FF:10241-104A7: Difference between revisions

Latest revision as of 13:57, 3 June 2020

Name:	visual cortex - wildtype
Species:	Mouse (Mus musculus)
Library ID:	CNhs13037
Sample type:	tissues
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	Visual cortex
dev stage	postnatal day 60-70
sex	male
age	P60-70
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		SAMD00005563

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13037		CAGE		DRX009139		DRR010013

Accession ID Mm9

Library id		BAM		CTSS
CNhs13037		DRZ001438		DRZ002821

Accession ID Mm10

Library id		BAM		CTSS
CNhs13037		DRZ012788		DRZ014171

Download raw sequence, BAM & CTSS

Mm9

Fasta	BAM	CTSS
download	download	donwload

Mm10

BAM	CTSS
download	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

CNhs13037

0	0
1	0.836
10	0
100	0
1000	0
1001	0.0395
1002	-0.0639
1003	0.287
1004	0
1005	0
1006	0.598
1007	-0.101
1008	0
1009	-0.19
101	-0.0853
1010	0
1011	0.864
1012	0.279
1013	0.169
1014	-0.0874
1015	-0.0569
1016	-0.126
1017	0
1018	0
1019	0
102	0
1020	0.447
1021	0
1022	-0.0704
1023	0
1024	-0.0899
1025	0
1026	0
1027	0.33
1028	0
1029	0.164
103	-0.0829
1030	0
1031	-0.54
1032	0.188
1033	-0.00214
1034	0
1035	0
1036	-0.183
1037	0
1038	0.0222
1039	0.025
104	0
1040	-0.216
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. 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 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 Analyst: Michiel de Hoon link to dataset. data

library id: CNhs13037

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0138
MA0003.1	MA0003.1	0.251
MA0004.1	MA0004.1	0.51
MA0006.1	MA0006.1	0.0859
MA0007.1	MA0007.1	0.472
MA0009.1	MA0009.1	0.783
MA0014.1	MA0014.1	0.687
MA0017.1	MA0017.1	7.82949e-7
MA0018.2	MA0018.2	0.00273
MA0019.1	MA0019.1	0.0938
MA0024.1	MA0024.1	0.0223
MA0025.1	MA0025.1	0.0225
MA0027.1	MA0027.1	0.0673
MA0028.1	MA0028.1	0.0592
MA0029.1	MA0029.1	0.933
MA0030.1	MA0030.1	0.401
MA0031.1	MA0031.1	0.0326
MA0035.2	MA0035.2	0.0202
MA0038.1	MA0038.1	0.727
MA0039.2	MA0039.2	0.00242
MA0040.1	MA0040.1	0.0568
MA0041.1	MA0041.1	0.354
MA0042.1	MA0042.1	0.496
MA0043.1	MA0043.1	0.303
MA0046.1	MA0046.1	8.07743e-11
MA0047.2	MA0047.2	7.48377e-4
MA0048.1	MA0048.1	0.0546
MA0050.1	MA0050.1	2.7057e-5
MA0051.1	MA0051.1	6.47204e-4
MA0052.1	MA0052.1	0.945
MA0055.1	MA0055.1	0.00718
MA0057.1	MA0057.1	0.469
MA0058.1	MA0058.1	0.302
MA0059.1	MA0059.1	0.263
MA0060.1	MA0060.1	0.029
MA0061.1	MA0061.1	0.0453
MA0062.2	MA0062.2	3.05115e-4
MA0065.2	MA0065.2	1.75335e-6
MA0066.1	MA0066.1	0.104
MA0067.1	MA0067.1	0.495
MA0068.1	MA0068.1	0.248
MA0069.1	MA0069.1	0.0608
MA0070.1	MA0070.1	0.921
MA0071.1	MA0071.1	0.0555
MA0072.1	MA0072.1	0.199
MA0073.1	MA0073.1	0.785
MA0074.1	MA0074.1	0.123
MA0076.1	MA0076.1	0.113
MA0077.1	MA0077.1	0.858
MA0078.1	MA0078.1	0.969
MA0079.2	MA0079.2	0.966
MA0080.2	MA0080.2	2.90366e-10
MA0081.1	MA0081.1	0.238
MA0083.1	MA0083.1	0.00597
MA0084.1	MA0084.1	0.475
MA0087.1	MA0087.1	0.558
MA0088.1	MA0088.1	0.32
MA0090.1	MA0090.1	0.223
MA0091.1	MA0091.1	0.295
MA0092.1	MA0092.1	0.241
MA0093.1	MA0093.1	0.51
MA0099.2	MA0099.2	0.00263
MA0100.1	MA0100.1	0.401
MA0101.1	MA0101.1	0.00952
MA0102.2	MA0102.2	0.175
MA0103.1	MA0103.1	0.403
MA0104.2	MA0104.2	0.889
MA0105.1	MA0105.1	0.0601
MA0106.1	MA0106.1	0.0521
MA0107.1	MA0107.1	0.0234
MA0108.2	MA0108.2	6.07477e-6
MA0111.1	MA0111.1	0.748
MA0112.2	MA0112.2	0.00201
MA0113.1	MA0113.1	0.26
MA0114.1	MA0114.1	2.27965e-6
MA0115.1	MA0115.1	3.39321e-4
MA0116.1	MA0116.1	0.179
MA0117.1	MA0117.1	0.79
MA0119.1	MA0119.1	0.164
MA0122.1	MA0122.1	0.595
MA0124.1	MA0124.1	0.859
MA0125.1	MA0125.1	0.253
MA0131.1	MA0131.1	0.723
MA0135.1	MA0135.1	0.23
MA0136.1	MA0136.1	1.82808e-12
MA0137.2	MA0137.2	0.194
MA0138.2	MA0138.2	9.50974e-4
MA0139.1	MA0139.1	0.493
MA0140.1	MA0140.1	0.00144
MA0141.1	MA0141.1	0.00328
MA0142.1	MA0142.1	0.388
MA0143.1	MA0143.1	0.509
MA0144.1	MA0144.1	0.0866
MA0145.1	MA0145.1	0.0824
MA0146.1	MA0146.1	0.00924
MA0147.1	MA0147.1	0.882
MA0148.1	MA0148.1	2.67634e-4
MA0149.1	MA0149.1	0.301
MA0150.1	MA0150.1	0.198
MA0152.1	MA0152.1	0.987
MA0153.1	MA0153.1	2.19889e-12
MA0154.1	MA0154.1	0.0813
MA0155.1	MA0155.1	0.36
MA0156.1	MA0156.1	1.08325e-10
MA0157.1	MA0157.1	0.037
MA0159.1	MA0159.1	0.00897
MA0160.1	MA0160.1	0.00469
MA0162.1	MA0162.1	0.184
MA0163.1	MA0163.1	0.00541
MA0164.1	MA0164.1	0.735
MA0258.1	MA0258.1	0.0479
MA0259.1	MA0259.1	0.773

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 in169 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: CNhs13037

Novel motif	Logo	P-value
1	1	0.303
10	10	0.0994
100	100	0.447
101	101	0.521
102	102	0.922
103	103	0.153
104	104	0.901
105	105	0.59
106	106	0.0574
107	107	0.19
108	108	0.476
109	109	0.00257
11	11	0.104
110	110	0.0622
111	111	0.523
112	112	0.0138
113	113	0.37
114	114	0.843
115	115	0.814
116	116	0.35
117	117	0.00491
118	118	0.548
119	119	0.216
12	12	0.751
120	120	0.753
121	121	0.16
122	122	0.958
123	123	9.70657e-4
124	124	0.043
125	125	0.736
126	126	0.0449
127	127	0.483
128	128	0.0483
129	129	0.364
13	13	4.25523e-9
130	130	0.0305
131	131	0.502
132	132	0.433
133	133	0.192
134	134	0.0757
135	135	0.399
136	136	0.00704
137	137	0.498
138	138	0.533
139	139	0.489
14	14	0.881
140	140	0.37
141	141	0.861
142	142	0.886
143	143	0.556
144	144	0.648
145	145	1.33291e-4
146	146	0.184
147	147	0.113
148	148	0.464
149	149	0.504
15	15	0.251
150	150	0.0519
151	151	0.827
152	152	0.0664
153	153	0.773
154	154	0.909
155	155	0.42
156	156	1.33485e-6
157	157	0.195
158	158	0.232
159	159	0.4
160	160	0.285
161	161	0.0846
162	162	0.5
163	163	0.983
164	164	0.107
165	165	0.118
166	166	0.661
167	167	0.195
168	168	0.577
169	169	0.00502
17	17	0.0705
18	18	0.858
19	19	0.0564
2	2	0.855
20	20	0.051
21	21	0.153
22	22	0.0879
23	23	0.702
24	24	0.0141
25	25	0.881
26	26	1.62361e-6
27	27	0.452
28	28	0.639
29	29	0.0387
3	3	0.0558
30	30	0.996
31	31	0.821
32	32	0.79
33	33	0.232
34	34	0.432
35	35	0.482
36	36	0.578
37	37	0.018
38	38	0.41
39	39	0.26
4	4	0.155
40	40	0.116
41	41	0.586
42	42	0.187
43	43	0.138
44	44	0.844
45	45	0.528
46	46	0.232
47	47	0.558
48	48	0.365
49	49	0.381
5	5	0.43
50	50	0.155
51	51	0.816
52	52	0.174
53	53	0.642
54	54	0.92
55	55	0.811
56	56	0.493
57	57	0.86
58	58	0.398
59	59	0.134
6	6	0.928
60	60	0.0397
61	61	0.0344
62	62	0.345
63	63	0.129
64	64	0.651
65	65	0.39
66	66	0.476
67	67	0.765
68	68	0.53
69	69	0.127
7	7	0.0154
70	70	0.383
71	71	0.0124
72	72	0.522
73	73	0.0177
74	74	0.969
75	75	0.0542
76	76	0.756
77	77	0.368
78	78	0.00262
79	79	0.35
8	8	0.151
80	80	0.758
81	81	0.834
82	82	0.427
83	83	0.0185
84	84	0.982
85	85	0.231
86	86	0.194
87	87	0.0165
88	88	0.559
89	89	0.976
9	9	0.363
90	90	0.456
91	91	0.146
92	92	0.423
93	93	0.371
94	94	0.87
95	95	0.0126
96	96	0.47
97	97	0.838
98	98	0.364
99	99	0.51

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: CNhs13037

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011270 mouse visual cortex from wildtype- neonate N60-70 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)
0007023 (adult 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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000315 (mouse neonate N60-70 sample)
0011270 (mouse visual cortex from wildtype- neonate N60-70 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)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000411,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0000956,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001869,UBERON:0001890,UBERON:0001893,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0002616,UBERON:0002619,UBERON:0002780,UBERON:0002791,UBERON:0003056,UBERON:0003075,UBERON:0003080,UBERON:0004121,UBERON:0005068,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007023,UBERON:0007135,UBERON:0007284
+|DRA_sample_Accession=CAGE@SAMD00005563
+|accession_numbers=CAGE;DRX009139;DRR010013;DRZ001438;DRZ002821;DRZ012788;DRZ014171
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000955,UBERON:0002021,UBERON:0000411,UBERON:0000956,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0002619,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0001950
 |ancestors_in_cell_lineage_facet=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000998,FF:0000004,FF:0000303,FF:0000315,FF:0011270
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
+|donor= donor1
 |expression_enrichment_score=chr19:4989964..4989972,-!p1@Npas4!2.19!152.21!Npas4;;chr10:67375368..67375433,-!p1@Zfp365!2.07!201.74!Zfp365;;chr6:85463580..85463585,-!p1@Egr4!2.07!117.53!Egr4;;chr16:91270004..91270023,+!p1@Olig1!2.00!113.03!Olig1;;chr6:55631042..55631102,-!p1@Neurod6!1.87!72.95!Neurod6;;chr11:98190918..98190951,-!p1@Neurod2!1.85!69.80!Neurod2;;chr2:61642631..61642684,+!p1@Tbr1!1.75!55.84!Tbr1;;chr7:116154364..116154444,+!p1@Tub!1.73!89.61!Tub;;chr19:19185671..19185693,-!p1@Rorb!1.71!117.08!Rorb;;chr2:127347067..127347093,-!p1@Kcnip3!1.69!78.36!Kcnip3;;chr12:30219426..30219506,+!p2@Myt1l!1.68!46.83!Myt1l;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.66!55.39!Pou3f3;;chr17:48015839..48015915,-!p3@Foxp4!1.61!46.38!Foxp4;;chr10:67375342..67375365,-!p3@Zfp365!1.61!40.08!Zfp365;;chr5:122452349..122452377,-!p4@Cux2!1.61!40.08!Cux2;;chr3:95032091..95032183,-!p1@Mllt11!1.56!286.40!Mllt11;;chr8:24780125..24780143,+!p1@Zmat4!1.56!50.89!Zmat4;;chr2:65683890..65683907,+!p1@Csrnp3!1.54!62.59!Csrnp3;;chr2:38206580..38206600,+!p2@Lhx2!1.54!40.98!Lhx2;;chr13:83663902..83663927,+!p1@Mef2c!1.50!698.00!Mef2c;;chr15:101097270..101097290,+!p1@Nr4a1!1.50!298.56!Nr4a1;;chr10:67375146..67375208,-!p2@Zfp365!1.50!46.38!Zfp365;;chr4:58956447..58956510,+!p1@Zkscan16!1.48!63.04!Zkscan16;;chr19:19185697..19185711,-!p2@Rorb!1.47!36.48!Rorb;;chr13:83663546..83663560,+!p4@Mef2c!1.47!36.48!Mef2c;;chrX:90531838..90531861,+!p1@Arx!1.46!35.13!Arx;;chr5:138199361..138199441,+!p2@Tsc22d4!1.45!50.44!Tsc22d4;;chrX:34442872..34442899,-!p1@Nkrf!1.45!34.67!Nkrf;;chr5:98609885..98609900,+!p1@Prdm8!1.45!27.47!Prdm8;;chr13:83663868..83663894,+!p2@Mef2c!1.44!362.51!Mef2c;;chr2:65768174..65768247,+!p2@Csrnp3!1.44!26.57!Csrnp3;;chr11:98636531..98636559,-!p1@Nr1d1!1.43!142.30!Nr1d1;;chr2:127347094..127347111,-!p2@Kcnip3!1.41!40.08!Kcnip3;;chr13:83663500..83663519,+!p8@Mef2c!1.41!24.77!Mef2c;;chr18:35020854..35020869,+!p1@Egr1!1.39!868.22!Egr1;;chr2:61642743..61642758,+!p2@Tbr1!1.39!23.42!Tbr1;;chr1:179374784..179374800,+!p2@Zfp238!1.36!25.67!Zfp238;;chr4:48058129..48058179,+!p2@Nr4a3!1.35!39.63!Nr4a3;;chr15:76352677..76352737,-!p3@Scrt1!1.35!21.62!Scrt1;;chr1:57029281..57029326,-!p1@Satb2!1.34!32.42!Satb2;;chr2:38206744..38206766,+!p1@Lhx2!1.34!25.22!Lhx2;;chr7:148008023..148008092,-!p1@Zfp941!1.32!46.83!Zfp941;;chr15:76353005..76353021,-!p2@Scrt1!1.31!19.36!Scrt1;;chr12:30213247..30213333,+!p1@Myt1l!1.30!18.91!Myt1l;;chr10:67000609..67000625,+!p1@Egr2!1.28!41.43!Egr2;;chr13:83643031..83643049,+!p11@Mef2c!1.27!17.56!Mef2c;;chr5:122499831..122499891,-!p1@Cux2!1.23!24.77!Cux2;;chr11:90250944..90250982,-!p2@Hlf!1.22!26.12!Hlf;;chr2:61642558..61642595,+!p3@Tbr1!1.22!15.76!Tbr1;;chr3:95032197..95032208,-!p3@Mllt11!1.20!18.46!Mllt11;;chr12:86939997..86940040,+!p4@Jdp2!1.20!14.86!Jdp2;;chr7:52960700..52960719,+!p2@Dbp!1.19!18.01!Dbp;;chr14:13178147..13178185,-!p1@Fezf2!1.17!13.96!Fezf2;;chr11:98190955..98190968,-!p2@Neurod2!1.16!13.51!Neurod2;;chr4:150482563..150482655,-!p2@Camta1!1.15!46.83!Camta1;;chr12:30220074..30220102,+!p3@Myt1l!1.15!13.06!Myt1l;;chr12:86814833..86814846,+!p1@Fos!1.14!292.71!Fos;;chr18:69680960..69681007,+!p10@Tcf4!1.14!16.66!Tcf4;;chr12:72149325..72149343,+!p2@Arid4a!1.10!16.21!Arid4a;;chr3:95032213..95032226,-!p6@Mllt11!1.10!13.96!Mllt11;;chr16:91225808..91225824,+!p1@Olig2!1.10!11.71!Olig2;;chr6:117813087..117813121,+!p1@Zfp239!1.08!41.88!Zfp239;;chr10:13685585..13685645,+!p2@Hivep2!1.08!38.73!Hivep2;;chrX:95345005..95345053,+!p1@Ar!1.07!10.81!Ar;;chr4:22415443..22415506,-!p1@Pou3f2!1.07!10.81!Pou3f2;;chr8:87297878..87297935,-!p3@Nfix!1.06!23.42!Nfix;;chr4:48058016..48058032,+!p3@Nr4a3!1.06!18.01!Nr4a3;;chr7:91520922..91520956,-!p5@Arnt2!1.06!10.36!Arnt2;;chr17:25707623..25707639,-!p1@Sox8!1.05!44.13!Sox8;;chr19:23216132..23216157,+!p3@Klf9!1.05!16.21!Klf9;;chr19:59533221..59533271,+!p1@Emx2!1.05!12.61!Emx2;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!1.04!103.57!Camta2;;chr7:52960780..52960793,+!p5@Dbp!1.04!11.71!Dbp;;chr2:162769220..162769252,+!p1@L3mbtl1!1.04!9.91!L3mbtl1;;chr14:70477113..70477173,+!p1@Egr3!1.04!9.91!Egr3;;chr15:76352434..76352488,-!p4@Scrt1!1.04!9.91!Scrt1;;chr10:13685657..13685677,+!p7@Hivep2!1.03!12.61!Hivep2;;chr7:71083876..71083932,-!p2@Klf13!1.02!77.46!Klf13;;chr2:65768149..65768173,+!p4@Csrnp3!1.02!9.46!Csrnp3;;chrX:34442842..34442866,-!p3@Nkrf!1.02!9.46!Nkrf;;chr2:56967334..56967366,-!p1@Nr4a2!1.01!19.36!Nr4a2;;chr18:36441119..36441158,+!p2@Pura!1.00!22.07!Pura;;chr11:23978111..23978134,+!p3@Bcl11a!1.00!18.91!Bcl11a;;chr2:127347042..127347058,-!p3@Kcnip3!1.00!9.01!Kcnip3;;chr14:70476975..70476997,+!p2@Egr3!1.00!9.01!Egr3;;chr9:48644306..48644364,-!p1@Zbtb16!0.99!36.48!Zbtb16;;chr11:23980664..23980706,+!p2@Bcl11a!0.98!38.28!Bcl11a;;chr7:30094448..30094481,+!p4@Dpf1!0.98!10.36!Dpf1;;chr11:90252223..90252240,-!p1@Hlf!0.97!70.70!Hlf;;chr6:108610766..108610781,+!p2@Bhlhe40!0.97!15.31!Bhlhe40;;chr11:90251852..90251855,-!p4@Hlf!0.97!10.36!Hlf;;chr2:77654815..77654872,-!p2@Zfp385b!0.96!10.36!Zfp385b;;chr16:91270091..91270143,+!p2@Olig1!0.96!8.11!Olig1;;chr1:179374764..179374776,+!p5@Zfp238!0.96!8.11!Zfp238;;chr8:107793688..107793736,+!p1@Hsf4!0.95!10.36!Hsf4;;chr7:52960730..52960762,+!p3@Dbp!0.94!9.91!Dbp;;chr12:54349410..54349461,+!p1@Npas3!0.94!9.46!Npas3;;chr6:144152648..144152680,-!p5@Sox5!0.94!7.66!Sox5;;chr11:21901608..21901634,-!p1@Otx1!0.94!7.66!Otx1;;chr2:25562263..25562314,+!p2@Bmyc!0.93!30.62!Bmyc;;chr7:30092993..30093076,+!p1@Dpf1!0.93!13.06!Dpf1;;chr10:80893711..80893784,-!p3@Nfic!0.92!40.08!Nfic;;chr4:154335024..154335039,+!p1@Hes5!0.92!9.01!Hes5;;chr8:87502608..87502623,-!p1@Junb!0.91!122.04!Junb;;chr14:18493386..18493464,+!p1@Thrb!0.91!27.92!Thrb;;chr13:78339428..78339466,-!p2@Nr2f1!0.91!9.91!Nr2f1;;chr4:124334894..124334899,+!p1@Pou3f1!0.91!9.46!Pou3f1;;chrX:108009761..108009788,+!p1@Pou3f4!0.91!7.21!Pou3f4;;chr1:57028606..57028625,-!p4@Satb2!0.91!7.21!Satb2;;chr11:90250894..90250916,-!p5@Hlf!0.91!7.21!Hlf;;chr13:83643136..83643158,+!p7@Mef2c!0.91!7.21!Mef2c;;chr19:26681865..26681900,+!p6@Smarca2!0.90!21.17!Smarca2;;chr5:125342568..125342602,+!p2@Zfp664!0.90!11.71!Zfp664;;chr11:98603119..98603130,+!p2@Thra!0.89!60.79!Thra;;chr15:103170533..103170556,-!p1@Zfp385a!0.89!26.12!Zfp385a;;chr3:95032184..95032195,-!p4@Mllt11!0.89!8.56!Mllt11;;chr4:119487109..119487131,+!p4@Hivep3!0.89!6.75!Hivep3;;chr14:13178241..13178254,-!p4@Fezf2!0.89!6.75!Fezf2;;chr10:84218800..84218829,+!p2@Rfx4!0.89!6.75!Rfx4;;chr7:19895384..19895399,-!p2@Fosb!0.88!9.46!Fosb;;chr9:36954842..36954908,-!p1@Pknox2!0.87!79.71!Pknox2;;chr9:48644284..48644305,-!p4@Zbtb16!0.87!8.56!Zbtb16;;chr1:179372411..179372509,+!p1@Zfp238!0.86!84.21!Zfp238;;chr15:81633165..81633188,+!p2@Tef!0.86!54.49!Tef;;chr7:91558472..91558512,-!p2@Arnt2!0.86!9.01!Arnt2;;chr7:52960888..52960902,+!p7@Dbp!0.86!6.30!Dbp;;chr19:19185429..19185440,-!p3@Rorb!0.86!6.30!Rorb;;chr4:150482353..150482386,-!p6@Camta1!0.86!6.30!Camta1;;chr2:79296783..79296801,-!p1@Neurod1!0.86!6.30!Neurod1;;chr13:83643302..83643309,+!p12@Mef2c!0.86!6.30!Mef2c;;chr12:50483639..50483654,+!p1@Foxg1!0.86!6.30!Foxg1;;chr7:17200307..17200370,-!p2@Grlf1!0.85!47.73!Grlf1;;chr15:81641878..81641921,+!p1@Tef!0.84!162.12!Tef;;chr2:166888481..166888548,-!p3@Znfx1!0.84!16.66!Znfx1;;chr10:13686815..13686846,+!p3@Hivep2!0.84!13.96!Hivep2;;chr1:179374820..179374831,+!p3@Zfp238!0.84!5.85!Zfp238;;chr7:91521166..91521194,-!p11@Arnt2!0.84!5.85!Arnt2;;chr11:23978078..23978096,+!p4@Bcl11a!0.83!18.46!Bcl11a;;chr11:98636508..98636524,-!p3@Nr1d1!0.83!7.21!Nr1d1;;chr13:78339134..78339185,-!p5@Nr2f1!0.83!7.21!Nr2f1;;chr12:72149359..72149406,+!p4@Arid4a!0.82!7.66!Arid4a;;chr11:23977742..23977794,+!p6@Bcl11a!0.82!7.21!Bcl11a;;chr10:67375223..67375240,-!p4@Zfp365!0.82!6.30!Zfp365;;chr8:87297280..87297326,-!p2@Nfix!0.81!13.51!Nfix;;chr4:150513630..150513686,-!p4@Camta1!0.81!6.30!Camta1;;chr6:85137505..85137517,+!p2@Emx1!0.81!5.40!Emx1;;chr2:163051181..163051205,+!p2@Tox2!0.81!5.40!Tox2;;chr9:96631780..96631791,-!p13@Zbtb38!0.81!5.40!Zbtb38;;chr12:39510042..39510069,+!p8@Etv1!0.81!5.40!Etv1;;chr12:86815639..86815664,+!p2@Fos!0.81!5.40!Fos;;chr15:100430414..100430470,-!p1@Pou6f1!0.80!17.56!Pou6f1;;chr13:78339382..78339420,-!p3@Nr2f1!0.80!6.30!Nr2f1;;chr18:36441100..36441113,+!p3@Pura!0.80!6.30!Pura;;chr11:98603185..98603208,+!p1@Thra!0.79!340.44!Thra;;chr10:13685899..13685916,+!p1@Hivep2!0.79!58.09!Hivep2;;chr15:78994907..78994926,-!p1@Sox10!0.79!13.96!Sox10;;chr3:34548909..34548927,+!p1@Sox2!0.78!9.01!Sox2;;chr11:23978229..23978268,+!p8@Bcl11a!0.78!5.85!Bcl11a;;chr7:52960555..52960662,+!p1@Dbp!0.77!45.48!Dbp;;chr7:91558392..91558434,-!p1@Arnt2!0.77!14.41!Arnt2;;chr7:25292160..25292213,+!p3@Zfp428!0.77!13.06!Zfp428;;chr7:37483231..37483263,+!p2@Tshz3!0.77!7.66!Tshz3;;chr6:144157924..144157955,-!p2@Sox5!0.77!6.30!Sox5;;chr11:98636568..98636574,-!p9@Nr1d1!0.77!5.85!Nr1d1;;chr10:42303385..42303401,-!p1@Nr2e1!0.77!4.95!Nr2e1;;chr9:96631820..96631834,-!p11@Zbtb38!0.77!4.95!Zbtb38;;chr2:71367142..71367167,+!p2@Dlx1!0.77!4.95!Dlx1;;chr6:85137520..85137563,+!p1@Emx1!0.77!4.95!Emx1;;chr1:57028157..57028173,-!p3@Satb2!0.77!4.95!Satb2;;chr10:30522690..30522752,-!p2@Ncoa7!0.76!31.52!Ncoa7;;chr15:103170516..103170531,-!p2@Zfp385a!0.76!12.16!Zfp385a;;chr19:23215469..23215494,+!p2@Klf9!0.76!7.66!Klf9;;chr4:48058047..48058062,+!p1@Nr4a3!0.76!7.66!Nr4a3;;chr7:30088977..30089002,+!p2@Dpf1!0.76!6.75!Dpf1;;chr7:91558537..91558558,-!p4@Arnt2!0.76!5.85!Arnt2;;chr15:99532568..99532636,+!p2@Smarcd1!0.75!46.83!Smarcd1;;chr1:39250584..39250643,+!p1@Npas2!0.75!25.67!Npas2;;chrX:92906980..92907024,+!p2@Zc3h12b!0.75!12.61!Zc3h12b;;chr2:71384802..71384815,-!p1@Dlx2!0.75!5.85!Dlx2;;chr17:51952537..51952552,-!p15@Satb1!0.75!4.95!Satb1;;chr16:22439681..22439698,-!p1@Etv5!0.74!86.46!Etv5;;chr14:76904356..76904367,+!p3@Tsc22d1!0.74!36.03!Tsc22d1;;chr8:72356532..72356611,+!p1@Pbx4!0.74!20.26!Pbx4;;chr14:55711114..55711159,-!p2@Zfhx2!0.74!10.81!Zfhx2;;chr11:23977565..23977612,+!p5@Bcl11a!0.74!10.36!Bcl11a;;chr16:95923651..95923701,+!p3@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Smad9!0.33!3.60!Smad9;;chr6:92041489..92041500,+!p4@Nr2c2!0.33!2.70!Nr2c2;;chr15:81633203..81633215,+!p3@Tef!0.33!2.25!Tef;;chr1:179372625..179372654,+!p4@Zfp238!0.33!2.25!Zfp238;;chr7:86956107..86956152,+!p@chr7:86956107..86956152,+!0.33!2.25!Mesp2;;chr8:87237711..87237727,-!p11@Nfix!0.33!1.80!Nfix;;chr6:99471147..99471161,-!p9@Foxp1!0.33!1.80!Foxp1;;chr13:29044875..29044928,-!p4@Sox4!0.33!1.80!Sox4;;chr9:31720843..31720888,-!p1@Barx2!0.33!1.35!Barx2;;chr13:48356475..48356492,+!p1@Id4!0.32!40.53!Id4;;chr2:166888107..166888224,-!p1@Znfx1!0.32!27.02!Znfx1;;chr1:170362040..170362113,-!p2@Pbx1!0.32!14.41!Pbx1;;chr9:31088110..31088151,+!p1@Prdm10!0.32!12.61!Prdm10;;chr14:55711198..55711258,-!p1@Zfhx2!0.32!10.36!Zfhx2;;chr4:6917606..6917681,-!p1@Tox!0.32!7.21!Tox;;chr2:48805065..48805076,+!p4@Mbd5!0.32!4.05!Mbd5;;chr14:76903992..76904056,+!p6@Tsc22d1!0.32!3.15!Tsc22d1;;chr2:160698668..160698679,-!p4@Zhx3!0.32!2.70!Zhx3;;chr7:25862363..25862382,+!p2@Zfp574!0.32!2.70!Zfp574;;chr19:28085997..28086028,-!p7@Rfx3!0.32!2.70!Rfx3;;chr15:40486615..40486628,+!p3@Zfpm2!0.32!2.25!Zfpm2;;chr18:69753145..69753159,+!p14@Tcf4!0.32!1.80!Tcf4;;chr4:149610794..149610876,+!p2@LOC100045967,p2@LOC100503183,p3@Eno1,p3@Gm5506!0.32!1.80!Eno1;;chr18:69752598..69752607,+!p26@Tcf4!0.32!1.35!Tcf4;;chr16:3872378..3872411,-!p6@Zfp597!0.32!1.35!Zfp597;;chr10:13686074..13686090,+!p9@Hivep2!0.32!1.35!Hivep2;;chr16:95924005..95924042,+!p2@Ets2!0.31!32.42!Ets2;;chr17:32967140..32967197,-!p1@Zfp799!0.31!24.77!Zfp799;;chr11:120494853..120494905,-!p1@Mafg!0.31!17.56!Mafg;;chrX:66613481..66613562,+!p1@Aff2!0.31!7.21!Aff2;;chrX:131543765..131543775,-!p2@Zmat1!0.31!3.15!Zmat1;;chr7:52963269..52963305,+!p4@Dbp!0.31!1.80!Dbp;;chr4:154010228..154010244,-!p4@Prdm16!0.31!1.80!Prdm16;;chr13:37870253..37870272,+!p13@Rreb1!0.31!1.80!Rreb1;;chr6:53523346..53523353,+!p3@Creb5!0.31!1.80!Creb5;;chr4:102787381..102787397,+!p9@Mier1!0.31!1.35!Mier1;;chr8:73905967..73905978,-!p4@Nr2f6!0.31!1.35!Nr2f6;;chr13:15555428..15555440,+!p7@Gli3!0.31!1.35!Gli3;;chr18:35721854..35721914,+!p1@Matr3!0.30!136.45!Matr3;;chr9:44689360..44689406,-!p1@Mll1!0.30!67.55!Mll1;;chr5:67698217..67698253,+!p2@Slc30a9!0.30!36.03!Slc30a9;;chr7:24866907..24866967,+!p1@LOC676710,p1@Zfp180!0.30!22.97!Zfp180;;chr15:81575569..81575599,+!p2@Zc3h7b!0.30!19.36!Zc3h7b;;chr10:22451142..22451191,-!p2@Tbpl1!0.30!17.56!Tbpl1;;chr15:50721588..50721610,-!p1@Trps1!0.30!17.56!Trps1;;chr7:5003165..5003203,+!p2@Zfp580!0.30!9.46!Zfp580;;chr4:126698529..126698536,+!p2@Sfpq!0.30!7.66!Sfpq;;chr7:30836380..30836430,-!p1@Zfp14!0.30!6.30!Zfp14;;chr17:23004042..23004077,-!p2@Zfp945!0.30!6.30!Zfp945;;chr4:122673278..122673336,+!p1@Mycl1!0.30!4.95!Mycl1;;chr1:138521510..138521526,+!p2@Zfp281!0.30!4.50!Zfp281;;chr1:138521574..138521597,+!p3@Zfp281!0.30!3.60!Zfp281;;chr18:7004715..7004731,-!p1@Mkx!0.30!3.60!Mkx;;chr18:79306029..79306059,-!p2@Setbp1!0.30!3.15!Setbp1;;chr2:165818215..165818226,+!p4@Ncoa3!0.30!2.70!Ncoa3;;chr11:23978353..23978379,+!p10@Bcl11a!0.30!1.35!Bcl11a;;chr6:92041522..92041531,+!p7@Nr2c2!0.30!1.35!Nr2c2;;chr4:13670441..13670463,+!p8@Runx1t1!0.30!1.35!Runx1t1;;chr3:95032515..95032553,-!p5@Mllt11!0.30!1.35!Mllt11;;chr15:40486854..40486867,+!p7@Zfpm2!0.30!1.35!Zfpm2;;chr11:121121297..121121369,+!p1@Foxk2!0.29!103.12!Foxk2;;chr4:82151178..82151262,-!p1@Nfib!0.29!70.70!Nfib;;chr1:182499095..182499141,+!p2@Parp1!0.29!30.62!Parp1;;chr13:65380147..65380174,+!p1@Zfp369!0.29!22.97!Zfp369;;chr10:57206160..57206220,+!p1@Hsf2!0.29!18.46!Hsf2;;chr6:47785649..47785724,+!p1@Zfp398!0.29!13.96!Zfp398;;chr7:26052688..26052742,+!p1@Cic!0.29!11.71!Cic;;chr4:120488308..120488366,-!p1@Nfyc!0.29!9.46!Nfyc;;chr7:148513409..148513455,-!p2@Deaf1!0.29!7.66!Deaf1;;chr7:6336020..6336068,+!p1@Zfp28!0.29!7.21!Zfp28;;chr2:73730619..73730630,-!p4@Atf2,p4@LOC100047997!0.29!6.75!Atf2;;chr1:64167851..64167886,-!p3@Klf7!0.29!6.75!Klf7;;chr7:50817629..50817652,+!p1@LOC100505180,p1@Zfp658!0.29!3.60!Zfp658;;chr9:48644429..48644462,-!p3@Zbtb16!0.29!2.70!Zbtb16;;chr15:50721560..50721572,-!p10@Trps1!0.29!2.25!Trps1;;chr13:29045131..29045159,-!p3@Sox4!0.29!1.80!Sox4;;chr7:91558631..91558652,-!p3@Arnt2!0.29!1.80!Arnt2;;chr11:99092312..99092333,-!p4@Smarce1!0.29!1.80!Smarce1;;chr2:120389480..120389491,-!p6@Zfp106!0.29!1.35!Zfp106;;chr7:123177120..123177138,-!p10@Sox6!0.29!1.35!Sox6;;chr12:39506841..39506848,+!p7@Etv1!0.29!1.35!Etv1;;chr14:52936008..52936019,-!p5@Sall2!0.29!1.35!Sall2;;chr4:149611320..149611348,+!p1@Eno1,p1@Gm5506,p1@LOC100045967,p1@LOC100503183!0.28!75.20!Eno1;;chr14:75684150..75684197,+!p1@Zc3h13!0.28!56.74!Zc3h13;;chr7:13404186..13404214,-!p1@Zfp329!0.28!33.77!Zfp329;;chr2:160698681..160698708,-!p2@Zhx3!0.28!13.51!Zhx3;;chr7:28764174..28764200,-!p1@Zfp780b!0.28!10.81!Zfp780b;;chr14:76814601..76814630,+!p5@Tsc22d1!0.28!9.91!Tsc22d1;;chr5:125538737..125538781,-!p2@Ncor2!0.28!5.40!Ncor2;;chr12:77470461..77470504,-!p3@Zbtb25!0.28!4.50!Zbtb25;;chr11:102178937..102178956,-!p5@Ubtf!0.28!4.50!Ubtf;;chr10:93610727..93610754,+!p2@Nr2c1!0.28!3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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 43: @@
 |has_quality=
 |id=FF:10241-104A7
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011270
+|is_a=EFO:0002091;;FF:0011270
-|name=visual cortex - wildtype, neonate N60-70, donor1
+|is_obsolete=
+|library_id=CNhs13037
+|library_id_phase_based=2:CNhs13037
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;10241
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;10241
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N60-70%252c%2520donor1.CNhs13037.10241-104A7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N60-70%252c%2520donor1.CNhs13037.10241-104A7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N60-70%252c%2520donor1.CNhs13037.10241-104A7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N60-70%252c%2520donor1.CNhs13037.10241-104A7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N60-70%252c%2520donor1.CNhs13037.10241-104A7.mm9.nobarcode.rdna.fa.gz
+|name=visual cortex - wildtype
 |namespace=FANTOM5
 |part_of=
 |profile_cagescan=,,,
 |profile_hcage=CNhs13037,LSID999,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.191346068050397,0,0,0,0,0,0.359816132670478,0,0.080732098131109,0,0,-0.0843392403965415,0,0,0,0,0,0,0.255463915877881,0,0,0,0,0,0,0,0,0,0,0,0,0.441671912595038,-0.396958596061813,0,0,0,0,0,0.115750435321908,0.118613213123435,0.0420754584392322,0.98783480068254,0.242229280403009,0.278900414858752,0,0,0,0,0,0,0,0,0,0.161464196262218,0,-0.0660055475634404,0,0,0,0,0,0,-0.0499644673196777,0.278900414858752,0.51209791841336,0,-0.0299606112555016,-0.310650657339386,0.779199133734347,-0.0167634680365776,0,0,0.0841598993465211,0.107495544289781,0.161464196262218,0,0.106268426007696,0.127237474695781,0.384365935079556,-0.0788315948399074,0,0,0,0,0,0,0.252270522545969,0.016389494342635,0.323552600250124,0,0,0.703539915125771,0.447357266760456,0
 |rna_box=104
 |rna_catalog_number=N/A
@@ Line 57: / Line 77: @@
 |rna_weight_ug=11.328
 |sample_age=P60-70
+|sample_category=tissues
 |sample_cell_catalog=N/A
 |sample_cell_line=N/A
@@ Line 72: / Line 93: @@
 |sample_note=
 |sample_sex=male
-|sample_species=mus musculus
+|sample_species=Mouse (Mus musculus)
 |sample_strain=
 |sample_tissue=Visual cortex
+|time= neonate N60-70
+|timecourse=Visual_cortex_development
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+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:10241-104A7;search_select_hide=table117:10241-104A7
 }}

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FF:10241-104A7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 13:57, 3 June 2020

CNhs13037

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0