FF:11854-124I9

Name:	Mouse CD4+ T Cells, donor1
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information
Sample information strain NA tissue spleen dev stage NA sex NA age NA cell type t cell, CD4+ cell line NA company NA collaboration Kawamoto (RCAI) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type total RNA extraction protocol (Details) OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
Method Sample accession id CAGE  DRS008704 Library accession numbers Library id Method Exp. accession id Run accession id {{{library_id}}} {{{accession_numbers}}} Accession ID Mm9 Library id BAM CTSS {{{library_id}}} Accession ID Mm10 Library id BAM CTSS {{{library_id}}}

Download raw sequence, BAM & CTSS
Mm9 BAM CTSS [{{{mm9bam}}} download] [{{{mm9ctss}}} donwload] Mm10 BAM CTSS [{{{mm10bam}}} download] [{{{mm10ctss}}} donwload]

Relative expression to median (log10)

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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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs13509

0	0
1	0
10	0
100	0
1000	0
1001	-0.0749
1002	-0.116
1003	-0.123
1004	0
1005	0.116
1006	-0.148
1007	0.032
1008	0
1009	-0.19
101	0.139
1010	0
1011	0.129
1012	0.186
1013	-0.188
1014	-0.0874
1015	-0.0376
1016	-0.594
1017	0
1018	0
1019	0
102	0.729
1020	0
1021	0
1022	-0.315
1023	0
1024	-0.0899
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.176
103	-0.0887
1030	0
1031	-1.148
1032	-0.655
1033	0.427
1034	0
1035	0
1036	0.433
1037	0
1038	0.0211
1039	-0.223
104	0
1040	-0.216
1041	0

Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

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JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13509

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	3.97871e-5
MA0003.1	MA0003.1	0.264
MA0004.1	MA0004.1	0.0952
MA0006.1	MA0006.1	0.434
MA0007.1	MA0007.1	0.648
MA0009.1	MA0009.1	0.71
MA0014.1	MA0014.1	0.793
MA0017.1	MA0017.1	0.357
MA0018.2	MA0018.2	4.81796e-8
MA0019.1	MA0019.1	0.79
MA0024.1	MA0024.1	0.774
MA0025.1	MA0025.1	0.644
MA0027.1	MA0027.1	0.808
MA0028.1	MA0028.1	2.303e-4
MA0029.1	MA0029.1	0.506
MA0030.1	MA0030.1	0.122
MA0031.1	MA0031.1	2.07317e-4
MA0035.2	MA0035.2	0.809
MA0038.1	MA0038.1	7.6594e-4
MA0039.2	MA0039.2	0.191
MA0040.1	MA0040.1	0.164
MA0041.1	MA0041.1	0.387
MA0042.1	MA0042.1	0.511
MA0043.1	MA0043.1	0.0193
MA0046.1	MA0046.1	9.60373e-11
MA0047.2	MA0047.2	0.0705
MA0048.1	MA0048.1	0.504
MA0050.1	MA0050.1	3.66975e-8
MA0051.1	MA0051.1	1.93679e-5
MA0052.1	MA0052.1	0.0857
MA0055.1	MA0055.1	0.411
MA0057.1	MA0057.1	0.911
MA0058.1	MA0058.1	0.0525
MA0059.1	MA0059.1	0.0967
MA0060.1	MA0060.1	0.00865
MA0061.1	MA0061.1	1.79873e-6
MA0062.2	MA0062.2	1.82661e-18
MA0065.2	MA0065.2	0.487
MA0066.1	MA0066.1	0.21
MA0067.1	MA0067.1	0.00178
MA0068.1	MA0068.1	0.0105
MA0069.1	MA0069.1	0.862
MA0070.1	MA0070.1	0.87
MA0071.1	MA0071.1	0.667
MA0072.1	MA0072.1	0.0321
MA0073.1	MA0073.1	0.772
MA0074.1	MA0074.1	0.659
MA0076.1	MA0076.1	1.01233e-5
MA0077.1	MA0077.1	0.224
MA0078.1	MA0078.1	0.541
MA0079.2	MA0079.2	0.0862
MA0080.2	MA0080.2	1.16003e-13
MA0081.1	MA0081.1	0.00354
MA0083.1	MA0083.1	0.245
MA0084.1	MA0084.1	0.823
MA0087.1	MA0087.1	0.871
MA0088.1	MA0088.1	0.536
MA0090.1	MA0090.1	0.0235
MA0091.1	MA0091.1	0.987
MA0092.1	MA0092.1	0.59
MA0093.1	MA0093.1	0.118
MA0099.2	MA0099.2	0.692
MA0100.1	MA0100.1	0.111
MA0101.1	MA0101.1	4.06577e-8
MA0102.2	MA0102.2	0.863
MA0103.1	MA0103.1	0.106
MA0104.2	MA0104.2	0.123
MA0105.1	MA0105.1	3.5427e-5
MA0106.1	MA0106.1	0.821
MA0107.1	MA0107.1	7.94176e-8
MA0108.2	MA0108.2	0.0245
MA0111.1	MA0111.1	0.354
MA0112.2	MA0112.2	0.81
MA0113.1	MA0113.1	0.587
MA0114.1	MA0114.1	0.0194
MA0115.1	MA0115.1	0.358
MA0116.1	MA0116.1	0.481
MA0117.1	MA0117.1	0.104
MA0119.1	MA0119.1	0.11
MA0122.1	MA0122.1	0.414
MA0124.1	MA0124.1	0.516
MA0125.1	MA0125.1	0.12
MA0131.1	MA0131.1	0.537
MA0135.1	MA0135.1	0.832
MA0136.1	MA0136.1	7.22525e-25
MA0137.2	MA0137.2	0.013
MA0138.2	MA0138.2	0.00272
MA0139.1	MA0139.1	0.567
MA0140.1	MA0140.1	0.508
MA0141.1	MA0141.1	0.488
MA0142.1	MA0142.1	0.259
MA0143.1	MA0143.1	0.35
MA0144.1	MA0144.1	0.0904
MA0145.1	MA0145.1	0.127
MA0146.1	MA0146.1	0.549
MA0147.1	MA0147.1	0.0656
MA0148.1	MA0148.1	0.18
MA0149.1	MA0149.1	0.0738
MA0150.1	MA0150.1	0.669
MA0152.1	MA0152.1	0.628
MA0153.1	MA0153.1	2.54423e-6
MA0154.1	MA0154.1	0.785
MA0155.1	MA0155.1	0.351
MA0156.1	MA0156.1	7.58134e-25
MA0157.1	MA0157.1	4.2973e-4
MA0159.1	MA0159.1	0.467
MA0160.1	MA0160.1	0.913
MA0162.1	MA0162.1	0.365
MA0163.1	MA0163.1	0.162
MA0164.1	MA0164.1	0.31
MA0258.1	MA0258.1	0.182
MA0259.1	MA0259.1	0.211

FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13509

Novel motif	Logo	P-value
1	1	0.467
10	10	0.0592
100	100	0.526
101	101	0.995
102	102	0.475
103	103	0.486
104	104	0.998
105	105	0.569
106	106	0.559
107	107	0.487
108	108	0.754
109	109	0.504
11	11	0.415
110	110	0.292
111	111	0.328
112	112	0.177
113	113	0.444
114	114	0.3
115	115	0.608
116	116	0.57
117	117	2.97036e-4
118	118	0.211
119	119	0.656
12	12	0.239
120	120	0.0611
121	121	0.337
122	122	0.97
123	123	0.66
124	124	0.465
125	125	0.561
126	126	0.456
127	127	0.784
128	128	0.246
129	129	0.332
13	13	0.143
130	130	0.71
131	131	0.267
132	132	0.828
133	133	0.55
134	134	0.592
135	135	0.878
136	136	0.546
137	137	0.336
138	138	0.267
139	139	0.321
14	14	0.603
140	140	0.528
141	141	0.324
142	142	0.263
143	143	2.52455e-4
144	144	0.507
145	145	0.199
146	146	0.784
147	147	0.469
148	148	0.178
149	149	0.176
15	15	0.185
150	150	0.881
151	151	0.288
152	152	0.379
153	153	0.47
154	154	0.166
155	155	0.0504
156	156	0.0661
157	157	0.833
158	158	0.0143
159	159	0.805
160	160	0.354
161	161	0.185
162	162	0.277
163	163	0.32
164	164	0.0919
165	165	0.819
166	166	0.487
167	167	0.0943
168	168	0.337
169	169	0.625
17	17	0.855
18	18	0.224
19	19	0.0776
2	2	0.018
20	20	0.0211
21	21	0.0869
22	22	0.615
23	23	0.995
24	24	0.552
25	25	0.198
26	26	0.363
27	27	0.658
28	28	0.384
29	29	0.0651
3	3	0.522
30	30	0.119
31	31	0.597
32	32	0.146
33	33	0.0987
34	34	0.353
35	35	0.0339
36	36	0.0899
37	37	0.232
38	38	0.618
39	39	0.365
4	4	0.7
40	40	0.504
41	41	0.149
42	42	0.281
43	43	0.713
44	44	0.683
45	45	0.27
46	46	0.506
47	47	0.862
48	48	0.431
49	49	0.207
5	5	0.119
50	50	0.469
51	51	0.69
52	52	0.184
53	53	0.607
54	54	0.639
55	55	0.896
56	56	0.993
57	57	0.688
58	58	0.321
59	59	0.565
6	6	0.661
60	60	0.854
61	61	0.209
62	62	0.0923
63	63	0.995
64	64	0.993
65	65	0.407
66	66	0.451
67	67	0.698
68	68	0.439
69	69	0.737
7	7	0.555
70	70	0.0234
71	71	0.192
72	72	0.954
73	73	0.322
74	74	0.713
75	75	0.00795
76	76	0.0271
77	77	0.0257
78	78	0.0404
79	79	0.954
8	8	0.71
80	80	0.163
81	81	0.992
82	82	0.495
83	83	0.0946
84	84	0.925
85	85	0.847
86	86	0.158
87	87	0.542
88	88	0.37
89	89	0.664
9	9	0.923
90	90	0.102
91	91	0.718
92	92	0.643
93	93	0.111
94	94	0.282
95	95	0.367
96	96	0.41
97	97	0.459
98	98	0.467
99	99	0.0285

de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs13509

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000031 CD4-positive T cell sample
FF:0000103 mouse sample

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>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)
0000791 (mature alpha-beta T cell)
0000084 (T cell)
0000789 (alpha-beta T cell)
0002419 (mature T cell)
0000624 (CD4-positive, alpha-beta T cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000031 (CD4-positive T cell sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)
CL:0000790 (immature alpha-beta T cell)

{{{1}}} Accession numbers
Method Sample accession id {{{2}}}  Library accession numbers Library id Method Exp. accession id Run accession id {{{4}}} {{{3}}} Accession ID Library id BAM CTSS {{{4}}} Accession ID Library id BAM CTSS {{{4}}}