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FF:1063-29H9

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Name:accessory axillary lymph node, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10475
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
tissueaccessory axillary lymph node
dev stageadult
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  SAMD00005298
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10475 CAGE DRX008926 DRR009800
Accession ID Mm9

Library idBAMCTSS
CNhs10475 DRZ001225 DRZ002608
Accession ID Mm10

Library idBAMCTSS
CNhs10475 DRZ012575 DRZ013958
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 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

CNhs10475

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.0725
1002 -0.116
1003 -0.123
1004 0
1005 0.228
1006 -0.143
1007 -0.0824
1008 0
1009 0.0497
101 0.223
1010 0
1011 0.221
1012 0.1
1013 0.00147
1014 -0.0874
1015 -0.147
1016 -0.272
1017 0
1018 0
1019 0
102 0.1
1020 0
1021 0.0513
1022 -0.124
1023 0.1
1024 0
1025 0
1026 0
1027 0
1028 0
1029 0.0304
103 -0.0787
1030 0.733
1031 -0.389
1032 -0.184
1033 0.145
1034 0
1035 0
1036 -0.00161
1037 0
1038 -0.194
1039 -0.153
104 0
1040 -0.0466
1041 0.361



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: CNhs10475
Jaspar motif P-value
MA0002.2 2.16405e-9
MA0003.1 0.64
MA0004.1 0.644
MA0006.1 0.188
MA0007.1 0.93
MA0009.1 0.804
MA0014.1 0.528
MA0017.1 0.879
MA0018.2 0.269
MA0019.1 0.143
MA0024.1 0.557
MA0025.1 0.924
MA0027.1 0.823
MA0028.1 7.00213e-5
MA0029.1 0.432
MA0030.1 0.369
MA0031.1 0.829
MA0035.2 0.732
MA0038.1 0.557
MA0039.2 0.455
MA0040.1 0.52
MA0041.1 0.67
MA0042.1 0.692
MA0043.1 0.832
MA0046.1 4.31292e-11
MA0047.2 0.969
MA0048.1 0.49
MA0050.1 9.44348e-24
MA0051.1 2.5034e-15
MA0052.1 0.0342
MA0055.1 0.343
MA0057.1 0.567
MA0058.1 0.795
MA0059.1 0.423
MA0060.1 0.0396
MA0061.1 4.50094e-14
MA0062.2 2.54414e-26
MA0065.2 0.897
MA0066.1 0.299
MA0067.1 0.368
MA0068.1 0.0175
MA0069.1 0.622
MA0070.1 0.468
MA0071.1 0.623
MA0072.1 0.221
MA0073.1 0.721
MA0074.1 0.872
MA0076.1 1.75874e-6
MA0077.1 0.0281
MA0078.1 0.58
MA0079.2 0.22
MA0080.2 4.7178e-16
MA0081.1 3.73571e-4
MA0083.1 0.27
MA0084.1 0.569
MA0087.1 0.391
MA0088.1 0.346
MA0090.1 0.00985
MA0091.1 0.627
MA0092.1 0.944
MA0093.1 0.631
MA0099.2 0.219
MA0100.1 0.805
MA0101.1 3.6079e-12
MA0102.2 0.0798
MA0103.1 0.631
MA0104.2 0.407
MA0105.1 3.73709e-8
MA0106.1 0.93
MA0107.1 1.06523e-15
MA0108.2 0.00308
MA0111.1 0.98
MA0112.2 0.0352
MA0113.1 0.377
MA0114.1 0.143
MA0115.1 0.78
MA0116.1 0.0192
MA0117.1 0.409
MA0119.1 0.378
MA0122.1 0.674
MA0124.1 0.379
MA0125.1 0.168
MA0131.1 0.662
MA0135.1 0.992
MA0136.1 5.77804e-26
MA0137.2 5.6304e-5
MA0138.2 0.0327
MA0139.1 0.202
MA0140.1 0.658
MA0141.1 0.0288
MA0142.1 8.18793e-6
MA0143.1 0.149
MA0144.1 0.0127
MA0145.1 0.733
MA0146.1 0.842
MA0147.1 0.297
MA0148.1 0.904
MA0149.1 0.974
MA0150.1 0.635
MA0152.1 0.876
MA0153.1 9.45679e-9
MA0154.1 2.4715e-4
MA0155.1 0.575
MA0156.1 3.96379e-39
MA0157.1 0.282
MA0159.1 0.191
MA0160.1 0.292
MA0162.1 0.368
MA0163.1 0.0158
MA0164.1 0.75
MA0258.1 0.336
MA0259.1 0.0531



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: CNhs10475
Novel motif P-value
1 0.742
10 0.196
100 0.441
101 0.786
102 0.742
103 0.242
104 0.762
105 0.695
106 0.128
107 0.326
108 0.479
109 0.479
11 0.779
110 0.18
111 0.564
112 0.0263
113 0.0185
114 0.392
115 0.982
116 0.594
117 0.00968
118 0.278
119 0.306
12 0.558
120 0.985
121 0.209
122 0.659
123 0.909
124 0.488
125 0.189
126 0.902
127 0.238
128 0.131
129 0.0518
13 0.254
130 0.343
131 0.699
132 0.61
133 0.898
134 0.686
135 0.388
136 0.713
137 0.13
138 0.868
139 0.838
14 0.408
140 0.813
141 0.0781
142 0.582
143 0.0142
144 0.775
145 0.349
146 0.538
147 0.618
148 0.0915
149 0.905
15 0.0577
150 0.166
151 0.0463
152 0.565
153 0.195
154 0.709
155 0.555
156 0.612
157 0.99
158 0.222
159 0.377
160 0.888
161 0.0715
162 0.0977
163 0.332
164 0.213
165 0.091
166 0.68
167 0.697
168 0.977
169 0.0571
17 0.664
18 0.633
19 0.424
2 0.904
20 0.272
21 0.857
22 0.567
23 0.967
24 0.104
25 0.196
26 0.133
27 0.15
28 0.0487
29 0.334
3 0.31
30 0.288
31 0.804
32 0.636
33 0.509
34 0.566
35 0.609
36 0.217
37 0.0312
38 0.077
39 0.335
4 0.398
40 0.6
41 0.865
42 0.18
43 0.174
44 0.546
45 0.227
46 0.285
47 0.319
48 0.355
49 0.333
5 0.244
50 0.912
51 0.986
52 0.634
53 0.789
54 0.409
55 0.808
56 0.699
57 0.457
58 0.0392
59 0.345
6 0.476
60 0.59
61 0.266
62 0.0792
63 0.695
64 0.694
65 0.332
66 0.662
67 0.504
68 0.469
69 0.345
7 0.196
70 0.225
71 0.197
72 0.146
73 0.0952
74 0.228
75 0.0447
76 0.299
77 0.297
78 0.0168
79 0.996
8 0.494
80 8.67614e-4
81 0.59
82 0.178
83 0.0399
84 0.876
85 0.746
86 0.385
87 0.919
88 0.396
89 0.659
9 0.341
90 0.216
91 0.868
92 0.692
93 0.168
94 0.28
95 0.483
96 0.988
97 0.941
98 0.138
99 0.336



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: CNhs10475


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)
0000029 (lymph node)
0000479 (tissue)
0001097 (axillary lymph node)
0000064 (organ part)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003968 (peripheral lymph node)
0010707 (appendage girdle complex)
0002465 (lymphoid system)
0001467 (shoulder)
0010708 (pectoral complex)
0002193 (hemolymphoid system)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue 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


NA