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FF:12988-138I9

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Name:EBF KO HPCs induced to T cell
Species:Mouse (Mus musculus)
Library ID:CNhs12980
Sample type:time courses
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeunclassifiable
cell lineNA
companyNA
collaborationTomokatsu Ikawa (RCAI)
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  SAMD00005159
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12980 CAGE DRX008900 DRR009772
Accession ID Mm9

Library idBAMCTSS
CNhs12980 DRZ001197 DRZ002582
Accession ID Mm10

Library idBAMCTSS
CNhs12980 DRZ012547 DRZ013932
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

CNhs12980

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0749
1002 --0.116
1003 --0.175
1004 0
1005 0
1006 --0.24
1007 --0.15
1008 0
1009 --0.191
101 0.207
1010 0
1011 0
1012 0
1013 0.0596
1014 --0.0874
1015 --0.0949
1016 --0.379
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.183
1022 --0.289
1023 0.101
1024 0.112
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.148
103 --0.0887
1030 0
1031 -1.049
1032 --0.383
1033 0.107
1034 0
1035 0
1036 0.375
1037 0
1038 --0.476
1039 --0.28
104 0
1040 --0.264
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: CNhs12980

Jaspar motif P-value
MA0002.2 3.73789e-8
MA0003.1 0.479
MA0004.1 0.0671
MA0006.1 0.975
MA0007.1 0.466
MA0009.1 0.665
MA0014.1 0.709
MA0017.1 0.383
MA0018.2 0.771
MA0019.1 0.872
MA0024.1 5.38863e-4
MA0025.1 0.166
MA0027.1 0.893
MA0028.1 4.08035e-7
MA0029.1 0.195
MA0030.1 0.0424
MA0031.1 0.502
MA0035.2 0.791
MA0038.1 0.104
MA0039.2 0.379
MA0040.1 0.201
MA0041.1 0.363
MA0042.1 0.462
MA0043.1 0.944
MA0046.1 1.02195e-12
MA0047.2 0.364
MA0048.1 0.15
MA0050.1 6.55323e-6
MA0051.1 0.00173
MA0052.1 0.173
MA0055.1 0.073
MA0057.1 0.928
MA0058.1 0.0233
MA0059.1 4.19146e-4
MA0060.1 0.726
MA0061.1 0.0396
MA0062.2 1.24921e-15
MA0065.2 0.097
MA0066.1 0.0986
MA0067.1 0.74
MA0068.1 0.704
MA0069.1 0.628
MA0070.1 0.765
MA0071.1 0.26
MA0072.1 0.862
MA0073.1 0.812
MA0074.1 0.213
MA0076.1 5.16746e-9
MA0077.1 0.278
MA0078.1 0.607
MA0079.2 0.0381
MA0080.2 9.12579e-12
MA0081.1 8.98542e-4
MA0083.1 0.00139
MA0084.1 0.547
MA0087.1 0.991
MA0088.1 0.0602
MA0090.1 0.0195
MA0091.1 0.0809
MA0092.1 0.385
MA0093.1 0.0593
MA0099.2 0.638
MA0100.1 0.00136
MA0101.1 0.0164
MA0102.2 0.547
MA0103.1 0.498
MA0104.2 0.00743
MA0105.1 6.40596e-5
MA0106.1 0.0594
MA0107.1 0.111
MA0108.2 1.26844e-4
MA0111.1 0.459
MA0112.2 0.00836
MA0113.1 0.199
MA0114.1 0.677
MA0115.1 0.651
MA0116.1 8.21001e-4
MA0117.1 0.931
MA0119.1 0.871
MA0122.1 0.477
MA0124.1 0.573
MA0125.1 0.048
MA0131.1 0.195
MA0135.1 0.0895
MA0136.1 2.3385e-25
MA0137.2 4.91805e-5
MA0138.2 0.0119
MA0139.1 0.195
MA0140.1 0.396
MA0141.1 0.198
MA0142.1 0.562
MA0143.1 0.299
MA0144.1 0.0797
MA0145.1 0.669
MA0146.1 0.208
MA0147.1 0.00305
MA0148.1 0.488
MA0149.1 0.0842
MA0150.1 0.368
MA0152.1 0.949
MA0153.1 1.00276e-5
MA0154.1 0.118
MA0155.1 0.927
MA0156.1 1.92336e-19
MA0157.1 0.846
MA0159.1 0.00958
MA0160.1 0.305
MA0162.1 0.202
MA0163.1 3.87556e-6
MA0164.1 0.927
MA0258.1 0.0222
MA0259.1 0.351



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: CNhs12980

Novel motif P-value
1 0.275
10 0.0223
100 0.861
101 0.971
102 0.338
103 0.0377
104 0.715
105 0.749
106 0.779
107 0.345
108 0.397
109 0.0843
11 0.0885
110 0.0361
111 0.00897
112 0.0439
113 0.667
114 0.888
115 0.985
116 0.707
117 4.06246e-4
118 0.145
119 0.583
12 0.491
120 0.42
121 0.165
122 0.885
123 0.816
124 0.71
125 0.344
126 0.223
127 0.304
128 0.386
129 0.551
13 0.016
130 0.786
131 0.746
132 0.506
133 0.766
134 0.268
135 0.638
136 0.719
137 0.152
138 0.372
139 0.137
14 0.621
140 0.534
141 0.826
142 0.862
143 0.135
144 0.83
145 0.0445
146 0.736
147 0.726
148 0.283
149 0.447
15 0.0105
150 0.464
151 0.387
152 0.474
153 0.885
154 0.686
155 0.192
156 0.092
157 0.855
158 0.344
159 0.49
160 0.953
161 0.056
162 0.395
163 0.23
164 0.0171
165 0.379
166 0.552
167 0.274
168 0.596
169 0.0292
17 0.827
18 0.184
19 0.82
2 0.118
20 0.0697
21 0.182
22 0.865
23 0.355
24 0.0603
25 0.11
26 0.0216
27 0.94
28 0.653
29 0.00543
3 0.0576
30 0.144
31 0.895
32 0.96
33 0.345
34 0.718
35 0.15
36 0.0234
37 0.0775
38 0.437
39 0.522
4 0.731
40 0.18
41 0.138
42 0.167
43 0.455
44 0.12
45 0.563
46 0.175
47 0.225
48 0.113
49 0.203
5 0.0619
50 0.59
51 0.741
52 0.33
53 0.511
54 0.898
55 0.159
56 0.717
57 0.148
58 0.168
59 0.718
6 0.499
60 0.719
61 0.113
62 0.0727
63 0.688
64 0.336
65 0.594
66 0.619
67 0.538
68 0.664
69 0.787
7 0.159
70 0.0178
71 0.00685
72 0.294
73 0.141
74 0.641
75 0.0076
76 0.136
77 0.423
78 0.148
79 0.898
8 0.0237
80 0.118
81 0.799
82 0.557
83 0.221
84 0.64
85 0.693
86 0.0778
87 0.196
88 0.459
89 0.358
9 0.927
90 0.0178
91 0.813
92 0.598
93 0.41
94 0.113
95 0.0841
96 0.231
97 0.578
98 0.627
99 0.373



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: CNhs12980


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000084 (T cell)
0000837 (hematopoietic multipotent progenitor cell)

FF: FANTOM5
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000357 (0 hr sample)
0000342 (T-cell induction sample)
0000729 (mouse EBF KO HPCs induced to T cell 0h 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

CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)