FF:19-21D8: Difference between revisions

Latest revision as of 19:09, 4 June 2020

Name:	corpus striatum, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10487
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	corpus striatum
dev stage	adult
sex	male
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004779

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10487		CAGE		DRX008945		DRR009819

Accession ID Mm9

Library id		BAM		CTSS
CNhs10487		DRZ001244		DRZ002627

Accession ID Mm10

Library id		BAM		CTSS
CNhs10487		DRZ012594		DRZ013977

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

CNhs10487

0	0
1	0.749
10	0
100	0
1000	0
1001	0.0819
1002	-0.0941
1003	0.103
1004	0
1005	0.125
1006	0.631
1007	0.0436
1008	0
1009	-0.0572
101	-0.057
1010	0
1011	0.948
1012	0.452
1013	0.179
1014	-0.0851
1015	-0.0207
1016	0.00992
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.0487
1022	0.058
1023	0
1024	0.0737
1025	0
1026	0
1027	0.193
1028	0
1029	0.0488
103	-0.0861
1030	0
1031	-0.338
1032	0.203
1033	0
1034	0
1035	0
1036	-0.223
1037	0
1038	-0.059
1039	0.103
104	0
1040	-0.216
1041	0

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

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression Analyst: Michiel de Hoon link to dataset. data

library id: CNhs10487

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0105
MA0003.1	MA0003.1	0.342
MA0004.1	MA0004.1	0.59
MA0006.1	MA0006.1	0.126
MA0007.1	MA0007.1	0.45
MA0009.1	MA0009.1	0.885
MA0014.1	MA0014.1	0.641
MA0017.1	MA0017.1	7.89366e-7
MA0018.2	MA0018.2	0.00334
MA0019.1	MA0019.1	0.475
MA0024.1	MA0024.1	0.0232
MA0025.1	MA0025.1	3.19862e-4
MA0027.1	MA0027.1	0.0613
MA0028.1	MA0028.1	0.044
MA0029.1	MA0029.1	0.992
MA0030.1	MA0030.1	0.773
MA0031.1	MA0031.1	0.21
MA0035.2	MA0035.2	0.0268
MA0038.1	MA0038.1	0.398
MA0039.2	MA0039.2	0.0264
MA0040.1	MA0040.1	0.308
MA0041.1	MA0041.1	0.0252
MA0042.1	MA0042.1	0.225
MA0043.1	MA0043.1	0.0214
MA0046.1	MA0046.1	1.55268e-9
MA0047.2	MA0047.2	5.29828e-4
MA0048.1	MA0048.1	0.0238
MA0050.1	MA0050.1	0.00191
MA0051.1	MA0051.1	0.0399
MA0052.1	MA0052.1	0.998
MA0055.1	MA0055.1	0.00297
MA0057.1	MA0057.1	0.479
MA0058.1	MA0058.1	0.476
MA0059.1	MA0059.1	0.148
MA0060.1	MA0060.1	0.534
MA0061.1	MA0061.1	0.0486
MA0062.2	MA0062.2	6.40671e-4
MA0065.2	MA0065.2	5.59256e-6
MA0066.1	MA0066.1	0.0376
MA0067.1	MA0067.1	0.522
MA0068.1	MA0068.1	0.302
MA0069.1	MA0069.1	0.0721
MA0070.1	MA0070.1	0.363
MA0071.1	MA0071.1	0.0349
MA0072.1	MA0072.1	0.363
MA0073.1	MA0073.1	0.905
MA0074.1	MA0074.1	0.112
MA0076.1	MA0076.1	0.103
MA0077.1	MA0077.1	0.648
MA0078.1	MA0078.1	0.935
MA0079.2	MA0079.2	0.342
MA0080.2	MA0080.2	6.93201e-10
MA0081.1	MA0081.1	0.343
MA0083.1	MA0083.1	0.0269
MA0084.1	MA0084.1	0.852
MA0087.1	MA0087.1	0.257
MA0088.1	MA0088.1	0.337
MA0090.1	MA0090.1	0.197
MA0091.1	MA0091.1	0.148
MA0092.1	MA0092.1	0.193
MA0093.1	MA0093.1	0.643
MA0099.2	MA0099.2	0.00857
MA0100.1	MA0100.1	0.259
MA0101.1	MA0101.1	0.0202
MA0102.2	MA0102.2	0.426
MA0103.1	MA0103.1	0.234
MA0104.2	MA0104.2	0.909
MA0105.1	MA0105.1	0.0173
MA0106.1	MA0106.1	0.0477
MA0107.1	MA0107.1	0.0598
MA0108.2	MA0108.2	9.73762e-4
MA0111.1	MA0111.1	0.762
MA0112.2	MA0112.2	0.00132
MA0113.1	MA0113.1	0.563
MA0114.1	MA0114.1	7.01942e-6
MA0115.1	MA0115.1	1.40044e-4
MA0116.1	MA0116.1	0.0776
MA0117.1	MA0117.1	0.928
MA0119.1	MA0119.1	0.156
MA0122.1	MA0122.1	0.545
MA0124.1	MA0124.1	0.364
MA0125.1	MA0125.1	0.0328
MA0131.1	MA0131.1	0.516
MA0135.1	MA0135.1	0.27
MA0136.1	MA0136.1	5.5405e-13
MA0137.2	MA0137.2	0.132
MA0138.2	MA0138.2	4.66998e-5
MA0139.1	MA0139.1	0.604
MA0140.1	MA0140.1	1.88748e-4
MA0141.1	MA0141.1	0.00151
MA0142.1	MA0142.1	0.0973
MA0143.1	MA0143.1	0.933
MA0144.1	MA0144.1	0.0966
MA0145.1	MA0145.1	0.191
MA0146.1	MA0146.1	0.0176
MA0147.1	MA0147.1	0.765
MA0148.1	MA0148.1	0.00155
MA0149.1	MA0149.1	0.132
MA0150.1	MA0150.1	0.182
MA0152.1	MA0152.1	0.256
MA0153.1	MA0153.1	5.71264e-9
MA0154.1	MA0154.1	0.079
MA0155.1	MA0155.1	0.503
MA0156.1	MA0156.1	2.19603e-8
MA0157.1	MA0157.1	0.0919
MA0159.1	MA0159.1	0.00248
MA0160.1	MA0160.1	0.00441
MA0162.1	MA0162.1	0.132
MA0163.1	MA0163.1	0.00224
MA0164.1	MA0164.1	0.933
MA0258.1	MA0258.1	0.0366
MA0259.1	MA0259.1	0.841

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: CNhs10487

Novel motif	Logo	P-value
1	1	0.209
10	10	0.048
100	100	0.304
101	101	0.485
102	102	0.947
103	103	0.106
104	104	0.97
105	105	0.794
106	106	0.102
107	107	0.264
108	108	0.576
109	109	0.00919
11	11	0.0755
110	110	0.0612
111	111	0.196
112	112	0.00875
113	113	0.302
114	114	0.501
115	115	0.688
116	116	0.185
117	117	0.00351
118	118	0.472
119	119	0.372
12	12	0.967
120	120	0.908
121	121	0.866
122	122	0.675
123	123	4.6079e-4
124	124	0.0139
125	125	0.158
126	126	0.029
127	127	0.251
128	128	0.0664
129	129	0.749
13	13	6.68914e-8
130	130	0.149
131	131	0.66
132	132	0.491
133	133	0.687
134	134	0.0849
135	135	0.197
136	136	0.0284
137	137	0.658
138	138	0.649
139	139	0.45
14	14	0.877
140	140	0.0952
141	141	0.822
142	142	0.71
143	143	0.429
144	144	0.795
145	145	5.11567e-4
146	146	0.317
147	147	0.249
148	148	0.946
149	149	0.735
15	15	0.282
150	150	0.0334
151	151	0.987
152	152	0.0859
153	153	0.875
154	154	1
155	155	0.215
156	156	0.00884
157	157	0.199
158	158	0.507
159	159	0.555
160	160	0.169
161	161	0.108
162	162	0.507
163	163	0.518
164	164	0.0532
165	165	0.106
166	166	0.822
167	167	0.779
168	168	0.433
169	169	0.0038
17	17	0.0463
18	18	0.849
19	19	0.0855
2	2	0.665
20	20	0.0202
21	21	0.181
22	22	0.137
23	23	0.973
24	24	0.0546
25	25	0.81
26	26	4.76458e-8
27	27	0.417
28	28	0.766
29	29	0.0262
3	3	0.0658
30	30	0.696
31	31	0.783
32	32	0.643
33	33	0.164
34	34	0.829
35	35	0.756
36	36	0.194
37	37	0.024
38	38	0.651
39	39	0.289
4	4	0.224
40	40	0.105
41	41	0.66
42	42	0.216
43	43	0.142
44	44	0.655
45	45	0.771
46	46	0.144
47	47	0.478
48	48	0.363
49	49	0.196
5	5	0.234
50	50	0.195
51	51	0.798
52	52	0.345
53	53	0.327
54	54	0.998
55	55	0.76
56	56	0.537
57	57	0.73
58	58	0.445
59	59	0.126
6	6	0.877
60	60	0.0549
61	61	0.0383
62	62	0.358
63	63	0.21
64	64	0.735
65	65	0.584
66	66	0.742
67	67	0.905
68	68	0.976
69	69	0.39
7	7	0.0235
70	70	0.142
71	71	0.00469
72	72	0.46
73	73	0.0217
74	74	0.845
75	75	0.0444
76	76	0.324
77	77	0.314
78	78	0.00111
79	79	0.768
8	8	0.0623
80	80	0.196
81	81	0.657
82	82	0.27
83	83	0.159
84	84	0.992
85	85	0.319
86	86	0.211
87	87	0.12
88	88	0.482
89	89	0.908
9	9	0.545
90	90	0.163
91	91	0.101
92	92	0.212
93	93	0.433
94	94	0.841
95	95	0.0198
96	96	0.388
97	97	0.928
98	98	0.769
99	99	0.456

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: CNhs10487

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011288 mouse corpus striatum- adult 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)
0000369 (corpus striatum)
0002435 (striatum)
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)
0001062 (anatomical entity)
0000480 (anatomical group)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0010011 (collection of basal ganglia)
0000204 (ventral part of telencephalon)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011288 (mouse corpus striatum- adult 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:0010082 (future corpus striatum)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00004779
+|accession_numbers=CAGE;DRX008945;DRR009819;DRZ001244;DRZ002627;DRZ012594;DRZ013977
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000955,UBERON:0000369,UBERON:0002435,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:0001062,UBERON:0000480,UBERON:0002420,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0007245,UBERON:0010317,UBERON:0010009,UBERON:0001017,UBERON:0001016,UBERON:0001893,UBERON:0001890,UBERON:0010011,UBERON:0000204,UBERON:0000454
 |ancestors_in_cell_lineage_facet=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.24!195.35!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!2.00!182.09!Tsc22d4;;chr6:85463580..85463585,-!p1@Egr4!1.99!96.53!Egr4;;chr10:67375368..67375433,-!p1@Zfp365!1.90!136.34!Zfp365;;chr12:30219426..30219506,+!p2@Myt1l!1.65!43.46!Myt1l;;chrX:108009761..108009788,+!p1@Pou3f4!1.62!40.72!Pou3f4;;chr2:127347067..127347093,-!p1@Kcnip3!1.57!59.93!Kcnip3;;chr10:67375146..67375208,-!p2@Zfp365!1.57!54.90!Zfp365;;chr2:65683890..65683907,+!p1@Csrnp3!1.51!59.02!Csrnp3;;chr7:116154364..116154444,+!p1@Tub!1.51!53.53!Tub;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.49!37.97!Pou3f3;;chr12:109242266..109242295,-!p1@Bcl11b!1.45!218.23!Bcl11b;;chr10:67375342..67375365,-!p3@Zfp365!1.43!25.62!Zfp365;;chr19:4989964..4989972,-!p1@Npas4!1.42!25.16!Npas4;;chr15:76353005..76353021,-!p2@Scrt1!1.42!25.16!Scrt1;;chr2:115890294..115890334,-!p9@Meis2!1.41!33.40!Meis2;;chr17:48015839..48015915,-!p3@Foxp4!1.41!28.82!Foxp4;;chr4:58956447..58956510,+!p1@Zkscan16!1.40!52.16!Zkscan16;;chr16:91225808..91225824,+!p1@Olig2!1.40!24.25!Olig2;;chr1:169528520..169528542,+!p2@Rxrg!1.39!23.79!Rxrg;;chr17:25707623..25707639,-!p1@Sox8!1.37!94.25!Sox8;;chr1:169528491..169528505,+!p4@Rxrg!1.35!21.50!Rxrg;;chr19:19185671..19185693,-!p1@Rorb!1.34!49.41!Rorb;;chr12:30220074..30220102,+!p3@Myt1l!1.33!20.59!Myt1l;;chr3:95032091..95032183,-!p1@Mllt11!1.32!164.24!Mllt11;;chr4:150482563..150482655,-!p2@Camta1!1.31!68.63!Camta1;;chrX:90531838..90531861,+!p1@Arx!1.31!24.25!Arx;;chr9:91260616..91260653,-!p2@Zic1!1.30!18.76!Zic1;;chr1:169528581..169528607,+!p7@Rxrg!1.29!18.30!Rxrg;;chr9:91260594..91260612,-!p1@Zic1!1.28!17.84!Zic1;;chrX:34442872..34442899,-!p1@Nkrf!1.27!22.88!Nkrf;;chr14:70476975..70476997,+!p2@Egr3!1.26!17.39!Egr3;;chr2:127347094..127347111,-!p2@Kcnip3!1.25!27.45!Kcnip3;;chr4:124334894..124334899,+!p1@Pou3f1!1.24!21.05!Pou3f1;;chr2:77654815..77654872,-!p2@Zfp385b!1.24!20.59!Zfp385b;;chr11:90252223..90252240,-!p1@Hlf!1.23!131.30!Hlf;;chr11:98636531..98636559,-!p1@Nr1d1!1.23!90.59!Nr1d1;;chr1:169528551..169528569,+!p8@Rxrg!1.23!16.01!Rxrg;;chr17:86020156..86020183,+!p1@Six3!1.23!16.01!Six3;;chr11:90251852..90251855,-!p4@Hlf!1.21!18.76!Hlf;;chr14:70477113..70477173,+!p1@Egr3!1.21!15.10!Egr3;;chr12:109241728..109241781,-!p2@Bcl11b!1.20!16.01!Bcl11b;;chr8:24780125..24780143,+!p1@Zmat4!1.19!21.05!Zmat4;;chr12:54349410..54349461,+!p1@Npas3!1.19!17.39!Npas3;;chr12:30213247..30213333,+!p1@Myt1l!1.19!14.64!Myt1l;;chr4:154335024..154335039,+!p1@Hes5!1.18!16.93!Hes5;;chr1:6477388..6477419,+!p3@St18!1.18!14.18!St18;;chr7:146768691..146768707,-!p1@Nkx6-2!1.17!13.73!Nkx6-2;;chr7:52960555..52960662,+!p1@Dbp!1.16!112.55!Dbp;;chr15:78994907..78994926,-!p1@Sox10!1.16!34.77!Sox10;;chr2:38206744..38206766,+!p1@Lhx2!1.16!16.47!Lhx2;;chr7:148008023..148008092,-!p1@Zfp941!1.15!32.03!Zfp941;;chr6:55631042..55631102,-!p1@Neurod6!1.14!12.81!Neurod6;;chr1:169528457..169528482,+!p3@Rxrg!1.14!12.81!Rxrg;;chr15:101097270..101097290,+!p1@Nr4a1!1.13!128.56!Nr4a1;;chr18:36441119..36441158,+!p2@Pura!1.13!30.65!Pura;;chr7:52960700..52960719,+!p2@Dbp!1.13!15.56!Dbp;;chr11:98190918..98190951,-!p1@Neurod2!1.13!12.35!Neurod2;;chr1:169528433..169528456,+!p10@Rxrg!1.13!12.35!Rxrg;;chr6:145813905..145813932,-!p2@Bhlhe41!1.11!22.42!Bhlhe41;;chr16:91270091..91270143,+!p2@Olig1!1.11!11.90!Olig1;;chr4:48058129..48058179,+!p2@Nr4a3!1.10!21.96!Nr4a3;;chr11:90250944..90250982,-!p2@Hlf!1.10!19.67!Hlf;;chr12:72149325..72149343,+!p2@Arid4a!1.10!16.47!Arid4a;;chr7:30092993..30093076,+!p1@Dpf1!1.09!19.67!Dpf1;;chr7:52960888..52960902,+!p7@Dbp!1.09!11.44!Dbp;;chr15:76352677..76352737,-!p3@Scrt1!1.09!11.44!Scrt1;;chr6:6813769..6813781,+!p8@Dlx6!1.09!11.44!Dlx6;;chr7:71083876..71083932,-!p2@Klf13!1.08!87.38!Klf13;;chr19:23216132..23216157,+!p3@Klf9!1.08!17.39!Klf9;;chr10:67000609..67000625,+!p1@Egr2!1.06!24.71!Egr2;;chr11:96685487..96685512,-!p7@Nfe2l1!1.06!10.52!Nfe2l1;;chr14:34791937..34791977,-!p1@Zfp488!1.06!10.52!Zfp488;;chr2:65768174..65768247,+!p2@Csrnp3!1.06!10.52!Csrnp3;;chr18:35020854..35020869,+!p1@Egr1!1.04!384.30!Egr1;;chr6:6831950..6831985,-!p2@Dlx5!1.04!10.98!Dlx5;;chr11:90250894..90250916,-!p5@Hlf!1.04!10.07!Hlf;;chr15:76352434..76352488,-!p4@Scrt1!1.04!10.07!Scrt1;;chr7:52960780..52960793,+!p5@Dbp!1.03!11.44!Dbp;;chrX:137083127..137083138,-!p9@Tsc22d3!1.03!9.61!Tsc22d3;;chr12:30220046..30220070,+!p6@Myt1l!1.03!9.61!Myt1l;;chr19:10315179..10315241,-!p1@Gm98!1.02!99.28!Gm98;;chr7:91558472..91558512,-!p2@Arnt2!1.02!13.73!Arnt2;;chr2:77654936..77654988,-!p4@Zfp385b!1.01!11.44!Zfp385b;;chr4:22415443..22415506,-!p1@Pou3f2!1.01!9.15!Pou3f2;;chr16:91225654..91225671,+!p2@Olig2!1.01!9.15!Olig2;;chr6:6813269..6813272,+!p2@Dlx6!1.01!9.15!Dlx6;;chr2:163051181..163051205,+!p2@Tox2!1.01!9.15!Tox2;;chr12:109242296..109242307,-!p3@Bcl11b!1.00!13.27!Bcl11b;;chr16:95923651..95923701,+!p3@Ets2!0.99!14.18!Ets2;;chr19:23215469..23215494,+!p2@Klf9!0.99!13.73!Klf9;;chr2:71384802..71384815,-!p1@Dlx2!0.99!10.98!Dlx2;;chr2:127347042..127347058,-!p3@Kcnip3!0.99!8.69!Kcnip3;;chr2:168427068..168427115,-!p3@Nfatc2!0.99!8.69!Nfatc2;;chr2:162769220..162769252,+!p1@L3mbtl1!0.97!8.24!L3mbtl1;;chrX:95345005..95345053,+!p1@Ar!0.97!8.24!Ar;;chr4:150482353..150482386,-!p6@Camta1!0.97!8.24!Camta1;;chr8:12395603..12395621,+!p1@Sox1!0.97!8.24!Sox1;;chr8:12395892..12395919,+!p4@Sox1!0.97!8.24!Sox1;;chr15:103170533..103170556,-!p1@Zfp385a!0.96!31.11!Zfp385a;;chr7:52960730..52960762,+!p3@Dbp!0.96!10.52!Dbp;;chr6:6832076..6832092,-!p1@Dlx5!0.96!9.61!Dlx5;;chr6:99471206..99471219,-!p12@Foxp1!0.95!9.15!Foxp1;;chr11:23980664..23980706,+!p2@Bcl11a!0.94!34.31!Bcl11a;;chr6:99471223..99471254,-!p7@Foxp1!0.94!11.90!Foxp1;;chr11:90252108..90252134,-!p6@Hlf!0.94!7.78!Hlf;;chr17:86020137..86020149,+!p5@Six3!0.94!7.78!Six3;;chr2:151907546..151907561,+!p1@Scrt2!0.94!7.78!Scrt2;;chr13:83663546..83663560,+!p4@Mef2c!0.92!9.61!Mef2c;;chr3:34548946..34548972,+!p2@Sox2!0.92!8.24!Sox2;;chr2:73109983..73109996,+!p1@Sp9!0.92!7.32!Sp9;;chr2:151907338..151907360,+!p2@Scrt2!0.92!7.32!Scrt2;;chr2:151907604..151907629,+!p4@Scrt2!0.92!7.32!Scrt2;;chr6:6813551..6813570,+!p5@Dlx6!0.92!7.32!Dlx6;;chr11:96685444..96685473,-!p5@Nfe2l1!0.92!7.32!Nfe2l1;;chr12:50485973..50486015,+!p2@Foxg1!0.92!7.32!Foxg1;;chr6:117813087..117813121,+!p1@Zfp239!0.91!28.37!Zfp239;;chr14:17407878..17407926,-!p1@Rarb!0.91!16.47!Rarb;;chr8:87297878..87297935,-!p3@Nfix!0.91!16.47!Nfix;;chr7:38554763..38554780,-!p1@Zfp536!0.91!13.27!Zfp536;;chr8:79423672..79423727,+!p2@Nr3c2!0.91!9.15!Nr3c2;;chr2:77654650..77654685,-!p3@Zfp385b!0.91!9.15!Zfp385b;;chr3:95032213..95032226,-!p6@Mllt11!0.91!8.69!Mllt11;;chr19:23215446..23215457,+!p8@Klf9!0.91!8.69!Klf9;;chr6:145814003..145814056,-!p1@Bhlhe41!0.90!21.05!Bhlhe41;;chr7:91558392..91558434,-!p1@Arnt2!0.90!19.67!Arnt2;;chr2:81893447..81893468,+!p2@Zfp804a!0.90!6.86!Zfp804a;;chr2:71367142..71367167,+!p2@Dlx1!0.90!6.86!Dlx1;;chr10:84218800..84218829,+!p2@Rfx4!0.90!6.86!Rfx4;;chr13:48356475..48356492,+!p1@Id4!0.89!156.01!Id4;;chr14:17407549..17407575,-!p3@Rarb!0.89!10.52!Rarb;;chr4:150513630..150513686,-!p4@Camta1!0.89!7.78!Camta1;;chr19:59533221..59533271,+!p1@Emx2!0.88!8.24!Emx2;;chr2:38206580..38206600,+!p2@Lhx2!0.88!8.24!Lhx2;;chr4:13670499..13670526,+!p2@Runx1t1!0.87!14.64!Runx1t1;;chr2:56967334..56967366,-!p1@Nr4a2!0.87!13.73!Nr4a2;;chr6:72850124..72850210,-!p7@Kcmf1!0.87!8.69!Kcmf1;;chr19:23216166..23216191,+!p6@Klf9!0.87!8.69!Klf9;;chr2:61642631..61642684,+!p1@Tbr1!0.87!6.41!Tbr1;;chr2:65768149..65768173,+!p4@Csrnp3!0.87!6.41!Csrnp3;;chr2:77541432..77541474,-!p5@Zfp385b!0.87!6.41!Zfp385b;;chrX:108009734..108009752,+!p2@Pou3f4!0.87!6.41!Pou3f4;;chrX:45245644..45245666,-!p2@Smarca1!0.86!21.05!Smarca1;;chr14:55711114..55711159,-!p2@Zfhx2!0.86!14.64!Zfhx2;;chr5:125342568..125342602,+!p2@Zfp664!0.86!10.52!Zfp664;;chr1:39250584..39250643,+!p1@Npas2!0.85!32.48!Npas2;;chr6:99471147..99471161,-!p9@Foxp1!0.85!8.24!Foxp1;;chr15:81641878..81641921,+!p1@Tef!0.84!164.24!Tef;;chr14:19071466..19071550,-!p1@Nr1d2!0.84!43.01!Nr1d2;;chr18:64499674..64499696,+!p1@Onecut2!0.84!10.52!Onecut2;;chr15:100430414..100430470,-!p1@Pou6f1!0.83!18.76!Pou6f1;;chr3:95032197..95032208,-!p3@Mllt11!0.83!7.32!Mllt11;;chr7:30094448..30094481,+!p4@Dpf1!0.82!6.86!Dpf1;;chr14:17407970..17408015,-!p2@Rarb!0.81!15.56!Rarb;;chr4:48058016..48058032,+!p3@Nr4a3!0.81!9.61!Nr4a3;;chr7:30088977..30089002,+!p2@Dpf1!0.81!7.78!Dpf1;;chr7:52960663..52960677,+!p6@Dbp!0.81!5.49!Dbp;;chr6:6831928..6831949,-!p3@Dlx5!0.81!5.49!Dlx5;;chrX:34442842..34442866,-!p3@Nkrf!0.81!5.49!Nkrf;;chr10:42303385..42303401,-!p1@Nr2e1!0.81!5.49!Nr2e1;;chr10:80893711..80893784,-!p3@Nfic!0.80!29.74!Nfic;;chr2:25562263..25562314,+!p2@Bmyc!0.80!22.42!Bmyc;;chr10:13685585..13685645,+!p2@Hivep2!0.80!19.67!Hivep2;;chr11:100800901..100800921,-!p4@Stat3!0.80!6.41!Stat3;;chr6:134780163..134780197,+!p2@Crebl2!0.79!12.81!Crebl2;;chr3:34548909..34548927,+!p1@Sox2!0.79!9.15!Sox2;;chr19:23215554..23215567,+!p5@Klf9!0.79!7.32!Klf9;;chr15:103170516..103170531,-!p2@Zfp385a!0.78!12.81!Zfp385a;;chr19:23215430..23215441,+!p7@Klf9!0.78!6.41!Klf9;;chr17:86020115..86020128,+!p2@Six3!0.78!5.03!Six3;;chr17:86020468..86020504,+!p6@Six3!0.78!5.03!Six3;;chr15:82742573..82742620,-!p2@Tcf20!0.78!5.03!Tcf20;;chr17:86012772..86012825,+!p4@Six3!0.78!5.03!Six3;;chr4:13678723..13678739,+!p10@Runx1t1!0.78!5.03!Runx1t1;;chr2:79296783..79296801,-!p1@Neurod1!0.78!5.03!Neurod1;;chr2:81893535..81893548,+!p1@Zfp804a!0.78!5.03!Zfp804a;;chr6:97879817..97879857,+!p2@Mitf!0.78!5.03!Mitf;;chrX:108009798..108009815,+!p3@Pou3f4!0.78!5.03!Pou3f4;;chr2:163030186..163030204,+!p4@Tox2!0.78!5.03!Tox2;;chr2:65683842..65683856,+!p3@Csrnp3!0.78!5.03!Csrnp3;;chr2:168427120..168427138,-!p4@Nfatc2!0.78!5.03!Nfatc2;;chr15:76352832..76352900,-!p1@Scrt1!0.78!5.03!Scrt1;;chr10:84218895..84218909,+!p1@Rfx4!0.78!5.03!Rfx4;;chr11:90252071..90252093,-!p7@Hlf!0.78!5.03!Hlf;;chr2:115891534..115891589,-!p1@Meis2!0.77!76.86!Meis2;;chr6:14851287..14851342,+!p1@Foxp2!0.77!17.39!Foxp2;;chr16:43503493..43503570,+!p9@Zbt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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011288
 |is_obsolete=
+|library_id=CNhs10487
+|library_id_phase_based=2:CNhs10487
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;19
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;19
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/corpus%2520striatum%252c%2520adult.CNhs10487.19-21D8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/corpus%2520striatum%252c%2520adult.CNhs10487.19-21D8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/corpus%2520striatum%252c%2520adult.CNhs10487.19-21D8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/corpus%2520striatum%252c%2520adult.CNhs10487.19-21D8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/corpus%2520striatum%252c%2520adult.CNhs10487.19-21D8.mm9.nobarcode.rdna.fa.gz
 |name=corpus striatum, adult
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10487,LSID647,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.069807679731332,0,0,0,0,0,0.0789905292703478,0,0,0,0,-0.0843392403965415,0,0,0,0,0.0818043715271035,0,-0.191893350882575,0,0,0,0,0,0.163608743054207,0,0,0,0,0,0,0,-0.394814049269825,0,0,0,0,0.00976194805536292,-0.0457139824416192,0.0929699776180331,-0.0718088666455605,0.803886829822875,0.650255191743164,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,0,0.123752150448911,-0.147041914285179,0.762032786982432,0.10531135288247,0,0,0.111953482474136,0.14860104088051,0,0,0.109836653797666,0.179041649424714,0.150330460577228,-0.0788315948399074,0,0,0,0,0,0,-0.0773372897074742,-0.310010555421208,-0.0821997261596875,0,0,0.573452241475822,0,0
@@ Line 62: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 82: / Line 97: @@
 |top_motifs=POU6F1:2.86388575112;REST:2.82992631515;MYFfamily:2.82793260266;ATF2:2.69354220913;NHLH1,2:2.65941781078;AHR_ARNT_ARNT2:2.64975044326;EGR1..3:2.50140758585;ZBTB6:2.46183840998;MTF1:2.45776826551;OCT4_SOX2{dimer}:2.40751332995;ZFP161:2.39539217798;PRRX1,2:2.3288659123;HBP1_HMGB_SSRP1_UBTF:2.2583678619;PBX1:2.25154164786;MED-1{core}:2.23302789975;LMO2:2.01866246798;HAND1,2:2.0088203736;MAFB:1.98862507902;BREu{core}:1.96609862876;RFX2..5_RFXANK_RFXAP:1.81257216994;RFX1:1.80851621006;CREB1:1.79838447967;HIC1:1.77778548913;PAX5:1.75658098999;RBPJ:1.75105438627;TFAP2B:1.74806507905;PRDM1:1.67666724235;CUX2:1.64545732898;SMAD1..7,9:1.61929503566;MTE{core}:1.61320225492;CDC5L:1.6064280744;JUN:1.57250913019;TGIF1:1.55975889288;GTF2I:1.51786113199;MZF1:1.50269957853;ATF5_CREB3:1.48617640863;FOX{F1,F2,J1}:1.47282365952;TEF:1.42259815025;TFAP2{A,C}:1.42153772592;NFE2L2:1.41233589557;DBP:1.38805129136;NFIL3:1.35088429446;RREB1:1.31347839604;TFDP1:1.30087630046;POU3F1..4:1.2813220396;FOXN1:1.24538356501;PAX6:1.23741877901;KLF4:1.18018783086;ADNP_IRX_SIX_ZHX:1.13406727109;SREBF1,2:1.12690150042;AR:1.12582178928;ALX1:1.08933400578;SOX2:1.06796343201;ZIC1..3:1.06577915781;NKX3-2:1.05919855518;FOXP3:1.05550251499;MYOD1:1.04598728994;HOX{A4,D4}:1.01654022435;NRF1:0.961950340957;NANOG:0.958882462187;STAT1,3:0.928036114907;FOXD3:0.915766178336;GCM1,2:0.911296429062;PDX1:0.909932300487;ZNF143:0.907449101645;bHLH_family:0.897820578311;LHX3,4:0.895735503624;EP300:0.894186637607;PAX2:0.89199282073;TAL1_TCF{3,4,12}:0.861035065307;NR3C1:0.848864165532;GFI1B:0.841739836578;PATZ1:0.809595041686;ZEB1:0.802656000792;PAX4:0.779374893955;MAZ:0.737455163227;NKX6-1,2:0.721281618666;HES1:0.687737032044;FOXM1:0.680508802243;RORA:0.672476830454;VSX1,2:0.663588511564;IKZF1:0.660809793987;GTF2A1,2:0.643820667947;GLI1..3:0.605820061355;SOX{8,9,10}:0.578733588053;POU1F1:0.565416424784;NKX2-3_NKX2-5:0.525545037256;PPARG:0.507452889984;SPZ1:0.489066884208;EVI1:0.474818428793;GZF1:0.459996636635;FOXA2:0.458319478725;HOXA9_MEIS1:0.433767037266;HMGA1,2:0.430353122624;NANOG{mouse}:0.39168043126;NFE2:0.299912666297;SOX17:0.295284759744;TFAP4:0.267733743198;ONECUT1,2:0.26188357554;PAX8:0.246033035505;NKX2-2,8:0.245091735333;NFE2L1:0.2279100928;CDX1,2,4:0.216270437826;ATF4:0.207903668563;ZNF423:0.204942049389;POU5F1:0.182042635107;GATA4:0.159390968906;EBF1:0.128662193124;YY1:0.100943450191;UFEwm:0.100023333241;FOXQ1:0.0810160888394;FOXP1:0.0755489644976;SOX5:0.0642708489618;TFCP2:0.0377656701008;T:0.0257955574727;NFATC1..3:-0.0068980790228;SP1:-0.035510430655;CRX:-0.0488785441099;ESRRA:-0.0609457650007;LEF1_TCF7_TCF7L1,2:-0.0924188074918;BPTF:-0.120440853882;SNAI1..3:-0.142215525582;TLX1..3_NFIC{dimer}:-0.154137950275;HMX1:-0.172989351959;AIRE:-0.212216043464;STAT2,4,6:-0.220856497128;ZNF148:-0.269311122675;HSF1,2:-0.288927036744;ZNF384:-0.290130193022;FOS_FOS{B,L1}_JUN{B,D}:-0.305057437708;MEF2{A,B,C,D}:-0.315836180121;TOPORS:-0.334659200802;GFI1:-0.372436489234;MYBL2:-0.388462310781;FOX{I1,J2}:-0.397688134425;NR5A1,2:-0.431175259155;FOSL2:-0.456951450019;PAX1,9:-0.473439743013;ZNF238:-0.497412967764;NKX2-1,4:-0.507153389127;ZBTB16:-0.533986708451;ATF6:-0.564784832206;XCPE1{core}:-0.579873443969;POU2F1..3:-0.583691076874;ARID5B:-0.584177231625;MYB:-0.644150123748;EN1,2:-0.648752905925;HOX{A5,B5}:-0.67216516109;IRF7:-0.673373834757;HLF:-0.705331900303;SPI1:-0.74234231663;ESR1:-0.763123398729;BACH2:-0.8067786489;ELK1,4_GABP{A,B1}:-0.823966264558;TBX4,5:-0.836183642294;GATA6:-0.837754046947;HNF1A:-0.873031511653;NFKB1_REL_RELA:-0.913255092922;TLX2:-0.915778989793;HIF1A:-0.915899268831;NFY{A,B,C}:-0.918072778677;CEBPA,B_DDIT3:-0.92016366971;HNF4A_NR2F1,2:-0.926923363456;IRF1,2:-0.937957198671;RUNX1..3:-0.958066703707;FOXL1:-0.986437081636;FOX{D1,D2}:-1.06362125809;ETS1,2:-1.11398334002;STAT5{A,B}:-1.14863293633;NKX3-1:-1.16156775565;NR1H4:-1.17342448178;TP53:-1.17920363289;IKZF2:-1.21158111433;TEAD1:-1.21891307716;SPIB:-1.26677332733;ELF1,2,4:-1.37584566801;NR6A1:-1.39241618115;TBP:-1.40846592912;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.41755398591;FOXO1,3,4:-1.4692120441;DMAP1_NCOR{1,2}_SMARC:-1.5373659948;SRF:-1.55047683912;RXR{A,B,G}:-1.60958949191;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.61579321622;E2F1..5:-1.62487930108;RXRA_VDR{dimer}:-1.64584681733;ALX4:-1.84066933212;PITX1..3:-1.85044116913;NFIX:-2.36210955495
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:19-21D8;search_select_hide=table117:19-21D8
 }}

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FF:19-21D8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:09, 4 June 2020

CNhs10487

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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