FF:10238-104A4: Difference between revisions

Latest revision as of 13:56, 3 June 2020

Name:	visual cortex - wildtype
Species:	Mouse (Mus musculus)
Library ID:	CNhs13034
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 30
sex	male
age	P30
cell type	mixed
cell line	N/A
company	N/A
collaboration	Michela Fagiolini/Alka Saxena/Piero Carninci
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	N/A
catalog number	N/A
sample type	Visual cortex tissue
extraction protocol (Details)	Total RNA Trizol Qiagen minElute

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005503

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13034		CAGE		DRX009136		DRR010010

Accession ID Mm9

Library id		BAM		CTSS
CNhs13034		DRZ001435		DRZ002818

Accession ID Mm10

Library id		BAM		CTSS
CNhs13034		DRZ012785		DRZ014168

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

CNhs13034

0	0
1	0.813
10	0
100	0
1000	-0.0355
1001	-0.0595
1002	-0.116
1003	0.289
1004	0
1005	0
1006	0.74
1007	-0.231
1008	0
1009	-0.19
101	-0.0876
1010	0
1011	0.995
1012	0.375
1013	0.158
1014	-0.0874
1015	-0.192
1016	-0.379
1017	0
1018	0
1019	0
102	0
1020	0.618
1021	0
1022	0
1023	0
1024	-0.14
1025	-0.0611
1026	0
1027	0.396
1028	0
1029	0.128
103	-0.0848
1030	0
1031	-0.684
1032	0.195
1033	0
1034	0
1035	0
1036	-0.183
1037	0
1038	0.0022
1039	0.0697
104	0
1040	-0.279
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: CNhs13034

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0112
MA0003.1	MA0003.1	0.314
MA0004.1	MA0004.1	0.567
MA0006.1	MA0006.1	0.0988
MA0007.1	MA0007.1	0.388
MA0009.1	MA0009.1	0.923
MA0014.1	MA0014.1	0.691
MA0017.1	MA0017.1	5.12468e-7
MA0018.2	MA0018.2	0.003
MA0019.1	MA0019.1	0.161
MA0024.1	MA0024.1	0.0321
MA0025.1	MA0025.1	0.0108
MA0027.1	MA0027.1	0.137
MA0028.1	MA0028.1	0.0735
MA0029.1	MA0029.1	0.805
MA0030.1	MA0030.1	0.532
MA0031.1	MA0031.1	0.0534
MA0035.2	MA0035.2	0.00852
MA0038.1	MA0038.1	0.925
MA0039.2	MA0039.2	0.00378
MA0040.1	MA0040.1	0.075
MA0041.1	MA0041.1	0.115
MA0042.1	MA0042.1	0.282
MA0043.1	MA0043.1	0.121
MA0046.1	MA0046.1	9.71351e-9
MA0047.2	MA0047.2	2.20919e-4
MA0048.1	MA0048.1	0.0454
MA0050.1	MA0050.1	1.10185e-5
MA0051.1	MA0051.1	0.00363
MA0052.1	MA0052.1	0.403
MA0055.1	MA0055.1	0.00969
MA0057.1	MA0057.1	0.45
MA0058.1	MA0058.1	0.434
MA0059.1	MA0059.1	0.323
MA0060.1	MA0060.1	0.0574
MA0061.1	MA0061.1	0.0364
MA0062.2	MA0062.2	0.00105
MA0065.2	MA0065.2	2.96916e-6
MA0066.1	MA0066.1	0.0584
MA0067.1	MA0067.1	0.465
MA0068.1	MA0068.1	0.253
MA0069.1	MA0069.1	0.0426
MA0070.1	MA0070.1	0.929
MA0071.1	MA0071.1	0.0887
MA0072.1	MA0072.1	0.354
MA0073.1	MA0073.1	0.851
MA0074.1	MA0074.1	0.156
MA0076.1	MA0076.1	0.155
MA0077.1	MA0077.1	0.538
MA0078.1	MA0078.1	0.91
MA0079.2	MA0079.2	0.977
MA0080.2	MA0080.2	1.33197e-10
MA0081.1	MA0081.1	0.212
MA0083.1	MA0083.1	0.00304
MA0084.1	MA0084.1	0.892
MA0087.1	MA0087.1	0.311
MA0088.1	MA0088.1	0.298
MA0090.1	MA0090.1	0.221
MA0091.1	MA0091.1	0.21
MA0092.1	MA0092.1	0.29
MA0093.1	MA0093.1	0.578
MA0099.2	MA0099.2	0.00454
MA0100.1	MA0100.1	0.42
MA0101.1	MA0101.1	0.0137
MA0102.2	MA0102.2	0.27
MA0103.1	MA0103.1	0.411
MA0104.2	MA0104.2	0.864
MA0105.1	MA0105.1	0.036
MA0106.1	MA0106.1	0.0535
MA0107.1	MA0107.1	0.023
MA0108.2	MA0108.2	1.04482e-4
MA0111.1	MA0111.1	0.66
MA0112.2	MA0112.2	9.75766e-4
MA0113.1	MA0113.1	0.207
MA0114.1	MA0114.1	4.35608e-6
MA0115.1	MA0115.1	1.57509e-4
MA0116.1	MA0116.1	0.13
MA0117.1	MA0117.1	0.764
MA0119.1	MA0119.1	0.114
MA0122.1	MA0122.1	0.426
MA0124.1	MA0124.1	0.798
MA0125.1	MA0125.1	0.444
MA0131.1	MA0131.1	0.707
MA0135.1	MA0135.1	0.455
MA0136.1	MA0136.1	1.15175e-11
MA0137.2	MA0137.2	0.192
MA0138.2	MA0138.2	0.00278
MA0139.1	MA0139.1	0.53
MA0140.1	MA0140.1	4.81602e-4
MA0141.1	MA0141.1	0.00263
MA0142.1	MA0142.1	0.385
MA0143.1	MA0143.1	0.642
MA0144.1	MA0144.1	0.127
MA0145.1	MA0145.1	0.0883
MA0146.1	MA0146.1	0.00993
MA0147.1	MA0147.1	0.887
MA0148.1	MA0148.1	1.50989e-4
MA0149.1	MA0149.1	0.42
MA0150.1	MA0150.1	0.281
MA0152.1	MA0152.1	0.562
MA0153.1	MA0153.1	3.29286e-9
MA0154.1	MA0154.1	0.049
MA0155.1	MA0155.1	0.342
MA0156.1	MA0156.1	7.55339e-10
MA0157.1	MA0157.1	0.0347
MA0159.1	MA0159.1	0.0134
MA0160.1	MA0160.1	0.00697
MA0162.1	MA0162.1	0.197
MA0163.1	MA0163.1	0.00645
MA0164.1	MA0164.1	0.988
MA0258.1	MA0258.1	0.0328
MA0259.1	MA0259.1	0.816

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: CNhs13034

Novel motif	Logo	P-value
1	1	0.36
10	10	0.0946
100	100	0.418
101	101	0.579
102	102	0.889
103	103	0.164
104	104	0.791
105	105	0.682
106	106	0.0518
107	107	0.141
108	108	0.381
109	109	0.00276
11	11	0.0988
110	110	0.0461
111	111	0.403
112	112	0.00603
113	113	0.337
114	114	0.615
115	115	0.934
116	116	0.293
117	117	0.00459
118	118	0.517
119	119	0.306
12	12	0.83
120	120	0.785
121	121	0.158
122	122	0.992
123	123	0.00211
124	124	0.0187
125	125	0.662
126	126	0.0626
127	127	0.422
128	128	0.0332
129	129	0.231
13	13	9.79521e-9
130	130	0.0603
131	131	0.529
132	132	0.55
133	133	0.5
134	134	0.056
135	135	0.307
136	136	0.0427
137	137	0.539
138	138	0.649
139	139	0.994
14	14	0.944
140	140	0.217
141	141	0.929
142	142	0.894
143	143	0.699
144	144	0.568
145	145	5.03722e-5
146	146	0.186
147	147	0.113
148	148	0.403
149	149	0.467
15	15	0.261
150	150	0.0367
151	151	0.822
152	152	0.067
153	153	0.96
154	154	0.94
155	155	0.431
156	156	0.00218
157	157	0.134
158	158	0.124
159	159	0.907
160	160	0.237
161	161	0.12
162	162	0.574
163	163	0.921
164	164	0.127
165	165	0.227
166	166	0.464
167	167	0.367
168	168	0.438
169	169	0.00336
17	17	0.0591
18	18	0.816
19	19	0.0558
2	2	0.923
20	20	0.0446
21	21	0.273
22	22	0.0843
23	23	0.671
24	24	0.0165
25	25	0.993
26	26	1.96553e-6
27	27	0.458
28	28	0.655
29	29	0.0305
3	3	0.0509
30	30	0.933
31	31	0.854
32	32	0.888
33	33	0.28
34	34	0.493
35	35	0.523
36	36	0.522
37	37	0.0186
38	38	0.438
39	39	0.188
4	4	0.16
40	40	0.188
41	41	0.741
42	42	0.171
43	43	0.135
44	44	0.738
45	45	0.567
46	46	0.227
47	47	0.5
48	48	0.358
49	49	0.313
5	5	0.308
50	50	0.136
51	51	0.817
52	52	0.156
53	53	0.603
54	54	0.95
55	55	0.955
56	56	0.512
57	57	0.813
58	58	0.367
59	59	0.124
6	6	0.966
60	60	0.0362
61	61	0.0379
62	62	0.324
63	63	0.113
64	64	0.624
65	65	0.449
66	66	0.476
67	67	0.643
68	68	0.192
69	69	0.142
7	7	0.0175
70	70	0.485
71	71	0.0132
72	72	0.675
73	73	0.025
74	74	0.895
75	75	0.0593
76	76	0.702
77	77	0.373
78	78	0.00227
79	79	0.417
8	8	0.167
80	80	0.712
81	81	0.719
82	82	0.485
83	83	0.0597
84	84	0.97
85	85	0.235
86	86	0.199
87	87	0.0549
88	88	0.572
89	89	0.959
9	9	0.35
90	90	0.415
91	91	0.208
92	92	0.604
93	93	0.284
94	94	0.932
95	95	0.0192
96	96	0.5
97	97	0.932
98	98	0.367
99	99	0.563

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: CNhs13034

FANTOM5 (FF) ontology

Direct parent terms

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

Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship Analyst: Hideya Kawaji link to source data data

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

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011269 (mouse visual cortex from wildtype- neonate N30 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship Analyst: Hideya Kawaji link to source data data
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005503
+|accession_numbers=CAGE;DRX009136;DRR010010;DRZ001435;DRZ002818;DRZ012785;DRZ014168
 |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=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
+|donor= donor1
 |expression_enrichment_score=chr19:4989964..4989972,-!p1@Npas4!2.17!145.92!Npas4;;chr10:67375368..67375433,-!p1@Zfp365!2.16!248.00!Zfp365;;chr16:91270004..91270023,+!p1@Olig1!2.08!135.65!Olig1;;chr6:85463580..85463585,-!p1@Egr4!1.99!96.60!Egr4;;chr6:55631042..55631102,-!p1@Neurod6!1.83!67.14!Neurod6;;chr11:98190918..98190951,-!p1@Neurod2!1.75!55.49!Neurod2;;chr5:138199361..138199441,+!p2@Tsc22d4!1.74!100.02!Tsc22d4;;chr19:19185671..19185693,-!p1@Rorb!1.72!119.89!Rorb;;chr7:116154364..116154444,+!p1@Tub!1.71!84.95!Tub;;chr12:30219426..30219506,+!p2@Myt1l!1.70!48.64!Myt1l;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.67!57.55!Pou3f3;;chr8:24780125..24780143,+!p1@Zmat4!1.65!62.34!Zmat4;;chr13:83663546..83663560,+!p4@Mef2c!1.61!51.38!Mef2c;;chr17:48015839..48015915,-!p3@Foxp4!1.60!45.22!Foxp4;;chr2:127347067..127347093,-!p1@Kcnip3!1.56!57.55!Kcnip3;;chr10:67375342..67375365,-!p3@Zfp365!1.56!34.94!Zfp365;;chr2:61642631..61642684,+!p1@Tbr1!1.55!34.25!Tbr1;;chr2:65683890..65683907,+!p1@Csrnp3!1.52!60.29!Csrnp3;;chr10:67375146..67375208,-!p2@Zfp365!1.52!48.64!Zfp365;;chrX:90531838..90531861,+!p1@Arx!1.51!39.05!Arx;;chr13:83663902..83663927,+!p1@Mef2c!1.50!698.78!Mef2c;;chr5:122452349..122452377,-!p4@Cux2!1.50!30.83!Cux2;;chr3:95032091..95032183,-!p1@Mllt11!1.49!243.20!Mllt11;;chr5:98609885..98609900,+!p1@Prdm8!1.48!29.46!Prdm8;;chr2:38206744..38206766,+!p1@Lhx2!1.45!32.88!Lhx2;;chr1:179374784..179374800,+!p2@Zfp238!1.45!32.20!Zfp238;;chr13:83663868..83663894,+!p2@Mef2c!1.44!361.04!Mef2c;;chrX:34442872..34442899,-!p1@Nkrf!1.42!32.88!Nkrf;;chr2:65768174..65768247,+!p2@Csrnp3!1.42!25.35!Csrnp3;;chr19:19185697..19185711,-!p2@Rorb!1.41!31.51!Rorb;;chr2:38206580..38206600,+!p2@Lhx2!1.40!29.46!Lhx2;;chr12:86939997..86940040,+!p4@Jdp2!1.37!22.61!Jdp2;;chr15:76353005..76353021,-!p2@Scrt1!1.36!21.92!Scrt1;;chr4:22415443..22415506,-!p1@Pou3f2!1.36!21.92!Pou3f2;;chr2:127347094..127347111,-!p2@Kcnip3!1.35!34.94!Kcnip3;;chr2:61642743..61642758,+!p2@Tbr1!1.35!21.24!Tbr1;;chr12:30213247..30213333,+!p1@Myt1l!1.35!21.24!Myt1l;;chr13:83663500..83663519,+!p8@Mef2c!1.35!21.24!Mef2c;;chr1:57029281..57029326,-!p1@Satb2!1.33!31.51!Satb2;;chr7:148008023..148008092,-!p1@Zfp941!1.32!47.27!Zfp941;;chr4:58956447..58956510,+!p1@Zkscan16!1.32!43.16!Zkscan16;;chr16:91270091..91270143,+!p2@Olig1!1.27!17.81!Olig1;;chr16:91225808..91225824,+!p1@Olig2!1.26!17.13!Olig2;;chr18:35020854..35020869,+!p1@Egr1!1.25!628.22!Egr1;;chr11:98636531..98636559,-!p1@Nr1d1!1.25!93.86!Nr1d1;;chr12:30220074..30220102,+!p3@Myt1l!1.24!16.44!Myt1l;;chr4:48058129..48058179,+!p2@Nr4a3!1.23!30.14!Nr4a3;;chr13:78339134..78339185,-!p5@Nr2f1!1.23!19.87!Nr2f1;;chr15:101097270..101097290,+!p1@Nr4a1!1.22!157.57!Nr4a1;;chr5:122499831..122499891,-!p1@Cux2!1.22!23.98!Cux2;;chr10:13685585..13685645,+!p2@Hivep2!1.20!50.70!Hivep2;;chr15:76352677..76352737,-!p3@Scrt1!1.19!14.39!Scrt1;;chr13:83643031..83643049,+!p11@Mef2c!1.19!14.39!Mef2c;;chr18:69680960..69681007,+!p10@Tcf4!1.17!17.81!Tcf4;;chr15:76352434..76352488,-!p4@Scrt1!1.17!13.70!Scrt1;;chr14:13178147..13178185,-!p1@Fezf2!1.12!12.33!Fezf2;;chr11:98190955..98190968,-!p2@Neurod2!1.12!12.33!Neurod2;;chr2:61642558..61642595,+!p3@Tbr1!1.12!12.33!Tbr1;;chr18:36441119..36441158,+!p2@Pura!1.09!27.40!Pura;;chr5:125342568..125342602,+!p2@Zfp664!1.09!18.50!Zfp664;;chr2:127347042..127347058,-!p3@Kcnip3!1.08!10.96!Kcnip3;;chr8:87297878..87297935,-!p3@Nfix!1.07!23.98!Nfix;;chr19:23216132..23216157,+!p3@Klf9!1.06!16.44!Klf9;;chr14:18493386..18493464,+!p1@Thrb!1.05!39.05!Thrb;;chr2:162769220..162769252,+!p1@L3mbtl1!1.05!10.28!L3mbtl1;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!1.04!105.50!Camta2;;chr4:48058016..48058032,+!p3@Nr4a3!1.04!17.13!Nr4a3;;chr17:25707623..25707639,-!p1@Sox8!1.03!41.79!Sox8;;chr11:90250944..90250982,-!p2@Hlf!1.03!16.44!Hlf;;chr3:95032213..95032226,-!p6@Mllt11!1.03!11.65!Mllt11;;chr1:179374764..179374776,+!p5@Zfp238!1.02!9.59!Zfp238;;chr3:95032197..95032208,-!p3@Mllt11!1.01!11.65!Mllt11;;chr2:77654815..77654872,-!p2@Zfp385b!1.01!11.65!Zfp385b;;chr12:86814833..86814846,+!p1@Fos!1.00!214.43!Fos;;chr9:48644306..48644364,-!p1@Zbtb16!1.00!36.99!Zbtb16;;chr12:54349410..54349461,+!p1@Npas3!1.00!10.96!Npas3;;chr11:90251852..90251855,-!p4@Hlf!1.00!10.96!Hlf;;chr7:91520922..91520956,-!p5@Arnt2!1.00!8.91!Arnt2;;chrX:95345005..95345053,+!p1@Ar!1.00!8.91!Ar;;chr2:65768149..65768173,+!p4@Csrnp3!1.00!8.91!Csrnp3;;chr19:19185429..19185440,-!p3@Rorb!1.00!8.91!Rorb;;chr4:150482563..150482655,-!p2@Camta1!0.99!32.20!Camta1;;chr19:26681865..26681900,+!p6@Smarca2!0.99!26.03!Smarca2;;chr10:67000609..67000625,+!p1@Egr2!0.99!20.55!Egr2;;chr19:59533221..59533271,+!p1@Emx2!0.99!10.96!Emx2;;chr2:25562263..25562314,+!p2@Bmyc!0.96!32.20!Bmyc;;chr13:78338076..78338104,-!p4@Nr2f1!0.96!10.28!Nr2f1;;chr7:91520957..91520973,-!p9@Arnt2!0.96!8.22!Arnt2;;chr6:98994408..98994420,-!p23@Foxp1!0.96!8.22!Foxp1;;chr1:57028606..57028625,-!p4@Satb2!0.96!8.22!Satb2;;chr2:163051181..163051205,+!p2@Tox2!0.96!8.22!Tox2;;chrX:34442842..34442866,-!p3@Nkrf!0.96!8.22!Nkrf;;chr11:90252223..90252240,-!p1@Hlf!0.95!67.14!Hlf;;chr7:71083876..71083932,-!p2@Klf13!0.94!63.71!Klf13;;chr12:72149359..72149406,+!p4@Arid4a!0.94!10.28!Arid4a;;chr3:95032184..95032195,-!p4@Mllt11!0.94!9.59!Mllt11;;chr6:117813087..117813121,+!p1@Zfp239!0.93!29.46!Zfp239;;chr14:70477113..70477173,+!p1@Egr3!0.93!7.54!Egr3;;chr2:79296907..79296918,-!p2@Neurod1!0.93!7.54!Neurod1;;chr1:179374820..179374831,+!p3@Zfp238!0.93!7.54!Zfp238;;chr10:13685899..13685916,+!p1@Hivep2!0.92!79.47!Hivep2;;chr4:154335024..154335039,+!p1@Hes5!0.92!8.91!Hes5;;chr10:13686815..13686846,+!p3@Hivep2!0.91!16.44!Hivep2;;chr2:56967334..56967366,-!p1@Nr4a2!0.91!15.07!Nr4a2;;chr7:91558472..91558512,-!p2@Arnt2!0.91!10.28!Arnt2;;chr8:87297280..87297326,-!p2@Nfix!0.90!17.13!Nfix;;chr7:30092993..30093076,+!p1@Dpf1!0.90!12.33!Dpf1;;chr2:77654650..77654685,-!p3@Zfp385b!0.90!8.91!Zfp385b;;chr7:146768691..146768707,-!p1@Nkx6-2!0.89!6.85!Nkx6-2;;chr6:144152648..144152680,-!p5@Sox5!0.89!6.85!Sox5;;chr7:91521166..91521194,-!p11@Arnt2!0.89!6.85!Arnt2;;chr13:83643302..83643309,+!p12@Mef2c!0.89!6.85!Mef2c;;chr11:98603119..98603130,+!p2@Thra!0.88!58.23!Thra;;chr13:83663600..83663625,+!p6@Mef2c!0.88!10.28!Mef2c;;chr10:80893711..80893784,-!p3@Nfic!0.87!35.62!Nfic;;chr9:68501522..68501538,+!p4@Rora!0.87!12.33!Rora;;chr17:51971932..51971958,-!p2@Satb1!0.87!8.91!Satb1;;chr13:78339382..78339420,-!p3@Nr2f1!0.87!7.54!Nr2f1;;chr11:23980664..23980706,+!p2@Bcl11a!0.86!28.77!Bcl11a;;chr7:91558392..91558434,-!p1@Arnt2!0.86!17.81!Arnt2;;chr4:124334894..124334899,+!p1@Pou3f1!0.86!8.22!Pou3f1;;chr17:48015824..48015836,-!p11@Foxp4!0.86!6.17!Foxp4;;chr11:90250894..90250916,-!p5@Hlf!0.86!6.17!Hlf;;chr11:90252108..90252134,-!p6@Hlf!0.86!6.17!Hlf;;chr14:70476975..70476997,+!p2@Egr3!0.86!6.17!Egr3;;chr11:98603185..98603208,+!p1@Thra!0.85!389.13!Thra;;chr15:103170533..103170556,-!p1@Zfp385a!0.85!23.98!Zfp385a;;chr3:34548946..34548972,+!p2@Sox2!0.85!6.85!Sox2;;chr10:67375223..67375240,-!p4@Zfp365!0.85!6.85!Zfp365;;chr13:78339428..78339466,-!p2@Nr2f1!0.84!8.22!Nr2f1;;chr4:150513630..150513686,-!p4@Camta1!0.84!6.85!Camta1;;chr15:81641878..81641921,+!p1@Tef!0.83!158.25!Tef;;chr12:72149325..72149343,+!p2@Arid4a!0.83!8.22!Arid4a;;chr6:72850124..72850210,-!p7@Kcmf1!0.82!7.54!Kcmf1;;chr7:30094448..30094481,+!p4@Dpf1!0.82!6.85!Dpf1;;chr9:36954842..36954908,-!p1@Pknox2!0.81!68.51!Pknox2;;chr2:37278526..37278575,-!p2@Rc3h2!0.81!24.66!Rc3h2;;chr6:108610766..108610781,+!p2@Bhlhe40!0.81!10.28!Bhlhe40;;chr6:85137520..85137563,+!p1@Emx1!0.81!5.48!Emx1;;chr7:52960888..52960902,+!p7@Dbp!0.81!5.48!Dbp;;chrX:108009761..108009788,+!p1@Pou3f4!0.81!5.48!Pou3f4;;chr4:119487109..119487131,+!p4@Hivep3!0.81!5.48!Hivep3;;chr3:34549096..34549111,+!p3@Sox2!0.81!5.48!Sox2;;chr4:22415290..22415307,-!p2@Pou3f2!0.81!5.48!Pou3f2;;chr2:79296783..79296801,-!p1@Neurod1!0.81!5.48!Neurod1;;chr10:84218800..84218829,+!p2@Rfx4!0.81!5.48!Rfx4;;chr13:83643159..83643226,+!p3@Mef2c!0.81!5.48!Mef2c;;chr14:13178361..13178386,-!p2@Fezf2!0.81!5.48!Fezf2;;chr12:50483639..50483654,+!p1@Foxg1!0.81!5.48!Foxg1;;chr15:81633165..81633188,+!p2@Tef!0.80!47.27!Tef;;chr7:17200307..17200370,-!p2@Grlf1!0.80!41.79!Grlf1;;chr13:44936126..44936164,+!p6@Jarid2!0.80!6.17!Jarid2;;chr13:78338288..78338309,-!p7@Nr2f1!0.80!6.17!Nr2f1;;chr1:179372411..179372509,+!p1@Zfp238!0.79!70.56!Zfp238;;chr15:100430414..100430470,-!p1@Pou6f1!0.79!17.13!Pou6f1;;chr7:25292160..25292213,+!p3@Zfp428!0.79!13.70!Zfp428;;chr8:107793688..107793736,+!p1@Hsf4!0.79!6.85!Hsf4;;chr10:13685657..13685677,+!p7@Hivep2!0.79!6.85!Hivep2;;chr11:23978111..23978134,+!p3@Bcl11a!0.78!10.96!Bcl11a;;chr3:34548909..34548927,+!p1@Sox2!0.78!8.91!Sox2;;chr14:118636214..118636235,-!p1@Sox21!0.78!6.17!Sox21;;chr2:77654936..77654988,-!p4@Zfp385b!0.77!6.17!Zfp385b;;chr7:52960700..52960719,+!p2@Dbp!0.77!6.17!Dbp;;chr10:30522690..30522752,-!p2@Ncoa7!0.76!31.51!Ncoa7;;chr12:39507404..39507441,+!p4@Etv1!0.76!6.85!Etv1;;chr12:30220046..30220070,+!p6@Myt1l!0.76!4.80!Myt1l;;chr11:21901608..21901634,-!p1@Otx1!0.76!4.80!Otx1;;chr11:96685444..96685473,-!p5@Nfe2l1!0.76!4.80!Nfe2l1;;chr4:13678482..13678505,+!p9@Runx1t1!0.76!4.80!Runx1t1;;chr2:77541432..77541474,-!p5@Zfp385b!0.76!4.80!Zfp385b;;chr4:13670499..13670526,+!p2@Runx1t1!0.75!10.96!Runx1t1;;chr8:87502608..87502623,-!p1@Junb!0.74!80.84!Junb;;chr11:23978078..23978096,+!p4@Bcl11a!0.74!15.07!Bcl11a;;chr2:44972821..44972865,-!p10@Zeb2!0.74!9.59!Zeb2;;chr16:95923651..95923701,+!p3@Ets2!0.74!7.54!Ets2;;chr4:135840573..135840601,+!p1@Zfp46!0.73!38.36!Zfp46;;chr7:25292331..25292421,+!p1@Zfp428!0.73!34.94!Zfp428;;chr8:112603610..112603656,+!p1@Zfp612!0.73!21.92!Zfp612;;chr7:91558537..91558558,-!p4@Arnt2!0.73!5.48!Arnt2;;chr14:76904356..76904367,+!p3@Tsc22d1!0.72!34.94!Tsc22d1;;chr3:95032558..95032641,-!p2@Mllt11!0.72!26.72!Mllt11;;chr19:28085586..28085622,-!p3@Rfx3!0.72!20.55!Rfx3;;chr15:103170516..103170531,-!p2@Zfp385a!0.72!10.96!Zfp385a;;chr11:62602947..62602980,-!p2@Zfp286!0.72!8.91!Zfp286;;chr19:23215469..23215494,+!p2@Klf9!0.72!6.85!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4;;chr10:41995430..41995458,-!p3@Foxo3!0.31!4.11!Foxo3;;chr12:119539732..119539762,-!p3@Sp4!0.31!3.43!Sp4;;chr15:50721544..50721558,-!p5@Trps1!0.31!3.43!Trps1;;chr15:25914217..25914232,+!p3@Zfp622!0.31!2.74!Zfp622;;chr6:38204214..38204267,-!p4@D630045J12Rik!0.31!2.74!D630045J12Rik;;chr13:78339476..78339515,-!p1@Nr2f1!0.31!2.06!Nr2f1;;chr10:86956396..86956411,-!p1@Ascl1!0.31!2.06!Ascl1;;chr17:32525943..32525992,-!p4@Wiz!0.31!2.06!Wiz;;chr18:5593564..5593584,+!p2@Zeb1!0.31!1.37!Zeb1;;chr15:103164702..103164778,-!p3@Zfp385a!0.31!1.37!Zfp385a;;chr2:90936886..90936898,+!p5@Sfpi1!0.31!1.37!Sfpi1;;chr6:86475924..86475935,-!p2@Pcbp1!0.30!29.46!Pcbp1;;chr1:173341474..173341513,+!p2@Usf1!0.30!23.98!Usf1;;chr10:79017833..79017871,-!p1@Mier2!0.30!9.59!Mier2;;chr4:61869460..61869521,-!p1@Zfp37!0.30!8.91!Zfp37;;chr18:24145736..24145783,-!p1@Zscan30!0.30!8.22!Zscan30;;chr14:100683912..100683947,-!p2@Klf12!0.30!4.80!Klf12;;chr5:22940320..22940331,+!p2@Mll5!0.30!4.80!Mll5;;chr11:95170871..95170900,-!p2@Myst2!0.30!4.11!Myst2;;chr17:51951634..51951651,-!p6@Satb1!0.30!2.74!Satb1;;chr13:67229127..67229153,+!p2@Zfp759!0.30!2.74!Zfp759;;chr9:48644429..48644462,-!p3@Zbtb16!0.30!2.74!Zbtb16;;chr2:44972869..44972895,-!p12@Zeb2!0.30!2.74!Zeb2;;chr11:98602203..98602266,+!p4@Thra!0.30!2.06!Thra;;chr3:9610033..9610040,-!p3@Zfp704!0.30!2.06!Zfp704;;chr3:95032515..95032553,-!p5@Mllt11!0.30!1.37!Mllt11;;chr9:48644013..48644027,-!p5@Zbtb16!0.30!1.37!Zbtb16;;chr7:25292118..25292129,+!p8@Zfp428!0.30!1.37!Zfp428;;chr18:35020615..35020641,+!p2@Egr1!0.30!1.37!Egr1;;chr2:83484681..83484704,+!p1@Zc3h15!0.29!80.84!Zc3h15;;chr7:134388025..134388092,+!p1@Zfp771!0.29!36.31!Zfp771;;chr11:83943084..83943122,-!p1@Tada2a!0.29!26.03!Tada2a;;chr16:23988711..23988727,-!p1@Bcl6!0.29!20.55!Bcl6;;chr15:81494344..81494388,+!p1@L3mbtl2!0.29!19.87!L3mbtl2;;chr9:121669118..121669179,+!p1@Zfp651!0.29!18.50!Zfp651;;chr7:30644985..30645072,+!p1@Zfp420!0.29!9.59!Zfp420;;chr17:32526309..32526356,-!p2@Wiz!0.29!8.91!Wiz;;chr17:51952617..51952680,-!p3@Satb1!0.29!8.22!Satb1;;chr8:79426176..79426275,+!p1@Nr3c2!0.29!8.22!Nr3c2;;chrX:66613481..66613562,+!p1@Aff2!0.29!6.85!Aff2;;chr11:69579401..69579427,+!p2@Zbtb4!0.29!6.17!Zbtb4;;chr4:122673278..122673336,+!p1@Mycl1!0.29!4.80!Mycl1;;chr1:170362437..170362478,-!p5@Pbx1!0.29!4.80!Pbx1;;chr2:44965662..44965685,-!p9@Zeb2!0.29!3.43!Zeb2;;chr1:138521574..138521597,+!p3@Zfp281!0.29!3.43!Zfp281;;chr19:26681226..26681299,+!p7@Smarca2!0.29!3.43!Smarca2;;chr12:86940300..86940312,+!p2@Jdp2!0.29!3.43!Jdp2;;chr4:133276779..133276796,-!p8@Arid1a!0.29!2.74!Arid1a;;chr3:5218563..5218587,+!p5@Zfhx4!0.29!2.06!Zfhx4;;chr5:9161608..9161619,-!p3@Dmtf1!0.29!2.06!Dmtf1;;chr12:100802129..100802145,-!p4@Foxn3!0.29!2.06!Foxn3;;chr11:58136641..58136663,-!p3@Zfp672!0.29!1.37!Zfp672;;chr7:123174485..123174514,-!p6@Sox6!0.29!1.37!Sox6;;chr13:29045252..29045271,-!p5@Sox4!0.29!1.37!Sox4;;chr12:39506841..39506848,+!p7@Etv1!0.29!1.37!Etv1;;chr7:31741624..31741643,-!p7@LOC100504922,p7@Usf2!0.29!1.37!Usf2;;chr1:170361678..170361689,-!p13@Pbx1!0.29!1.37!Pbx1;;chr2:120389531..120389614,-!p1@Zfp106!0.28!126.74!Zfp106;;chr11:121121297..121121369,+!p1@Foxk2!0.28!100.71!Foxk2;;chr3:87946250..87946405,+!p1@Mef2d!0.28!70.56!Mef2d;;chr5:67698217..67698253,+!p2@Slc30a9!0.28!34.25!Slc30a9;;chr15:81575569..81575599,+!p2@Zc3h7b!0.28!18.50!Zc3h7b;;chr1:170362040..170362113,-!p2@Pbx1!0.28!13.02!Pbx1;;chr11:58717675..58717719,-!p1@Zfp39!0.28!11.65!Zfp39;;chr4:133801494..133801519,-!p2@Zfp593!0.28!11.65!Zfp593;;chr18:69504157..69504184,+!p3@Tcf4!0.28!10.28!Tcf4;;chr1:138521528..138521572,+!p1@Zfp281!0.28!9.59!Zfp281;;chr1:64579555..64579570,+!p3@Creb1!0.28!7.54!Creb1;;chr2:48805044..48805063,+!p3@Mbd5!0.28!6.85!Mbd5;;chr17:34730333..34730362,+!p2@Pbx2!0.28!6.17!Pbx2;;chr11:102179101..102179130,-!p3@Ubtf!0.28!5.48!Ubtf;;chr9:20385740..20385777,+!p2@Zfp846!0.28!5.48!Zfp846;;chr8:114167356..114167390,+!p3@Zfp1!0.28!5.48!Zfp1;;chr4:119960301..119960359,-!p1@Foxo6!0.28!4.80!Foxo6;;chr6:134780234..134780288,+!p1@Crebl2!0.28!4.80!Crebl2;;chr4:126700722..126700753,+!p4@Sfpq!0.28!3.43!Sfpq;;chr5:143942477..143942493,-!p2@Rbak!0.28!2.74!Rbak;;chr5:147760331..147760336,+!p5@Gtf3a!0.28!2.06!Gtf3a;;chr6:146744595..146744613,+!p2@Arntl2!0.28!2.06!Arntl2;;chr1:38684431..38684450,-!p3@Aff3!0.28!2.06!Aff3;;chr1:52065454..52065495,+!p1@Stat4!0.28!2.06!Stat4;;chr9:69137709..69137714,+!p7@Rora!0.28!1.37!Rora;;chr7:38558574..38558611,-!p2@Zfp536!0.28!1.37!Zfp536;;chr7:25292223..25292234,+!p7@Zfp428!0.28!1.37!Zfp428;;chr7:25292246..25292259,+!p6@Zfp428!0.28!1.37!Zfp428;;chr18:39649174..39649196,-!p5@Nr3c1!0.28!1.37!Nr3c1;;chr18:35721854..35721914,+!p1@Matr3!0.27!126.06!Matr3;;chr13:48356475..48356492,+!p1@Id4!0.27!36.31!Id4;;chr2:83484658..83484678,+!p2@Zc3h15!0.27!26.03!Zc3h15;;chr7:17199897..17199955,-!p1@Grlf1!0.27!18.50!Grlf1;;chr7:28516417..28516460,+!p1@Zfp60!0.27!13.70!Zfp60;;chrY:234225..234243,+!p1@Kdm5d,p1@LOC100040412!0.27!12.33!Kdm5d;;chr9:31088110..31088151,+!p1@Prdm10!0.27!10.96!Prdm10;;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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 45: @@
 |is_a=EFO:0002091;;FF:0011269
 |is_obsolete=
-|name=visual cortex - wildtype, neonate N30, donor1
+|library_id=CNhs13034
+|library_id_phase_based=2:CNhs13034
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;10238
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;10238
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N30%252c%2520donor1.CNhs13034.10238-104A4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N30%252c%2520donor1.CNhs13034.10238-104A4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N30%252c%2520donor1.CNhs13034.10238-104A4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N30%252c%2520donor1.CNhs13034.10238-104A4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/visual%2520cortex%2520-%2520wildtype%252c%2520neonate%2520N30%252c%2520donor1.CNhs13034.10238-104A4.mm9.nobarcode.rdna.fa.gz
+|name=visual cortex - wildtype
 |namespace=FANTOM5
 |part_of=
 |profile_cagescan=,,,
 |profile_hcage=CNhs13034,LSID999,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0695936976069825,0,0,0,0,0,0.279622059725091,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.0347278225761296,0,0,0,0,0,0.226621173458704,0,0,0,0,0,0,0.809178968328299,-0.331801618865327,0,0,0,0,0,-0.209322725495826,0.0851217001838886,-0.0573522010287757,0.660819652815364,-0.269868638010351,0.374778587894724,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,-0.130696565450787,0.124715802340032,0,0,-0.0281942706964978,-0.084029483880682,0.943875968859944,0.101835519650015,0,0,0.0848200839751655,0.226644136664218,0,0,0.105902329003296,0.175097243979509,0.550726803707136,0.295946993054816,0.074261885240697,0,0,0,0,0,0.35861877533569,0.156135929894745,0.215243403603217,0,0,0.645953767926874,0.54736048427158,0
 |rna_box=104
 |rna_catalog_number=N/A
@@ Line 60: / Line 77: @@
 |rna_weight_ug=7.44
 |sample_age=P30
+|sample_category=tissues
 |sample_cell_catalog=N/A
 |sample_cell_line=N/A
@@ Line 75: / Line 93: @@
 |sample_note=
 |sample_sex=male
-|sample_species=mus musculus
+|sample_species=Mouse (Mus musculus)
 |sample_strain=
 |sample_tissue=Visual cortex
+|time= neonate N30
+|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=table111:10238-104A4;search_select_hide=table117:10238-104A4
 }}

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FF:10238-104A4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 13:56, 3 June 2020

CNhs13034

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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