FF:1830-49C7

Name:	mouse fibroblast cell line: CRL-1658 NIH/3T3, biol_rep1
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information
Sample information strain NA tissue whole body dev stage embryo sex NA age NA cell type fibroblast cell line CRL-1658 NIH/3T3 company NA collaboration NA 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) NA

Download raw sequence, BAM & CTSS
Mm9 BAM CTSS [{{{mm9bam}}} download] [{{{mm9ctss}}} donwload] Mm10 BAM CTSS [{{{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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs11093

0	0
1	0
10	0
100	0
1000	0.0659
1001	-0.0195
1002	0.0797
1003	0.291
1004	0
1005	0
1006	-0.143
1007	-0.0134
1008	0
1009	0.349
101	0.177
1010	0
1011	-0.175
1012	0
1013	-0.102
1014	-0.0851
1015	0.183
1016	0.0736
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.0172
1022	-0.124
1023	0
1024	-0.307
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.148
103	0.215
1030	0
1031	0.242
1032	-0.111
1033	-0.0752
1034	0
1035	0
1036	-0.0597
1037	0
1038	-0.23
1039	-0.0742
104	0
1040	0.411
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 no result for this sample

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: CNhs11093

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.631
MA0003.1	MA0003.1	0.75
MA0004.1	MA0004.1	0.115
MA0006.1	MA0006.1	0.547
MA0007.1	MA0007.1	0.64
MA0009.1	MA0009.1	0.665
MA0014.1	MA0014.1	0.709
MA0017.1	MA0017.1	0.0104
MA0018.2	MA0018.2	0.707
MA0019.1	MA0019.1	0.417
MA0024.1	MA0024.1	0.0112
MA0025.1	MA0025.1	0.454
MA0027.1	MA0027.1	0.195
MA0028.1	MA0028.1	0.00199
MA0029.1	MA0029.1	0.374
MA0030.1	MA0030.1	0.0511
MA0031.1	MA0031.1	0.171
MA0035.2	MA0035.2	9.98939e-4
MA0038.1	MA0038.1	0.276
MA0039.2	MA0039.2	0.11
MA0040.1	MA0040.1	0.178
MA0041.1	MA0041.1	0.57
MA0042.1	MA0042.1	0.712
MA0043.1	MA0043.1	0.143
MA0046.1	MA0046.1	1.17976e-8
MA0047.2	MA0047.2	0.0658
MA0048.1	MA0048.1	4.58889e-5
MA0050.1	MA0050.1	0.456
MA0051.1	MA0051.1	0.946
MA0052.1	MA0052.1	2.38173e-4
MA0055.1	MA0055.1	2.66278e-4
MA0057.1	MA0057.1	0.742
MA0058.1	MA0058.1	0.052
MA0059.1	MA0059.1	0.0198
MA0060.1	MA0060.1	0.682
MA0061.1	MA0061.1	0.561
MA0062.2	MA0062.2	0.012
MA0065.2	MA0065.2	0.308
MA0066.1	MA0066.1	0.74
MA0067.1	MA0067.1	0.72
MA0068.1	MA0068.1	0.304
MA0069.1	MA0069.1	0.606
MA0070.1	MA0070.1	0.14
MA0071.1	MA0071.1	0.986
MA0072.1	MA0072.1	0.888
MA0073.1	MA0073.1	0.346
MA0074.1	MA0074.1	0.783
MA0076.1	MA0076.1	0.022
MA0077.1	MA0077.1	0.148
MA0078.1	MA0078.1	0.0186
MA0079.2	MA0079.2	0.284
MA0080.2	MA0080.2	0.00342
MA0081.1	MA0081.1	0.418
MA0083.1	MA0083.1	0.537
MA0084.1	MA0084.1	0.588
MA0087.1	MA0087.1	0.996
MA0088.1	MA0088.1	0.073
MA0090.1	MA0090.1	0.0375
MA0091.1	MA0091.1	0.468
MA0092.1	MA0092.1	0.69
MA0093.1	MA0093.1	0.17
MA0099.2	MA0099.2	2.72436e-9
MA0100.1	MA0100.1	0.0101
MA0101.1	MA0101.1	0.102
MA0102.2	MA0102.2	0.417
MA0103.1	MA0103.1	3.19984e-4
MA0104.2	MA0104.2	0.051
MA0105.1	MA0105.1	0.644
MA0106.1	MA0106.1	0.00728
MA0107.1	MA0107.1	0.408
MA0108.2	MA0108.2	1.44633e-7
MA0111.1	MA0111.1	0.537
MA0112.2	MA0112.2	0.602
MA0113.1	MA0113.1	0.844
MA0114.1	MA0114.1	0.0475
MA0115.1	MA0115.1	0.298
MA0116.1	MA0116.1	0.387
MA0117.1	MA0117.1	0.895
MA0119.1	MA0119.1	0.494
MA0122.1	MA0122.1	0.902
MA0124.1	MA0124.1	0.689
MA0125.1	MA0125.1	0.00793
MA0131.1	MA0131.1	0.192
MA0135.1	MA0135.1	0.696
MA0136.1	MA0136.1	0.419
MA0137.2	MA0137.2	0.578
MA0138.2	MA0138.2	5.07383e-4
MA0139.1	MA0139.1	0.12
MA0140.1	MA0140.1	0.00101
MA0141.1	MA0141.1	0.608
MA0142.1	MA0142.1	0.416
MA0143.1	MA0143.1	0.516
MA0144.1	MA0144.1	0.587
MA0145.1	MA0145.1	0.275
MA0146.1	MA0146.1	0.0084
MA0147.1	MA0147.1	0.0567
MA0148.1	MA0148.1	0.194
MA0149.1	MA0149.1	0.392
MA0150.1	MA0150.1	0.0157
MA0152.1	MA0152.1	0.97
MA0153.1	MA0153.1	5.01577e-8
MA0154.1	MA0154.1	0.298
MA0155.1	MA0155.1	0.634
MA0156.1	MA0156.1	0.29
MA0157.1	MA0157.1	0.777
MA0159.1	MA0159.1	0.478
MA0160.1	MA0160.1	0.673
MA0162.1	MA0162.1	0.467
MA0163.1	MA0163.1	0.0502
MA0164.1	MA0164.1	0.241
MA0258.1	MA0258.1	0.79
MA0259.1	MA0259.1	0.0544

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: CNhs11093

Novel motif	Logo	P-value
1	1	0.561
10	10	0.176
100	100	0.716
101	101	0.0799
102	102	0.783
103	103	0.422
104	104	0.711
105	105	0.539
106	106	0.475
107	107	0.119
108	108	0.792
109	109	0.202
11	11	0.186
110	110	0.0311
111	111	0.321
112	112	0.668
113	113	0.335
114	114	0.609
115	115	0.726
116	116	0.0642
117	117	9.28766e-4
118	118	0.747
119	119	0.353
12	12	0.943
120	120	0.448
121	121	0.477
122	122	0.182
123	123	0.329
124	124	0.0235
125	125	0.187
126	126	0.423
127	127	0.333
128	128	0.358
129	129	0.436
13	13	0.474
130	130	0.339
131	131	0.196
132	132	0.31
133	133	0.13
134	134	0.705
135	135	0.429
136	136	0.933
137	137	0.746
138	138	0.713
139	139	0.0322
14	14	0.397
140	140	0.921
141	141	0.872
142	142	0.74
143	143	0.012
144	144	0.649
145	145	0.118
146	146	0.125
147	147	0.88
148	148	0.55
149	149	0.481
15	15	0.702
150	150	0.0601
151	151	0.96
152	152	0.104
153	153	0.951
154	154	0.571
155	155	0.171
156	156	0.793
157	157	0.499
158	158	0.548
159	159	0.0285
160	160	0.916
161	161	0.527
162	162	0.983
163	163	0.668
164	164	0.00139
165	165	0.362
166	166	0.489
167	167	0.944
168	168	0.639
169	169	0.0487
17	17	0.78
18	18	0.0261
19	19	0.645
2	2	0.106
20	20	0.0185
21	21	0.0221
22	22	0.748
23	23	0.269
24	24	0.258
25	25	0.969
26	26	0.0375
27	27	0.288
28	28	0.427
29	29	0.0286
3	3	0.656
30	30	0.272
31	31	0.68
32	32	0.639
33	33	0.91
34	34	0.22
35	35	0.41
36	36	0.937
37	37	0.027
38	38	0.856
39	39	0.607
4	4	0.399
40	40	0.048
41	41	0.264
42	42	0.36
43	43	0.915
44	44	0.474
45	45	0.253
46	46	0.723
47	47	0.875
48	48	0.792
49	49	0.601
5	5	0.736
50	50	0.956
51	51	0.735
52	52	0.45
53	53	0.278
54	54	0.304
55	55	0.5
56	56	0.488
57	57	0.205
58	58	0.394
59	59	0.531
6	6	0.685
60	60	0.816
61	61	0.464
62	62	0.87
63	63	0.627
64	64	0.928
65	65	0.83
66	66	0.417
67	67	0.824
68	68	0.161
69	69	0.388
7	7	0.975
70	70	0.138
71	71	0.066
72	72	0.967
73	73	0.0113
74	74	0.41
75	75	0.033
76	76	0.0506
77	77	0.699
78	78	0.0919
79	79	0.113
8	8	0.109
80	80	0.0418
81	81	0.879
82	82	0.715
83	83	0.436
84	84	0.36
85	85	0.934
86	86	0.272
87	87	0.292
88	88	0.373
89	89	0.215
9	9	0.694
90	90	0.0443
91	91	0.444
92	92	0.741
93	93	0.0848
94	94	0.394
95	95	0.0118
96	96	0.781
97	97	0.584
98	98	0.705
99	99	0.422

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: CNhs11093

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0001062 (anatomical entity)

FF: FANTOM5
NA

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
NA