FF:10237-104A3: Difference between revisions

Latest revision as of 13:56, 3 June 2020

Name:	visual cortex - wildtype
Species:	Mouse (Mus musculus)
Library ID:	CNhs13033
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 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

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005460

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13033		CAGE		DRX009134		DRR010008

Accession ID Mm9

Library id		BAM		CTSS
CNhs13033		DRZ001433		DRZ002816

Accession ID Mm10

Library id		BAM		CTSS
CNhs13033		DRZ012783		DRZ014166

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

CNhs13033

0	0
1	0.809
10	0
100	0
1000	0.0342
1001	-0.00595
1002	-0.0468
1003	0.44
1004	0
1005	0
1006	0.666
1007	-0.259
1008	0
1009	-0.177
101	-0.0768
1010	0
1011	0.842
1012	0.587
1013	0.0876
1014	0
1015	-0.113
1016	-0.134
1017	0
1018	0
1019	0
102	0
1020	0.434
1021	0
1022	-0.0704
1023	0
1024	-0.0899
1025	0
1026	0
1027	0.197
1028	0
1029	0.252
103	-0.0848
1030	0
1031	-0.403
1032	0.144
1033	0
1034	0
1035	0
1036	-0.183
1037	0
1038	-0.0391
1039	0.0123
104	0
1040	-0.484
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: CNhs13033

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0264
MA0003.1	MA0003.1	0.246
MA0004.1	MA0004.1	0.528
MA0006.1	MA0006.1	0.0956
MA0007.1	MA0007.1	0.305
MA0009.1	MA0009.1	0.879
MA0014.1	MA0014.1	0.605
MA0017.1	MA0017.1	1.89415e-7
MA0018.2	MA0018.2	0.00771
MA0019.1	MA0019.1	0.109
MA0024.1	MA0024.1	0.0336
MA0025.1	MA0025.1	0.375
MA0027.1	MA0027.1	0.0448
MA0028.1	MA0028.1	0.0275
MA0029.1	MA0029.1	0.539
MA0030.1	MA0030.1	0.37
MA0031.1	MA0031.1	0.0161
MA0035.2	MA0035.2	0.0102
MA0038.1	MA0038.1	0.714
MA0039.2	MA0039.2	0.00224
MA0040.1	MA0040.1	0.0605
MA0041.1	MA0041.1	0.393
MA0042.1	MA0042.1	0.587
MA0043.1	MA0043.1	0.763
MA0046.1	MA0046.1	3.86586e-10
MA0047.2	MA0047.2	2.53641e-4
MA0048.1	MA0048.1	0.0568
MA0050.1	MA0050.1	1.40012e-5
MA0051.1	MA0051.1	7.68255e-4
MA0052.1	MA0052.1	0.997
MA0055.1	MA0055.1	0.00837
MA0057.1	MA0057.1	0.471
MA0058.1	MA0058.1	0.305
MA0059.1	MA0059.1	0.295
MA0060.1	MA0060.1	0.0617
MA0061.1	MA0061.1	0.0557
MA0062.2	MA0062.2	3.3502e-5
MA0065.2	MA0065.2	1.4145e-6
MA0066.1	MA0066.1	0.163
MA0067.1	MA0067.1	0.601
MA0068.1	MA0068.1	0.22
MA0069.1	MA0069.1	0.145
MA0070.1	MA0070.1	0.977
MA0071.1	MA0071.1	0.0404
MA0072.1	MA0072.1	0.109
MA0073.1	MA0073.1	0.826
MA0074.1	MA0074.1	0.104
MA0076.1	MA0076.1	0.0443
MA0077.1	MA0077.1	0.77
MA0078.1	MA0078.1	0.974
MA0079.2	MA0079.2	0.823
MA0080.2	MA0080.2	2.01646e-10
MA0081.1	MA0081.1	0.234
MA0083.1	MA0083.1	0.00221
MA0084.1	MA0084.1	0.614
MA0087.1	MA0087.1	0.572
MA0088.1	MA0088.1	0.331
MA0090.1	MA0090.1	0.14
MA0091.1	MA0091.1	0.338
MA0092.1	MA0092.1	0.298
MA0093.1	MA0093.1	0.514
MA0099.2	MA0099.2	3.67271e-4
MA0100.1	MA0100.1	0.378
MA0101.1	MA0101.1	0.0167
MA0102.2	MA0102.2	0.214
MA0103.1	MA0103.1	0.271
MA0104.2	MA0104.2	0.886
MA0105.1	MA0105.1	0.0916
MA0106.1	MA0106.1	0.0792
MA0107.1	MA0107.1	0.0431
MA0108.2	MA0108.2	1.54453e-4
MA0111.1	MA0111.1	0.766
MA0112.2	MA0112.2	0.00104
MA0113.1	MA0113.1	0.169
MA0114.1	MA0114.1	3.14022e-6
MA0115.1	MA0115.1	2.83795e-4
MA0116.1	MA0116.1	0.163
MA0117.1	MA0117.1	0.738
MA0119.1	MA0119.1	0.115
MA0122.1	MA0122.1	0.511
MA0124.1	MA0124.1	0.962
MA0125.1	MA0125.1	0.267
MA0131.1	MA0131.1	0.808
MA0135.1	MA0135.1	0.148
MA0136.1	MA0136.1	1.38507e-11
MA0137.2	MA0137.2	0.0615
MA0138.2	MA0138.2	0.00328
MA0139.1	MA0139.1	0.391
MA0140.1	MA0140.1	0.0017
MA0141.1	MA0141.1	5.7324e-4
MA0142.1	MA0142.1	0.227
MA0143.1	MA0143.1	0.789
MA0144.1	MA0144.1	0.0404
MA0145.1	MA0145.1	0.0693
MA0146.1	MA0146.1	0.00912
MA0147.1	MA0147.1	0.934
MA0148.1	MA0148.1	5.68554e-4
MA0149.1	MA0149.1	0.5
MA0150.1	MA0150.1	0.118
MA0152.1	MA0152.1	0.954
MA0153.1	MA0153.1	4.45823e-10
MA0154.1	MA0154.1	0.061
MA0155.1	MA0155.1	0.331
MA0156.1	MA0156.1	2.24336e-11
MA0157.1	MA0157.1	0.0229
MA0159.1	MA0159.1	0.0048
MA0160.1	MA0160.1	0.00366
MA0162.1	MA0162.1	0.181
MA0163.1	MA0163.1	0.00392
MA0164.1	MA0164.1	0.772
MA0258.1	MA0258.1	0.0473
MA0259.1	MA0259.1	0.758

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: CNhs13033

Novel motif	Logo	P-value
1	1	0.352
10	10	0.123
100	100	0.476
101	101	0.52
102	102	0.821
103	103	0.198
104	104	0.949
105	105	0.55
106	106	0.0478
107	107	0.16
108	108	0.492
109	109	0.00232
11	11	0.104
110	110	0.0699
111	111	0.451
112	112	0.0191
113	113	0.308
114	114	0.602
115	115	0.794
116	116	0.336
117	117	0.00675
118	118	0.526
119	119	0.189
12	12	0.579
120	120	0.912
121	121	0.144
122	122	0.949
123	123	0.00125
124	124	0.0342
125	125	0.978
126	126	0.0431
127	127	0.684
128	128	0.052
129	129	0.432
13	13	6.9781e-9
130	130	0.0337
131	131	0.447
132	132	0.51
133	133	0.366
134	134	0.0842
135	135	0.234
136	136	0.0014
137	137	0.547
138	138	0.694
139	139	0.988
14	14	0.755
140	140	0.283
141	141	0.659
142	142	0.935
143	143	0.581
144	144	0.666
145	145	6.91146e-4
146	146	0.255
147	147	0.107
148	148	0.759
149	149	0.567
15	15	0.289
150	150	0.0352
151	151	0.748
152	152	0.0632
153	153	0.721
154	154	0.911
155	155	0.5
156	156	1.20876e-14
157	157	0.27
158	158	0.375
159	159	0.216
160	160	0.343
161	161	0.0669
162	162	0.602
163	163	0.787
164	164	0.098
165	165	0.21
166	166	0.656
167	167	0.217
168	168	0.578
169	169	0.00369
17	17	0.0506
18	18	0.821
19	19	0.0628
2	2	0.975
20	20	0.0588
21	21	0.231
22	22	0.0783
23	23	0.648
24	24	0.0131
25	25	0.958
26	26	8.84069e-7
27	27	0.59
28	28	0.639
29	29	0.0487
3	3	0.0525
30	30	0.927
31	31	0.767
32	32	0.873
33	33	0.187
34	34	0.473
35	35	0.497
36	36	0.617
37	37	0.0155
38	38	0.332
39	39	0.224
4	4	0.214
40	40	0.105
41	41	0.61
42	42	0.198
43	43	0.121
44	44	0.899
45	45	0.541
46	46	0.246
47	47	0.527
48	48	0.432
49	49	0.324
5	5	0.458
50	50	0.149
51	51	0.723
52	52	0.168
53	53	0.654
54	54	0.918
55	55	0.858
56	56	0.452
57	57	0.848
58	58	0.412
59	59	0.132
6	6	0.981
60	60	0.0263
61	61	0.0421
62	62	0.367
63	63	0.123
64	64	0.674
65	65	0.263
66	66	0.494
67	67	0.822
68	68	0.275
69	69	0.309
7	7	0.0195
70	70	0.458
71	71	0.0102
72	72	0.518
73	73	0.0164
74	74	0.571
75	75	0.0646
76	76	0.693
77	77	0.345
78	78	0.00316
79	79	0.661
8	8	0.22
80	80	0.971
81	81	0.553
82	82	0.413
83	83	0.03
84	84	0.827
85	85	0.248
86	86	0.162
87	87	0.00253
88	88	0.453
89	89	0.945
9	9	0.354
90	90	0.525
91	91	0.406
92	92	0.547
93	93	0.658
94	94	0.776
95	95	0.0166
96	96	0.572
97	97	0.932
98	98	0.534
99	99	0.411

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: CNhs13033

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011268 mouse visual cortex from wildtype- neonate N15 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)
0000316 (mouse neonate N15 sample)
0011268 (mouse visual cortex from wildtype- neonate N15 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:0007135,UBERON:0007284
+|DRA_sample_Accession=CAGE@SAMD00005460
+|accession_numbers=CAGE;DRX009134;DRR010008;DRZ001433;DRZ002816;DRZ012783;DRZ014166
+|ancestors_in_anatomy_facet=UBERON:0000468,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:0000004,FF:0000303,FF:0000316,FF:0011268
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
+|donor= donor3
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.25!202.23!Olig1;;chr6:55631042..55631102,-!p1@Neurod6!1.95!88.80!Neurod6;;chr10:67375368..67375433,-!p1@Zfp365!1.92!141.51!Zfp365;;chr6:85463580..85463585,-!p1@Egr4!1.92!83.07!Egr4;;chr11:98190918..98190951,-!p1@Neurod2!1.89!76.77!Neurod2;;chr19:4989964..4989972,-!p1@Npas4!1.86!71.61!Npas4;;chr19:19185671..19185693,-!p1@Rorb!1.84!155.83!Rorb;;chr5:138199361..138199441,+!p2@Tsc22d4!1.78!109.42!Tsc22d4;;chr12:30219426..30219506,+!p2@Myt1l!1.74!54.43!Myt1l;;chr7:116154364..116154444,+!p1@Tub!1.73!88.23!Tub;;chr13:83663902..83663927,+!p1@Mef2c!1.72!1152.67!Mef2c;;chr3:95032091..95032183,-!p1@Mllt11!1.72!413.63!Mllt11;;chr13:83663546..83663560,+!p4@Mef2c!1.71!64.74!Mef2c;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.70!61.87!Pou3f3;;chr2:61642631..61642684,+!p1@Tbr1!1.64!42.97!Tbr1;;chr13:83663500..83663519,+!p8@Mef2c!1.62!40.68!Mef2c;;chr13:83663868..83663894,+!p2@Mef2c!1.60!532.22!Mef2c;;chr17:48015839..48015915,-!p3@Foxp4!1.59!44.69!Foxp4;;chrX:90531838..90531861,+!p1@Arx!1.58!45.83!Arx;;chr16:91225808..91225824,+!p1@Olig2!1.56!35.52!Olig2;;chr1:179374784..179374800,+!p2@Zfp238!1.54!38.96!Zfp238;;chr1:57029281..57029326,-!p1@Satb2!1.53!50.99!Satb2;;chr2:65683890..65683907,+!p1@Csrnp3!1.52!60.73!Csrnp3;;chr2:38206580..38206600,+!p2@Lhx2!1.50!37.24!Lhx2;;chr5:122452349..122452377,-!p4@Cux2!1.50!30.94!Cux2;;chr10:67375342..67375365,-!p3@Zfp365!1.50!30.36!Zfp365;;chr2:127347067..127347093,-!p1@Kcnip3!1.47!46.98!Kcnip3;;chr5:98609885..98609900,+!p1@Prdm8!1.46!28.07!Prdm8;;chr2:38206744..38206766,+!p1@Lhx2!1.45!32.66!Lhx2;;chr12:30213247..30213333,+!p1@Myt1l!1.45!27.50!Myt1l;;chr16:91270091..91270143,+!p2@Olig1!1.44!26.35!Olig1;;chr10:13685585..13685645,+!p2@Hivep2!1.43!87.08!Hivep2;;chr15:76352677..76352737,-!p3@Scrt1!1.42!25.21!Scrt1;;chrX:34442872..34442899,-!p1@Nkrf!1.40!30.94!Nkrf;;chr2:61642743..61642758,+!p2@Tbr1!1.40!24.06!Tbr1;;chr2:65768174..65768247,+!p2@Csrnp3!1.35!21.20!Csrnp3;;chr17:25707623..25707639,-!p1@Sox8!1.32!83.07!Sox8;;chr15:76352832..76352900,-!p1@Scrt1!1.32!20.05!Scrt1;;chr4:48058129..48058179,+!p2@Nr4a3!1.31!36.67!Nr4a3;;chr10:67375146..67375208,-!p2@Zfp365!1.31!29.79!Zfp365;;chr13:83643031..83643049,+!p11@Mef2c!1.31!19.48!Mef2c;;chr12:30220074..30220102,+!p3@Myt1l!1.30!18.91!Myt1l;;chr1:57028606..57028625,-!p4@Satb2!1.29!18.33!Satb2;;chr8:24780125..24780143,+!p1@Zmat4!1.28!25.78!Zmat4;;chr8:87297280..87297326,-!p2@Nfix!1.25!38.96!Nfix;;chr5:122499831..122499891,-!p1@Cux2!1.25!25.78!Cux2;;chr11:98190955..98190968,-!p2@Neurod2!1.25!16.61!Neurod2;;chr18:36441119..36441158,+!p2@Pura!1.23!38.38!Pura;;chr18:35020854..35020869,+!p1@Egr1!1.22!580.34!Egr1;;chr4:150482563..150482655,-!p2@Camta1!1.22!55.00!Camta1;;chr4:48058016..48058032,+!p3@Nr4a3!1.22!26.35!Nr4a3;;chr19:19185697..19185711,-!p2@Rorb!1.22!20.05!Rorb;;chr2:79296783..79296801,-!p1@Neurod1!1.22!15.47!Neurod1;;chr12:72149359..72149406,+!p4@Arid4a!1.20!19.48!Arid4a;;chr15:76353005..76353021,-!p2@Scrt1!1.20!14.90!Scrt1;;chr4:22415443..22415506,-!p1@Pou3f2!1.20!14.90!Pou3f2;;chr5:125342568..125342602,+!p2@Zfp664!1.18!22.92!Zfp664;;chr4:58956447..58956510,+!p1@Zkscan16!1.17!29.79!Zkscan16;;chr4:124334894..124334899,+!p1@Pou3f1!1.17!17.76!Pou3f1;;chr14:13178147..13178185,-!p1@Fezf2!1.17!13.75!Fezf2;;chr2:127347094..127347111,-!p2@Kcnip3!1.15!21.77!Kcnip3;;chr1:179374820..179374831,+!p3@Zfp238!1.15!13.18!Zfp238;;chr12:86939997..86940040,+!p4@Jdp2!1.15!13.18!Jdp2;;chr4:154335024..154335039,+!p1@Hes5!1.14!15.47!Hes5;;chr11:23980664..23980706,+!p2@Bcl11a!1.12!53.28!Bcl11a;;chr8:87297878..87297935,-!p3@Nfix!1.12!26.93!Nfix;;chr18:69680960..69681007,+!p10@Tcf4!1.12!16.04!Tcf4;;chr2:61642558..61642595,+!p3@Tbr1!1.11!12.03!Tbr1;;chr15:101097270..101097290,+!p1@Nr4a1!1.09!116.30!Nr4a1;;chr11:23978111..23978134,+!p3@Bcl11a!1.09!23.49!Bcl11a;;chr11:90250944..90250982,-!p2@Hlf!1.09!18.91!Hlf;;chr13:83663600..83663625,+!p6@Mef2c!1.09!17.19!Mef2c;;chr10:13685657..13685677,+!p7@Hivep2!1.09!14.90!Hivep2;;chr11:23978229..23978268,+!p8@Bcl11a!1.08!12.60!Bcl11a;;chr11:98636531..98636559,-!p1@Nr1d1!1.07!61.87!Nr1d1;;chr2:162769220..162769252,+!p1@L3mbtl1!1.07!10.89!L3mbtl1;;chr2:127347042..127347058,-!p3@Kcnip3!1.07!10.89!Kcnip3;;chr3:95032197..95032208,-!p3@Mllt11!1.06!13.18!Mllt11;;chr13:78339134..78339185,-!p5@Nr2f1!1.05!12.60!Nr2f1;;chr6:144152648..144152680,-!p5@Sox5!1.05!10.31!Sox5;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!1.04!105.41!Camta2;;chr2:77654815..77654872,-!p2@Zfp385b!1.04!12.60!Zfp385b;;chr4:135840573..135840601,+!p1@Zfp46!1.03!78.49!Zfp46;;chr3:95032184..95032195,-!p4@Mllt11!1.03!12.03!Mllt11;;chrX:108009761..108009788,+!p1@Pou3f4!1.03!9.74!Pou3f4;;chr12:54349410..54349461,+!p1@Npas3!1.02!11.46!Npas3;;chr17:51971932..51971958,-!p2@Satb1!1.01!12.60!Satb1;;chr7:122968213..122968266,-!p4@Sox6!1.01!10.89!Sox6;;chr9:96631820..96631834,-!p11@Zbtb38!1.01!9.17!Zbtb38;;chr14:34791937..34791977,-!p1@Zfp488!1.01!9.17!Zfp488;;chr14:13178361..13178386,-!p2@Fezf2!1.01!9.17!Fezf2;;chr11:21901608..21901634,-!p1@Otx1!1.01!9.17!Otx1;;chr10:13685899..13685916,+!p1@Hivep2!0.99!93.95!Hivep2;;chr6:117813087..117813121,+!p1@Zfp239!0.99!34.37!Zfp239;;chr3:34548909..34548927,+!p1@Sox2!0.99!14.90!Sox2;;chr11:98603185..98603208,+!p1@Thra!0.98!524.20!Thra;;chr7:148513409..148513455,-!p2@Deaf1!0.98!41.25!Deaf1;;chr1:57028157..57028173,-!p3@Satb2!0.98!8.59!Satb2;;chr2:65768149..65768173,+!p4@Csrnp3!0.98!8.59!Csrnp3;;chr1:179374764..179374776,+!p5@Zfp238!0.98!8.59!Zfp238;;chr4:119487109..119487131,+!p4@Hivep3!0.98!8.59!Hivep3;;chr12:30220046..30220070,+!p6@Myt1l!0.98!8.59!Myt1l;;chrX:34442842..34442866,-!p3@Nkrf!0.98!8.59!Nkrf;;chr7:71083876..71083932,-!p2@Klf13!0.96!66.46!Klf13;;chr7:30088977..30089002,+!p2@Dpf1!0.96!11.46!Dpf1;;chr4:22415290..22415307,-!p2@Pou3f2!0.96!8.02!Pou3f2;;chr14:18493386..18493464,+!p1@Thrb!0.95!30.94!Thrb;;chr9:36954842..36954908,-!p1@Pknox2!0.93!89.94!Pknox2;;chr15:78994907..78994926,-!p1@Sox10!0.93!20.05!Sox10;;chr7:91520922..91520956,-!p5@Arnt2!0.93!7.45!Arnt2;;chr1:57028125..57028149,-!p2@Satb2!0.93!7.45!Satb2;;chr19:28085586..28085622,-!p3@Rfx3!0.92!32.66!Rfx3;;chr19:23215469..23215494,+!p2@Klf9!0.92!11.46!Klf9;;chr12:72149325..72149343,+!p2@Arid4a!0.92!10.31!Arid4a;;chr19:59533221..59533271,+!p1@Emx2!0.92!9.17!Emx2;;chr18:36441100..36441113,+!p3@Pura!0.92!8.59!Pura;;chr10:30522690..30522752,-!p2@Ncoa7!0.91!45.26!Ncoa7;;chr9:48644306..48644364,-!p1@Zbtb16!0.91!29.79!Zbtb16;;chr11:90252223..90252240,-!p1@Hlf!0.90!60.73!Hlf;;chr11:90251852..90251855,-!p4@Hlf!0.90!8.59!Hlf;;chr19:19185429..19185440,-!p3@Rorb!0.90!6.87!Rorb;;chr13:83643302..83643309,+!p12@Mef2c!0.90!6.87!Mef2c;;chr15:76352434..76352488,-!p4@Scrt1!0.90!6.87!Scrt1;;chr6:53018556..53018650,-!p1@Jazf1!0.89!47.55!Jazf1;;chr3:95032558..95032641,-!p2@Mllt11!0.88!38.38!Mllt11;;chr2:56967334..56967366,-!p1@Nr4a2!0.87!13.75!Nr4a2;;chr12:86814833..86814846,+!p1@Fos!0.86!155.25!Fos;;chr11:98603119..98603130,+!p2@Thra!0.86!55.57!Thra;;chr7:91558472..91558512,-!p2@Arnt2!0.86!9.17!Arnt2;;chr10:84218800..84218829,+!p2@Rfx4!0.86!6.30!Rfx4;;chr13:83643159..83643226,+!p3@Mef2c!0.86!6.30!Mef2c;;chr2:65683842..65683856,+!p3@Csrnp3!0.86!6.30!Csrnp3;;chr17:51951383..51951409,-!p19@Satb1!0.86!6.30!Satb1;;chr13:78339428..78339466,-!p2@Nr2f1!0.85!8.59!Nr2f1;;chr19:23215446..23215457,+!p8@Klf9!0.85!7.45!Klf9;;chr3:95032213..95032226,-!p6@Mllt11!0.85!7.45!Mllt11;;chr3:34548946..34548972,+!p2@Sox2!0.85!6.87!Sox2;;chr11:23978078..23978096,+!p4@Bcl11a!0.84!18.91!Bcl11a;;chr15:103170516..103170531,-!p2@Zfp385a!0.84!14.90!Zfp385a;;chr4:13670499..13670526,+!p2@Runx1t1!0.84!13.75!Runx1t1;;chr10:62328047..62328076,-!p3@Tet1!0.84!9.17!Tet1;;chr10:62327990..62328025,-!p2@Tet1!0.83!9.17!Tet1;;chr4:48058047..48058062,+!p1@Nr4a3!0.83!9.17!Nr4a3;;chr8:79423672..79423727,+!p2@Nr3c2!0.83!7.45!Nr3c2;;chr10:42303385..42303401,-!p1@Nr2e1!0.83!5.73!Nr2e1;;chr1:57028556..57028583,-!p5@Satb2!0.83!5.73!Satb2;;chr1:42752654..42752665,+!p@chr1:42752654..42752665,+!0.83!5.73!Pou3f3;;chr6:85137505..85137517,+!p2@Emx1!0.83!5.73!Emx1;;chr6:55631251..55631265,-!p2@Neurod6!0.83!5.73!Neurod6;;chr7:148008023..148008092,-!p1@Zfp941!0.82!14.32!Zfp941;;chr7:30094448..30094481,+!p4@Dpf1!0.82!6.87!Dpf1;;chr19:23215673..23215753,+!p1@Klf9!0.81!84.79!Klf9;;chr1:39250584..39250643,+!p1@Npas2!0.81!29.79!Npas2;;chr6:144157924..144157955,-!p2@Sox5!0.81!6.87!Sox5;;chr1:179372411..179372509,+!p1@Zfp238!0.80!73.33!Zfp238;;chr19:23216132..23216157,+!p3@Klf9!0.80!8.59!Klf9;;chr19:23215509..23215523,+!p4@Klf9!0.80!6.87!Klf9;;chr11:98614826..98614845,+!p9@Thra!0.80!6.87!Thra;;chr11:98603160..98603171,+!p3@Thra!0.79!26.35!Thra;;chr2:25562263..25562314,+!p2@Bmyc!0.79!21.77!Bmyc;;chr7:25292160..25292213,+!p3@Zfp428!0.79!13.75!Zfp428;;chr10:67000609..67000625,+!p1@Egr2!0.79!12.60!Egr2;;chr2:71384458..71384526,-!p2@Dlx2!0.79!5.16!Dlx2;;chr12:50485973..50486015,+!p2@Foxg1!0.79!5.16!Foxg1;;chr13:83643136..83643158,+!p7@Mef2c!0.79!5.16!Mef2c;;chr12:50483639..50483654,+!p1@Foxg1!0.79!5.16!Foxg1;;chr15:76352740..76352781,-!p5@Scrt1!0.79!5.16!Scrt1;;chr7:146768691..146768707,-!p1@Nkx6-2!0.79!5.16!Nkx6-2;;chr7:91521166..91521194,-!p11@Arnt2!0.79!5.16!Arnt2;;chr15:81641878..81641921,+!p1@Tef!0.78!142.08!Tef;;chrX:45245644..45245666,-!p2@Smarca1!0.78!17.19!Smarca1;;chr1:189821714..189821761,+!p1@Esrrg!0.78!9.74!Esrrg;;chr7:30092993..30093076,+!p1@Dpf1!0.78!9.17!Dpf1;;chr19:28085485..28085544,-!p5@Rfx3!0.77!21.20!Rfx3;;chr5:3648045..3648074,-!p2@Gatad1!0.77!8.59!Gatad1;;chr18:69753168..69753186,+!p12@Tcf4!0.77!6.87!Tcf4;;chr17:27693865..27693877,+!p8@Hmga1-rs1,p9@Hmga1!0.75!8.02!Hmga1;;chr7:91558537..91558558,-!p4@Arnt2!0.75!5.73!Arnt2;;chr1:179374862..179374873,+!p6@Zfp238!0.75!4.58!Zfp238;;chr1:57029027..57029056,-!p7@Satb2!0.75!4.58!Satb2;;chr1:57028594..57028604,-!p10@Satb2!0.75!4.58!Satb2;;chr13:78339096..78339116,-!p12@Nr2f1!0.75!4.58!Nr2f1;;chr14:13178323..13178347,-!p3@Fezf2!0.75!4.58!Fezf2;;chr13:83643232..83643254,+!p5@Mef2c!0.75!4.58!Mef2c;;chr11:90250894..90250916,-!p5@H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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:10237-104A3
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011268
+|is_a=EFO:0002091;;FF:0011268
-|name=visual cortex - wildtype, neonate N15, donor3
+|is_obsolete=
+|library_id=CNhs13033
+|library_id_phase_based=2:CNhs13033
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;10237
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;10237
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor3.CNhs13033.10237-104A3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor3.CNhs13033.10237-104A3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor3.CNhs13033.10237-104A3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor3.CNhs13033.10237-104A3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N15%252c%2520donor3.CNhs13033.10237-104A3.mm9.nobarcode.rdna.fa.gz
+|name=visual cortex - wildtype
 |namespace=FANTOM5
 |part_of=
 |profile_cagescan=,,,
 |profile_hcage=CNhs13033,LSID999,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.34557214567236,0,0,0,0,0,0.358980707152115,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.13969407397359,0,0,0,0,0,0,0,0,0,0,0,0,0.659226585696921,-0.558422792324031,0,0,0,0,0,-0.209322725495826,0.150156760405983,0.116743483271537,1.23886824897147,-0.269868638010351,0.331587424856164,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0428469550828748,0,-0.0726960239896975,0.382973280977661,0.746880393378071,0,-0.10409248387501,-0.310650657339386,0.993480945169588,0.061757227825316,0,0.0190120621523582,0.104037018085932,0,0.196699873644339,0,0.159108892805817,0.208794856026609,0.519056391146607,-0.0788315948399074,0,0,0,0,0,0,0.328928477474124,0.132877911289549,0.317287788385361,0,0,0.827947632634613,0.434359137099159,0
 |rna_box=104
 |rna_catalog_number=N/A
@@ Line 57: / Line 77: @@
 |rna_weight_ug=10.32
 |sample_age=P15
+|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 N15
+|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=table111:10237-104A3;search_select_hide=table117:10237-104A3
 }}

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FF:10237-104A3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 13:56, 3 June 2020

CNhs13033

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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