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FF:1310-23B1

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Name:epididymis and seminiferous tubule, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11218
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
tissueepididymis and seminiferous tubule
dev stage0 day neonate
sexmale
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  SAMD00004895
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11218 CAGE DRX008951 DRR009825
Accession ID Mm9

Library idBAMCTSS
CNhs11218 DRZ001250 DRZ002633
Accession ID Mm10

Library idBAMCTSS
CNhs11218 DRZ012600 DRZ013983
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs11218

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0435
1001 0.0886
1002 0.85
1003 0.188
1004 0.305
1005 0
1006 --0.011
1007 0.141
1008 0
1009 0.331
101 0.0264
1010 0
1011 0.0021
1012 0.0421
1013 --0.141
1014 0.502
1015 0.171
1016 0.427
1017 0
1018 0.0421
1019 0
102 0
1020 0
1021 0.0805
1022 --0.0283
1023 0
1024 0.0585
1025 0.098
1026 0.0863
1027 0
1028 0
1029 0.226
103 0.671
1030 0
1031 0.701
1032 0.0174
1033 --0.0244
1034 0
1035 0
1036 0.0675
1037 0
1038 0.103
1039 --0.102
104 0
1040 0.31
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: CNhs11218

Jaspar motif P-value
MA0002.2 0.00179
MA0003.1 0.56
MA0004.1 0.466
MA0006.1 0.888
MA0007.1 0.548
MA0009.1 0.352
MA0014.1 0.246
MA0017.1 3.55163e-5
MA0018.2 0.144
MA0019.1 0.786
MA0024.1 7.96657e-4
MA0025.1 0.115
MA0027.1 0.144
MA0028.1 0.159
MA0029.1 0.628
MA0030.1 0.719
MA0031.1 0.772
MA0035.2 3.75903e-5
MA0038.1 0.275
MA0039.2 0.456
MA0040.1 0.0773
MA0041.1 0.0751
MA0042.1 0.406
MA0043.1 0.907
MA0046.1 0.0196
MA0047.2 0.0424
MA0048.1 0.147
MA0050.1 0.723
MA0051.1 0.722
MA0052.1 0.0679
MA0055.1 0.158
MA0057.1 0.59
MA0058.1 0.394
MA0059.1 0.167
MA0060.1 0.291
MA0061.1 0.542
MA0062.2 0.00281
MA0065.2 2.2295e-4
MA0066.1 0.0194
MA0067.1 0.276
MA0068.1 0.798
MA0069.1 0.537
MA0070.1 0.99
MA0071.1 0.00436
MA0072.1 5.54261e-4
MA0073.1 0.737
MA0074.1 0.755
MA0076.1 0.179
MA0077.1 0.883
MA0078.1 0.0578
MA0079.2 0.11
MA0080.2 2.23902e-5
MA0081.1 0.0416
MA0083.1 0.00113
MA0084.1 0.904
MA0087.1 0.351
MA0088.1 0.0927
MA0090.1 0.176
MA0091.1 0.605
MA0092.1 0.665
MA0093.1 0.479
MA0099.2 0.0252
MA0100.1 0.276
MA0101.1 0.853
MA0102.2 0.618
MA0103.1 0.00164
MA0104.2 0.098
MA0105.1 0.013
MA0106.1 0.775
MA0107.1 0.831
MA0108.2 0.976
MA0111.1 0.531
MA0112.2 5.97573e-4
MA0113.1 0.928
MA0114.1 5.19039e-5
MA0115.1 1.01068e-4
MA0116.1 0.0275
MA0117.1 0.168
MA0119.1 0.298
MA0122.1 0.403
MA0124.1 0.098
MA0125.1 0.287
MA0131.1 0.583
MA0135.1 0.863
MA0136.1 9.23726e-6
MA0137.2 0.406
MA0138.2 0.00503
MA0139.1 0.019
MA0140.1 0.012
MA0141.1 1.81188e-4
MA0142.1 0.0122
MA0143.1 0.935
MA0144.1 0.777
MA0145.1 0.333
MA0146.1 0.76
MA0147.1 0.0754
MA0148.1 0.0193
MA0149.1 0.0251
MA0150.1 3.90525e-4
MA0152.1 0.00173
MA0153.1 0.00721
MA0154.1 0.0521
MA0155.1 0.529
MA0156.1 0.0162
MA0157.1 0.615
MA0159.1 0.00129
MA0160.1 7.77984e-4
MA0162.1 0.702
MA0163.1 0.859
MA0164.1 0.905
MA0258.1 1.76605e-4
MA0259.1 0.744



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: CNhs11218

Novel motif P-value
1 0.0454
10 0.119
100 0.857
101 0.405
102 0.997
103 0.269
104 0.928
105 0.555
106 0.445
107 0.788
108 0.693
109 0.159
11 0.124
110 0.24
111 0.0246
112 0.47
113 0.644
114 0.0106
115 0.682
116 0.945
117 0.00977
118 0.484
119 0.0399
12 0.58
120 0.294
121 0.395
122 0.705
123 0.188
124 0.287
125 0.46
126 0.409
127 0.201
128 0.244
129 0.349
13 0.459
130 0.468
131 0.728
132 0.748
133 0.192
134 0.754
135 0.106
136 0.469
137 0.846
138 0.0753
139 0.0125
14 0.466
140 0.434
141 0.374
142 0.589
143 0.387
144 0.189
145 0.625
146 0.521
147 0.715
148 0.574
149 0.853
15 0.0604
150 0.499
151 0.0575
152 0.727
153 0.912
154 0.669
155 0.701
156 0.00982
157 0.681
158 0.347
159 0.411
160 0.776
161 0.55
162 0.948
163 0.0571
164 0.539
165 0.164
166 0.0108
167 0.292
168 0.583
169 0.306
17 0.308
18 0.154
19 0.876
2 0.789
20 0.642
21 0.846
22 0.913
23 0.352
24 0.822
25 0.083
26 0.899
27 0.624
28 0.187
29 0.27
3 0.219
30 0.925
31 0.588
32 0.698
33 0.689
34 0.894
35 0.0207
36 0.0621
37 0.196
38 0.549
39 0.642
4 0.946
40 0.195
41 0.0171
42 0.511
43 0.205
44 0.0599
45 0.808
46 0.259
47 0.142
48 0.12
49 0.0624
5 0.136
50 0.462
51 0.754
52 0.882
53 0.97
54 0.402
55 0.459
56 0.313
57 0.527
58 0.22
59 0.457
6 0.906
60 0.506
61 0.567
62 0.0332
63 0.314
64 0.338
65 0.238
66 0.75
67 0.991
68 0.012
69 0.754
7 0.335
70 0.00114
71 0.122
72 0.467
73 0.206
74 0.877
75 0.0274
76 0.821
77 0.627
78 0.307
79 0.543
8 0.0218
80 0.111
81 0.257
82 0.389
83 0.434
84 0.829
85 0.0249
86 0.262
87 0.043
88 0.705
89 0.141
9 0.769
90 0.00453
91 0.486
92 0.404
93 0.916
94 0.239
95 0.112
96 0.0542
97 0.693
98 0.158
99 0.945



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: CNhs11218


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)
0000473 (testis)
0000991 (gonad)
0001301 (epididymis)
0001343 (seminiferous tubule of testis)
0000479 (tissue)
0000058 (duct)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0005904 (duct of male reproductive system)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0004175 (internal genitalia)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)
0006947 (male genital duct)
0004054 (internal male genitalia)

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)
0011506 (mouse epididymis and seminiferous tubule- 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:0004871 (somatic layer of lateral plate mesoderm)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0007297 (presumptive pronephric mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)