Personal tools

FF:633-15C6

From FANTOM5_SSTAR

Revision as of 13:41, 10 August 2017 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:eyeball, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11207
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 stage0 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  SAMD00005813
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11207 CAGE DRX008959 DRR009833
Accession ID Mm9

Library idBAMCTSS
CNhs11207 DRZ001258 DRZ002641
Accession ID Mm10

Library idBAMCTSS
CNhs11207 DRZ012608 DRZ013991
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

CNhs11207

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.169
10 0
100 0.149
1000 0.00486
1001 0.117
1002 0.262
1003 0.0222
1004 0.205
1005 --0.0101
1006 0.172
1007 0.143
1008 0
1009 0.0934
101 0.0287
1010 0
1011 0.0617
1012 0.127
1013 --0.105
1014 0.445
1015 0.19
1016 0.301
1017 0
1018 0.0807
1019 0
102 0
1020 0
1021 0.0558
1022 0.0103
1023 0
1024 0.0286
1025 --0.0611
1026 0.0286
1027 0.853
1028 0
1029 0.266
103 0.463
1030 0
1031 0.322
1032 0.0231
1033 0
1034 0
1035 0.0286
1036 0
1037 0
1038 0.0953
1039 --0.174
104 0
1040 0.0792
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: CNhs11207

Jaspar motif P-value
MA0002.2 6.99963e-5
MA0003.1 0.254
MA0004.1 0.371
MA0006.1 0.347
MA0007.1 0.292
MA0009.1 0.355
MA0014.1 0.138
MA0017.1 1.94821e-7
MA0018.2 0.464
MA0019.1 0.571
MA0024.1 0.0065
MA0025.1 0.0959
MA0027.1 0.331
MA0028.1 0.173
MA0029.1 0.447
MA0030.1 0.843
MA0031.1 0.448
MA0035.2 8.95112e-4
MA0038.1 0.00621
MA0039.2 0.0475
MA0040.1 0.0938
MA0041.1 0.413
MA0042.1 0.926
MA0043.1 0.685
MA0046.1 6.03816e-23
MA0047.2 4.00589e-4
MA0048.1 0.505
MA0050.1 8.93772e-4
MA0051.1 0.00624
MA0052.1 0.733
MA0055.1 0.641
MA0057.1 0.129
MA0058.1 0.349
MA0059.1 0.245
MA0060.1 7.96768e-8
MA0061.1 0.0277
MA0062.2 0.0028
MA0065.2 7.51832e-7
MA0066.1 0.233
MA0067.1 0.954
MA0068.1 0.387
MA0069.1 0.0278
MA0070.1 0.708
MA0071.1 0.6
MA0072.1 0.262
MA0073.1 0.334
MA0074.1 0.301
MA0076.1 0.468
MA0077.1 0.00755
MA0078.1 0.833
MA0079.2 0.528
MA0080.2 5.42327e-12
MA0081.1 0.0482
MA0083.1 0.93
MA0084.1 0.0734
MA0087.1 0.185
MA0088.1 0.0496
MA0090.1 0.937
MA0091.1 0.218
MA0092.1 0.494
MA0093.1 0.397
MA0099.2 4.1374e-5
MA0100.1 0.846
MA0101.1 0.0657
MA0102.2 0.489
MA0103.1 0.00446
MA0104.2 0.716
MA0105.1 0.00128
MA0106.1 0.311
MA0107.1 0.0786
MA0108.2 0.0171
MA0111.1 0.71
MA0112.2 2.53449e-4
MA0113.1 0.31
MA0114.1 3.21659e-6
MA0115.1 1.91301e-5
MA0116.1 0.0073
MA0117.1 0.605
MA0119.1 0.0498
MA0122.1 0.894
MA0124.1 0.522
MA0125.1 0.00316
MA0131.1 0.668
MA0135.1 0.71
MA0136.1 6.93397e-16
MA0137.2 0.0111
MA0138.2 0.856
MA0139.1 0.0642
MA0140.1 3.94882e-4
MA0141.1 1.21139e-4
MA0142.1 0.567
MA0143.1 0.123
MA0144.1 0.0308
MA0145.1 0.0615
MA0146.1 0.0587
MA0147.1 0.5
MA0148.1 3.90158e-4
MA0149.1 0.0075
MA0150.1 0.0348
MA0152.1 0.335
MA0153.1 8.08266e-26
MA0154.1 0.00543
MA0155.1 0.712
MA0156.1 7.1723e-7
MA0157.1 0.216
MA0159.1 0.00685
MA0160.1 0.00283
MA0162.1 0.386
MA0163.1 4.71896e-4
MA0164.1 0.993
MA0258.1 0.00832
MA0259.1 0.802



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: CNhs11207

Novel motif P-value
1 0.08
10 0.105
100 0.786
101 0.644
102 0.779
103 0.0248
104 0.712
105 0.536
106 0.11
107 0.373
108 0.938
109 0.00856
11 0.0357
110 0.095
111 0.00114
112 0.00508
113 0.99
114 0.0321
115 0.88
116 0.177
117 0.0189
118 0.455
119 0.0543
12 0.445
120 0.318
121 0.515
122 0.888
123 0.666
124 0.588
125 0.0804
126 0.183
127 0.0968
128 0.179
129 0.409
13 0.00515
130 0.943
131 0.225
132 0.615
133 0.741
134 0.527
135 0.284
136 0.168
137 0.794
138 0.338
139 0.0292
14 0.9
140 0.191
141 0.0281
142 0.764
143 0.184
144 0.709
145 0.0721
146 0.385
147 0.498
148 0.283
149 0.231
15 0.0462
150 0.376
151 0.343
152 0.0788
153 0.608
154 0.973
155 0.296
156 0.941
157 0.924
158 0.353
159 0.748
160 0.404
161 0.143
162 0.979
163 0.577
164 0.0111
165 0.0154
166 0.593
167 0.739
168 0.694
169 0.00352
17 0.0459
18 0.467
19 0.296
2 0.717
20 0.499
21 0.307
22 0.256
23 0.351
24 0.0687
25 0.403
26 0.0257
27 0.473
28 0.317
29 0.0445
3 0.0557
30 0.84
31 0.52
32 0.282
33 0.235
34 0.768
35 0.523
36 0.074
37 0.0229
38 0.238
39 0.544
4 0.699
40 0.151
41 0.253
42 0.212
43 0.157
44 0.0533
45 0.537
46 0.142
47 0.0627
48 0.0637
49 0.156
5 0.0988
50 0.746
51 0.578
52 0.485
53 0.964
54 0.65
55 0.353
56 0.26
57 0.55
58 0.214
59 0.0337
6 0.47
60 0.0749
61 0.298
62 0.0845
63 0.0905
64 0.4
65 0.117
66 0.842
67 0.983
68 0.104
69 0.804
7 0.0906
70 0.00462
71 0.0181
72 0.164
73 0.0288
74 0.566
75 0.0272
76 0.564
77 0.135
78 0.0384
79 0.201
8 0.0353
80 0.256
81 0.295
82 0.0104
83 0.414
84 0.445
85 0.0333
86 0.167
87 0.0656
88 0.6
89 0.0843
9 0.627
90 0.0885
91 0.855
92 0.108
93 0.277
94 0.393
95 0.0459
96 0.413
97 0.823
98 0.439
99 0.518



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: CNhs11207


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)
0011264 (mouse eyeball- neonate N00 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)


Warning: A non-numeric value encountered in /var/www/html/resource_browser/extensions/FantomExtention/includes/FE_ParserFunctions.php on line 50