Personal tools

FF:1532-43E7

From FANTOM5_SSTAR

Revision as of 13:21, 10 August 2017 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:eyeball, neonate N01
Species:Mouse (Mus musculus)
Library ID:CNhs11140
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueeyeball
dev stage1 day neonate
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

Accession numbers
MethodSample accession id
CAGE  SAMD00004944
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11140 CAGE DRX008960 DRR009834
Accession ID Mm9

Library idBAMCTSS
CNhs11140 DRZ001259 DRZ002642
Accession ID Mm10

Library idBAMCTSS
CNhs11140 DRZ012609 DRZ013992
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs11140

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.18
10 0
100 0.18
1000 0.0262
1001 0.173
1002 0.297
1003 0.106
1004 0.139
1005 0
1006 0.192
1007 0.119
1008 0
1009 --0.00487
101 0.0638
1010 0
1011 0.0471
1012 0.141
1013 --0.0989
1014 0.248
1015 0.138
1016 0.198
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0991
1023 0
1024 --0.0899
1025 --0.0581
1026 0
1027 0.899
1028 0
1029 0.442
103 0.449
1030 0.0524
1031 0.323
1032 0.0287
1033 0.0524
1034 0
1035 0.0524
1036 0.054
1037 0
1038 0.0273
1039 --0.123
104 0
1040 -6.461034e-4
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



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: CNhs11140

Jaspar motif P-value
MA0002.2 1.43848e-4
MA0003.1 0.178
MA0004.1 0.285
MA0006.1 0.229
MA0007.1 0.222
MA0009.1 0.124
MA0014.1 0.172
MA0017.1 3.76448e-8
MA0018.2 0.466
MA0019.1 0.333
MA0024.1 0.00483
MA0025.1 0.0249
MA0027.1 0.614
MA0028.1 0.152
MA0029.1 0.284
MA0030.1 0.603
MA0031.1 0.129
MA0035.2 4.02174e-4
MA0038.1 0.00356
MA0039.2 0.00335
MA0040.1 0.0647
MA0041.1 0.34
MA0042.1 0.927
MA0043.1 0.493
MA0046.1 1.49811e-23
MA0047.2 5.91798e-5
MA0048.1 0.516
MA0050.1 7.55452e-4
MA0051.1 0.00405
MA0052.1 0.931
MA0055.1 0.528
MA0057.1 0.123
MA0058.1 0.245
MA0059.1 0.338
MA0060.1 5.85624e-7
MA0061.1 0.0238
MA0062.2 3.58204e-4
MA0065.2 4.55166e-8
MA0066.1 0.353
MA0067.1 0.874
MA0068.1 0.455
MA0069.1 0.0282
MA0070.1 0.693
MA0071.1 0.876
MA0072.1 0.0583
MA0073.1 0.519
MA0074.1 0.267
MA0076.1 0.406
MA0077.1 0.0207
MA0078.1 0.876
MA0079.2 0.586
MA0080.2 4.10711e-13
MA0081.1 0.0229
MA0083.1 0.474
MA0084.1 0.102
MA0087.1 0.463
MA0088.1 0.0926
MA0090.1 0.531
MA0091.1 0.0343
MA0092.1 0.554
MA0093.1 0.306
MA0099.2 7.48342e-7
MA0100.1 0.689
MA0101.1 0.0193
MA0102.2 0.206
MA0103.1 8.70155e-4
MA0104.2 0.963
MA0105.1 0.019
MA0106.1 0.375
MA0107.1 0.0266
MA0108.2 0.0921
MA0111.1 0.904
MA0112.2 0.00144
MA0113.1 0.122
MA0114.1 1.08843e-7
MA0115.1 7.84165e-6
MA0116.1 0.0346
MA0117.1 0.75
MA0119.1 0.0816
MA0122.1 0.884
MA0124.1 0.41
MA0125.1 0.00434
MA0131.1 0.611
MA0135.1 0.487
MA0136.1 1.02566e-16
MA0137.2 0.00243
MA0138.2 0.553
MA0139.1 0.0986
MA0140.1 3.61328e-4
MA0141.1 1.78851e-4
MA0142.1 0.237
MA0143.1 0.0289
MA0144.1 0.00387
MA0145.1 0.0343
MA0146.1 0.0285
MA0147.1 0.714
MA0148.1 8.38187e-4
MA0149.1 0.0336
MA0150.1 0.0269
MA0152.1 0.275
MA0153.1 5.46415e-25
MA0154.1 0.00643
MA0155.1 0.801
MA0156.1 2.24701e-9
MA0157.1 0.0672
MA0159.1 0.00819
MA0160.1 6.92746e-4
MA0162.1 0.42
MA0163.1 9.0095e-4
MA0164.1 0.83
MA0258.1 0.0176
MA0259.1 0.979



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: CNhs11140

Novel motif P-value
1 0.189
10 0.164
100 0.595
101 0.903
102 0.592
103 0.0292
104 0.662
105 0.423
106 0.0408
107 0.231
108 0.913
109 0.00608
11 0.0365
110 0.103
111 0.00406
112 0.00671
113 0.996
114 0.0361
115 0.911
116 0.0964
117 0.0228
118 0.317
119 0.0826
12 0.313
120 0.509
121 0.247
122 0.982
123 0.473
124 0.974
125 0.127
126 0.159
127 0.0592
128 0.156
129 0.613
13 0.00234
130 0.877
131 0.275
132 0.673
133 0.883
134 0.646
135 0.553
136 0.0122
137 0.532
138 0.263
139 0.0789
14 0.902
140 0.368
141 0.0748
142 0.786
143 0.191
144 0.664
145 0.0659
146 0.292
147 0.75
148 0.425
149 0.216
15 0.0734
150 0.217
151 0.403
152 0.0201
153 0.88
154 0.715
155 0.278
156 0.795
157 0.812
158 0.338
159 0.711
160 0.48
161 0.311
162 0.863
163 0.591
164 0.00512
165 0.0541
166 0.437
167 0.822
168 0.881
169 0.00682
17 0.0478
18 0.589
19 0.321
2 0.456
20 0.466
21 0.192
22 0.2
23 0.457
24 0.0431
25 0.513
26 0.0234
27 0.409
28 0.282
29 0.0454
3 0.0862
30 0.607
31 0.531
32 0.437
33 0.208
34 0.616
35 0.773
36 0.355
37 0.0138
38 0.27
39 0.382
4 0.599
40 0.232
41 0.269
42 0.331
43 0.208
44 0.0904
45 0.35
46 0.198
47 0.0757
48 0.0646
49 0.242
5 0.181
50 0.701
51 0.532
52 0.247
53 0.981
54 0.623
55 0.566
56 0.332
57 0.834
58 0.279
59 0.0152
6 0.694
60 0.0265
61 0.347
62 0.142
63 0.0795
64 0.476
65 0.147
66 0.901
67 0.701
68 0.0625
69 0.996
7 0.1
70 0.00956
71 0.0293
72 0.165
73 0.00756
74 0.45
75 0.0372
76 0.59
77 0.116
78 0.0323
79 0.183
8 0.0607
80 0.275
81 0.395
82 0.0268
83 0.614
84 0.21
85 0.0907
86 0.139
87 0.00543
88 0.495
89 0.0646
9 0.611
90 0.241
91 0.949
92 0.0841
93 0.524
94 0.482
95 0.0108
96 0.791
97 0.961
98 0.361
99 0.558



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: CNhs11140


FANTOM5 (FF) ontology


Direct parent terms


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
0000468 (multi-cellular organism)
0000970 (eye)
0000019 (camera-type eye)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0001032 (sensory system)
0010317 (germ layer / neural crest derived structure)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002104 (visual system)
0004456 (entire sense organ system)
0001456 (face)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011252 (mouse eyeball- neonate N01 sample)

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

link to source data
data

UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0003056 (pre-chordal neural plate)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)