Personal tools

FF:988-6G6

From FANTOM5_SSTAR

Revision as of 13:49, 10 August 2017 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:oviduct, adult pregnant day01
Species:Mouse (Mus musculus)
Library ID:CNhs10500
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
tissueoviduct
dev stage1 day pregnant adult
sexfemale
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  SAMD00004897
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10500 CAGE DRX009053 DRR009927
Accession ID Mm9

Library idBAMCTSS
CNhs10500 DRZ001352 DRZ002735
Accession ID Mm10

Library idBAMCTSS
CNhs10500 DRZ012702 DRZ014085
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

CNhs10500

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0663
1001 0.271
1002 0.0412
1003 0.201
1004 0.648
1005 0.0436
1006 0.0189
1007 0.0667
1008 0
1009 0.446
101 0.0292
1010 0
1011 0.086
1012 0.0663
1013 0.118
1014 0
1015 --0.0664
1016 0.198
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.124
1023 0
1024 0.213
1025 0.138
1026 0.232
1027 0
1028 0
1029 0.35
103 0.235
1030 0
1031 0.587
1032 --0.11
1033 0
1034 0.0663
1035 0
1036 --0.0283
1037 0
1038 0.101
1039 0.0197
104 0
1040 0.38
1041 0.0663



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: CNhs10500

Jaspar motif P-value
MA0002.2 0.948
MA0003.1 0.084
MA0004.1 0.623
MA0006.1 0.178
MA0007.1 0.814
MA0009.1 0.83
MA0014.1 0.758
MA0017.1 2.55299e-5
MA0018.2 0.0064
MA0019.1 0.496
MA0024.1 0.012
MA0025.1 0.175
MA0027.1 0.781
MA0028.1 0.024
MA0029.1 0.286
MA0030.1 0.142
MA0031.1 0.12
MA0035.2 0.00186
MA0038.1 0.296
MA0039.2 0.0465
MA0040.1 0.47
MA0041.1 0.184
MA0042.1 0.377
MA0043.1 0.367
MA0046.1 4.03884e-5
MA0047.2 0.983
MA0048.1 0.511
MA0050.1 3.18734e-8
MA0051.1 3.71695e-5
MA0052.1 0.35
MA0055.1 0.406
MA0057.1 0.679
MA0058.1 0.491
MA0059.1 0.0472
MA0060.1 0.0155
MA0061.1 0.627
MA0062.2 0.0159
MA0065.2 0.00314
MA0066.1 0.0105
MA0067.1 0.62
MA0068.1 0.501
MA0069.1 0.52
MA0070.1 0.772
MA0071.1 0.00356
MA0072.1 0.0758
MA0073.1 0.683
MA0074.1 0.882
MA0076.1 0.081
MA0077.1 0.845
MA0078.1 0.0155
MA0079.2 0.0341
MA0080.2 0.00124
MA0081.1 0.885
MA0083.1 4.9262e-6
MA0084.1 0.186
MA0087.1 0.299
MA0088.1 0.271
MA0090.1 0.641
MA0091.1 0.23
MA0092.1 0.682
MA0093.1 0.715
MA0099.2 0.692
MA0100.1 0.643
MA0101.1 0.754
MA0102.2 0.993
MA0103.1 0.712
MA0104.2 0.019
MA0105.1 0.107
MA0106.1 0.663
MA0107.1 0.18
MA0108.2 0.176
MA0111.1 0.903
MA0112.2 0.594
MA0113.1 0.331
MA0114.1 1.01807e-5
MA0115.1 8.75703e-6
MA0116.1 0.166
MA0117.1 0.119
MA0119.1 0.266
MA0122.1 0.453
MA0124.1 0.952
MA0125.1 0.035
MA0131.1 0.377
MA0135.1 0.808
MA0136.1 0.037
MA0137.2 0.287
MA0138.2 0.645
MA0139.1 0.934
MA0140.1 0.00178
MA0141.1 1.32638e-7
MA0142.1 0.555
MA0143.1 0.72
MA0144.1 0.275
MA0145.1 0.0202
MA0146.1 0.787
MA0147.1 0.00778
MA0148.1 0.954
MA0149.1 0.0329
MA0150.1 0.139
MA0152.1 0.119
MA0153.1 2.34612e-5
MA0154.1 0.874
MA0155.1 0.621
MA0156.1 0.0129
MA0157.1 0.0448
MA0159.1 0.0122
MA0160.1 7.65576e-4
MA0162.1 0.68
MA0163.1 0.0639
MA0164.1 0.595
MA0258.1 0.111
MA0259.1 0.0461



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: CNhs10500

Novel motif P-value
1 0.169
10 0.0317
100 0.0933
101 0.445
102 0.997
103 0.628
104 0.265
105 0.851
106 0.464
107 0.276
108 0.416
109 0.912
11 0.172
110 0.569
111 0.145
112 0.38
113 0.859
114 0.0393
115 0.635
116 0.425
117 0.00107
118 0.0401
119 0.283
12 0.817
120 0.23
121 0.293
122 0.653
123 0.279
124 0.64
125 0.386
126 0.771
127 0.0691
128 0.969
129 0.793
13 0.894
130 0.0392
131 0.692
132 0.721
133 0.33
134 0.531
135 0.223
136 0.44
137 0.381
138 0.0287
139 0.688
14 0.679
140 0.453
141 0.592
142 0.344
143 0.156
144 0.644
145 0.621
146 0.366
147 0.364
148 0.311
149 0.094
15 0.857
150 0.805
151 0.829
152 0.0562
153 0.741
154 0.948
155 0.893
156 0.246
157 0.794
158 0.78
159 0.139
160 0.8
161 0.618
162 0.717
163 0.205
164 0.649
165 0.802
166 0.00105
167 0.0606
168 0.308
169 0.0742
17 0.57
18 0.0126
19 0.165
2 0.0379
20 0.18
21 0.744
22 0.48
23 0.595
24 0.25
25 0.131
26 0.861
27 0.429
28 0.538
29 0.0734
3 0.337
30 0.239
31 0.588
32 0.19
33 0.388
34 0.696
35 0.0178
36 0.015
37 0.863
38 0.673
39 0.569
4 0.819
40 0.108
41 0.122
42 0.651
43 0.336
44 0.0875
45 0.208
46 0.435
47 0.853
48 0.559
49 0.186
5 0.262
50 0.436
51 0.938
52 0.255
53 0.159
54 0.656
55 0.864
56 0.684
57 0.215
58 0.623
59 0.934
6 0.413
60 0.633
61 0.602
62 0.146
63 0.851
64 0.206
65 0.982
66 0.349
67 0.427
68 0.347
69 0.413
7 0.531
70 0.191
71 0.0422
72 0.579
73 0.923
74 0.84
75 0.0383
76 0.165
77 0.896
78 0.00427
79 0.691
8 0.042
80 0.178
81 0.481
82 0.908
83 0.908
84 0.99
85 0.834
86 0.92
87 0.438
88 0.668
89 0.918
9 0.505
90 0.0166
91 0.554
92 0.635
93 0.472
94 0.0987
95 0.12
96 0.0449
97 0.232
98 0.659
99 0.284



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: CNhs10500


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)
0007023 (adult organism)
0000993 (oviduct)
0000479 (tissue)
0005156 (reproductive structure)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0000474 (female reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000317 (mouse pregnant tissue sample)
0000318 (mouse pregnant day 1 sample)
0011442 (mouse oviduct- adult pregnant day01 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:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)