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|top_motifs=HOX{A4,D4}:2.68569107211;NKX2-3_NKX2-5:2.55736200275;TBP:2.32951102147;MYOD1:2.30375529371;ZNF148:2.23144087114;TFAP4:2.16868216543;LHX3,4:2.16643522216;SMAD1..7,9:2.08138674102;EP300:2.04394080423;VSX1,2:1.93282657623;HMX1:1.91462650712;LEF1_TCF7_TCF7L1,2:1.85323421896;TFCP2:1.80488591949;NKX3-2:1.78212765743;GLI1..3:1.77729332567;ESR1:1.73803220282;MAZ:1.73773887965;PATZ1:1.70869986244;TGIF1:1.69573676233;GTF2I:1.69092665135;TFAP2{A,C}:1.67708137463;RREB1:1.63545460541;MYFfamily:1.61174194701;HOX{A5,B5}:1.58406998915;NANOG:1.56547922005;MAFB:1.54679858982;MZF1:1.52212700371;XCPE1{core}:1.51977862057;SOX{8,9,10}:1.5159654057;TBX4,5:1.4846203676;KLF4:1.43798453665;NHLH1,2:1.43055545245;T:1.41018349147;SP1:1.30023624957;PAX5:1.28388265298;MTF1:1.27341348513;PRDM1:1.26568770542;PRRX1,2:1.25352938978;HIC1:1.24871630303;ZNF238:1.24159751596;ZNF423:1.23568411323;PPARG:1.21430524939;EN1,2:1.19549819391;GTF2A1,2:1.18837826061;TOPORS:1.18509984788;MED-1{core}:1.14943540208;HAND1,2:1.14892217482;POU5F1:1.13170143425;REST:1.12906505493;FOXL1:1.11542136744;TAL1_TCF{3,4,12}:1.11469384426;ZIC1..3:1.10665695993;FOS_FOS{B,L1}_JUN{B,D}:1.078195146;ATF2:1.07798293529;ZBTB6:1.07737777143;GFI1B:1.07162478685;MTE{core}:1.04390083216;TFAP2B:1.03674304599;EGR1..3:1.03609204182;GCM1,2:1.01408569945;SOX2:1.01154909249;NKX2-1,4:1.00868261943;MEF2{A,B,C,D}:1.00128238137;ALX1:0.997125735133;LMO2:0.976492872008;RFX2..5_RFXANK_RFXAP:0.971025072725;BREu{core}:0.951249773624;EBF1:0.868217456185;POU6F1:0.849924091578;ADNP_IRX_SIX_ZHX:0.839405087081;ATF6:0.829794325232;TLX1..3_NFIC{dimer}:0.815340469772;TEAD1:0.790667648071;ZFP161:0.787775321524;HIF1A:0.781853251546;SOX5:0.761245714818;HOXA9_MEIS1:0.754892898835;IKZF1:0.736648821572;RFX1:0.736567579381;HES1:0.724704941662;PAX1,9:0.720572858967;TFDP1:0.715685035853;FOSL2:0.712462996483;TLX2:0.705409400647;PAX2:0.671631217492;TP53:0.668382436487;OCT4_SOX2{dimer}:0.661010208808;UFEwm:0.632327870657;SNAI1..3:0.628764451978;GFI1:0.625231921669;POU2F1..3:0.594510463046;AHR_ARNT_ARNT2:0.589856958085;FOXP3:0.562546389054;CRX:0.537999967687;CDC5L:0.520609837959;CUX2:0.517118415739;RXRA_VDR{dimer}:0.500421929583;NFATC1..3:0.487573473824;PAX6:0.463799301415;FOXM1:0.446051829919;SPZ1:0.433853532928;HSF1,2:0.431450692837;NR3C1:0.419192414055;SRF:0.413359280494;ZEB1:0.403884221948;HMGA1,2:0.378799896481;ZNF384:0.373987041466;NFE2L2:0.372929776738;GATA4:0.313918890353;DBP:0.300811685671;MYBL2:0.286808872327;NFE2L1:0.253322040887;POU3F1..4:0.225161117918;JUN:0.195012153572;FOXQ1:0.183995593076;SOX17:0.166211920348;PAX4:0.152062031825;RBPJ:0.112849138372;IKZF2:0.0987136402802;FOXA2:0.0418340446791;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0331973210569;NKX6-1,2:0.0314137494615;FOX{F1,F2,J1}:0.021143416032;PITX1..3:0.0209400051872;RORA:0.00600310770537;ZNF143:-0.0126391636251;BACH2:-0.0400508329885;NANOG{mouse}:-0.0426439883084;NFE2:-0.0467209596886;FOXN1:-0.0763305035385;bHLH_family:-0.0934174599822;HLF:-0.130276631385;NR5A1,2:-0.137712024458;NRF1:-0.195176484059;RXR{A,B,G}:-0.210654342965;POU1F1:-0.219678866509;PAX8:-0.224760791666;HBP1_HMGB_SSRP1_UBTF:-0.266083329327;NFIX:-0.280872870914;GZF1:-0.310496966396;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.323209981856;NKX2-2,8:-0.338612128001;RUNX1..3:-0.346608785582;NFKB1_REL_RELA:-0.359799999423;NFY{A,B,C}:-0.411425648207;PBX1:-0.428339641763;SPIB:-0.434825630321;NR1H4:-0.459290173593;EVI1:-0.473645816773;ONECUT1,2:-0.484201264973;ATF5_CREB3:-0.502365199483;FOX{I1,J2}:-0.52526014969;E2F1..5:-0.547903127463;SPI1:-0.56298482944;STAT2,4,6:-0.586921628762;CEBPA,B_DDIT3:-0.608628305221;MYB:-0.612894052749;STAT5{A,B}:-0.640098285708;ALX4:-0.647716429468;FOX{D1,D2}:-0.686138955155;BPTF:-0.734758009289;NKX3-1:-0.736319367236;ETS1,2:-0.75975990109;TEF:-0.763716425727;HNF4A_NR2F1,2:-0.77456273727;AIRE:-0.832969666159;FOXD3:-0.834088590866;FOXP1:-0.858480837273;HNF1A:-0.862245966836;CREB1:-0.867769540971;SREBF1,2:-0.869641948776;ATF4:-0.873359394194;NFIL3:-0.873909663536;IRF7:-0.888315671246;DMAP1_NCOR{1,2}_SMARC:-0.913054470374;AR:-0.918501340411;GATA6:-0.951601437774;ESRRA:-0.968095613284;FOXO1,3,4:-0.998486495493;IRF1,2:-1.08746881907;ELF1,2,4:-1.16426446057;YY1:-1.17503639464;ELK1,4_GABP{A,B1}:-1.1751415719;ARID5B:-1.29606726052;STAT1,3:-1.35339722579;CDX1,2,4:-1.44183473779;NR6A1:-1.53816732902;PDX1:-1.61374068992;ZBTB16:-1.71748275825
 
}}
 
}}

Revision as of 06:21, 15 February 2012


Name:whole body, embryo E17, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage17 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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

CNhs10517

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.243
10 0
100 0.176
1000 0.176
1001 --0.0633
1002 0.0447
1003 0.335
1004 0.136
1005 0
1006 0.269
1007 --0.0202
1008 0
1009 0.111
101 --0.0674
1010 0
1011 0.246
1012 0
1013 --0.0375
1014 0.481
1015 0.232
1016 0.274
1017 0.0968
1018 0.243
1019 0
102 0
1020 0
1021 0
1022 0.0265
1023 0
1024 0.161
1025 0.176
1026 0.118
1027 0.0968
1028 0
1029 --0.0179
103 0.721
1030 0
1031 0.421
1032 0.0374
1033 0.0303
1034 0
1035 0
1036 --0.0723
1037 0
1038 --0.018
1039 --0.00831
104 0
1040 0.135
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: CNhs10517

Jaspar motif P-value
MA0002.2 0.0306
MA0003.1 0.728
MA0004.1 0.196
MA0006.1 0.493
MA0007.1 0.107
MA0009.1 0.64
MA0014.1 0.207
MA0017.1 2.14197e-10
MA0018.2 0.53
MA0019.1 0.228
MA0024.1 0.398
MA0025.1 0.663
MA0027.1 0.963
MA0028.1 7.79861e-6
MA0029.1 0.595
MA0030.1 0.924
MA0031.1 0.249
MA0035.2 0.00787
MA0038.1 0.0527
MA0039.2 0.906
MA0040.1 0.733
MA0041.1 0.292
MA0042.1 0.641
MA0043.1 0.79
MA0046.1 1.34826e-14
MA0047.2 0.0035
MA0048.1 0.0089
MA0050.1 1.3185e-9
MA0051.1 1.02954e-5
MA0052.1 1.61395e-9
MA0055.1 2.5934e-4
MA0057.1 0.752
MA0058.1 0.0923
MA0059.1 0.0213
MA0060.1 0.0475
MA0061.1 0.048
MA0062.2 2.15916e-11
MA0065.2 8.43857e-5
MA0066.1 0.0771
MA0067.1 0.216
MA0068.1 0.405
MA0069.1 0.432
MA0070.1 0.162
MA0071.1 0.0113
MA0072.1 0.0127
MA0073.1 0.961
MA0074.1 0.313
MA0076.1 6.90427e-6
MA0077.1 0.153
MA0078.1 0.763
MA0079.2 0.0414
MA0080.2 4.01137e-10
MA0081.1 0.0936
MA0083.1 8.21615e-4
MA0084.1 0.66
MA0087.1 0.65
MA0088.1 0.0966
MA0090.1 0.595
MA0091.1 0.77
MA0092.1 0.775
MA0093.1 0.188
MA0099.2 0.477
MA0100.1 0.0302
MA0101.1 0.00421
MA0102.2 0.833
MA0103.1 0.532
MA0104.2 0.399
MA0105.1 0.0322
MA0106.1 0.155
MA0107.1 0.0324
MA0108.2 3.99907e-27
MA0111.1 0.892
MA0112.2 0.00144
MA0113.1 0.0874
MA0114.1 2.35562e-8
MA0115.1 1.41215e-7
MA0116.1 0.192
MA0117.1 0.345
MA0119.1 0.309
MA0122.1 0.957
MA0124.1 0.773
MA0125.1 0.00349
MA0131.1 0.311
MA0135.1 0.0145
MA0136.1 6.93788e-15
MA0137.2 4.89415e-5
MA0138.2 4.14627e-4
MA0139.1 0.235
MA0140.1 6.87162e-4
MA0141.1 7.67928e-5
MA0142.1 0.366
MA0143.1 0.345
MA0144.1 0.0161
MA0145.1 0.999
MA0146.1 0.047
MA0147.1 0.372
MA0148.1 5.23807e-4
MA0149.1 0.00321
MA0150.1 0.00377
MA0152.1 0.279
MA0153.1 5.60157e-15
MA0154.1 0.2
MA0155.1 0.503
MA0156.1 1.5869e-12
MA0157.1 0.287
MA0159.1 0.00412
MA0160.1 0.00161
MA0162.1 0.577
MA0163.1 0.00482
MA0164.1 0.472
MA0258.1 0.0189
MA0259.1 0.524



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: CNhs10517

Novel motif P-value
1 0.196
10 0.0344
100 0.531
101 0.364
102 0.843
103 0.0144
104 0.65
105 0.971
106 0.424
107 0.928
108 0.464
109 0.0502
11 0.0611
110 0.0492
111 0.00339
112 0.00498
113 0.974
114 0.134
115 0.915
116 0.646
117 0.00129
118 0.137
119 0.286
12 0.839
120 0.825
121 0.434
122 0.549
123 0.124
124 0.58
125 0.118
126 0.0157
127 0.35
128 0.536
129 0.144
13 1.6065e-5
130 0.976
131 0.882
132 0.805
133 0.38
134 0.412
135 0.785
136 0.122
137 0.363
138 0.713
139 0.0499
14 0.703
140 0.376
141 0.599
142 0.0358
143 0.264
144 0.755
145 0.0195
146 0.953
147 0.653
148 0.292
149 0.63
15 0.0141
150 0.282
151 0.54
152 0.495
153 0.681
154 0.313
155 0.128
156 2.73725e-6
157 0.691
158 0.0108
159 0.681
160 0.852
161 0.0746
162 0.742
163 0.35
164 0.0012
165 0.0372
166 0.779
167 0.00963
168 0.263
169 0.0387
17 0.232
18 0.695
19 0.436
2 0.0836
20 0.0167
21 0.719
22 0.413
23 0.556
24 0.231
25 0.357
26 0.0024
27 0.654
28 0.235
29 0.00573
3 0.0423
30 0.126
31 0.958
32 0.4
33 0.116
34 0.581
35 0.23
36 0.0846
37 0.0167
38 0.679
39 0.508
4 0.846
40 0.225
41 0.483
42 0.268
43 0.171
44 0.21
45 0.6
46 0.279
47 0.305
48 0.117
49 0.0723
5 0.0464
50 0.902
51 0.695
52 0.706
53 0.421
54 0.85
55 0.815
56 0.915
57 0.506
58 0.41
59 0.703
6 0.891
60 0.325
61 0.0767
62 0.268
63 0.587
64 0.772
65 0.79
66 0.779
67 0.957
68 0.807
69 0.979
7 0.0733
70 0.0524
71 0.0206
72 0.373
73 0.0242
74 0.498
75 0.0203
76 0.015
77 0.806
78 0.0231
79 0.698
8 0.0777
80 0.515
81 0.939
82 0.264
83 0.237
84 0.751
85 0.433
86 0.327
87 0.605
88 0.361
89 0.677
9 0.944
90 0.0192
91 0.606
92 0.321
93 0.0459
94 0.567
95 0.0251
96 0.592
97 0.863
98 0.817
99 0.741



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: CNhs10517


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

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0000922 (embryo)
0001062 (anatomical entity)

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