0.111
82 0.398
83 0.537
84 0.708
85 0.0111
86 0.642
87 0.025
88 0.512
89 0.866
9 0.694
90 0.671
91 0.051
92 0.18
93 0.806
94 0.95
95 0.0159
96 0.672
97 0.388
98 0.143
99 0.439



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs12109


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)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000134 (mesenchymal cell)
0000151 (secretory cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000327 (extracellular matrix secreting cell)
0000499 (stromal cell)
0000548 (animal cell)
0000708 (leptomeningeal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
0003210 (blood-cerebrospinal fluid barrier)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

NA