FF:10242-104A8: Difference between revisions

Latest revision as of 13:57, 3 June 2020

Name:	visual cortex - wildtype
Species:	Mouse (Mus musculus)
Library ID:	CNhs13038
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		SAMD00004869

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13038		CAGE		DRX009140		DRR010014

Accession ID Mm9

Library id		BAM		CTSS
CNhs13038		DRZ001439		DRZ002822

Accession ID Mm10

Library id		BAM		CTSS
CNhs13038		DRZ012789		DRZ014172

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

CNhs13038

0	0
1	0.838
10	0
100	0
1000	0
1001	0.0345
1002	-0.116
1003	0.397
1004	0
1005	0
1006	0.62
1007	-0.246
1008	0
1009	-0.0938
101	-0.0304
1010	0
1011	0.938
1012	0.373
1013	0.186
1014	-0.0874
1015	-0.112
1016	-0.23
1017	0
1018	0
1019	0
102	0
1020	0.449
1021	0
1022	-0.0704
1023	0
1024	-0.0269
1025	-0.0194
1026	0
1027	0.388
1028	0
1029	0.273
103	-0.0848
1030	0
1031	-0.661
1032	0.196
1033	-0.0013
1034	0
1035	0
1036	-0.292
1037	0
1038	0.0919
1039	0.00256
104	0
1040	-0.139
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: CNhs13038

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0187
MA0003.1	MA0003.1	0.253
MA0004.1	MA0004.1	0.573
MA0006.1	MA0006.1	0.0852
MA0007.1	MA0007.1	0.471
MA0009.1	MA0009.1	0.984
MA0014.1	MA0014.1	0.693
MA0017.1	MA0017.1	9.53978e-7
MA0018.2	MA0018.2	0.00112
MA0019.1	MA0019.1	0.129
MA0024.1	MA0024.1	0.0276
MA0025.1	MA0025.1	0.0107
MA0027.1	MA0027.1	0.0348
MA0028.1	MA0028.1	0.0656
MA0029.1	MA0029.1	0.814
MA0030.1	MA0030.1	0.345
MA0031.1	MA0031.1	0.024
MA0035.2	MA0035.2	0.0129
MA0038.1	MA0038.1	0.887
MA0039.2	MA0039.2	0.00256
MA0040.1	MA0040.1	0.0374
MA0041.1	MA0041.1	0.336
MA0042.1	MA0042.1	0.404
MA0043.1	MA0043.1	0.139
MA0046.1	MA0046.1	1.32877e-10
MA0047.2	MA0047.2	3.48871e-4
MA0048.1	MA0048.1	0.0488
MA0050.1	MA0050.1	6.60438e-6
MA0051.1	MA0051.1	0.00135
MA0052.1	MA0052.1	0.966
MA0055.1	MA0055.1	0.00731
MA0057.1	MA0057.1	0.501
MA0058.1	MA0058.1	0.327
MA0059.1	MA0059.1	0.257
MA0060.1	MA0060.1	0.0209
MA0061.1	MA0061.1	0.0416
MA0062.2	MA0062.2	4.24129e-4
MA0065.2	MA0065.2	2.83918e-6
MA0066.1	MA0066.1	0.0701
MA0067.1	MA0067.1	0.288
MA0068.1	MA0068.1	0.223
MA0069.1	MA0069.1	0.138
MA0070.1	MA0070.1	0.659
MA0071.1	MA0071.1	0.0261
MA0072.1	MA0072.1	0.0848
MA0073.1	MA0073.1	0.839
MA0074.1	MA0074.1	0.131
MA0076.1	MA0076.1	0.136
MA0077.1	MA0077.1	0.94
MA0078.1	MA0078.1	0.978
MA0079.2	MA0079.2	0.916
MA0080.2	MA0080.2	1.31596e-10
MA0081.1	MA0081.1	0.196
MA0083.1	MA0083.1	0.00876
MA0084.1	MA0084.1	0.229
MA0087.1	MA0087.1	0.679
MA0088.1	MA0088.1	0.27
MA0090.1	MA0090.1	0.14
MA0091.1	MA0091.1	0.231
MA0092.1	MA0092.1	0.32
MA0093.1	MA0093.1	0.588
MA0099.2	MA0099.2	0.00565
MA0100.1	MA0100.1	0.422
MA0101.1	MA0101.1	0.0114
MA0102.2	MA0102.2	0.208
MA0103.1	MA0103.1	0.4
MA0104.2	MA0104.2	0.913
MA0105.1	MA0105.1	0.0582
MA0106.1	MA0106.1	0.0449
MA0107.1	MA0107.1	0.0232
MA0108.2	MA0108.2	3.75612e-5
MA0111.1	MA0111.1	0.669
MA0112.2	MA0112.2	0.00231
MA0113.1	MA0113.1	0.258
MA0114.1	MA0114.1	2.64155e-6
MA0115.1	MA0115.1	5.29622e-4
MA0116.1	MA0116.1	0.132
MA0117.1	MA0117.1	0.637
MA0119.1	MA0119.1	0.0842
MA0122.1	MA0122.1	0.678
MA0124.1	MA0124.1	0.841
MA0125.1	MA0125.1	0.319
MA0131.1	MA0131.1	0.695
MA0135.1	MA0135.1	0.23
MA0136.1	MA0136.1	5.42514e-13
MA0137.2	MA0137.2	0.305
MA0138.2	MA0138.2	0.00278
MA0139.1	MA0139.1	0.626
MA0140.1	MA0140.1	0.00125
MA0141.1	MA0141.1	0.00147
MA0142.1	MA0142.1	0.356
MA0143.1	MA0143.1	0.548
MA0144.1	MA0144.1	0.119
MA0145.1	MA0145.1	0.0903
MA0146.1	MA0146.1	0.0112
MA0147.1	MA0147.1	0.926
MA0148.1	MA0148.1	1.59235e-4
MA0149.1	MA0149.1	0.31
MA0150.1	MA0150.1	0.319
MA0152.1	MA0152.1	0.634
MA0153.1	MA0153.1	5.34461e-10
MA0154.1	MA0154.1	0.0543
MA0155.1	MA0155.1	0.349
MA0156.1	MA0156.1	5.55586e-11
MA0157.1	MA0157.1	0.0542
MA0159.1	MA0159.1	0.00625
MA0160.1	MA0160.1	0.0042
MA0162.1	MA0162.1	0.174
MA0163.1	MA0163.1	0.00444
MA0164.1	MA0164.1	0.965
MA0258.1	MA0258.1	0.0417
MA0259.1	MA0259.1	0.837

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: CNhs13038

Novel motif	Logo	P-value
1	1	0.396
10	10	0.102
100	100	0.488
101	101	0.557
102	102	0.879
103	103	0.095
104	104	0.992
105	105	0.53
106	106	0.0664
107	107	0.142
108	108	0.439
109	109	0.00237
11	11	0.1
110	110	0.0615
111	111	0.57
112	112	0.0241
113	113	0.359
114	114	0.653
115	115	0.852
116	116	0.25
117	117	0.00477
118	118	0.556
119	119	0.308
12	12	0.761
120	120	0.741
121	121	0.194
122	122	0.876
123	123	8.76756e-4
124	124	0.014
125	125	0.342
126	126	0.0368
127	127	0.519
128	128	0.0611
129	129	0.402
13	13	8.33679e-9
130	130	0.0537
131	131	0.623
132	132	0.584
133	133	0.31
134	134	0.0758
135	135	0.483
136	136	0.00626
137	137	0.565
138	138	0.725
139	139	0.404
14	14	0.841
140	140	0.251
141	141	0.956
142	142	0.704
143	143	0.515
144	144	0.569
145	145	9.04384e-5
146	146	0.165
147	147	0.0908
148	148	0.391
149	149	0.506
15	15	0.267
150	150	0.0353
151	151	0.832
152	152	0.0701
153	153	0.947
154	154	0.885
155	155	0.411
156	156	0.0196
157	157	0.171
158	158	0.284
159	159	0.451
160	160	0.321
161	161	0.089
162	162	0.473
163	163	0.821
164	164	0.193
165	165	0.129
166	166	0.497
167	167	0.194
168	168	0.622
169	169	0.00566
17	17	0.0802
18	18	0.87
19	19	0.0526
2	2	0.841
20	20	0.0367
21	21	0.224
22	22	0.0923
23	23	0.755
24	24	0.00797
25	25	0.948
26	26	1.06538e-6
27	27	0.403
28	28	0.7
29	29	0.044
3	3	0.0523
30	30	0.959
31	31	0.82
32	32	0.779
33	33	0.241
34	34	0.391
35	35	0.497
36	36	0.601
37	37	0.0207
38	38	0.423
39	39	0.21
4	4	0.178
40	40	0.115
41	41	0.598
42	42	0.165
43	43	0.14
44	44	0.93
45	45	0.534
46	46	0.254
47	47	0.594
48	48	0.361
49	49	0.364
5	5	0.353
50	50	0.141
51	51	0.759
52	52	0.181
53	53	0.541
54	54	0.951
55	55	0.955
56	56	0.475
57	57	0.918
58	58	0.436
59	59	0.105
6	6	0.961
60	60	0.0385
61	61	0.0335
62	62	0.351
63	63	0.123
64	64	0.679
65	65	0.438
66	66	0.52
67	67	0.827
68	68	0.253
69	69	0.234
7	7	0.0181
70	70	0.372
71	71	0.0142
72	72	0.517
73	73	0.021
74	74	0.764
75	75	0.0529
76	76	0.845
77	77	0.278
78	78	0.00263
79	79	0.554
8	8	0.166
80	80	0.678
81	81	0.699
82	82	0.412
83	83	0.0251
84	84	0.861
85	85	0.173
86	86	0.215
87	87	0.0151
88	88	0.673
89	89	0.899
9	9	0.353
90	90	0.582
91	91	0.154
92	92	0.52
93	93	0.497
94	94	0.887
95	95	0.0162
96	96	0.605
97	97	0.836
98	98	0.342
99	99	0.475

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: CNhs13038

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:0000468,UBERON:0007023,UBERON:0000922,UBERON:0000955,UBERON:0002021,UBERON:0000411,UBERON:0000483,UBERON:0000956,UBERON:0000033,UBERON:0000479,UBERON:0002346,UBERON:0000064,UBERON:0000073,UBERON:0004121,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000025,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000477,UBERON:0002020,UBERON:0002791,UBERON:0003528,UBERON:0000481,UBERON:0000467,UBERON:0002616,UBERON:0002619,UBERON:0001062,UBERON:0000119,UBERON:0005291,UBERON:0002780,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0001016,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0005743,UBERON:0001950,UBERON:0003075,UBERON:0003056,UBERON:0001049,UBERON:0006238,UBERON:0006601,UBERON:0005068,UBERON:0006241,UBERON:0003080,UBERON:0006240,UBERON:0007284,UBERON:0007135
+|DRA_sample_Accession=CAGE@SAMD00004869
+|accession_numbers=CAGE;DRX009140;DRR010014;DRZ001439;DRZ002822;DRZ012789;DRZ014172
+|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=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
+|donor= donor2
 |expression_enrichment_score=chr6:85463580..85463585,-!p1@Egr4!2.28!188.51!Egr4;;chr19:4989964..4989972,-!p1@Npas4!2.20!158.60!Npas4;;chr10:67375368..67375433,-!p1@Zfp365!2.13!231.56!Zfp365;;chr16:91270004..91270023,+!p1@Olig1!2.01!114.19!Olig1;;chr6:55631042..55631102,-!p1@Neurod6!1.90!79.30!Neurod6;;chr15:101097270..101097290,+!p1@Nr4a1!1.81!621.71!Nr4a1;;chr2:61642631..61642684,+!p1@Tbr1!1.81!63.89!Tbr1;;chr2:127347067..127347093,-!p1@Kcnip3!1.78!96.07!Kcnip3;;chr12:30219426..30219506,+!p2@Myt1l!1.76!57.10!Myt1l;;chr11:98190918..98190951,-!p1@Neurod2!1.76!57.10!Neurod2;;chr7:116154364..116154444,+!p1@Tub!1.75!92.44!Tub;;chr19:19185671..19185693,-!p1@Rorb!1.73!122.35!Rorb;;chr10:67000609..67000625,+!p1@Egr2!1.73!116.91!Egr2;;chr10:67375342..67375365,-!p3@Zfp365!1.65!43.95!Zfp365;;chr5:138199361..138199441,+!p2@Tsc22d4!1.62!74.77!Tsc22d4;;chr4:48058129..48058179,+!p2@Nr4a3!1.59!69.78!Nr4a3;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.59!47.13!Pou3f3;;chr8:24780125..24780143,+!p1@Zmat4!1.58!52.56!Zmat4;;chr3:95032091..95032183,-!p1@Mllt11!1.56!285.48!Mllt11;;chr17:48015839..48015915,-!p3@Foxp4!1.56!41.69!Foxp4;;chr2:65683890..65683907,+!p1@Csrnp3!1.55!65.25!Csrnp3;;chrX:34442872..34442899,-!p1@Nkrf!1.55!44.86!Nkrf;;chr18:35020854..35020869,+!p1@Egr1!1.52!1165.03!Egr1;;chr10:67375146..67375208,-!p2@Zfp365!1.52!48.03!Zfp365;;chr5:122452349..122452377,-!p4@Cux2!1.51!31.72!Cux2;;chr13:83663902..83663927,+!p1@Mef2c!1.50!698.75!Mef2c;;chr13:83663868..83663894,+!p2@Mef2c!1.46!381.09!Mef2c;;chr1:57029281..57029326,-!p1@Satb2!1.46!42.60!Satb2;;chrX:90531838..90531861,+!p1@Arx!1.46!34.89!Arx;;chr2:38206580..38206600,+!p2@Lhx2!1.46!33.99!Lhx2;;chr2:65768174..65768247,+!p2@Csrnp3!1.44!26.28!Csrnp3;;chr4:58956447..58956510,+!p1@Zkscan16!1.43!54.83!Zkscan16;;chr2:38206744..38206766,+!p1@Lhx2!1.41!29.45!Lhx2;;chr11:98636531..98636559,-!p1@Nr1d1!1.40!131.86!Nr1d1;;chr7:148008023..148008092,-!p1@Zfp941!1.40!56.64!Zfp941;;chr13:83663546..83663560,+!p4@Mef2c!1.40!31.27!Mef2c;;chr15:76352677..76352737,-!p3@Scrt1!1.39!23.56!Scrt1;;chr15:76353005..76353021,-!p2@Scrt1!1.39!23.56!Scrt1;;chr2:127347094..127347111,-!p2@Kcnip3!1.37!36.25!Kcnip3;;chr19:19185697..19185711,-!p2@Rorb!1.37!28.55!Rorb;;chr12:86814833..86814846,+!p1@Fos!1.36!486.67!Fos;;chr2:56967334..56967366,-!p1@Nr4a2!1.33!41.24!Nr4a2;;chr14:13178147..13178185,-!p1@Fezf2!1.33!20.39!Fezf2;;chr12:86939997..86940040,+!p4@Jdp2!1.32!19.94!Jdp2;;chr13:83663500..83663519,+!p8@Mef2c!1.32!19.94!Mef2c;;chr4:48058016..48058032,+!p3@Nr4a3!1.31!32.63!Nr4a3;;chr1:179374784..179374800,+!p2@Zfp238!1.31!22.66!Zfp238;;chr17:25707623..25707639,-!p1@Sox8!1.29!77.94!Sox8;;chr2:61642743..61642758,+!p2@Tbr1!1.29!18.58!Tbr1;;chr5:98609885..98609900,+!p1@Prdm8!1.29!18.58!Prdm8;;chr11:90250944..90250982,-!p2@Hlf!1.27!29.45!Hlf;;chr5:122499831..122499891,-!p1@Cux2!1.27!26.74!Cux2;;chr12:30213247..30213333,+!p1@Myt1l!1.27!17.67!Myt1l;;chr16:91225808..91225824,+!p1@Olig2!1.26!17.22!Olig2;;chr4:150482563..150482655,-!p2@Camta1!1.25!59.36!Camta1;;chr4:22415443..22415506,-!p1@Pou3f2!1.25!16.77!Pou3f2;;chr2:127347042..127347058,-!p3@Kcnip3!1.25!16.77!Kcnip3;;chr12:30220074..30220102,+!p3@Myt1l!1.24!16.31!Myt1l;;chr10:13685585..13685645,+!p2@Hivep2!1.23!54.83!Hivep2;;chr14:70477113..70477173,+!p1@Egr3!1.22!15.41!Egr3;;chr6:108610766..108610781,+!p2@Bhlhe40!1.21!27.19!Bhlhe40;;chr11:98190955..98190968,-!p2@Neurod2!1.20!14.95!Neurod2;;chr7:19895384..19895399,-!p2@Fosb!1.19!20.39!Fosb;;chr15:76352434..76352488,-!p4@Scrt1!1.19!14.50!Scrt1;;chr8:87502608..87502623,-!p1@Junb!1.17!223.40!Junb;;chr3:95032213..95032226,-!p6@Mllt11!1.17!16.31!Mllt11;;chr2:61642558..61642595,+!p3@Tbr1!1.16!13.59!Tbr1;;chr2:77654815..77654872,-!p2@Zfp385b!1.15!16.31!Zfp385b;;chr7:52960700..52960719,+!p2@Dbp!1.15!16.31!Dbp;;chr13:83643031..83643049,+!p11@Mef2c!1.15!13.14!Mef2c;;chr3:95032197..95032208,-!p3@Mllt11!1.14!15.86!Mllt11;;chr12:72149325..72149343,+!p2@Arid4a!1.11!16.77!Arid4a;;chr6:144152648..144152680,-!p5@Sox5!1.11!11.78!Sox5;;chr7:52960730..52960762,+!p3@Dbp!1.09!14.50!Dbp;;chr11:90251852..90251855,-!p4@Hlf!1.09!14.05!Hlf;;chr4:150513630..150513686,-!p4@Camta1!1.07!12.23!Camta1;;chr19:23216132..23216157,+!p3@Klf9!1.06!16.31!Klf9;;chr16:91270091..91270143,+!p2@Olig1!1.06!10.42!Olig1;;chr8:87297878..87297935,-!p3@Nfix!1.05!23.11!Nfix;;chr4:48058047..48058062,+!p1@Nr4a3!1.05!15.86!Nr4a3;;chr18:69680960..69681007,+!p10@Tcf4!1.04!13.14!Tcf4;;chr8:107793688..107793736,+!p1@Hsf4!1.04!13.14!Hsf4;;chr10:84218800..84218829,+!p2@Rfx4!1.04!9.97!Rfx4;;chrX:34442842..34442866,-!p3@Nkrf!1.04!9.97!Nkrf;;chrX:95345005..95345053,+!p1@Ar!1.04!9.97!Ar;;chr7:71083876..71083932,-!p2@Klf13!1.03!78.85!Klf13;;chr9:48644306..48644364,-!p1@Zbtb16!1.03!39.42!Zbtb16;;chr6:117813087..117813121,+!p1@Zfp239!1.03!37.61!Zfp239;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!1.01!97.43!Camta2;;chr8:87297280..87297326,-!p2@Nfix!1.00!21.75!Nfix;;chr7:30094448..30094481,+!p4@Dpf1!1.00!10.88!Dpf1;;chr2:65768149..65768173,+!p4@Csrnp3!1.00!9.06!Csrnp3;;chr14:18493386..18493464,+!p1@Thrb!0.99!34.44!Thrb;;chr7:30092993..30093076,+!p1@Dpf1!0.99!15.41!Dpf1;;chr3:95032184..95032195,-!p4@Mllt11!0.99!10.88!Mllt11;;chr10:67375223..67375240,-!p4@Zfp365!0.99!9.97!Zfp365;;chr10:84218895..84218909,+!p1@Rfx4!0.98!8.61!Rfx4;;chr11:21901608..21901634,-!p1@Otx1!0.98!8.61!Otx1;;chr14:70476975..70476997,+!p2@Egr3!0.98!8.61!Egr3;;chr14:13178361..13178386,-!p2@Fezf2!0.98!8.61!Fezf2;;chr7:146768691..146768707,-!p1@Nkx6-2!0.98!8.61!Nkx6-2;;chr19:19185429..19185440,-!p3@Rorb!0.98!8.61!Rorb;;chr18:36441119..36441158,+!p2@Pura!0.97!20.84!Pura;;chr19:59533221..59533271,+!p1@Emx2!0.97!10.42!Emx2;;chr7:52960780..52960793,+!p5@Dbp!0.97!9.97!Dbp;;chr10:80893711..80893784,-!p3@Nfic!0.96!43.50!Nfic;;chr15:103170533..103170556,-!p1@Zfp385a!0.96!30.81!Zfp385a;;chr11:90252223..90252240,-!p1@Hlf!0.95!67.97!Hlf;;chr13:78339134..78339185,-!p5@Nr2f1!0.95!9.97!Nr2f1;;chr11:23978078..23978096,+!p4@Bcl11a!0.94!24.02!Bcl11a;;chr13:78339428..78339466,-!p2@Nr2f1!0.94!10.88!Nr2f1;;chr13:83643136..83643158,+!p7@Mef2c!0.94!7.70!Mef2c;;chr12:72149359..72149406,+!p4@Arid4a!0.93!9.97!Arid4a;;chr19:23216166..23216191,+!p6@Klf9!0.93!9.97!Klf9;;chr18:69753168..69753186,+!p12@Tcf4!0.92!9.97!Tcf4;;chr11:98636508..98636524,-!p3@Nr1d1!0.92!9.06!Nr1d1;;chr7:91521166..91521194,-!p11@Arnt2!0.92!7.25!Arnt2;;chr11:23980664..23980706,+!p2@Bcl11a!0.91!32.17!Bcl11a;;chr3:34548909..34548927,+!p1@Sox2!0.91!12.23!Sox2;;chr14:118636214..118636235,-!p1@Sox21!0.91!8.61!Sox21;;chr7:91558472..91558512,-!p2@Arnt2!0.90!9.97!Arnt2;;chr8:79423672..79423727,+!p2@Nr3c2!0.90!9.06!Nr3c2;;chr10:13685899..13685916,+!p1@Hivep2!0.89!73.41!Hivep2;;chr7:91520922..91520956,-!p5@Arnt2!0.89!6.80!Arnt2;;chrX:108009761..108009788,+!p1@Pou3f4!0.89!6.80!Pou3f4;;chr2:25562263..25562314,+!p2@Bmyc!0.88!27.19!Bmyc;;chr13:44936126..44936164,+!p6@Jarid2!0.88!7.70!Jarid2;;chr1:39250584..39250643,+!p1@Npas2!0.87!33.99!Npas2;;chr7:19895354..19895369,-!p1@Fosb!0.87!9.06!Fosb;;chr9:91260594..91260612,-!p1@Zic1!0.87!6.34!Zic1;;chr7:91520957..91520973,-!p9@Arnt2!0.87!6.34!Arnt2;;chr2:162769220..162769252,+!p1@L3mbtl1!0.87!6.34!L3mbtl1;;chr14:13178241..13178254,-!p4@Fezf2!0.87!6.34!Fezf2;;chr13:83643159..83643226,+!p3@Mef2c!0.87!6.34!Mef2c;;chr4:48058196..48058205,+!p4@Nr4a3!0.87!6.34!Nr4a3;;chr11:23978111..23978134,+!p3@Bcl11a!0.85!13.14!Bcl11a;;chr7:37483231..37483263,+!p2@Tshz3!0.85!9.52!Tshz3;;chr7:30088977..30089002,+!p2@Dpf1!0.85!8.61!Dpf1;;chr11:98636400..98636418,-!p4@Nr1d1!0.85!8.16!Nr1d1;;chr11:98603119..98603130,+!p2@Thra!0.84!53.47!Thra;;chr15:100430414..100430470,-!p1@Pou6f1!0.84!19.49!Pou6f1;;chr19:23215469..23215494,+!p2@Klf9!0.84!9.52!Klf9;;chr4:48058102..48058110,+!p5@Nr4a3!0.84!6.80!Nr4a3;;chr1:42752654..42752665,+!p@chr1:42752654..42752665,+!0.84!5.89!Pou3f3;;chr12:30220046..30220070,+!p6@Myt1l!0.84!5.89!Myt1l;;chr11:90250894..90250916,-!p5@Hlf!0.84!5.89!Hlf;;chr19:26681865..26681900,+!p6@Smarca2!0.83!17.67!Smarca2;;chr2:115890294..115890334,-!p9@Meis2!0.83!8.16!Meis2;;chr10:13685657..13685677,+!p7@Hivep2!0.83!7.70!Hivep2;;chr4:124334894..124334899,+!p1@Pou3f1!0.83!7.70!Pou3f1;;chr15:81641878..81641921,+!p1@Tef!0.82!154.97!Tef;;chr15:81633165..81633188,+!p2@Tef!0.82!49.39!Tef;;chr9:36954842..36954908,-!p1@Pknox2!0.81!68.88!Pknox2;;chr11:21901587..21901604,-!p2@Otx1!0.81!5.44!Otx1;;chr1:179374764..179374776,+!p5@Zfp238!0.81!5.44!Zfp238;;chr1:57028157..57028173,-!p3@Satb2!0.81!5.44!Satb2;;chr2:163030219..163030258,+!p5@Tox2!0.81!5.44!Tox2;;chr4:150482353..150482386,-!p6@Camta1!0.81!5.44!Camta1;;chr2:77654650..77654685,-!p3@Zfp385b!0.80!6.80!Zfp385b;;chr7:17200307..17200370,-!p2@Grlf1!0.79!41.24!Grlf1;;chr11:98636575..98636607,-!p2@Nr1d1!0.79!20.39!Nr1d1;;chr10:13686815..13686846,+!p3@Hivep2!0.79!12.23!Hivep2;;chr13:83663600..83663625,+!p6@Mef2c!0.79!8.16!Mef2c;;chr12:54349410..54349461,+!p1@Npas3!0.79!6.34!Npas3;;chr4:154335024..154335039,+!p1@Hes5!0.79!6.34!Hes5;;chr1:179372411..179372509,+!p1@Zfp238!0.78!69.33!Zfp238;;chr15:99532568..99532636,+!p2@Smarcd1!0.78!49.85!Smarcd1;;chr4:13670499..13670526,+!p2@Runx1t1!0.78!11.78!Runx1t1;;chr1:57028606..57028625,-!p4@Satb2!0.78!4.98!Satb2;;chr14:76904356..76904367,+!p3@Tsc22d1!0.77!39.42!Tsc22d1;;chr3:95032558..95032641,-!p2@Mllt11!0.77!29.45!Mllt11;;chr2:44972821..44972865,-!p10@Zeb2!0.77!10.42!Zeb2;;chr2:44972869..44972895,-!p12@Zeb2!0.77!9.97!Zeb2;;chr19:23215446..23215457,+!p8@Klf9!0.77!5.89!Klf9;;chr6:6831950..6831985,-!p2@Dlx5!0.77!5.44!Dlx5;;chr11:98603185..98603208,+!p1@Thra!0.76!319.47!Thra;;chr4:119406412..119406439,+!p2@Hivep3!0.76!9.97!Hivep3;;chr19:23215673..23215753,+!p1@Klf9!0.75!73.86!Klf9;;chr9:48644284..48644305,-!p4@Zbtb16!0.75!6.34!Zbtb16;;chr13:78338076..78338104,-!p4@Nr2f1!0.75!5.89!Nr2f1;;chr7:52960555..52960662,+!p1@Dbp!0.74!42.14!Dbp;;chr10:30522690..30522752,-!p2@Ncoa7!0.74!30.36!Ncoa7;;chr19:28085586..28085622,-!p3@Rfx3!0.74!21.30!Rfx3;;chr7:25292160..25292213,+!p3@Zfp428!0.74!12.23!Zfp428;;chr15:103170561..103170572,-!p4@Zfp385a!0.74!6.80!Zfp385a;;chr18:35020615.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Zfp580;;chr7:52963269..52963305,+!p4@Dbp!0.23!1.36!Dbp;;chr13:29045296..29045307,-!p8@Sox4!0.23!0.91!Sox4;;chr17:87153028..87153049,+!p2@Epas1!0.22!30.36!Epas1;;chr15:81977802..81977828,+!p2@Srebf2!0.22!12.23!Srebf2;;chr1:38684260..38684312,-!p2@Aff3!0.22!9.97!Aff3;;chr16:17530781..17530882,-!p2@Thap7!0.22!8.16!Thap7;;chr7:5003165..5003203,+!p2@Zfp580!0.22!7.70!Zfp580;;chr17:84105510..84105540,+!p2@Mta3!0.22!7.25!Mta3;;chr3:32409460..32409483,+!p2@Zfp639!0.22!6.34!Zfp639;;chr7:17200019..17200060,-!p4@Grlf1!0.22!5.89!Grlf1;;chr1:133904217..133904250,+!p5@Elk4!0.22!4.08!Elk4;;chr1:181476392..181476407,-!p2@Tfb2m!0.22!3.17!Tfb2m;;chr18:74427866..74427881,+!p3@Mbd1!0.22!3.17!Mbd1;;chr16:55973899..55973913,+!p7@Rpl24,p7@Zbtb11!0.22!2.72!Zbtb11;;chr19:26681226..26681299,+!p7@Smarca2!0.22!2.72!Smarca2;;chr7:148513637..148513648,-!p6@Deaf1!0.22!1.81!Deaf1;;chr6:115310872..115310899,+!p2@Pparg!0.22!1.81!Pparg;;chr6:98978868..98978918,-!p6@Foxp1!0.22!1.81!Foxp1;;chr13:44826650..44826661,+!p8@Jarid2!0.22!1.81!Jarid2;;chr1:181733834..181733845,-!p3@Ahctf1!0.22!1.81!Ahctf1;;chr9:122775033..122775044,-!p2@Zfp445!0.22!1.81!Zfp445;;chr6:115311270..115311298,+!p1@Pparg!0.22!1.36!Pparg;;chr3:54559550..54559570,+!p4@Smad9!0.22!1.36!Smad9;;chr3:94668075..94668087,+!p6@Pogz!0.22!1.36!Pogz;;chr4:48057987..48057996,+!p7@Nr4a3!0.22!0.91!Nr4a3;;chr5:3648013..3648038,-!p5@Gatad1!0.22!0.91!Gatad1;;chr13:44829403..44829438,+!p11@Jarid2!0.22!0.91!Jarid2;;chr5:138526311..138526375,+!p1@Zkscan1!0.21!52.11!Zkscan1;;chr9:122775056..122775117,-!p1@Zfp445!0.21!49.85!Zfp445;;chr16:3744089..3744145,+!p1@Zfp263!0.21!30.36!Zfp263;;chr15:38230448..38230470,-!p1@Klf10!0.21!29.91!Klf10;;chr7:13404186..13404214,-!p1@Zfp329!0.21!28.55!Zfp329;;chr8:86590723..86590781,+!p1@Rfx1!0.21!26.74!Rfx1;;chr4:151235807..151235870,-!p1@Camta1!0.21!23.11!Camta1;;chr1:136456734..136456757,+!p3@Kdm5b!0.21!17.67!Kdm5b;;chr5:143942400..143942474,-!p1@Rbak!0.21!14.95!Rbak;;chr11:53164378..53164392,+!p2@Aff4!0.21!12.23!Aff4;;chr10:5958538..5958568,+!p1@Zbtb2!0.21!5.89!Zbtb2;;chr17:84105477..84105509,+!p3@Mta3!0.21!4.98!Mta3;;chr4:54960870..54960926,+!p1@Zfp462!0.21!4.53!Zfp462;;chr3:88753953..88754004,+!p1@Ash1l!0.21!4.08!Ash1l;;chr5:110539087..110539133,+!p1@Zfp605!0.21!3.63!Zfp605;;chr13:22036953..22037009,+!p1@Zfp184!0.21!3.17!Zfp184;;chr16:43619101..43619151,+!p6@Zbtb20!0.21!2.72!Zbtb20;;chr8:4613211..4613224,+!p3@Zfp958!0.21!2.27!Zfp958;;chr4:118954858..118954885,-!p5@Ybx1!0.21!1.81!Ybx1;;chr6:83391668..83391678,-!p3@Tet3!0.21!1.36!Tet3;;chr7:91558631..91558652,-!p3@Arnt2!0.21!1.36!Arnt2;;chr11:99092312..99092333,-!p4@Smarce1!0.21!1.36!Smarce1;;chr13:53568104..53568156,-!p1@Msx2!0.21!1.36!Msx2;;chr12:25336286..25336297,+!p2@Klf11!0.21!1.36!Klf11;;chr4:13670441..13670463,+!p8@Runx1t1!0.21!0.91!Runx1t1;;chr4:154011072..154011095,-!p6@Prdm16!0.21!0.91!Prdm16;;chr2:56976467..56976482,-!p4@Nr4a2!0.21!0.91!Nr4a2;;chr1:38684414..38684427,-!p7@Aff3!0.21!0.91!Aff3;;chr5:125538703..125538715,-!p5@Ncor2!0.21!0.91!Ncor2;;chr9:72122748..72122757,+!p4@Zfp280d!0.21!0.91!Zfp280d;;chr9:30838314..30838336,+!p4@Zbtb44!0.21!0.91!Zbtb44;;chr15:81977668..81977705,+!p1@Srebf2!0.20!108.75!Srebf2;;chr13:58503480..58503510,-!p3@Hnrnpk!0.20!73.86!Hnrnpk;;chr3:90097085..90097175,+!p1@Gatad2b!0.20!56.19!Gatad2b;;chr12:41172341..41172385,-!p1@Zfp277!0.20!48.49!Zfp277;;chr3:54611692..54611726,-!p1@Rfxap!0.20!32.17!Rfxap;;chr18:61336648..61336711,-!p1@Hmgxb3!0.20!26.28!Hmgxb3;;chr16:95924005..95924042,+!p2@Ets2!0.20!25.38!Ets2;;chr4:149943647..149943707,+!p2@Rere!0.20!25.38!Rere;;chr9:113840108..113840184,+!p2@Ubp1!0.20!12.69!Ubp1;;chr14:55482892..55482988,-!p1@Homez!0.20!9.06!Homez;;chr15:81977766..81977789,+!p3@Srebf2!0.20!8.16!Srebf2;;chr14:76814736..76814781,+!p4@Tsc22d1!0.20!7.70!Tsc22d1;;
+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 45: @@
 |is_a=EFO:0002091;;FF:0011270
 |is_obsolete=
-|name=visual cortex - wildtype, neonate N60-70, donor2
+|library_id=CNhs13038
+|library_id_phase_based=2:CNhs13038
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;10242
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;10242
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N60-70%252c%2520donor2.CNhs13038.10242-104A8.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%2520donor2.CNhs13038.10242-104A8.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%2520donor2.CNhs13038.10242-104A8.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%2520donor2.CNhs13038.10242-104A8.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%2520donor2.CNhs13038.10242-104A8.mm9.nobarcode.rdna.fa.gz
+|name=visual cortex - wildtype
 |namespace=FANTOM5
 |part_of=
 |profile_cagescan=,,,
 |profile_hcage=CNhs13038,LSID999,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.286570071366746,0,0,0,0,0,0.305276213114552,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.378515830675447,0,0,0,0,0,0,0,0,0,0,0,0,0.638062984050757,-0.278235003245783,0,0,0,0,0,-0.0470145479456583,0.136743932909303,-0.031746630491251,0.887414511565249,0.0103191510678969,0.372806586713801,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,-0.0495424766757029,0.162308177550168,0.372806586713801,0,-0.121288331922096,-0.030462868261138,0.899661584616122,0.0947568497787502,0,0.102499977586267,0.110068036502019,0.167710285683003,0.280187789078248,0,0.106256544902725,0.203557656461916,0.242357998546886,-0.0788315948399074,0,0,0,0,0,0,0.177547622666161,-0.104494861607205,0.141151933063649,0,0,0.891935116888402,0.453317117684587,0
 |rna_box=104
 |rna_catalog_number=N/A
@@ Line 59: / Line 77: @@
 |rna_weight_ug=10.404
 |sample_age=P60-70
+|sample_category=tissues
 |sample_cell_catalog=N/A
 |sample_cell_line=N/A
@@ Line 74: / 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=table111:10242-104A8;search_select_hide=table117:10242-104A8
 }}

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FF:10242-104A8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 13:57, 3 June 2020

CNhs13038

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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