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FF:11817-124E8

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Name:CD4+CD25-CD44- naive conventional T cells, pool2 (Balb_cAJcl)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/cAJcl
tissueblood
dev stageNA
sexNA
ageNA
cell typeT cell
cell lineNA
companyNA
collaborationMorikawa (University of Kyoto)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberBLnT
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs13220

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0173
1001 --0.0631
1002 --0.116
1003 --0.157
1004 0
1005 0
1006 --0.254
1007 --0.265
1008 0
1009 --0.19
101 0.185
1010 0
1011 0.0364
1012 0
1013 --0.139
1014 --0.0874
1015 --0.202
1016 --0.594
1017 0
1018 0
1019 0
102 0.636
1020 0.0364
1021 0.124
1022 --0.137
1023 0.0364
1024 --0.14
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.089
103 --0.0887
1030 0
1031 -1.111
1032 --0.659
1033 0.515
1034 0
1035 0
1036 0.293
1037 0
1038 --0.223
1039 --0.229
104 0
1040 --0.216
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
no result for this sample


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: CNhs13220

Jaspar motif P-value
MA0002.2 4.71356e-5
MA0003.1 0.274
MA0004.1 0.0488
MA0006.1 0.493
MA0007.1 0.365
MA0009.1 0.803
MA0014.1 0.736
MA0017.1 0.983
MA0018.2 5.23107e-4
MA0019.1 0.698
MA0024.1 0.676
MA0025.1 0.792
MA0027.1 0.926
MA0028.1 4.47163e-8
MA0029.1 0.256
MA0030.1 0.293
MA0031.1 0.00665
MA0035.2 0.728
MA0038.1 0.00204
MA0039.2 0.354
MA0040.1 0.294
MA0041.1 0.0512
MA0042.1 0.397
MA0043.1 0.0297
MA0046.1 2.37414e-9
MA0047.2 0.143
MA0048.1 0.293
MA0050.1 1.56882e-8
MA0051.1 1.69982e-6
MA0052.1 0.0142
MA0055.1 0.144
MA0057.1 0.846
MA0058.1 0.0316
MA0059.1 0.019
MA0060.1 3.53943e-4
MA0061.1 6.26951e-5
MA0062.2 9.73059e-24
MA0065.2 0.756
MA0066.1 0.072
MA0067.1 0.0923
MA0068.1 0.0997
MA0069.1 0.689
MA0070.1 0.684
MA0071.1 0.913
MA0072.1 0.0895
MA0073.1 0.904
MA0074.1 0.273
MA0076.1 1.67357e-11
MA0077.1 0.143
MA0078.1 0.574
MA0079.2 0.0675
MA0080.2 1.16197e-13
MA0081.1 0.00318
MA0083.1 0.135
MA0084.1 0.602
MA0087.1 0.878
MA0088.1 0.645
MA0090.1 0.0789
MA0091.1 0.752
MA0092.1 0.745
MA0093.1 0.0598
MA0099.2 0.441
MA0100.1 0.138
MA0101.1 3.43622e-5
MA0102.2 0.82
MA0103.1 0.135
MA0104.2 0.0372
MA0105.1 1.00043e-6
MA0106.1 0.867
MA0107.1 7.88025e-5
MA0108.2 3.80426e-6
MA0111.1 0.227
MA0112.2 0.125
MA0113.1 0.237
MA0114.1 0.334
MA0115.1 0.745
MA0116.1 0.0162
MA0117.1 0.501
MA0119.1 0.566
MA0122.1 0.522
MA0124.1 0.642
MA0125.1 0.154
MA0131.1 0.487
MA0135.1 0.834
MA0136.1 1.00843e-26
MA0137.2 1.1018e-4
MA0138.2 0.00606
MA0139.1 0.248
MA0140.1 0.335
MA0141.1 0.924
MA0142.1 0.346
MA0143.1 0.573
MA0144.1 0.0202
MA0145.1 0.265
MA0146.1 0.791
MA0147.1 0.0161
MA0148.1 0.126
MA0149.1 0.111
MA0150.1 0.624
MA0152.1 0.732
MA0153.1 1.26494e-5
MA0154.1 0.187
MA0155.1 0.603
MA0156.1 1.03144e-30
MA0157.1 0.00633
MA0159.1 0.155
MA0160.1 0.899
MA0162.1 0.977
MA0163.1 0.00999
MA0164.1 0.276
MA0258.1 0.0939
MA0259.1 0.194



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: CNhs13220

Novel motif P-value
1 0.267
10 0.0248
100 0.552
101 0.9
102 0.483
103 0.318
104 0.868
105 0.85
106 0.976
107 0.449
108 0.543
109 0.246
11 0.243
110 0.0622
111 0.0663
112 0.0828
113 0.613
114 0.112
115 0.666
116 0.75
117 3.27666e-4
118 0.21
119 0.812
12 0.22
120 0.0494
121 0.442
122 0.77
123 0.307
124 0.297
125 0.249
126 0.299
127 0.759
128 0.784
129 0.349
13 0.118
130 0.738
131 0.313
132 0.965
133 0.928
134 0.698
135 0.779
136 0.293
137 0.445
138 0.393
139 0.335
14 0.654
140 0.532
141 0.0804
142 0.392
143 1.13569e-4
144 0.419
145 0.148
146 0.932
147 0.544
148 0.231
149 0.301
15 0.0813
150 0.732
151 0.292
152 0.232
153 0.479
154 0.248
155 0.0908
156 0.891
157 0.93
158 0.0511
159 0.834
160 0.445
161 0.105
162 0.601
163 0.832
164 0.0165
165 0.873
166 0.423
167 0.0758
168 0.631
169 0.769
17 0.635
18 0.25
19 0.144
2 0.0462
20 0.0122
21 0.101
22 0.789
23 0.689
24 0.269
25 0.142
26 0.281
27 0.904
28 0.228
29 0.0193
3 0.26
30 0.125
31 0.737
32 0.231
33 0.0873
34 0.438
35 0.0352
36 0.0323
37 0.133
38 0.534
39 0.576
4 0.966
40 0.411
41 0.275
42 0.243
43 0.566
44 0.602
45 0.447
46 0.418
47 0.516
48 0.255
49 0.224
5 0.0338
50 0.591
51 0.792
52 0.0732
53 0.731
54 0.629
55 0.441
56 0.904
57 0.639
58 0.344
59 0.795
6 0.646
60 0.974
61 0.183
62 0.0718
63 0.718
64 0.823
65 0.439
66 0.143
67 0.578
68 0.847
69 0.852
7 0.449
70 0.0114
71 0.0955
72 0.482
73 0.26
74 0.686
75 0.00566
76 0.0143
77 0.14
78 0.135
79 0.823
8 0.481
80 0.195
81 0.836
82 0.2
83 0.0724
84 0.675
85 0.99
86 0.174
87 0.971
88 0.416
89 0.96
9 0.928
90 0.0674
91 0.863
92 0.468
93 0.194
94 0.3
95 0.0922
96 0.191
97 0.507
98 0.45
99 0.0884



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: CNhs13220


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000084 (T cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000624 (CD4-positive, alpha-beta T cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000789 (alpha-beta T cell)
0000790 (immature alpha-beta T cell)
0000791 (mature alpha-beta T cell)
0000805 (immature single positive thymocyte)
0000806 (DN2 thymocyte)
0000807 (DN3 thymocyte)
0000808 (DN4 thymocyte)
0000809 (double-positive, alpha-beta thymocyte)
0000810 (CD4-positive, alpha-beta thymocyte)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000893 (thymocyte)
0000894 (DN1 thymic pro-T cell)
0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)
0000898 (naive T cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002419 (mature T cell)
0002420 (immature T cell)
0002425 (early T lineage precursor)
0002427 (resting double-positive thymocyte)
0002428 (double-positive blast)
0002429 (CD69-positive double-positive thymocyte)
0002431 (CD4-positive, CD8-intermediate double-positive thymocyte)
0002432 (CD24-positive, CD4 single-positive thymocyte)
0002433 (CD69-positive, CD4-positive single-positive thymocyte)
0002436 (mature CD4 single-positive thymocyte)
0002489 (double negative thymocyte)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

FF: FANTOM5
NA

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