FF:10236-104A2

Name:	visual cortex - wildtype, neonate N15, donor2
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 mixed cell line N/A company N/A collaboration Michela Fagiolini/Alka Saxena/Piero Carninci External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number N/A catalog number N/A sample type Visual cortex tissue extraction protocol (Details) Total RNA Trizol Qiagen minElute

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

CNhs13032

0	0
1	0.815
10	0
100	0
1000	0.0919
1001	-0.00227
1002	-0.0941
1003	0.409
1004	0
1005	0
1006	0.603
1007	-0.164
1008	0
1009	-0.19
101	-0.0675
1010	0
1011	0.941
1012	0.651
1013	0.119
1014	0
1015	0.0837
1016	-0.0769
1017	0
1018	0
1019	0
102	0
1020	0.454
1021	0
1022	-0.124
1023	0
1024	-0.0899
1025	-0.0611
1026	0
1027	0.519
1028	0
1029	0.107
103	-0.0848
1030	0
1031	-0.627
1032	0.107
1033	0.137
1034	0
1035	0
1036	-0.183
1037	0
1038	-0.0774
1039	-0.02
104	0
1040	-0.457
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: CNhs13032

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0281
MA0003.1	MA0003.1	0.282
MA0004.1	MA0004.1	0.515
MA0006.1	MA0006.1	0.105
MA0007.1	MA0007.1	0.432
MA0009.1	MA0009.1	0.878
MA0014.1	MA0014.1	0.526
MA0017.1	MA0017.1	1.59959e-7
MA0018.2	MA0018.2	0.00938
MA0019.1	MA0019.1	0.132
MA0024.1	MA0024.1	0.0292
MA0025.1	MA0025.1	0.439
MA0027.1	MA0027.1	0.104
MA0028.1	MA0028.1	0.0295
MA0029.1	MA0029.1	0.548
MA0030.1	MA0030.1	0.427
MA0031.1	MA0031.1	0.00547
MA0035.2	MA0035.2	0.0151
MA0038.1	MA0038.1	0.803
MA0039.2	MA0039.2	0.00253
MA0040.1	MA0040.1	0.0705
MA0041.1	MA0041.1	0.264
MA0042.1	MA0042.1	0.504
MA0043.1	MA0043.1	0.668
MA0046.1	MA0046.1	1.32485e-9
MA0047.2	MA0047.2	2.93056e-4
MA0048.1	MA0048.1	0.0526
MA0050.1	MA0050.1	2.92095e-6
MA0051.1	MA0051.1	1.35642e-4
MA0052.1	MA0052.1	0.796
MA0055.1	MA0055.1	0.00973
MA0057.1	MA0057.1	0.491
MA0058.1	MA0058.1	0.327
MA0059.1	MA0059.1	0.254
MA0060.1	MA0060.1	0.0377
MA0061.1	MA0061.1	0.0657
MA0062.2	MA0062.2	8.11293e-5
MA0065.2	MA0065.2	7.78532e-7
MA0066.1	MA0066.1	0.106
MA0067.1	MA0067.1	0.61
MA0068.1	MA0068.1	0.173
MA0069.1	MA0069.1	0.124
MA0070.1	MA0070.1	0.97
MA0071.1	MA0071.1	0.0446
MA0072.1	MA0072.1	0.115
MA0073.1	MA0073.1	0.824
MA0074.1	MA0074.1	0.164
MA0076.1	MA0076.1	0.0617
MA0077.1	MA0077.1	0.782
MA0078.1	MA0078.1	0.958
MA0079.2	MA0079.2	0.91
MA0080.2	MA0080.2	1.31688e-10
MA0081.1	MA0081.1	0.177
MA0083.1	MA0083.1	7.4769e-4
MA0084.1	MA0084.1	0.628
MA0087.1	MA0087.1	0.711
MA0088.1	MA0088.1	0.303
MA0090.1	MA0090.1	0.14
MA0091.1	MA0091.1	0.245
MA0092.1	MA0092.1	0.265
MA0093.1	MA0093.1	0.529
MA0099.2	MA0099.2	6.06593e-4
MA0100.1	MA0100.1	0.354
MA0101.1	MA0101.1	0.0226
MA0102.2	MA0102.2	0.17
MA0103.1	MA0103.1	0.258
MA0104.2	MA0104.2	0.936
MA0105.1	MA0105.1	0.0951
MA0106.1	MA0106.1	0.0809
MA0107.1	MA0107.1	0.0512
MA0108.2	MA0108.2	7.21059e-5
MA0111.1	MA0111.1	0.693
MA0112.2	MA0112.2	9.7593e-4
MA0113.1	MA0113.1	0.244
MA0114.1	MA0114.1	1.56758e-6
MA0115.1	MA0115.1	1.54161e-4
MA0116.1	MA0116.1	0.152
MA0117.1	MA0117.1	0.785
MA0119.1	MA0119.1	0.0981
MA0122.1	MA0122.1	0.633
MA0124.1	MA0124.1	0.947
MA0125.1	MA0125.1	0.19
MA0131.1	MA0131.1	0.76
MA0135.1	MA0135.1	0.276
MA0136.1	MA0136.1	7.48477e-12
MA0137.2	MA0137.2	0.0877
MA0138.2	MA0138.2	0.00476
MA0139.1	MA0139.1	0.432
MA0140.1	MA0140.1	0.00149
MA0141.1	MA0141.1	0.00118
MA0142.1	MA0142.1	0.301
MA0143.1	MA0143.1	0.783
MA0144.1	MA0144.1	0.0501
MA0145.1	MA0145.1	0.0726
MA0146.1	MA0146.1	0.00922
MA0147.1	MA0147.1	0.988
MA0148.1	MA0148.1	4.11275e-4
MA0149.1	MA0149.1	0.33
MA0150.1	MA0150.1	0.141
MA0152.1	MA0152.1	0.83
MA0153.1	MA0153.1	4.37855e-10
MA0154.1	MA0154.1	0.0501
MA0155.1	MA0155.1	0.313
MA0156.1	MA0156.1	5.24508e-11
MA0157.1	MA0157.1	0.00695
MA0159.1	MA0159.1	0.00401
MA0160.1	MA0160.1	0.00195
MA0162.1	MA0162.1	0.182
MA0163.1	MA0163.1	0.00473
MA0164.1	MA0164.1	0.873
MA0258.1	MA0258.1	0.0296
MA0259.1	MA0259.1	0.827

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: CNhs13032

Novel motif	Logo	P-value
1	1	0.37
10	10	0.104
100	100	0.428
101	101	0.35
102	102	0.793
103	103	0.198
104	104	0.977
105	105	0.493
106	106	0.0501
107	107	0.0966
108	108	0.406
109	109	0.00303
11	11	0.0749
110	110	0.0536
111	111	0.35
112	112	0.0111
113	113	0.362
114	114	0.615
115	115	0.919
116	116	0.303
117	117	0.0067
118	118	0.579
119	119	0.136
12	12	0.714
120	120	0.885
121	121	0.135
122	122	0.812
123	123	3.91669e-4
124	124	0.0423
125	125	0.973
126	126	0.024
127	127	0.557
128	128	0.0535
129	129	0.332
13	13	4.64296e-9
130	130	0.0363
131	131	0.412
132	132	0.467
133	133	0.335
134	134	0.0652
135	135	0.137
136	136	0.00363
137	137	0.694
138	138	0.669
139	139	0.948
14	14	0.752
140	140	0.205
141	141	0.954
142	142	0.908
143	143	0.583
144	144	0.563
145	145	1.62379e-4
146	146	0.211
147	147	0.0829
148	148	0.509
149	149	0.577
15	15	0.289
150	150	0.0359
151	151	0.746
152	152	0.0745
153	153	0.928
154	154	0.84
155	155	0.425
156	156	1.28279e-10
157	157	0.253
158	158	0.231
159	159	0.376
160	160	0.354
161	161	0.0655
162	162	0.6
163	163	0.988
164	164	0.0966
165	165	0.129
166	166	0.511
167	167	0.321
168	168	0.651
169	169	0.00321
17	17	0.0661
18	18	0.834
19	19	0.0535
2	2	0.96
20	20	0.0509
21	21	0.192
22	22	0.075
23	23	0.596
24	24	0.0214
25	25	0.882
26	26	4.94484e-7
27	27	0.585
28	28	0.638
29	29	0.0502
3	3	0.0601
30	30	0.976
31	31	0.795
32	32	0.783
33	33	0.209
34	34	0.488
35	35	0.46
36	36	0.549
37	37	0.0182
38	38	0.328
39	39	0.208
4	4	0.246
40	40	0.112
41	41	0.585
42	42	0.232
43	43	0.13
44	44	0.886
45	45	0.542
46	46	0.27
47	47	0.418
48	48	0.344
49	49	0.326
5	5	0.422
50	50	0.166
51	51	0.773
52	52	0.192
53	53	0.599
54	54	0.969
55	55	0.732
56	56	0.497
57	57	0.812
58	58	0.443
59	59	0.119
6	6	0.969
60	60	0.028
61	61	0.029
62	62	0.336
63	63	0.109
64	64	0.643
65	65	0.27
66	66	0.407
67	67	0.912
68	68	0.39
69	69	0.239
7	7	0.0122
70	70	0.309
71	71	0.0121
72	72	0.527
73	73	0.0224
74	74	0.755
75	75	0.0738
76	76	0.771
77	77	0.362
78	78	0.00333
79	79	0.581
8	8	0.214
80	80	0.543
81	81	0.635
82	82	0.501
83	83	0.0327
84	84	0.892
85	85	0.269
86	86	0.181
87	87	0.00734
88	88	0.5
89	89	0.815
9	9	0.388
90	90	0.49
91	91	0.289
92	92	0.615
93	93	0.437
94	94	0.838
95	95	0.0179
96	96	0.673
97	97	0.918
98	98	0.47
99	99	0.485

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: CNhs13032

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
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000411 (visual cortex)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001890 (forebrain)
0001893 (telencephalon)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

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