FF:10349-105D7

Name:	visual cortex - wildtype, neonate N15, donor5
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 Visual cortex dev stage postnatal day 15 sex male age P15 cell type CELL MIXTURE - tissue sample cell line NA 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) OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

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

CNhs13820

0	0
1	0.823
10	0
100	0.0307
1000	0.0287
1001	0.0534
1002	-0.0804
1003	0.468
1004	0.0689
1005	0.0894
1006	0.565
1007	-0.193
1008	0
1009	-0.193
101	-0.104
1010	0
1011	0.89
1012	0.51
1013	0.109
1014	0.0689
1015	-0.053
1016	-0.031
1017	0
1018	0
1019	0
102	0
1020	0.835
1021	0
1022	-0.0704
1023	0
1024	-0.0113
1025	0
1026	0
1027	0.345
1028	0
1029	0.0444
103	-0.0788
1030	0
1031	-0.547
1032	0.115
1033	0.105
1034	0
1035	0
1036	-0.111
1037	0
1038	0.0388
1039	0.0887
104	0
1040	-0.39
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

---

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: CNhs13820

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00343
MA0003.1	MA0003.1	0.216
MA0004.1	MA0004.1	0.55
MA0006.1	MA0006.1	0.105
MA0007.1	MA0007.1	0.482
MA0009.1	MA0009.1	0.64
MA0014.1	MA0014.1	0.621
MA0017.1	MA0017.1	5.22257e-7
MA0018.2	MA0018.2	0.0189
MA0019.1	MA0019.1	0.076
MA0024.1	MA0024.1	0.0679
MA0025.1	MA0025.1	0.884
MA0027.1	MA0027.1	0.0626
MA0028.1	MA0028.1	0.0429
MA0029.1	MA0029.1	0.779
MA0030.1	MA0030.1	0.22
MA0031.1	MA0031.1	0.0112
MA0035.2	MA0035.2	0.0139
MA0038.1	MA0038.1	0.599
MA0039.2	MA0039.2	0.00286
MA0040.1	MA0040.1	0.0415
MA0041.1	MA0041.1	0.543
MA0042.1	MA0042.1	0.667
MA0043.1	MA0043.1	0.607
MA0046.1	MA0046.1	7.46245e-11
MA0047.2	MA0047.2	4.17909e-4
MA0048.1	MA0048.1	0.166
MA0050.1	MA0050.1	0.00109
MA0051.1	MA0051.1	0.00925
MA0052.1	MA0052.1	0.443
MA0055.1	MA0055.1	0.0352
MA0057.1	MA0057.1	0.375
MA0058.1	MA0058.1	0.339
MA0059.1	MA0059.1	0.346
MA0060.1	MA0060.1	0.0503
MA0061.1	MA0061.1	0.0572
MA0062.2	MA0062.2	1.71301e-4
MA0065.2	MA0065.2	3.36869e-7
MA0066.1	MA0066.1	0.0811
MA0067.1	MA0067.1	0.533
MA0068.1	MA0068.1	0.59
MA0069.1	MA0069.1	0.0752
MA0070.1	MA0070.1	0.758
MA0071.1	MA0071.1	0.0436
MA0072.1	MA0072.1	0.155
MA0073.1	MA0073.1	0.836
MA0074.1	MA0074.1	0.134
MA0076.1	MA0076.1	0.0842
MA0077.1	MA0077.1	0.949
MA0078.1	MA0078.1	0.719
MA0079.2	MA0079.2	0.997
MA0080.2	MA0080.2	3.51128e-10
MA0081.1	MA0081.1	0.156
MA0083.1	MA0083.1	0.00771
MA0084.1	MA0084.1	0.836
MA0087.1	MA0087.1	0.429
MA0088.1	MA0088.1	0.263
MA0090.1	MA0090.1	0.0469
MA0091.1	MA0091.1	0.301
MA0092.1	MA0092.1	0.339
MA0093.1	MA0093.1	0.554
MA0099.2	MA0099.2	9.70758e-5
MA0100.1	MA0100.1	0.285
MA0101.1	MA0101.1	0.0363
MA0102.2	MA0102.2	0.384
MA0103.1	MA0103.1	0.19
MA0104.2	MA0104.2	0.948
MA0105.1	MA0105.1	0.0608
MA0106.1	MA0106.1	0.0938
MA0107.1	MA0107.1	0.0604
MA0108.2	MA0108.2	8.90945e-4
MA0111.1	MA0111.1	0.799
MA0112.2	MA0112.2	0.00108
MA0113.1	MA0113.1	0.221
MA0114.1	MA0114.1	1.65753e-6
MA0115.1	MA0115.1	6.38924e-5
MA0116.1	MA0116.1	0.116
MA0117.1	MA0117.1	0.834
MA0119.1	MA0119.1	0.114
MA0122.1	MA0122.1	0.812
MA0124.1	MA0124.1	0.85
MA0125.1	MA0125.1	0.501
MA0131.1	MA0131.1	0.93
MA0135.1	MA0135.1	0.129
MA0136.1	MA0136.1	8.6103e-10
MA0137.2	MA0137.2	0.223
MA0138.2	MA0138.2	0.00718
MA0139.1	MA0139.1	0.452
MA0140.1	MA0140.1	4.94393e-4
MA0141.1	MA0141.1	0.0012
MA0142.1	MA0142.1	0.372
MA0143.1	MA0143.1	0.514
MA0144.1	MA0144.1	0.097
MA0145.1	MA0145.1	0.0512
MA0146.1	MA0146.1	0.0119
MA0147.1	MA0147.1	0.982
MA0148.1	MA0148.1	9.16556e-4
MA0149.1	MA0149.1	0.351
MA0150.1	MA0150.1	0.0684
MA0152.1	MA0152.1	0.397
MA0153.1	MA0153.1	2.80728e-11
MA0154.1	MA0154.1	0.0358
MA0155.1	MA0155.1	0.298
MA0156.1	MA0156.1	1.09515e-10
MA0157.1	MA0157.1	0.0425
MA0159.1	MA0159.1	0.00246
MA0160.1	MA0160.1	0.00123
MA0162.1	MA0162.1	0.183
MA0163.1	MA0163.1	0.00363
MA0164.1	MA0164.1	0.659
MA0258.1	MA0258.1	0.0359
MA0259.1	MA0259.1	0.694

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: CNhs13820

Novel motif	Logo	P-value
1	1	0.363
10	10	0.137
100	100	0.53
101	101	0.74
102	102	0.943
103	103	0.0991
104	104	0.957
105	105	0.436
106	106	0.079
107	107	0.152
108	108	0.565
109	109	0.00372
11	11	0.102
110	110	0.0662
111	111	0.479
112	112	0.0125
113	113	0.519
114	114	0.468
115	115	0.761
116	116	0.391
117	117	0.00746
118	118	0.516
119	119	0.0874
12	12	0.605
120	120	0.887
121	121	0.0472
122	122	0.783
123	123	0.0145
124	124	0.129
125	125	0.858
126	126	0.0329
127	127	0.576
128	128	0.0595
129	129	0.37
13	13	1.10358e-7
130	130	0.0695
131	131	0.245
132	132	0.569
133	133	0.259
134	134	0.127
135	135	0.589
136	136	0.00752
137	137	0.549
138	138	0.859
139	139	0.708
14	14	0.647
140	140	0.694
141	141	0.737
142	142	0.833
143	143	0.515
144	144	0.58
145	145	0.00116
146	146	0.126
147	147	0.0974
148	148	0.711
149	149	0.279
15	15	0.182
150	150	0.0528
151	151	0.663
152	152	0.0979
153	153	0.996
154	154	0.743
155	155	0.415
156	156	6.98886e-32
157	157	0.264
158	158	0.135
159	159	0.754
160	160	0.302
161	161	0.0526
162	162	0.718
163	163	0.67
164	164	0.133
165	165	0.185
166	166	0.642
167	167	0.236
168	168	0.389
169	169	0.00375
17	17	0.0738
18	18	0.995
19	19	0.0634
2	2	0.766
20	20	0.165
21	21	0.31
22	22	0.0693
23	23	0.297
24	24	0.00632
25	25	0.785
26	26	4.31847e-6
27	27	0.745
28	28	0.612
29	29	0.0627
3	3	0.0652
30	30	0.838
31	31	0.826
32	32	0.771
33	33	0.2
34	34	0.468
35	35	0.63
36	36	0.594
37	37	0.0201
38	38	0.177
39	39	0.354
4	4	0.155
40	40	0.123
41	41	0.417
42	42	0.208
43	43	0.137
44	44	0.541
45	45	0.466
46	46	0.263
47	47	0.423
48	48	0.329
49	49	0.32
5	5	0.518
50	50	0.197
51	51	0.682
52	52	0.172
53	53	0.87
54	54	0.887
55	55	0.979
56	56	0.45
57	57	0.814
58	58	0.301
59	59	0.0874
6	6	0.961
60	60	0.0267
61	61	0.0606
62	62	0.237
63	63	0.117
64	64	0.615
65	65	0.151
66	66	0.563
67	67	0.715
68	68	0.321
69	69	0.214
7	7	0.0129
70	70	0.336
71	71	0.0182
72	72	0.349
73	73	0.0305
74	74	0.682
75	75	0.0627
76	76	0.989
77	77	0.252
78	78	0.00175
79	79	0.606
8	8	0.287
80	80	0.867
81	81	0.897
82	82	0.285
83	83	0.0458
84	84	0.579
85	85	0.152
86	86	0.165
87	87	0.00584
88	88	0.501
89	89	0.711
9	9	0.315
90	90	0.636
91	91	0.44
92	92	0.497
93	93	0.531
94	94	0.872
95	95	0.0237
96	96	0.452
97	97	0.932
98	98	0.254
99	99	0.499

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: CNhs13820

FANTOM5 (FF) ontology

---

Direct parent terms

is_a relathionship
FF:0000004 tissue sample
FF:0000103 mouse sample
FF:0000316 mouse neonate N15 sample
UBERON:0000411 visual cortex

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

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