FF:12972-138H2

Name:	EBF KO HPCs induced to T cell
Species:	Mouse (Mus musculus)
Library ID:	CNhs11058
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information
Sample information strain NA tissue NA dev stage NA sex NA age NA cell type unclassifiable cell line NA company NA collaboration Tomokatsu Ikawa (RCAI) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type NA extraction protocol (Details) NA

CAGE Accession numbers
Method Sample accession id CAGE  SAMD00005018 Library accession numbers Library id Method Exp. accession id Run accession id CNhs11058 CAGE DRX008899 DRR009771 Accession ID Mm9 Library id BAM CTSS CNhs11058 DRZ001196 DRZ002581 Accession ID Mm10 Library id BAM CTSS CNhs11058 DRZ012546 DRZ013931

Download raw sequence, BAM & CTSS
Mm9 Fasta BAM CTSS download download donwload Mm10 BAM CTSS download 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.
Analyst:NA

link to dataset.
data

CNhs11058

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	--0.129
1004	0
1005	0
1006	--0.143
1007	--0.0529
1008	0
1009	--0.171
101	0.166
1010	0
1011	0.00572
1012	0
1013	0.0747
1014	--0.0874
1015	0.0462
1016	--0.344
1017	0
1018	0
1019	0
102	0.0411
1020	0.0411
1021	0.0672
1022	--0.263
1023	0.113
1024	0.139
1025	0
1026	0
1027	--0.048
1028	0
1029	--0.142
103	--0.0796
1030	0
1031	--0.973
1032	--0.387
1033	0.113
1034	0
1035	0
1036	0.278
1037	0
1038	--0.377
1039	--0.169
104	0
1040	--0.175
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

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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: CNhs11058

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	1.79247e-8
MA0003.1	MA0003.1	0.573
MA0004.1	MA0004.1	0.0417
MA0006.1	MA0006.1	0.972
MA0007.1	MA0007.1	0.356
MA0009.1	MA0009.1	0.767
MA0014.1	MA0014.1	0.545
MA0017.1	MA0017.1	0.538
MA0018.2	MA0018.2	0.951
MA0019.1	MA0019.1	0.893
MA0024.1	MA0024.1	5.31246e-4
MA0025.1	MA0025.1	0.296
MA0027.1	MA0027.1	0.98
MA0028.1	MA0028.1	4.02835e-7
MA0029.1	MA0029.1	0.425
MA0030.1	MA0030.1	0.0424
MA0031.1	MA0031.1	0.865
MA0035.2	MA0035.2	0.571
MA0038.1	MA0038.1	0.0314
MA0039.2	MA0039.2	0.501
MA0040.1	MA0040.1	0.654
MA0041.1	MA0041.1	0.0336
MA0042.1	MA0042.1	0.25
MA0043.1	MA0043.1	0.917
MA0046.1	MA0046.1	7.73929e-14
MA0047.2	MA0047.2	0.448
MA0048.1	MA0048.1	0.134
MA0050.1	MA0050.1	3.64008e-6
MA0051.1	MA0051.1	0.00583
MA0052.1	MA0052.1	0.404
MA0055.1	MA0055.1	0.0828
MA0057.1	MA0057.1	0.934
MA0058.1	MA0058.1	0.0087
MA0059.1	MA0059.1	1.91928e-4
MA0060.1	MA0060.1	0.774
MA0061.1	MA0061.1	0.0295
MA0062.2	MA0062.2	5.37088e-16
MA0065.2	MA0065.2	0.116
MA0066.1	MA0066.1	0.0477
MA0067.1	MA0067.1	0.621
MA0068.1	MA0068.1	0.083
MA0069.1	MA0069.1	0.687
MA0070.1	MA0070.1	0.767
MA0071.1	MA0071.1	0.41
MA0072.1	MA0072.1	0.906
MA0073.1	MA0073.1	0.933
MA0074.1	MA0074.1	0.0977
MA0076.1	MA0076.1	7.86076e-9
MA0077.1	MA0077.1	0.374
MA0078.1	MA0078.1	0.706
MA0079.2	MA0079.2	0.0385
MA0080.2	MA0080.2	1.83773e-12
MA0081.1	MA0081.1	5.85268e-4
MA0083.1	MA0083.1	1.48896e-4
MA0084.1	MA0084.1	0.458
MA0087.1	MA0087.1	0.917
MA0088.1	MA0088.1	0.0476
MA0090.1	MA0090.1	0.0239
MA0091.1	MA0091.1	0.075
MA0092.1	MA0092.1	0.352
MA0093.1	MA0093.1	0.0343
MA0099.2	MA0099.2	0.922
MA0100.1	MA0100.1	0.00108
MA0101.1	MA0101.1	0.0127
MA0102.2	MA0102.2	0.834
MA0103.1	MA0103.1	0.47
MA0104.2	MA0104.2	0.00603
MA0105.1	MA0105.1	1.06413e-4
MA0106.1	MA0106.1	0.0946
MA0107.1	MA0107.1	0.0577
MA0108.2	MA0108.2	1.82599e-6
MA0111.1	MA0111.1	0.498
MA0112.2	MA0112.2	0.00677
MA0113.1	MA0113.1	0.375
MA0114.1	MA0114.1	0.768
MA0115.1	MA0115.1	0.652
MA0116.1	MA0116.1	6.10863e-4
MA0117.1	MA0117.1	0.956
MA0119.1	MA0119.1	0.879
MA0122.1	MA0122.1	0.597
MA0124.1	MA0124.1	0.577
MA0125.1	MA0125.1	0.0856
MA0131.1	MA0131.1	0.257
MA0135.1	MA0135.1	0.0438
MA0136.1	MA0136.1	7.84112e-27
MA0137.2	MA0137.2	1.45639e-4
MA0138.2	MA0138.2	7.02612e-4
MA0139.1	MA0139.1	0.236
MA0140.1	MA0140.1	0.186
MA0141.1	MA0141.1	0.389
MA0142.1	MA0142.1	0.513
MA0143.1	MA0143.1	0.304
MA0144.1	MA0144.1	0.073
MA0145.1	MA0145.1	0.719
MA0146.1	MA0146.1	0.0716
MA0147.1	MA0147.1	0.0024
MA0148.1	MA0148.1	0.449
MA0149.1	MA0149.1	0.099
MA0150.1	MA0150.1	0.283
MA0152.1	MA0152.1	0.995
MA0153.1	MA0153.1	1.35916e-6
MA0154.1	MA0154.1	0.108
MA0155.1	MA0155.1	0.995
MA0156.1	MA0156.1	1.71039e-23
MA0157.1	MA0157.1	0.988
MA0159.1	MA0159.1	0.0236
MA0160.1	MA0160.1	0.389
MA0162.1	MA0162.1	0.258
MA0163.1	MA0163.1	2.43779e-6
MA0164.1	MA0164.1	0.822
MA0258.1	MA0258.1	0.013
MA0259.1	MA0259.1	0.327

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: CNhs11058

Novel motif	Logo	P-value
1	1	0.246
10	10	0.0269
100	100	0.824
101	101	0.899
102	102	0.231
103	103	0.16
104	104	0.731
105	105	0.713
106	106	0.667
107	107	0.432
108	108	0.334
109	109	0.0912
11	11	0.0662
110	110	0.0573
111	111	0.0207
112	112	0.079
113	113	0.673
114	114	0.752
115	115	0.905
116	116	0.942
117	117	1.51689e-4
118	118	0.0574
119	119	0.67
12	12	0.574
120	120	0.374
121	121	0.131
122	122	0.667
123	123	0.57
124	124	0.802
125	125	0.303
126	126	0.242
127	127	0.581
128	128	0.273
129	129	0.416
13	13	0.0126
130	130	0.518
131	131	0.911
132	132	0.507
133	133	0.756
134	134	0.314
135	135	0.644
136	136	0.522
137	137	0.0605
138	138	0.616
139	139	0.297
14	14	0.589
140	140	0.837
141	141	0.913
142	142	0.498
143	143	0.0781
144	144	0.733
145	145	0.0391
146	146	0.696
147	147	0.531
148	148	0.208
149	149	0.489
15	15	0.00918
150	150	0.338
151	151	0.398
152	152	0.826
153	153	0.825
154	154	0.6
155	155	0.242
156	156	0.0542
157	157	0.659
158	158	0.301
159	159	0.359
160	160	0.818
161	161	0.115
162	162	0.331
163	163	0.329
164	164	0.0127
165	165	0.661
166	166	0.513
167	167	0.385
168	168	0.418
169	169	0.0214
17	17	0.816
18	18	0.277
19	19	0.776
2	2	0.0854
20	20	0.042
21	21	0.162
22	22	0.684
23	23	0.53
24	24	0.0686
25	25	0.155
26	26	0.0134
27	27	0.947
28	28	0.536
29	29	0.01
3	3	0.0439
30	30	0.134
31	31	0.721
32	32	0.815
33	33	0.34
34	34	0.729
35	35	0.155
36	36	0.0345
37	37	0.0676
38	38	0.346
39	39	0.552
4	4	0.805
40	40	0.184
41	41	0.209
42	42	0.168
43	43	0.411
44	44	0.152
45	45	0.597
46	46	0.235
47	47	0.228
48	48	0.114
49	49	0.195
5	5	0.104
50	50	0.638
51	51	0.93
52	52	0.349
53	53	0.457
54	54	0.637
55	55	0.267
56	56	0.792
57	57	0.218
58	58	0.213
59	59	0.803
6	6	0.417
60	60	0.718
61	61	0.107
62	62	0.102
63	63	0.67
64	64	0.423
65	65	0.511
66	66	0.744
67	67	0.809
68	68	0.87
69	69	0.548
7	7	0.217
70	70	0.0179
71	71	0.00885
72	72	0.427
73	73	0.0915
74	74	0.56
75	75	0.0058
76	76	0.0831
77	77	0.398
78	78	0.0807
79	79	0.832
8	8	0.0385
80	80	0.191
81	81	0.951
82	82	0.825
83	83	0.213
84	84	0.416
85	85	0.716
86	86	0.0533
87	87	0.167
88	88	0.401
89	89	0.606
9	9	0.917
90	90	0.0103
91	91	0.918
92	92	0.928
93	93	0.91
94	94	0.161
95	95	0.0285
96	96	0.173
97	97	0.555
98	98	0.496
99	99	0.329

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: CNhs11058

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000729 mouse EBF KO HPCs induced to T cell 0h sample

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)