Personal tools

FF:752-24D1

From FANTOM5_SSTAR

Jump to: navigation, search


Name:spleen, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11116
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
tissuespleen
dev stage10 days 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  SAMD00005884
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11116 CAGE DRX009087 DRR009961
Accession ID Mm9

Library idBAMCTSS
CNhs11116 DRZ001386 DRZ002769
Accession ID Mm10

Library idBAMCTSS
CNhs11116 DRZ012736 DRZ014119
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs11116

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.0119
1002 0.00471
1003 -0.0927
1004 0
1005 0.075
1006 -0.143
1007 0.0174
1008 0
1009 -0.185
101 0.103
1010 0
1011 -0.103
1012 0.244
1013 -0.0779
1014 -0.0196
1015 -0.164
1016 -0.465
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.075
1022 -0.165
1023 0
1024 0.049
1025 0
1026 0
1027 0
1028 0
1029 0.266
103 -0.00877
1030 0.46
1031 -0.188
1032 -0.177
1033 0.00845
1034 0
1035 0
1036 0.411
1037 0
1038 -0.255
1039 -0.173
104 0
1040 -0.0915
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs11116
Jaspar motif P-value
MA0002.2 0.00953
MA0003.1 0.608
MA0004.1 0.937
MA0006.1 0.374
MA0007.1 0.785
MA0009.1 0.413
MA0014.1 0.991
MA0017.1 0.226
MA0018.2 9.60074e-4
MA0019.1 0.499
MA0024.1 5.21844e-7
MA0025.1 0.0555
MA0027.1 0.636
MA0028.1 0.0434
MA0029.1 0.964
MA0030.1 0.253
MA0031.1 0.502
MA0035.2 4.92642e-13
MA0038.1 0.0469
MA0039.2 0.718
MA0040.1 0.885
MA0041.1 0.3
MA0042.1 0.843
MA0043.1 5.52888e-4
MA0046.1 7.46664e-11
MA0047.2 0.834
MA0048.1 0.102
MA0050.1 1.27315e-5
MA0051.1 0.00112
MA0052.1 3.91262e-6
MA0055.1 0.188
MA0057.1 0.71
MA0058.1 0.964
MA0059.1 0.182
MA0060.1 0.267
MA0061.1 0.0101
MA0062.2 3.30613e-4
MA0065.2 0.29
MA0066.1 0.199
MA0067.1 0.574
MA0068.1 0.793
MA0069.1 0.497
MA0070.1 0.157
MA0071.1 0.724
MA0072.1 0.771
MA0073.1 0.868
MA0074.1 0.731
MA0076.1 0.0992
MA0077.1 0.0814
MA0078.1 0.508
MA0079.2 0.0329
MA0080.2 7.53797e-10
MA0081.1 0.0843
MA0083.1 0.143
MA0084.1 0.193
MA0087.1 0.0967
MA0088.1 0.108
MA0090.1 0.0563
MA0091.1 0.0211
MA0092.1 0.635
MA0093.1 0.989
MA0099.2 0.629
MA0100.1 0.0573
MA0101.1 0.0404
MA0102.2 0.917
MA0103.1 0.642
MA0104.2 0.638
MA0105.1 1.0843e-5
MA0106.1 0.314
MA0107.1 0.0738
MA0108.2 9.42747e-4
MA0111.1 0.668
MA0112.2 0.00124
MA0113.1 0.496
MA0114.1 0.722
MA0115.1 0.591
MA0116.1 4.71306e-4
MA0117.1 0.973
MA0119.1 0.107
MA0122.1 0.773
MA0124.1 0.88
MA0125.1 0.0657
MA0131.1 0.755
MA0135.1 0.076
MA0136.1 4.14394e-10
MA0137.2 0.754
MA0138.2 0.00512
MA0139.1 0.13
MA0140.1 1.01847e-45
MA0141.1 0.266
MA0142.1 0.36
MA0143.1 0.254
MA0144.1 0.785
MA0145.1 0.966
MA0146.1 0.474
MA0147.1 0.547
MA0148.1 0.657
MA0149.1 0.0235
MA0150.1 0.0303
MA0152.1 0.891
MA0153.1 1.30421e-6
MA0154.1 0.00593
MA0155.1 0.688
MA0156.1 6.46543e-8
MA0157.1 0.423
MA0159.1 0.272
MA0160.1 0.965
MA0162.1 0.186
MA0163.1 4.8273e-5
MA0164.1 0.456
MA0258.1 0.115
MA0259.1 0.857



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs11116
Novel motif P-value
1 0.0784
10 0.0244
100 0.571
101 0.97
102 0.723
103 0.0102
104 0.865
105 0.723
106 0.243
107 0.466
108 0.362
109 0.061
11 0.191
110 0.0698
111 0.0197
112 0.0423
113 0.995
114 0.453
115 0.528
116 0.793
117 0.00148
118 0.112
119 0.201
12 0.809
120 0.873
121 0.189
122 0.59
123 0.165
124 0.881
125 0.0208
126 0.242
127 0.444
128 0.161
129 0.197
13 0.00325
130 0.277
131 0.938
132 0.168
133 0.443
134 0.0639
135 0.928
136 0.818
137 0.0126
138 0.626
139 0.461
14 0.762
140 0.202
141 0.747
142 0.0666
143 0.453
144 0.646
145 0.00674
146 0.851
147 0.746
148 0.123
149 0.692
15 0.0463
150 0.166
151 0.326
152 0.469
153 0.593
154 0.244
155 0.0992
156 0.771
157 0.563
158 0.0494
159 0.0975
160 0.434
161 0.0804
162 0.982
163 0.716
164 0.0224
165 0.353
166 0.381
167 0.0746
168 0.486
169 0.0637
17 0.432
18 0.238
19 0.257
2 0.321
20 0.0745
21 0.421
22 0.638
23 0.892
24 0.435
25 0.361
26 8.08329e-4
27 0.85
28 0.287
29 0.016
3 0.0378
30 0.387
31 0.891
32 0.551
33 0.197
34 0.971
35 0.693
36 0.044
37 0.153
38 0.488
39 0.656
4 0.846
40 0.251
41 0.697
42 0.0532
43 0.0976
44 0.917
45 0.68
46 0.135
47 0.185
48 0.254
49 0.0583
5 0.0998
50 0.958
51 0.819
52 0.842
53 0.98
54 0.97
55 0.282
56 0.594
57 0.0651
58 0.315
59 0.494
6 0.382
60 0.394
61 0.438
62 0.15
63 0.41
64 0.576
65 0.539
66 0.782
67 0.429
68 0.689
69 0.279
7 0.0433
70 0.345
71 0.0173
72 0.409
73 0.445
74 0.712
75 0.0449
76 0.251
77 0.77
78 0.0426
79 0.989
8 0.0209
80 0.0596
81 0.437
82 0.599
83 0.485
84 0.0574
85 0.391
86 0.79
87 0.352
88 0.724
89 0.633
9 0.421
90 0.0241
91 0.127
92 0.461
93 0.451
94 0.119
95 0.193
96 0.00692
97 0.859
98 0.26
99 0.971



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs11116


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)
0002106 (spleen)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002323 (body cavity)
0005177 (trunk region element)
0004177 (hemopoietic organ)
0005057 (immune organ)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002390 (hematopoietic system)
0002417 (abdominal segment of trunk)
0002193 (hemolymphoid system)
0000916 (abdomen)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011417 (mouse spleen- neonate N10 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:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)