FF:10243-104A9: Difference between revisions

Latest revision as of 13:57, 3 June 2020

Name:	visual cortex - wildtype
Species:	Mouse (Mus musculus)
Library ID:	CNhs13039
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		SAMD00004914

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13039		CAGE		DRX009141		DRR010015

Accession ID Mm9

Library id		BAM		CTSS
CNhs13039		DRZ001440		DRZ002823

Accession ID Mm10

Library id		BAM		CTSS
CNhs13039		DRZ012790		DRZ014173

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

CNhs13039

0	0
1	0.834
10	0
100	0
1000	-0.0355
1001	0.0737
1002	-0.0873
1003	0.399
1004	0
1005	0
1006	0.668
1007	-0.174
1008	0
1009	-0.19
101	-0.104
1010	0
1011	0.884
1012	0.487
1013	0.092
1014	0
1015	-0.205
1016	-0.37
1017	0
1018	0
1019	0
102	0
1020	0.487
1021	0
1022	-0.0464
1023	0
1024	0
1025	0
1026	0
1027	0.261
1028	0
1029	0.126
103	-0.0848
1030	0
1031	-0.528
1032	0.125
1033	0
1034	0
1035	0
1036	-0.183
1037	0
1038	0.0983
1039	0.0942
104	0
1040	-0.134
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: CNhs13039

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0239
MA0003.1	MA0003.1	0.239
MA0004.1	MA0004.1	0.614
MA0006.1	MA0006.1	0.0955
MA0007.1	MA0007.1	0.365
MA0009.1	MA0009.1	0.824
MA0014.1	MA0014.1	0.614
MA0017.1	MA0017.1	6.06206e-7
MA0018.2	MA0018.2	0.00207
MA0019.1	MA0019.1	0.084
MA0024.1	MA0024.1	0.0184
MA0025.1	MA0025.1	0.0288
MA0027.1	MA0027.1	0.0711
MA0028.1	MA0028.1	0.0316
MA0029.1	MA0029.1	0.8
MA0030.1	MA0030.1	0.422
MA0031.1	MA0031.1	0.0273
MA0035.2	MA0035.2	0.0156
MA0038.1	MA0038.1	0.454
MA0039.2	MA0039.2	0.00224
MA0040.1	MA0040.1	0.0475
MA0041.1	MA0041.1	0.438
MA0042.1	MA0042.1	0.416
MA0043.1	MA0043.1	0.132
MA0046.1	MA0046.1	9.4658e-11
MA0047.2	MA0047.2	3.35562e-4
MA0048.1	MA0048.1	0.0718
MA0050.1	MA0050.1	5.64718e-6
MA0051.1	MA0051.1	4.69052e-4
MA0052.1	MA0052.1	0.676
MA0055.1	MA0055.1	0.00975
MA0057.1	MA0057.1	0.495
MA0058.1	MA0058.1	0.38
MA0059.1	MA0059.1	0.283
MA0060.1	MA0060.1	0.00427
MA0061.1	MA0061.1	0.0409
MA0062.2	MA0062.2	1.28257e-4
MA0065.2	MA0065.2	3.87464e-6
MA0066.1	MA0066.1	0.0879
MA0067.1	MA0067.1	0.394
MA0068.1	MA0068.1	0.166
MA0069.1	MA0069.1	0.0976
MA0070.1	MA0070.1	0.957
MA0071.1	MA0071.1	0.0621
MA0072.1	MA0072.1	0.149
MA0073.1	MA0073.1	0.81
MA0074.1	MA0074.1	0.185
MA0076.1	MA0076.1	0.0694
MA0077.1	MA0077.1	0.928
MA0078.1	MA0078.1	0.967
MA0079.2	MA0079.2	0.924
MA0080.2	MA0080.2	2.64054e-10
MA0081.1	MA0081.1	0.175
MA0083.1	MA0083.1	0.00186
MA0084.1	MA0084.1	0.347
MA0087.1	MA0087.1	0.682
MA0088.1	MA0088.1	0.223
MA0090.1	MA0090.1	0.174
MA0091.1	MA0091.1	0.444
MA0092.1	MA0092.1	0.285
MA0093.1	MA0093.1	0.639
MA0099.2	MA0099.2	0.00505
MA0100.1	MA0100.1	0.313
MA0101.1	MA0101.1	0.0104
MA0102.2	MA0102.2	0.358
MA0103.1	MA0103.1	0.458
MA0104.2	MA0104.2	0.924
MA0105.1	MA0105.1	0.0479
MA0106.1	MA0106.1	0.0541
MA0107.1	MA0107.1	0.0195
MA0108.2	MA0108.2	6.18179e-6
MA0111.1	MA0111.1	0.592
MA0112.2	MA0112.2	0.00162
MA0113.1	MA0113.1	0.129
MA0114.1	MA0114.1	4.24064e-6
MA0115.1	MA0115.1	4.38193e-4
MA0116.1	MA0116.1	0.177
MA0117.1	MA0117.1	0.751
MA0119.1	MA0119.1	0.0808
MA0122.1	MA0122.1	0.789
MA0124.1	MA0124.1	0.89
MA0125.1	MA0125.1	0.46
MA0131.1	MA0131.1	0.669
MA0135.1	MA0135.1	0.0966
MA0136.1	MA0136.1	1.09683e-12
MA0137.2	MA0137.2	0.128
MA0138.2	MA0138.2	0.00883
MA0139.1	MA0139.1	0.573
MA0140.1	MA0140.1	0.00163
MA0141.1	MA0141.1	0.00255
MA0142.1	MA0142.1	0.379
MA0143.1	MA0143.1	0.406
MA0144.1	MA0144.1	0.11
MA0145.1	MA0145.1	0.0975
MA0146.1	MA0146.1	0.0108
MA0147.1	MA0147.1	0.952
MA0148.1	MA0148.1	2.75743e-4
MA0149.1	MA0149.1	0.23
MA0150.1	MA0150.1	0.177
MA0152.1	MA0152.1	0.452
MA0153.1	MA0153.1	5.12675e-10
MA0154.1	MA0154.1	0.0765
MA0155.1	MA0155.1	0.301
MA0156.1	MA0156.1	7.41177e-12
MA0157.1	MA0157.1	0.0288
MA0159.1	MA0159.1	0.00858
MA0160.1	MA0160.1	0.00535
MA0162.1	MA0162.1	0.189
MA0163.1	MA0163.1	0.00608
MA0164.1	MA0164.1	0.841
MA0258.1	MA0258.1	0.0547
MA0259.1	MA0259.1	0.856

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: CNhs13039

Novel motif	Logo	P-value
1	1	0.386
10	10	0.0881
100	100	0.483
101	101	0.467
102	102	0.978
103	103	0.0839
104	104	0.969
105	105	0.603
106	106	0.0677
107	107	0.258
108	108	0.351
109	109	0.00251
11	11	0.103
110	110	0.051
111	111	0.369
112	112	0.00969
113	113	0.399
114	114	0.748
115	115	0.922
116	116	0.245
117	117	0.00431
118	118	0.55
119	119	0.22
12	12	0.821
120	120	0.739
121	121	0.159
122	122	0.99
123	123	3.99086e-4
124	124	0.0289
125	125	0.528
126	126	0.0385
127	127	0.602
128	128	0.0747
129	129	0.306
13	13	5.06591e-9
130	130	0.0423
131	131	0.423
132	132	0.532
133	133	0.31
134	134	0.0645
135	135	0.298
136	136	0.0144
137	137	0.483
138	138	0.703
139	139	0.955
14	14	0.941
140	140	0.379
141	141	0.862
142	142	0.655
143	143	0.566
144	144	0.557
145	145	7.99265e-5
146	146	0.126
147	147	0.0755
148	148	0.56
149	149	0.537
15	15	0.293
150	150	0.0463
151	151	0.785
152	152	0.0681
153	153	0.989
154	154	0.852
155	155	0.331
156	156	0.127
157	157	0.192
158	158	0.351
159	159	0.354
160	160	0.242
161	161	0.107
162	162	0.623
163	163	0.907
164	164	0.145
165	165	0.0503
166	166	0.644
167	167	0.168
168	168	0.676
169	169	0.00476
17	17	0.074
18	18	0.7
19	19	0.0641
2	2	0.894
20	20	0.0443
21	21	0.258
22	22	0.0854
23	23	0.814
24	24	0.00747
25	25	0.906
26	26	2.27727e-7
27	27	0.446
28	28	0.631
29	29	0.0416
3	3	0.0516
30	30	0.979
31	31	0.754
32	32	0.793
33	33	0.232
34	34	0.493
35	35	0.42
36	36	0.419
37	37	0.0194
38	38	0.525
39	39	0.225
4	4	0.352
40	40	0.104
41	41	0.551
42	42	0.19
43	43	0.149
44	44	0.771
45	45	0.576
46	46	0.271
47	47	0.489
48	48	0.339
49	49	0.393
5	5	0.28
50	50	0.146
51	51	0.754
52	52	0.159
53	53	0.599
54	54	0.936
55	55	0.971
56	56	0.494
57	57	0.877
58	58	0.431
59	59	0.152
6	6	0.999
60	60	0.0309
61	61	0.0318
62	62	0.353
63	63	0.121
64	64	0.708
65	65	0.48
66	66	0.451
67	67	0.953
68	68	0.196
69	69	0.251
7	7	0.0143
70	70	0.45
71	71	0.00754
72	72	0.587
73	73	0.023
74	74	0.866
75	75	0.0558
76	76	0.844
77	77	0.38
78	78	0.00115
79	79	0.657
8	8	0.173
80	80	0.776
81	81	0.66
82	82	0.368
83	83	0.0472
84	84	0.967
85	85	0.21
86	86	0.204
87	87	0.0118
88	88	0.591
89	89	0.968
9	9	0.377
90	90	0.553
91	91	0.184
92	92	0.527
93	93	0.311
94	94	0.941
95	95	0.0173
96	96	0.633
97	97	0.921
98	98	0.608
99	99	0.417

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: CNhs13039

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@SAMD00004914
+|accession_numbers=CAGE;DRX009141;DRR010015;DRZ001440;DRZ002823;DRZ012790;DRZ014173
+|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= donor3
 |expression_enrichment_score=chr19:4989964..4989972,-!p1@Npas4!2.21!160.51!Npas4;;chr6:85463580..85463585,-!p1@Egr4!2.18!150.67!Egr4;;chr10:67375368..67375433,-!p1@Zfp365!2.15!239.21!Zfp365;;chr16:91270004..91270023,+!p1@Olig1!1.97!104.59!Olig1;;chr11:98190918..98190951,-!p1@Neurod2!1.85!69.38!Neurod2;;chr6:55631042..55631102,-!p1@Neurod6!1.78!59.54!Neurod6;;chr19:19185671..19185693,-!p1@Rorb!1.77!133.58!Rorb;;chr7:116154364..116154444,+!p1@Tub!1.75!92.68!Tub;;chr2:61642631..61642684,+!p1@Tbr1!1.74!53.85!Tbr1;;chr10:67375342..67375365,-!p3@Zfp365!1.71!50.74!Zfp365;;chr12:30219426..30219506,+!p2@Myt1l!1.71!49.70!Myt1l;;chr2:127347067..127347093,-!p1@Kcnip3!1.68!76.11!Kcnip3;;chr17:48015839..48015915,-!p3@Foxp4!1.67!53.85!Foxp4;;chr15:101097270..101097290,+!p1@Nr4a1!1.64!412.14!Nr4a1;;chr13:83663546..83663560,+!p4@Mef2c!1.60!50.22!Mef2c;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.60!48.15!Pou3f3;;chr5:138199361..138199441,+!p2@Tsc22d4!1.59!69.38!Tsc22d4;;chr8:24780125..24780143,+!p1@Zmat4!1.58!52.81!Zmat4;;chr5:122452349..122452377,-!p4@Cux2!1.58!37.28!Cux2;;chr10:67375146..67375208,-!p2@Zfp365!1.57!54.36!Zfp365;;chrX:90531838..90531861,+!p1@Arx!1.56!43.49!Arx;;chr4:48058129..48058179,+!p2@Nr4a3!1.53!61.61!Nr4a3;;chr3:95032091..95032183,-!p1@Mllt11!1.51!256.29!Mllt11;;chr1:57029281..57029326,-!p1@Satb2!1.49!45.56!Satb2;;chrX:34442872..34442899,-!p1@Nkrf!1.49!38.31!Nkrf;;chr2:65683890..65683907,+!p1@Csrnp3!1.48!54.88!Csrnp3;;chr18:35020854..35020869,+!p1@Egr1!1.46!1018.43!Egr1;;chr2:65768174..65768247,+!p2@Csrnp3!1.46!27.96!Csrnp3;;chr15:76353005..76353021,-!p2@Scrt1!1.46!27.96!Scrt1;;chr11:98636531..98636559,-!p1@Nr1d1!1.45!149.63!Nr1d1;;chr5:98609885..98609900,+!p1@Prdm8!1.45!26.92!Prdm8;;chr13:83663902..83663927,+!p1@Mef2c!1.44!609.40!Mef2c;;chr19:19185697..19185711,-!p2@Rorb!1.44!33.65!Rorb;;chr15:76352677..76352737,-!p3@Scrt1!1.44!26.41!Scrt1;;chr2:38206580..38206600,+!p2@Lhx2!1.43!32.10!Lhx2;;chr10:67000609..67000625,+!p1@Egr2!1.40!54.88!Egr2;;chr4:58956447..58956510,+!p1@Zkscan16!1.39!50.74!Zkscan16;;chr13:83663868..83663894,+!p2@Mef2c!1.38!315.32!Mef2c;;chr13:83663500..83663519,+!p8@Mef2c!1.38!22.78!Mef2c;;chr5:122499831..122499891,-!p1@Cux2!1.37!34.17!Cux2;;chr2:38206744..38206766,+!p1@Lhx2!1.36!26.41!Lhx2;;chr12:86939997..86940040,+!p4@Jdp2!1.36!21.75!Jdp2;;chr7:148008023..148008092,-!p1@Zfp941!1.32!47.12!Zfp941;;chr2:127347094..127347111,-!p2@Kcnip3!1.31!31.58!Kcnip3;;chr2:61642743..61642758,+!p2@Tbr1!1.29!18.64!Tbr1;;chr12:30213247..30213333,+!p1@Myt1l!1.29!18.64!Myt1l;;chr12:86814833..86814846,+!p1@Fos!1.27!399.19!Fos;;chr3:95032197..95032208,-!p3@Mllt11!1.27!21.75!Mllt11;;chr1:179374784..179374800,+!p2@Zfp238!1.24!19.16!Zfp238;;chr2:127347042..127347058,-!p3@Kcnip3!1.24!16.57!Kcnip3;;chr13:83643031..83643049,+!p11@Mef2c!1.24!16.57!Mef2c;;chr4:150482563..150482655,-!p2@Camta1!1.23!55.92!Camta1;;chr7:52960700..52960719,+!p2@Dbp!1.21!18.64!Dbp;;chr14:13178147..13178185,-!p1@Fezf2!1.19!14.50!Fezf2;;chr4:22415443..22415506,-!p1@Pou3f2!1.19!14.50!Pou3f2;;chr17:25707623..25707639,-!p1@Sox8!1.17!58.51!Sox8;;chr18:36441119..36441158,+!p2@Pura!1.17!33.14!Pura;;chr10:13685585..13685645,+!p2@Hivep2!1.16!46.08!Hivep2;;chr3:95032213..95032226,-!p6@Mllt11!1.16!16.05!Mllt11;;chr16:91225808..91225824,+!p1@Olig2!1.16!13.46!Olig2;;chr11:98190955..98190968,-!p2@Neurod2!1.16!13.46!Neurod2;;chr2:61642558..61642595,+!p3@Tbr1!1.14!12.94!Tbr1;;chr15:76352434..76352488,-!p4@Scrt1!1.14!12.94!Scrt1;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!1.13!129.96!Camta2;;chr8:87297878..87297935,-!p3@Nfix!1.13!27.96!Nfix;;chr12:30220074..30220102,+!p3@Myt1l!1.13!12.43!Myt1l;;chr2:65768149..65768173,+!p4@Csrnp3!1.13!12.43!Csrnp3;;chr4:48058016..48058032,+!p3@Nr4a3!1.12!20.71!Nr4a3;;chrX:95345005..95345053,+!p1@Ar!1.11!11.91!Ar;;chr8:87502608..87502623,-!p1@Junb!1.09!182.77!Junb;;chr14:18493386..18493464,+!p1@Thrb!1.09!42.97!Thrb;;chrX:108009761..108009788,+!p1@Pou3f4!1.09!11.39!Pou3f4;;chr9:48644306..48644364,-!p1@Zbtb16!1.08!44.53!Zbtb16;;chr2:77654815..77654872,-!p2@Zfp385b!1.07!13.46!Zfp385b;;chr4:154335024..154335039,+!p1@Hes5!1.07!12.94!Hes5;;chr7:30092993..30093076,+!p1@Dpf1!1.06!18.12!Dpf1;;chr11:90250944..90250982,-!p2@Hlf!1.06!17.60!Hlf;;chr7:19895384..19895399,-!p2@Fosb!1.06!15.02!Fosb;;chr14:70476975..70476997,+!p2@Egr3!1.06!10.36!Egr3;;chr18:69680960..69681007,+!p10@Tcf4!1.05!13.46!Tcf4;;chr12:72149325..72149343,+!p2@Arid4a!1.04!13.98!Arid4a;;chr14:13178361..13178386,-!p2@Fezf2!1.03!9.84!Fezf2;;chr2:162769220..162769252,+!p1@L3mbtl1!1.03!9.84!L3mbtl1;;chr7:91520922..91520956,-!p5@Arnt2!1.03!9.84!Arnt2;;chr11:23978111..23978134,+!p3@Bcl11a!1.02!20.19!Bcl11a;;chr10:13685657..13685677,+!p7@Hivep2!1.02!12.43!Hivep2;;chr4:150513630..150513686,-!p4@Camta1!1.02!10.87!Camta1;;chr19:23216132..23216157,+!p3@Klf9!1.01!14.50!Klf9;;chr11:98636508..98636524,-!p3@Nr1d1!1.01!11.39!Nr1d1;;chr1:179374764..179374776,+!p5@Zfp238!1.01!9.32!Zfp238;;chr6:117813087..117813121,+!p1@Zfp239!1.00!34.69!Zfp239;;chr8:107793688..107793736,+!p1@Hsf4!1.00!11.91!Hsf4;;chr12:54349410..54349461,+!p1@Npas3!1.00!10.87!Npas3;;chr2:56967334..56967366,-!p1@Nr4a2!0.99!18.12!Nr4a2;;chr19:59533221..59533271,+!p1@Emx2!0.99!10.87!Emx2;;chr13:78339134..78339185,-!p5@Nr2f1!0.99!10.87!Nr2f1;;chr14:70477113..70477173,+!p1@Egr3!0.99!8.80!Egr3;;chr11:21901608..21901634,-!p1@Otx1!0.99!8.80!Otx1;;chr10:80893711..80893784,-!p3@Nfic!0.98!46.08!Nfic;;chr7:52960730..52960762,+!p3@Dbp!0.98!10.87!Dbp;;chr7:91521166..91521194,-!p11@Arnt2!0.97!8.28!Arnt2;;chr8:87297280..87297326,-!p2@Nfix!0.96!19.67!Nfix;;chr12:72149359..72149406,+!p4@Arid4a!0.96!10.87!Arid4a;;chr2:25562263..25562314,+!p2@Bmyc!0.95!31.58!Bmyc;;chr11:90251852..90251855,-!p4@Hlf!0.95!9.84!Hlf;;chr7:52960780..52960793,+!p5@Dbp!0.95!9.32!Dbp;;chr9:48644284..48644305,-!p4@Zbtb16!0.94!10.36!Zbtb16;;chr16:91270091..91270143,+!p2@Olig1!0.94!7.77!Olig1;;chr11:90252223..90252240,-!p1@Hlf!0.93!64.72!Hlf;;chr7:71083876..71083932,-!p2@Klf13!0.93!61.61!Klf13;;chr11:23978078..23978096,+!p4@Bcl11a!0.93!23.82!Bcl11a;;chr15:103170533..103170556,-!p1@Zfp385a!0.92!27.96!Zfp385a;;chr7:130644017..130644092,-!p1@Zkscan2!0.92!14.50!Zkscan2;;chr7:30088977..30089002,+!p2@Dpf1!0.92!10.36!Dpf1;;chr14:118636214..118636235,-!p1@Sox21!0.92!8.80!Sox21;;chr11:90252108..90252134,-!p6@Hlf!0.92!7.25!Hlf;;chr11:90250894..90250916,-!p5@Hlf!0.92!7.25!Hlf;;chr7:91558472..91558512,-!p2@Arnt2!0.91!10.36!Arnt2;;chr9:68501522..68501538,+!p4@Rora!0.90!13.46!Rora;;chr7:37483231..37483263,+!p2@Tshz3!0.90!10.87!Tshz3;;chr11:98636400..98636418,-!p4@Nr1d1!0.90!9.32!Nr1d1;;chr11:23980664..23980706,+!p2@Bcl11a!0.89!31.07!Bcl11a;;chr7:91520957..91520973,-!p9@Arnt2!0.89!6.73!Arnt2;;chr1:179374820..179374831,+!p3@Zfp238!0.89!6.73!Zfp238;;chr13:83643136..83643158,+!p7@Mef2c!0.89!6.73!Mef2c;;chr3:34548909..34548927,+!p1@Sox2!0.88!11.39!Sox2;;chr6:108610766..108610781,+!p2@Bhlhe40!0.87!11.91!Bhlhe40;;chr5:125342568..125342602,+!p2@Zfp664!0.87!10.87!Zfp664;;chr7:17200307..17200370,-!p2@Grlf1!0.86!48.15!Grlf1;;chr19:26681865..26681900,+!p6@Smarca2!0.86!19.16!Smarca2;;chr2:115890294..115890334,-!p9@Meis2!0.86!8.80!Meis2;;chr13:78339428..78339466,-!p2@Nr2f1!0.86!8.80!Nr2f1;;chr3:95032184..95032195,-!p4@Mllt11!0.86!7.77!Mllt11;;chr18:36441100..36441113,+!p3@Pura!0.86!7.25!Pura;;chr1:57028556..57028583,-!p5@Satb2!0.86!6.21!Satb2;;chr1:57028606..57028625,-!p4@Satb2!0.86!6.21!Satb2;;chr6:85137520..85137563,+!p1@Emx1!0.86!6.21!Emx1;;chrX:34442842..34442866,-!p3@Nkrf!0.86!6.21!Nkrf;;chr15:81641878..81641921,+!p1@Tef!0.85!168.79!Tef;;chr9:36954842..36954908,-!p1@Pknox2!0.85!75.59!Pknox2;;chr11:98603119..98603130,+!p2@Thra!0.85!54.36!Thra;;chr15:99532568..99532636,+!p2@Smarcd1!0.84!57.99!Smarcd1;;chr13:83663600..83663625,+!p6@Mef2c!0.84!9.32!Mef2c;;chr7:52960555..52960662,+!p1@Dbp!0.83!52.81!Dbp;;chr3:95032558..95032641,-!p2@Mllt11!0.83!34.17!Mllt11;;chr4:119487109..119487131,+!p4@Hivep3!0.83!5.70!Hivep3;;chr2:71367871..71367898,+!p1@Dlx1!0.83!5.70!Dlx1;;chr7:52960888..52960902,+!p7@Dbp!0.83!5.70!Dbp;;chr12:50483639..50483654,+!p1@Foxg1!0.83!5.70!Foxg1;;chr2:163051181..163051205,+!p2@Tox2!0.83!5.70!Tox2;;chr10:82226613..82226641,-!p4@Nfyb!0.82!16.05!Nfyb;;chr3:34548946..34548972,+!p2@Sox2!0.82!6.21!Sox2;;chr10:13685899..13685916,+!p1@Hivep2!0.81!61.10!Hivep2;;chr7:30094448..30094481,+!p4@Dpf1!0.81!6.73!Dpf1;;chr11:70501599..70501634,-!p2@Camta2,p2@LOC100048818!0.80!11.39!Camta2;;chr16:95923651..95923701,+!p3@Ets2!0.80!8.80!Ets2;;chr19:23216166..23216191,+!p6@Klf9!0.80!7.25!Klf9;;chr14:76904356..76904367,+!p3@Tsc22d1!0.79!40.90!Tsc22d1;;chr8:112603610..112603656,+!p1@Zfp612!0.79!25.89!Zfp612;;chr11:98636575..98636607,-!p2@Nr1d1!0.79!20.19!Nr1d1;;chr2:44972821..44972865,-!p10@Zeb2!0.79!10.87!Zeb2;;chr15:103170561..103170572,-!p4@Zfp385a!0.79!7.77!Zfp385a;;chr8:79423672..79423727,+!p2@Nr3c2!0.79!6.73!Nr3c2;;chr15:76352740..76352781,-!p5@Scrt1!0.79!5.18!Scrt1;;chr13:83643302..83643309,+!p12@Mef2c!0.79!5.18!Mef2c;;chr2:163030186..163030204,+!p4@Tox2!0.79!5.18!Tox2;;chr1:57028157..57028173,-!p3@Satb2!0.79!5.18!Satb2;;chr19:19185429..19185440,-!p3@Rorb!0.79!5.18!Rorb;;chr6:144152648..144152680,-!p5@Sox5!0.79!5.18!Sox5;;chr6:72850124..72850210,-!p7@Kcmf1!0.78!6.73!Kcmf1;;chr2:37278526..37278575,-!p2@Rc3h2!0.77!22.26!Rc3h2;;chrX:45245644..45245666,-!p2@Smarca1!0.77!17.09!Smarca1;;chr13:44936126..44936164,+!p6@Jarid2!0.77!5.70!Jarid2;;chr11:98603185..98603208,+!p1@Thra!0.76!317.90!Thra;;chr17:51971932..51971958,-!p2@Satb1!0.76!6.73!Satb1;;chr4:48057987..48057996,+!p7@Nr4a3!0.76!5.70!Nr4a3;;chr2:81893447..81893468,+!p2@Zfp804a!0.75!4.66!Zfp804a;;chr3:17954496..17954515,+!p3@Bhlhe22!0.75!4.66!Bhlhe22;;chr2:81893535..81893548,+!p1@Zfp804a!0.75!4.66!Zfp804a;;chr4:48058196..48058205,+!p4@Nr4a3!0.75!4.66!Nr4a3;;chr15:95485240..95485257,-!p1@Dbx2!0.75!4.66!Dbx2;;chr17:51972603..51972624,-!p9@Satb1!0.75!4.66!Satb1;;chr15:76352832..76352900,-!p1@Scrt1!0.75!4.66!Scrt1;;chr13:83643232..83643254,+!p5@Mef2c!0.75!4.66!Mef2c;;chr13:83643159..83643226,+!p3@Mef2c!0.75!4.66!Mef2c;;chr8:123958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c3h3!0.22!16.57!Zc3h3;;chr9:55785900..55785950,-!p1@Scaper!0.22!14.50!Scaper;;chr9:113840108..113840184,+!p2@Ubp1!0.22!13.46!Ubp1;;chr8:108160490..108160512,+!p2@Ctcf!0.22!11.91!Ctcf;;chr5:146041333..146041379,+!p@chr5:146041333..146041379,+!0.22!10.87!Zfp498;;chr18:76401314..76401395,+!p2@Smad2!0.22!9.84!Smad2;;chr9:31088110..31088151,+!p1@Prdm10!0.22!9.84!Prdm10;;chr7:134170660..134170711,-!p6@Maz!0.22!7.77!Maz;;chr4:151401741..151401793,-!p1@Zbtb48!0.22!5.70!Zbtb48;;chr2:73730619..73730630,-!p4@Atf2,p4@LOC100047997!0.22!5.70!Atf2;;chr10:114821572..114821618,-!p3@Thap2!0.22!5.70!Thap2;;chr7:134592623..134592680,-!p1@Zfp689!0.22!5.18!Zfp689;;chr7:148513599..148513636,-!p3@Deaf1!0.22!5.18!Deaf1;;chr2:83484738..83484749,+!p5@Zc3h15!0.22!5.18!Zc3h15;;chr11:102179101..102179130,-!p3@Ubtf!0.22!4.66!Ubtf;;chr3:152059326..152059358,+!p3@Gm8261,p3@Zzz3!0.22!4.14!Zzz3;;chr13:42147211..42147244,+!p2@Hivep1!0.22!4.14!Hivep1;;chr11:53164533..53164548,+!p4@Aff4!0.22!3.62!Aff4;;chrX:20527723..20527739,-!p2@Elk1!0.22!3.62!Elk1;;chr6:38204087..38204108,-!p2@D630045J12Rik!0.22!3.62!D630045J12Rik;;chr12:119539732..119539762,-!p3@Sp4!0.22!2.59!Sp4;;chr7:4947724..4947743,-!p3@Zfp579!0.22!2.59!Zfp579;;chr16:3884438..3884470,-!p2@Zfp597!0.22!2.59!Zfp597;;chr15:40486615..40486628,+!p3@Zfpm2!0.22!1.55!Zfpm2;;chr8:87237732..87237745,-!p7@Nfix!0.22!1.55!Nfix;;chr7:31741624..31741643,-!p7@LOC100504922,p7@Usf2!0.22!1.04!Usf2;;chr8:124806111..124806122,+!p3@Zfpm1!0.22!1.04!Zfpm1;;chr18:39649174..39649196,-!p5@Nr3c1!0.22!1.04!Nr3c1;;chr1:133903955..133903969,+!p10@Elk4!0.22!1.04!Elk4;;chr6:15135639..15135655,+!p9@Foxp2!0.22!1.04!Foxp2;;chr4:87678639..87678653,-!p11@Mllt3!0.22!1.04!Mllt3;;chr11:112643496..112643562,+!p1@Sox9!0.21!53.85!Sox9;;chr14:65568675..65568723,-!p1@Hmbox1!0.21!48.15!Hmbox1;;chr8:86590723..86590781,+!p1@Rfx1!0.21!26.41!Rfx1;;chr7:148513456..148513506,-!p1@Deaf1!0.21!22.26!Deaf1;;chr1:33871361..33871418,-!p1@Zfp451!0.21!19.16!Zfp451;;chr1:136456734..136456757,+!p3@Kdm5b!0.21!17.60!Kdm5b;;chr10:75495343..75495405,+!p1@Zfp280b!0.21!11.91!Zfp280b;;chr7:50835064..50835134,+!p1@Zfp719!0.21!10.87!Zfp719;;chrX:98728074..98728116,+!p2@Taf1!0.21!8.80!Taf1;;chr17:32526309..32526356,-!p2@Wiz!0.21!7.25!Wiz;;chr12:75008946..75008957,+!p2@Hif1a!0.21!6.73!Hif1a;;chr7:25101609..25101678,-!p1@Zfp94!0.21!4.66!Zfp94;;chr3:88753953..88754004,+!p1@Ash1l!0.21!4.14!Ash1l;;chr5:110539087..110539133,+!p1@Zfp605!0.21!3.62!Zfp605;;chr5:22940320..22940331,+!p2@Mll5!0.21!3.62!Mll5;;chr8:124900562..124900573,+!p3@Zc3h18!0.21!3.11!Zc3h18;;chr7:87171256..87171280,+!p4@Zfp710!0.21!2.07!Zfp710;;chrX:70587989..70588000,+!p3@Zfp275!0.21!2.07!Zfp275;;chr4:82151583..82151594,-!p6@Nfib!0.21!2.07!Nfib;;chr18:69505476..69505494,+!p15@Tcf4!0.21!1.55!Tcf4;;chr19:28754600..28754612,-!p2@Glis3!0.21!1.55!Glis3;;chr3:19957878..19957885,+!p2@Hltf!0.21!1.04!Hltf;;chr6:145813964..145813994,-!p3@Bhlhe41!0.21!1.04!Bhlhe41;;chr7:25292223..25292234,+!p7@Zfp428!0.21!1.04!Zfp428;;chr13:58503480..58503510,-!p3@Hnrnpk!0.20!73.52!Hnrnpk;;chr5:22940253..22940289,+!p1@Mll5!0.20!71.97!Mll5;;chr15:57907747..57907798,-!p1@9130401M01Rik,p1@Zhx1!0.20!37.28!Zhx1;;chr7:134388025..134388092,+!p1@Zfp771!0.20!29.51!Zfp771;;chr2:164860270..164860320,-!p1@Ncoa5!0.20!27.96!Ncoa5;;chr18:61336648..61336711,-!p1@Hmgxb3!0.20!26.41!Hmgxb3;;chr15:76181777..76181802,+!p2@Maf1!0.20!22.78!Maf1;;chr17:46693107..46693137,-!p1@Srf!0.20!13.46!Srf;;chr16:33380950..33380988,+!p2@Zfp148!0.20!5.18!Zfp148;;chr6:118405493..118405536,-!p1@Zfp248!0.20!4.66!Zfp248;;chr7:46773114..46773155,+!p1@Zfp619!0.20!4.66!Zfp619;;chr11:102178937..102178956,-!p5@Ubtf!0.20!3.62!Ubtf;;chr8:83262929..83262957,-!p1@Smarca5!0.20!3.11!Smarca5;;chr6:133985971..133985991,+!p6@Etv6!0.20!3.11!Etv6;;chr12:86940300..86940312,+!p2@Jdp2!0.20!2.59!Jdp2;;chr13:5860872..5860883,+!p3@Klf6!0.20!2.07!Klf6;;
+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 45: @@
 |is_a=EFO:0002091;;FF:0011270
 |is_obsolete=
-|name=visual cortex - wildtype, neonate N60-70, donor3
+|library_id=CNhs13039
+|library_id_phase_based=2:CNhs13039
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;10243
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;10243
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N60-70%252c%2520donor3.CNhs13039.10243-104A9.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%2520donor3.CNhs13039.10243-104A9.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%2520donor3.CNhs13039.10243-104A9.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%2520donor3.CNhs13039.10243-104A9.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%2520donor3.CNhs13039.10243-104A9.mm9.nobarcode.rdna.fa.gz
+|name=visual cortex - wildtype
 |namespace=FANTOM5
 |part_of=
 |profile_cagescan=,,,
 |profile_hcage=CNhs13039,LSID999,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.125847228394889,0,0,0,0,0,0.387310472573062,0,0,0,0,0.0968639517804338,0,0,0,0,0,0,0.116782156043335,0,0,0,0,0,0.181203192176975,0,0,0,0,0,0,0.683141369918527,-0.558422792324031,0,0,0,0,0,-0.005773424259247,0.121859637955871,-0.0220093476426886,0.962739229190068,-0.0886654458333759,0.181203192176975,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0428469550828748,0,-0.0292855944760917,0,0.181203192176975,0,-0.0327440330038944,-0.310650657339386,0.758291536883996,0.253792080429094,0,0,0.0756696135427808,0.222619186226048,0.181203192176975,0,0.113097449106987,0.198275374318798,0.478644363398066,-0.0788315948399074,0,0,0,0,0,0,0.282276330160645,0.0108672658080402,0.306363864654796,0,0,0.487285649470539,0.407098602473158,0
 |rna_box=104
 |rna_catalog_number=N/A
@@ Line 58: / Line 77: @@
 |rna_weight_ug=9.696
 |sample_age=P60-70
+|sample_category=tissues
 |sample_cell_catalog=N/A
 |sample_cell_line=N/A
@@ Line 73: / 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=table111:10243-104A9;search_select_hide=table117:10243-104A9
 }}

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FF:10243-104A9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 13:57, 3 June 2020

CNhs13039

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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