FF:10240-104A6

Name:	visual cortex - wildtype, neonate N30, donor3
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	tissues
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information strain NA tissue Visual cortex dev stage postnatal day 30 sex male age P30 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

CAGE Accession numbers
Method Sample accession id CAGE  DRS009001 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)

---

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

CNhs13036

MCL coexpression id	Coexpression dpi cluster scores median value
0	0
1	0.817
10	0
100	0
1000	0
1001	--0.0275
1002	--0.116
1003	0.146
1004	0
1005	0
1006	0.611
1007	--0.145
1008	0
1009	--0.15
101	--0.0855
1010	0
1011	0.926
1012	0.224
1013	0.304
1014	0.139
1015	--0.0136
1016	--0.293
1017	0
1018	0
1019	0
102	0
1020	0.568
1021	0
1022	--0.0704
1023	0
1024	0.0845
1025	0
1026	0
1027	0.521
1028	0
1029	0.0472
103	--0.0861
1030	0
1031	--0.489
1032	0.0404
1033	0
1034	0
1035	0
1036	--0.183
1037	0
1038	0.0728
1039	0.0167
104	0
1040	--0.466
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

---

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: CNhs13036

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0132
MA0003.1	MA0003.1	0.273
MA0004.1	MA0004.1	0.562
MA0006.1	MA0006.1	0.0891
MA0007.1	MA0007.1	0.332
MA0009.1	MA0009.1	0.794
MA0014.1	MA0014.1	0.633
MA0017.1	MA0017.1	5.96451e-7
MA0018.2	MA0018.2	0.00378
MA0019.1	MA0019.1	0.152
MA0024.1	MA0024.1	0.0146
MA0025.1	MA0025.1	0.179
MA0027.1	MA0027.1	0.0416
MA0028.1	MA0028.1	0.0457
MA0029.1	MA0029.1	0.573
MA0030.1	MA0030.1	0.307
MA0031.1	MA0031.1	0.0193
MA0035.2	MA0035.2	0.0348
MA0038.1	MA0038.1	0.789
MA0039.2	MA0039.2	0.00276
MA0040.1	MA0040.1	0.0518
MA0041.1	MA0041.1	0.453
MA0042.1	MA0042.1	0.534
MA0043.1	MA0043.1	0.41
MA0046.1	MA0046.1	2.29168e-10
MA0047.2	MA0047.2	2.86369e-4
MA0048.1	MA0048.1	0.062
MA0050.1	MA0050.1	6.00889e-5
MA0051.1	MA0051.1	0.00208
MA0052.1	MA0052.1	0.751
MA0055.1	MA0055.1	0.0169
MA0057.1	MA0057.1	0.552
MA0058.1	MA0058.1	0.402
MA0059.1	MA0059.1	0.321
MA0060.1	MA0060.1	0.0201
MA0061.1	MA0061.1	0.0331
MA0062.2	MA0062.2	1.12357e-4
MA0065.2	MA0065.2	3.88928e-6
MA0066.1	MA0066.1	0.0853
MA0067.1	MA0067.1	0.488
MA0068.1	MA0068.1	0.336
MA0069.1	MA0069.1	0.0886
MA0070.1	MA0070.1	0.718
MA0071.1	MA0071.1	0.0419
MA0072.1	MA0072.1	0.291
MA0073.1	MA0073.1	0.94
MA0074.1	MA0074.1	0.132
MA0076.1	MA0076.1	0.0807
MA0077.1	MA0077.1	0.698
MA0078.1	MA0078.1	0.999
MA0079.2	MA0079.2	0.894
MA0080.2	MA0080.2	1.45221e-10
MA0081.1	MA0081.1	0.172
MA0083.1	MA0083.1	0.00237
MA0084.1	MA0084.1	0.488
MA0087.1	MA0087.1	0.446
MA0088.1	MA0088.1	0.324
MA0090.1	MA0090.1	0.172
MA0091.1	MA0091.1	0.331
MA0092.1	MA0092.1	0.28
MA0093.1	MA0093.1	0.581
MA0099.2	MA0099.2	0.00175
MA0100.1	MA0100.1	0.331
MA0101.1	MA0101.1	0.00783
MA0102.2	MA0102.2	0.284
MA0103.1	MA0103.1	0.355
MA0104.2	MA0104.2	0.881
MA0105.1	MA0105.1	0.0576
MA0106.1	MA0106.1	0.0687
MA0107.1	MA0107.1	0.0186
MA0108.2	MA0108.2	4.42869e-5
MA0111.1	MA0111.1	0.859
MA0112.2	MA0112.2	0.00206
MA0113.1	MA0113.1	0.148
MA0114.1	MA0114.1	6.02031e-6
MA0115.1	MA0115.1	3.60278e-4
MA0116.1	MA0116.1	0.171
MA0117.1	MA0117.1	0.806
MA0119.1	MA0119.1	0.114
MA0122.1	MA0122.1	0.808
MA0124.1	MA0124.1	0.884
MA0125.1	MA0125.1	0.246
MA0131.1	MA0131.1	0.778
MA0135.1	MA0135.1	0.178
MA0136.1	MA0136.1	3.22146e-12
MA0137.2	MA0137.2	0.145
MA0138.2	MA0138.2	0.00201
MA0139.1	MA0139.1	0.578
MA0140.1	MA0140.1	0.00246
MA0141.1	MA0141.1	0.00204
MA0142.1	MA0142.1	0.26
MA0143.1	MA0143.1	0.879
MA0144.1	MA0144.1	0.049
MA0145.1	MA0145.1	0.0891
MA0146.1	MA0146.1	0.0112
MA0147.1	MA0147.1	0.959
MA0148.1	MA0148.1	2.4784e-4
MA0149.1	MA0149.1	0.302
MA0150.1	MA0150.1	0.222
MA0152.1	MA0152.1	0.826
MA0153.1	MA0153.1	3.68464e-9
MA0154.1	MA0154.1	0.0656
MA0155.1	MA0155.1	0.403
MA0156.1	MA0156.1	1.20027e-11
MA0157.1	MA0157.1	0.0382
MA0159.1	MA0159.1	0.00659
MA0160.1	MA0160.1	0.00242
MA0162.1	MA0162.1	0.191
MA0163.1	MA0163.1	0.00419
MA0164.1	MA0164.1	0.827
MA0258.1	MA0258.1	0.0556
MA0259.1	MA0259.1	0.757

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: CNhs13036

Novel motif	Logo	P-value
1	1	0.434
10	10	0.115
100	100	0.406
101	101	0.554
102	102	0.935
103	103	0.183
104	104	0.872
105	105	0.616
106	106	0.0455
107	107	0.12
108	108	0.46
109	109	0.00251
11	11	0.103
110	110	0.0546
111	111	0.456
112	112	0.0134
113	113	0.366
114	114	0.689
115	115	0.896
116	116	0.28
117	117	0.00472
118	118	0.522
119	119	0.266
12	12	0.712
120	120	0.944
121	121	0.177
122	122	0.992
123	123	7.36134e-4
124	124	0.0354
125	125	0.877
126	126	0.025
127	127	0.444
128	128	0.0315
129	129	0.46
13	13	4.67443e-9
130	130	0.0296
131	131	0.36
132	132	0.556
133	133	0.401
134	134	0.119
135	135	0.294
136	136	0.00749
137	137	0.527
138	138	0.65
139	139	0.771
14	14	0.953
140	140	0.268
141	141	0.952
142	142	0.888
143	143	0.729
144	144	0.533
145	145	1.54892e-4
146	146	0.2
147	147	0.0972
148	148	0.515
149	149	0.58
15	15	0.358
150	150	0.0416
151	151	0.82
152	152	0.0662
153	153	0.863
154	154	0.937
155	155	0.283
156	156	4.71686e-10
157	157	0.209
158	158	0.23
159	159	0.882
160	160	0.249
161	161	0.0384
162	162	0.602
163	163	0.864
164	164	0.112
165	165	0.0866
166	166	0.547
167	167	0.243
168	168	0.744
169	169	0.00388
17	17	0.0675
18	18	0.806
19	19	0.0559
2	2	0.922
20	20	0.0629
21	21	0.287
22	22	0.0919
23	23	0.625
24	24	0.0199
25	25	0.952
26	26	4.58806e-7
27	27	0.475
28	28	0.671
29	29	0.0472
3	3	0.0681
30	30	0.887
31	31	0.915
32	32	0.845
33	33	0.257
34	34	0.405
35	35	0.455
36	36	0.594
37	37	0.021
38	38	0.311
39	39	0.213
4	4	0.177
40	40	0.133
41	41	0.684
42	42	0.175
43	43	0.138
44	44	0.808
45	45	0.559
46	46	0.266
47	47	0.527
48	48	0.348
49	49	0.394
5	5	0.462
50	50	0.145
51	51	0.758
52	52	0.163
53	53	0.603
54	54	0.97
55	55	0.973
56	56	0.514
57	57	0.894
58	58	0.471
59	59	0.127
6	6	0.957
60	60	0.0336
61	61	0.0341
62	62	0.392
63	63	0.134
64	64	0.69
65	65	0.266
66	66	0.489
67	67	0.976
68	68	0.245
69	69	0.219
7	7	0.014
70	70	0.458
71	71	0.0118
72	72	0.681
73	73	0.0237
74	74	0.952
75	75	0.0532
76	76	0.794
77	77	0.352
78	78	8.65183e-4
79	79	0.593
8	8	0.196
80	80	0.684
81	81	0.729
82	82	0.422
83	83	0.123
84	84	0.953
85	85	0.203
86	86	0.188
87	87	0.0275
88	88	0.486
89	89	0.922
9	9	0.346
90	90	0.625
91	91	0.33
92	92	0.64
93	93	0.819
94	94	0.811
95	95	0.0122
96	96	0.629
97	97	0.939
98	98	0.423
99	99	0.44

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: CNhs13036

FANTOM5 (FF) ontology

---

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011269 mouse visual cortex from wildtype- neonate N30 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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002021 (occipital lobe)
0000411 (visual cortex)
0000956 (cerebral cortex)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0001950 (neocortex)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011269 (mouse visual cortex from wildtype- neonate N30 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
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

{{{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}}}