FF:11646-122D8: Difference between revisions

Latest revision as of 18:13, 4 June 2020

Name:	Mouse Neurons - striatal, donor3
Species:	Mouse (Mus musculus)
Library ID:	CNhs12111
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	corpus striatum
dev stage	NA
sex	NA
age	NA
cell type	neuron
cell line	NA
company	Sciencell/3H
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	RNAMNS1
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005045

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12111		CAGE		DRX008845		DRR009717

Accession ID Mm9

Library id		BAM		CTSS
CNhs12111		DRZ001142		DRZ002527

Accession ID Mm10

Library id		BAM		CTSS
CNhs12111		DRZ012492		DRZ013877

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

CNhs12111

0	0
1	0.398
10	0
100	0.409
1000	-0.0355
1001	-0.0445
1002	-0.00676
1003	-0.0711
1004	0
1005	-0.0459
1006	0.34
1007	-0.177
1008	0
1009	-0.19
101	-0.155
1010	0
1011	0.152
1012	0
1013	-0.0888
1014	0
1015	0.421
1016	0.164
1017	0
1018	0
1019	0
102	0
1020	0.489
1021	0
1022	-0.124
1023	0
1024	-0.152
1025	0
1026	0
1027	0.319
1028	0
1029	-0.115
103	-0.0829
1030	0
1031	-0.393
1032	-0.0325
1033	0
1034	0
1035	0
1036	-0.115
1037	0
1038	0.0553
1039	-0.323
104	0
1040	-0.254
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: CNhs12111

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0037
MA0003.1	MA0003.1	0.172
MA0004.1	MA0004.1	0.645
MA0006.1	MA0006.1	0.0787
MA0007.1	MA0007.1	0.152
MA0009.1	MA0009.1	0.977
MA0014.1	MA0014.1	0.407
MA0017.1	MA0017.1	3.31809e-5
MA0018.2	MA0018.2	0.0193
MA0019.1	MA0019.1	0.325
MA0024.1	MA0024.1	0.921
MA0025.1	MA0025.1	0.213
MA0027.1	MA0027.1	0.537
MA0028.1	MA0028.1	0.528
MA0029.1	MA0029.1	0.811
MA0030.1	MA0030.1	0.264
MA0031.1	MA0031.1	0.0315
MA0035.2	MA0035.2	0.0801
MA0038.1	MA0038.1	0.293
MA0039.2	MA0039.2	0.00892
MA0040.1	MA0040.1	0.471
MA0041.1	MA0041.1	0.375
MA0042.1	MA0042.1	0.84
MA0043.1	MA0043.1	0.132
MA0046.1	MA0046.1	6.08913e-9
MA0047.2	MA0047.2	5.49351e-4
MA0048.1	MA0048.1	0.469
MA0050.1	MA0050.1	1.83841e-10
MA0051.1	MA0051.1	1.86929e-5
MA0052.1	MA0052.1	0.0149
MA0055.1	MA0055.1	0.34
MA0057.1	MA0057.1	0.102
MA0058.1	MA0058.1	0.578
MA0059.1	MA0059.1	0.458
MA0060.1	MA0060.1	0.00366
MA0061.1	MA0061.1	0.0491
MA0062.2	MA0062.2	0.0977
MA0065.2	MA0065.2	2.65608e-5
MA0066.1	MA0066.1	0.233
MA0067.1	MA0067.1	0.785
MA0068.1	MA0068.1	0.924
MA0069.1	MA0069.1	0.127
MA0070.1	MA0070.1	0.944
MA0071.1	MA0071.1	0.175
MA0072.1	MA0072.1	0.126
MA0073.1	MA0073.1	0.738
MA0074.1	MA0074.1	0.323
MA0076.1	MA0076.1	0.91
MA0077.1	MA0077.1	0.0128
MA0078.1	MA0078.1	0.0511
MA0079.2	MA0079.2	0.925
MA0080.2	MA0080.2	2.44692e-10
MA0081.1	MA0081.1	0.285
MA0083.1	MA0083.1	0.00325
MA0084.1	MA0084.1	0.8
MA0087.1	MA0087.1	0.263
MA0088.1	MA0088.1	0.249
MA0090.1	MA0090.1	0.00837
MA0091.1	MA0091.1	0.171
MA0092.1	MA0092.1	0.185
MA0093.1	MA0093.1	0.643
MA0099.2	MA0099.2	9.15911e-5
MA0100.1	MA0100.1	0.965
MA0101.1	MA0101.1	0.0285
MA0102.2	MA0102.2	0.958
MA0103.1	MA0103.1	0.126
MA0104.2	MA0104.2	0.572
MA0105.1	MA0105.1	0.0698
MA0106.1	MA0106.1	0.126
MA0107.1	MA0107.1	0.0313
MA0108.2	MA0108.2	0.0856
MA0111.1	MA0111.1	0.902
MA0112.2	MA0112.2	1.52331e-4
MA0113.1	MA0113.1	0.245
MA0114.1	MA0114.1	7.73243e-5
MA0115.1	MA0115.1	0.0168
MA0116.1	MA0116.1	0.087
MA0117.1	MA0117.1	0.774
MA0119.1	MA0119.1	0.04
MA0122.1	MA0122.1	0.506
MA0124.1	MA0124.1	0.945
MA0125.1	MA0125.1	0.0821
MA0131.1	MA0131.1	0.889
MA0135.1	MA0135.1	0.219
MA0136.1	MA0136.1	2.3536e-8
MA0137.2	MA0137.2	0.00421
MA0138.2	MA0138.2	0.289
MA0139.1	MA0139.1	0.27
MA0140.1	MA0140.1	0.00353
MA0141.1	MA0141.1	0.00534
MA0142.1	MA0142.1	0.0168
MA0143.1	MA0143.1	0.00625
MA0144.1	MA0144.1	0.0101
MA0145.1	MA0145.1	0.0374
MA0146.1	MA0146.1	0.0399
MA0147.1	MA0147.1	0.63
MA0148.1	MA0148.1	2.10993e-6
MA0149.1	MA0149.1	0.0759
MA0150.1	MA0150.1	0.04
MA0152.1	MA0152.1	0.107
MA0153.1	MA0153.1	1.66945e-8
MA0154.1	MA0154.1	0.0174
MA0155.1	MA0155.1	0.765
MA0156.1	MA0156.1	2.29417e-6
MA0157.1	MA0157.1	0.0354
MA0159.1	MA0159.1	0.00503
MA0160.1	MA0160.1	0.0483
MA0162.1	MA0162.1	0.308
MA0163.1	MA0163.1	0.00814
MA0164.1	MA0164.1	0.94
MA0258.1	MA0258.1	0.0138
MA0259.1	MA0259.1	0.512

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: CNhs12111

Novel motif	Logo	P-value
1	1	0.166
10	10	0.132
100	100	0.708
101	101	0.899
102	102	0.728
103	103	0.0713
104	104	0.829
105	105	0.188
106	106	0.00624
107	107	0.0326
108	108	0.476
109	109	0.00171
11	11	0.0877
110	110	0.0973
111	111	0.153
112	112	0.0136
113	113	0.952
114	114	0.275
115	115	0.995
116	116	0.436
117	117	0.0554
118	118	0.531
119	119	0.0993
12	12	0.604
120	120	0.904
121	121	0.286
122	122	0.885
123	123	0.0999
124	124	0.959
125	125	0.452
126	126	0.133
127	127	0.129
128	128	0.038
129	129	0.224
13	13	1.45978e-6
130	130	0.254
131	131	0.695
132	132	0.97
133	133	0.283
134	134	0.478
135	135	0.72
136	136	0.0537
137	137	0.199
138	138	0.74
139	139	0.163
14	14	0.63
140	140	0.192
141	141	0.252
142	142	0.0635
143	143	0.528
144	144	0.902
145	145	0.0216
146	146	0.353
147	147	0.708
148	148	0.421
149	149	0.16
15	15	0.252
150	150	0.126
151	151	0.412
152	152	0.0381
153	153	0.527
154	154	0.712
155	155	0.51
156	156	0.00393
157	157	0.0673
158	158	0.211
159	159	0.218
160	160	0.281
161	161	0.249
162	162	0.807
163	163	0.251
164	164	0.0224
165	165	0.0445
166	166	0.972
167	167	0.805
168	168	0.763
169	169	0.00462
17	17	0.0228
18	18	0.586
19	19	0.0501
2	2	0.842
20	20	0.492
21	21	0.558
22	22	0.0849
23	23	0.28
24	24	0.0353
25	25	0.705
26	26	3.20157e-4
27	27	0.796
28	28	0.317
29	29	0.156
3	3	0.0806
30	30	0.584
31	31	0.921
32	32	0.373
33	33	0.174
34	34	0.415
35	35	0.386
36	36	0.495
37	37	0.00882
38	38	0.303
39	39	0.132
4	4	0.529
40	40	0.188
41	41	0.845
42	42	0.238
43	43	0.142
44	44	0.737
45	45	0.427
46	46	0.16
47	47	0.209
48	48	0.114
49	49	0.17
5	5	0.17
50	50	0.219
51	51	0.55
52	52	0.0882
53	53	0.676
54	54	0.642
55	55	0.915
56	56	0.366
57	57	0.724
58	58	0.266
59	59	0.0688
6	6	0.527
60	60	0.0112
61	61	0.164
62	62	0.155
63	63	0.0821
64	64	0.902
65	65	0.259
66	66	0.843
67	67	0.903
68	68	0.626
69	69	0.517
7	7	0.0189
70	70	0.0145
71	71	0.0179
72	72	0.335
73	73	0.0208
74	74	0.581
75	75	0.148
76	76	0.699
77	77	0.265
78	78	0.0148
79	79	0.591
8	8	0.204
80	80	0.817
81	81	0.543
82	82	0.117
83	83	0.0586
84	84	0.97
85	85	0.0625
86	86	0.272
87	87	0.072
88	88	0.285
89	89	0.246
9	9	0.35
90	90	0.155
91	91	0.32
92	92	0.345
93	93	0.0119
94	94	0.944
95	95	0.0229
96	96	0.32
97	97	0.8
98	98	0.793
99	99	0.237

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: CNhs12111

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000209 mouse striatal neuron 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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002613 (striatum neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0000369 (corpus striatum)
0002435 (striatum)
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)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000209 (mouse striatal neuron 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
CL:0000133 (neurectodermal cell)
CL:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000483,UBERON:0000369,UBERON:0002435,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:0001062,UBERON:0000119,UBERON:0005291,UBERON:0002420,UBERON:0002780,UBERON:0007245,UBERON:0006598,UBERON:0002532,UBERON:0010009,UBERON:0001017,UBERON:0001016,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0001893,UBERON:0001890,UBERON:0005743,UBERON:0010011,UBERON:0000204,UBERON:0003075,UBERON:0003056,UBERON:0001049,UBERON:0006238,UBERON:0000454,UBERON:0010082,UBERON:0006601,UBERON:0005068,UBERON:0006241,UBERON:0003080,UBERON:0006240,UBERON:0007284,UBERON:0007135
+|DRA_sample_Accession=CAGE@SAMD00005045
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000540,CL:0000055,CL:0000047,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002321,CL:0002371,CL:0002319,CL:0000221,CL:0000117,CL:0000393,CL:0000220,CL:0000004,CL:0000031,CL:0000211,CL:0000404,CL:0000255,CL:0002613,CL:0000133,CL:0000337
+|accession_numbers=CAGE;DRX008845;DRR009717;DRZ001142;DRZ002527;DRZ012492;DRZ013877
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0000369,UBERON:0002435,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=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0002613
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000203,FF:0000209
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr19:55969923..55969944,+!p6@Tcf7l2!2.20!156.27!Tcf7l2;;chr9:91260594..91260612,-!p1@Zic1!2.12!132.31!Zic1;;chr19:55968967..55968991,+!p7@Tcf7l2!2.01!102.10!Tcf7l2;;chr19:55969946..55969973,+!p8@Tcf7l2!1.99!95.85!Tcf7l2;;chr9:91260616..91260653,-!p2@Zic1!1.99!95.85!Zic1;;chr3:34548909..34548927,+!p1@Sox2!1.94!142.21!Sox2;;chr1:140739014..140739032,-!p1@Lhx9!1.89!96.89!Lhx9;;chr3:127336052..127336058,+!p1@Neurog2!1.89!77.10!Neurog2;;chr19:55969887..55969904,+!p9@Tcf7l2!1.86!71.37!Tcf7l2;;chrX:90531838..90531861,+!p1@Arx!1.84!84.39!Arx;;chr7:116154364..116154444,+!p1@Tub!1.83!112.52!Tub;;chr12:28027561..28027591,-!p1@Sox11!1.82!407.35!Sox11;;chr3:95032091..95032183,-!p1@Mllt11!1.80!504.24!Mllt11;;chr3:101814061..101814094,+!p1@Nhlh2!1.73!52.61!Nhlh2;;chr14:122874619..122874634,+!p1@Zic2!1.68!46.36!Zic2;;chr2:71367871..71367898,+!p1@Dlx1!1.66!44.28!Dlx1;;chr4:107353376..107353452,-!p3@Dmrtb1!1.66!44.28!Dmrtb1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.62!51.57!Pou3f3;;chr19:55967803..55967834,+!p12@Tcf7l2!1.61!40.11!Tcf7l2;;chr17:48015839..48015915,-!p3@Foxp4!1.60!45.84!Foxp4;;chr16:91270004..91270023,+!p1@Olig1!1.59!42.71!Olig1;;chrX:108009761..108009788,+!p1@Pou3f4!1.59!37.51!Pou3f4;;chr11:84339016..84339044,-!p1@Lhx1!1.59!37.51!Lhx1;;chrX:55283799..55283813,+!p1@Zic3!1.58!36.98!Zic3;;chr6:55631042..55631102,-!p1@Neurod6!1.57!36.46!Neurod6;;chr2:71384802..71384815,-!p1@Dlx2!1.54!41.67!Dlx2;;chr2:38206580..38206600,+!p2@Lhx2!1.54!41.67!Lhx2;;chr12:30213247..30213333,+!p1@Myt1l!1.53!32.82!Myt1l;;chr2:65683890..65683907,+!p1@Csrnp3!1.48!55.22!Csrnp3;;chr4:154335024..154335039,+!p1@Hes5!1.48!34.90!Hes5;;chr4:107353508..107353547,-!p4@Dmrtb1!1.48!29.17!Dmrtb1;;chr7:91558472..91558512,-!p2@Arnt2!1.43!36.98!Arnt2;;chr7:30088977..30089002,+!p2@Dpf1!1.43!35.42!Dpf1;;chr1:91827756..91827773,-!p1@Gbx2!1.43!26.05!Gbx2;;chr1:91827728..91827743,-!p2@Gbx2!1.42!25.00!Gbx2;;chr3:34548946..34548972,+!p2@Sox2!1.40!26.57!Sox2;;chr7:25292331..25292421,+!p1@Zfp428!1.38!157.84!Zfp428;;chr12:54349410..54349461,+!p1@Npas3!1.38!27.61!Npas3;;chr9:91263879..91263911,+!p1@Zic4!1.37!22.40!Zic4;;chr19:55967842..55967878,+!p13@Tcf7l2!1.36!21.88!Tcf7l2;;chrX:58146612..58146615,-!p1@Sox3!1.36!21.88!Sox3;;chr2:38206744..38206766,+!p1@Lhx2!1.35!25.52!Lhx2;;chr8:12395603..12395621,+!p1@Sox1!1.35!21.36!Sox1;;chr15:76352832..76352900,-!p1@Scrt1!1.35!21.36!Scrt1;;chr7:30092993..30093076,+!p1@Dpf1!1.33!34.38!Dpf1;;chr2:71367142..71367167,+!p2@Dlx1!1.33!20.32!Dlx1;;chr19:55969687..55969714,+!p16@Tcf7l2!1.32!19.79!Tcf7l2;;chr2:146047829..146047847,+!p1@Insm1!1.31!34.38!Insm1;;chr10:86956396..86956411,-!p1@Ascl1!1.31!29.69!Ascl1;;chr2:147012125..147012149,-!p1@Nkx2-2!1.30!18.75!Nkx2-2;;chr13:95645580..95645598,+!p1@Otp!1.30!18.75!Otp;;chr14:49287186..49287225,-!p1@Otx2!1.30!18.75!Otx2;;chr13:44936126..44936164,+!p6@Jarid2!1.28!20.84!Jarid2;;chr2:65768174..65768247,+!p2@Csrnp3!1.27!17.71!Csrnp3;;chr9:118387300..118387317,+!p1@Eomes!1.27!17.71!Eomes;;chr7:56892217..56892221,-!p1@Dbx1!1.27!17.71!Dbx1;;chr16:91225808..91225824,+!p1@Olig2!1.25!16.67!Olig2;;chr17:86020115..86020128,+!p2@Six3!1.25!16.67!Six3;;chr13:48356475..48356492,+!p1@Id4!1.23!336.51!Id4;;chr2:79296783..79296801,-!p1@Neurod1!1.23!16.15!Neurod1;;chr5:120881900..120881914,+!p1@Lhx5!1.23!16.15!Lhx5;;chr2:73110004..73110016,+!p2@Sp9!1.22!15.63!Sp9;;chr9:99776566..99776612,-!p1@Sox14!1.21!15.11!Sox14;;chr11:21901608..21901634,-!p1@Otx1!1.21!15.11!Otx1;;chr13:117099847..117099907,-!p1@Isl1!1.19!26.57!Isl1;;chr4:107353346..107353375,-!p5@Dmrtb1!1.18!14.06!Dmrtb1;;chr4:13670499..13670526,+!p2@Runx1t1!1.16!29.69!Runx1t1;;chr6:6832076..6832092,-!p1@Dlx5!1.16!15.63!Dlx5;;chr7:91558392..91558434,-!p1@Arnt2!1.15!35.94!Arnt2;;chr4:107353563..107353590,-!p6@Dmrtb1!1.15!13.02!Dmrtb1;;chr15:76352740..76352781,-!p5@Scrt1!1.15!13.02!Scrt1;;chr2:56967334..56967366,-!p1@Nr4a2!1.14!26.05!Nr4a2;;chr17:37140628..37140631,+!p2@Zfp57!1.13!25.00!Zfp57;;chr13:78339382..78339420,-!p3@Nr2f1!1.13!14.59!Nr2f1;;chr2:73109983..73109996,+!p1@Sp9!1.13!12.50!Sp9;;chr5:106887474..106887489,-!p1@Barhl2!1.13!12.50!Barhl2;;chr6:6831950..6831985,-!p2@Dlx5!1.11!13.02!Dlx5;;chr12:30219426..30219506,+!p2@Myt1l!1.11!11.98!Myt1l;;chr2:146911200..146911219,-!p1@Nkx2-4!1.11!11.98!Nkx2-4;;chr2:181501745..181501778,+!p1@Myt1!1.10!11.46!Myt1;;chr5:98609885..98609900,+!p1@Prdm8!1.10!11.46!Prdm8;;chr5:24104751..24104773,-!p5@Smarcd3!1.10!11.46!Smarcd3;;chr4:107353455..107353476,-!p8@Dmrtb1!1.10!11.46!Dmrtb1;;chr4:109650609..109650653,+!p1@Dmrta2!1.10!11.46!Dmrta2;;chr17:86020156..86020183,+!p1@Six3!1.10!11.46!Six3;;chr7:148008023..148008092,-!p1@Zfp941!1.08!26.57!Zfp941;;chr18:64499706..64499721,+!p2@Onecut2!1.08!15.63!Onecut2;;chr3:95032184..95032195,-!p4@Mllt11!1.08!13.54!Mllt11;;chr4:150503457..150503498,-!p3@Camta1!1.08!12.50!Camta1;;chr4:22415443..22415506,-!p1@Pou3f2!1.08!10.94!Pou3f2;;chr11:98190918..98190951,-!p1@Neurod2!1.08!10.94!Neurod2;;chr10:84218895..84218909,+!p1@Rfx4!1.06!10.42!Rfx4;;chr3:66785857..66785873,-!p1@Shox2!1.06!10.42!Shox2;;chr4:13678723..13678739,+!p10@Runx1t1!1.06!10.42!Runx1t1;;chr19:55967419..55967424,+!p19@Tcf7l2!1.06!10.42!Tcf7l2;;chr15:76352677..76352737,-!p3@Scrt1!1.06!10.42!Scrt1;;chr5:140019843..140019858,+!p2@Uncx!1.06!10.42!Uncx;;chr6:6831928..6831949,-!p3@Dlx5!1.06!10.42!Dlx5;;chr17:37139472..37139514,+!p1@Zfp57!1.05!69.28!Zfp57;;chr4:150482563..150482655,-!p2@Camta1!1.05!36.46!Camta1;;chr7:130644017..130644092,-!p1@Zkscan2!1.05!19.79!Zkscan2;;chr19:59533221..59533271,+!p1@Emx2!1.05!12.50!Emx2;;chr7:135019147..135019187,-!p3@Zfp668!1.04!21.88!Zfp668;;chr7:144505957..144505972,-!p2@Ebf3!1.04!12.50!Ebf3;;chr5:140019865..140019886,+!p1@Uncx!1.04!9.90!Uncx;;chr2:152223734..152223756,-!p6@Sox12!1.03!11.46!Sox12;;chr4:122673278..122673336,+!p1@Mycl1!1.02!30.73!Mycl1;;chr9:69608672..69608686,-!p1@Foxb1!1.02!9.38!Foxb1;;chr2:31495237..31495243,+!p1@Prdm12!1.02!9.38!Prdm12;;chr2:181501710..181501742,+!p2@Myt1!1.02!9.38!Myt1;;chr17:86020510..86020589,+!p3@Six3!1.02!9.38!Six3;;chr9:18278055..18278126,-!p1@Zfp558!1.01!27.09!Zfp558;;chr19:19185671..19185693,-!p1@Rorb!1.01!22.40!Rorb;;chr17:35031589..35031630,+!p2@Zbtb12!1.01!17.19!Zbtb12;;chr1:189821714..189821761,+!p1@Esrrg!1.01!17.19!Esrrg;;chr13:78339428..78339466,-!p2@Nr2f1!1.00!12.50!Nr2f1;;chr13:78338076..78338104,-!p4@Nr2f1!1.00!11.46!Nr2f1;;chr2:163028808..163028869,+!p1@Tox2!0.99!32.30!Tox2;;chr3:95032197..95032208,-!p3@Mllt11!0.99!10.94!Mllt11;;chr19:55969646..55969665,+!p26@Tcf7l2!0.99!8.86!Tcf7l2;;chr5:148000254..148000260,+!p1@Gsx1!0.99!8.86!Gsx1;;chr10:84218800..84218829,+!p2@Rfx4!0.99!8.86!Rfx4;;chr15:76353005..76353021,-!p2@Scrt1!0.99!8.86!Scrt1;;chr13:78339241..78339273,-!p9@Nr2f1!0.99!8.86!Nr2f1;;chr9:74709695..74709722,+!p1@Onecut1!0.99!8.86!Onecut1;;chr7:30089006..30089022,+!p3@Dpf1!0.99!8.86!Dpf1;;chr15:75447162..75447217,+!p2@Zfp41!0.98!26.05!Zfp41;;chr2:152223783..152223812,-!p4@Sox12!0.98!19.79!Sox12;;chr4:13670571..13670625,+!p1@Runx1t1!0.97!23.44!Runx1t1;;chr3:128916868..128916890,+!p1@Pitx2!0.97!11.46!Pitx2;;chr19:55969980..55969987,+!p37@Tcf7l2!0.97!8.33!Tcf7l2;;chr14:122874593..122874610,+!p2@Zic2!0.97!8.33!Zic2;;chr12:57637732..57637777,-!p5@Nkx2-1!0.97!8.33!Nkx2-1;;chrX:108009734..108009752,+!p2@Pou3f4!0.97!8.33!Pou3f4;;chr19:55816546..55816556,+!p3@Tcf7l2!0.95!31.25!Tcf7l2;;chr7:144506077..144506128,-!p1@Ebf3!0.95!18.75!Ebf3;;chrX:34442872..34442899,-!p1@Nkrf!0.95!10.42!Nkrf;;chr4:13669922..13669957,+!p13@Runx1t1!0.95!7.81!Runx1t1;;chr1:140739042..140739054,-!p2@Lhx9!0.95!7.81!Lhx9;;chr19:55968937..55968951,+!p21@Tcf7l2!0.95!7.81!Tcf7l2;;chr1:140744193..140744208,-!p4@Lhx9!0.95!7.81!Lhx9;;chr1:173987720..173987729,-!p1@Nhlh1!0.95!7.81!Nhlh1;;chr7:91520922..91520956,-!p5@Arnt2!0.95!7.81!Arnt2;;chr14:122874718..122874729,+!p3@Zic2!0.95!7.81!Zic2;;chr1:191994550..191994623,-!p1@Prox1!0.94!55.22!Prox1;;chr8:87297280..87297326,-!p2@Nfix!0.94!18.75!Nfix;;chr13:29045559..29045574,-!p1@Sox4!0.93!639.68!Sox4;;chr1:179374784..179374800,+!p2@Zfp238!0.93!8.86!Zfp238;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.92!20.32!Zfhx3;;chr13:78339476..78339515,-!p1@Nr2f1!0.92!11.46!Nr2f1;;chr4:22415290..22415307,-!p2@Pou3f2!0.92!7.29!Pou3f2;;chr3:128902837..128902861,+!p3@Pitx2!0.92!7.29!Pitx2;;chr4:13678482..13678505,+!p9@Runx1t1!0.92!7.29!Runx1t1;;chr2:65768149..65768173,+!p4@Csrnp3!0.92!7.29!Csrnp3;;chr19:55972441..55972456,+!p18@Tcf7l2!0.92!7.29!Tcf7l2;;chr7:25292160..25292213,+!p3@Zfp428!0.91!18.23!Zfp428;;chr13:72101178..72101203,-!p1@Irx1!0.91!11.46!Irx1;;chr1:170361991..170362015,-!p6@Pbx1!0.90!16.15!Pbx1;;chr6:47780508..47780583,-!p1@Zfp786!0.90!13.54!Zfp786;;chr13:72766250..72766273,+!p1@Irx2!0.90!10.94!Irx2;;chr5:107003725..107003746,-!p5@Zfp644!0.90!9.38!Zfp644;;chr4:129118044..129118067,-!p1@Zbtb8b!0.90!8.86!Zbtb8b;;chr14:55711114..55711159,-!p2@Zfhx2!0.89!15.63!Zfhx2;;chr4:124334894..124334899,+!p1@Pou3f1!0.89!8.86!Pou3f1;;chr4:13678684..13678704,+!p17@Runx1t1!0.89!6.77!Runx1t1;;chr3:34548845..34548856,+!p4@Sox2!0.89!6.77!Sox2;;chr19:55972403..55972421,+!p22@Tcf7l2!0.89!6.77!Tcf7l2;;chr19:55968827..55968868,+!p29@Tcf7l2!0.89!6.77!Tcf7l2;;chrX:110837933..110837958,+!p2@Dach2!0.89!6.77!Dach2;;chr13:95645608..95645616,+!p2@Otp!0.89!6.77!Otp;;chr8:90483459..90483475,-!p1@Zfp423!0.88!18.75!Zfp423;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.88!11.98!Zfhx3;;chr4:13670626..13670657,+!p5@Runx1t1!0.88!10.42!Runx1t1;;chr13:78339134..78339185,-!p5@Nr2f1!0.88!8.33!Nr2f1;;chr3:95032558..95032641,-!p2@Mllt11!0.87!37.51!Mllt11;;chr4:54960870..54960926,+!p1@Zfp462!0.87!24.48!Zfp462;;chr7:25372631..25372684,-!p1@Zfp575!0.87!20.32!Zfp575;;chr8:111227354..111227401,+!p@chr8:111227354..111227401,+!0.87!8.86!Zfhx3;;chr5:24107676..24107722,-!p4@Smarcd3!0.87!8.86!Smarcd3;;chr17:37139455..37139469,+!p3@Zfp57!0.86!9.90!Zfp57;;chr6:6812962..6812979,+!p1@Dlx6!0.86!6.25!Dlx6;;chr6:23198371..23198390,-!p1@Fezf1!0.86!6.25!Fezf1;;chr6:6812988..6813002,+!p3@Dlx6!0.86!6.25!Dlx6;;chr2:71366660..7136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+|ffid_belonging_in_development=CL:0000133,CL:0000337,CL:0000031,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:11646-122D8
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000209
+|is_a=EFO:0002091;;FF:0000209
+|is_obsolete=
+|library_id=CNhs12111
+|library_id_phase_based=2:CNhs12111
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11646
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11646
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor3.CNhs12111.11646-122D8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor3.CNhs12111.11646-122D8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor3.CNhs12111.11646-122D8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor3.CNhs12111.11646-122D8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor3.CNhs12111.11646-122D8.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - striatal, donor3
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12111,LSID839,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.160630945989308,0,0,0,0,0,-0.153017719324371,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.118125536441913,0,0,0,0,0,0,0,0,0,0,0,0,0.368070143704165,-0.558422792324031,0,0,0,0,0,-0.054313281833582,0.198704881729365,0.0104920709896117,0.299812360535397,0.558149464078341,0.48906556937507,0,0,0,0,0,0,0,0,0,0,0,0.116098930289281,0,0,0,0,0,0,-0.130696565450787,0,0,0,-0.20244242069718,-0.310650657339386,-0.158091042771083,0.016310765424639,0,0,0.166127202859393,0,0,0,0.11099939945045,0.0891208986984317,0.374181479893529,-0.0788315948399074,0,0,0,0,0,0,0.182104477852721,0.0250268583701239,0.138901564237547,0,0,0,0.321353282817222,0
 |rna_box=122
 |rna_catalog_number=custom
@@ Line 57: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=N/A
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=corpus striatum
 |top_motifs=ADNP_IRX_SIX_ZHX:2.63070714208;LHX3,4:2.5397291796;TFDP1:2.50549689684;SOX2:2.44503831509;ALX1:2.33410305558;VSX1,2:2.18897817906;ZFP161:2.13574339603;MED-1{core}:2.12265571543;BREu{core}:2.10504812035;POU6F1:2.05050805978;ZIC1..3:2.04976473389;MZF1:2.0339696425;MTE{core}:2.01342020097;PRRX1,2:2.0085450645;NKX6-1,2:1.94337781756;AHR_ARNT_ARNT2:1.94076893255;PAX6:1.93845361067;SOX{8,9,10}:1.8528088577;OCT4_SOX2{dimer}:1.81047414643;POU3F1..4:1.73644173103;LEF1_TCF7_TCF7L1,2:1.73406099377;FOXQ1:1.69944431225;PRDM1:1.66565769928;RFX1:1.58267026721;RREB1:1.57658421833;NRF1:1.57245511752;ONECUT1,2:1.5563945614;ZBTB6:1.54616161974;FOXD3:1.52504206342;CDC5L:1.50719482891;DBP:1.48589064776;TFAP2B:1.46385037285;REST:1.44930811215;KLF4:1.42917177952;PATZ1:1.40095385754;UFEwm:1.38436015475;EGR1..3:1.38234875554;HIC1:1.36099150677;SOX17:1.32831491426;NANOG:1.27750986796;HOXA9_MEIS1:1.19884359395;FOXP3:1.19110463188;ATF2:1.1805818789;POU5F1:1.17320520134;RFX2..5_RFXANK_RFXAP:1.16751935254;LMO2:1.13999399927;HOX{A5,B5}:1.09582360662;SMAD1..7,9:1.05635089439;YY1:1.05180151015;HMGA1,2:1.04784886382;PAX8:1.02720319544;MYFfamily:1.00605100003;FOXM1:1.0022427702;GATA4:0.964853229863;EN1,2:0.954433814317;HES1:0.932441602873;PAX4:0.894722678754;GTF2I:0.8938606279;NHLH1,2:0.875081958043;JUN:0.87371843361;CUX2:0.829929006695;POU1F1:0.827737813356;ZNF143:0.824269493407;NKX3-2:0.798784256436;ZNF384:0.789402241667;RBPJ:0.777374847194;NKX2-3_NKX2-5:0.768299823764;MTF1:0.713516065322;HMX1:0.682011070564;HAND1,2:0.672820769936;ZNF423:0.659661788743;NANOG{mouse}:0.634934535278;ATF5_CREB3:0.626468362025;BPTF:0.61867392365;GFI1B:0.604405484667;HOX{A4,D4}:0.598709795157;HBP1_HMGB_SSRP1_UBTF:0.593020524637;FOXL1:0.574617290716;PAX5:0.570077350181;EP300:0.563750459867;SOX5:0.551708474391;POU2F1..3:0.550719032744;NR3C1:0.53176504667;TBX4,5:0.509443434216;NFE2L1:0.506594925437;ELK1,4_GABP{A,B1}:0.493846003482;NR5A1,2:0.4841267021;NKX2-1,4:0.468127981732;MAZ:0.468024243671;TGIF1:0.392796879167;NFY{A,B,C}:0.379122462972;CREB1:0.362316592963;EVI1:0.317309138363;HSF1,2:0.296607217538;RORA:0.247679264001;ZBTB16:0.240164994949;FOXN1:0.193120458376;PPARG:0.192839651761;FOX{I1,J2}:0.182976899673;GZF1:0.182761920045;NKX3-1:0.176412604683;IKZF2:0.168847775925;FOX{F1,F2,J1}:0.139477435003;CRX:0.135349615558;RXR{A,B,G}:0.124453393423;PAX2:0.086161910669;MAFB:0.082611734981;AIRE:0.00651158439816;STAT5{A,B}:-0.0887803563522;NFIX:-0.0930324294504;T:-0.0974040902429;ZEB1:-0.106836487344;HIF1A:-0.115929376578;ARID5B:-0.123465346489;NKX2-2,8:-0.145701381647;MYOD1:-0.150461159782;FOXP1:-0.163525177598;NFIL3:-0.171998285108;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.189435209098;CDX1,2,4:-0.200623510861;GTF2A1,2:-0.202958645725;TFAP4:-0.220326833249;MYB:-0.230015470054;ATF4:-0.236481752684;TEF:-0.292032584593;PBX1:-0.349272818142;SPZ1:-0.358159479987;RUNX1..3:-0.363690855037;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.364980219973;NR1H4:-0.367608462061;STAT1,3:-0.373310441463;GFI1:-0.392629253921;TFAP2{A,C}:-0.412495702102;PAX1,9:-0.451146542816;PITX1..3:-0.460516619238;GLI1..3:-0.46264393638;SP1:-0.482648751813;XCPE1{core}:-0.533051737068;ZNF238:-0.559602108881;HNF4A_NR2F1,2:-0.561419036652;SREBF1,2:-0.563344604471;IKZF1:-0.569541694269;ESR1:-0.575979187772;bHLH_family:-0.580600979513;MEF2{A,B,C,D}:-0.606239482927;GCM1,2:-0.610255720609;TAL1_TCF{3,4,12}:-0.615741384549;SNAI1..3:-0.617717846494;TLX2:-0.623492549287;FOXA2:-0.625093227212;TP53:-0.634589568826;TOPORS:-0.698368796765;HNF1A:-0.698639720461;AR:-0.711829158596;GATA6:-0.716610479613;SPI1:-0.733713188421;SPIB:-0.768070737781;E2F1..5:-0.769767218214;HLF:-0.781714013246;TLX1..3_NFIC{dimer}:-0.810992361321;NFE2:-0.829412245016;NFKB1_REL_RELA:-0.857586930554;ESRRA:-0.859635545085;TBP:-0.866297640641;ZNF148:-0.915699475426;MYBL2:-0.939407597837;ELF1,2,4:-0.974504985992;CEBPA,B_DDIT3:-1.00030497185;ALX4:-1.00702390555;ATF6:-1.05994508385;FOSL2:-1.07366320695;BACH2:-1.11872937124;TFCP2:-1.12065378609;NFE2L2:-1.13372856903;EBF1:-1.1399926162;TEAD1:-1.17649336767;ETS1,2:-1.18696014409;RXRA_VDR{dimer}:-1.2981169771;FOS_FOS{B,L1}_JUN{B,D}:-1.33714889241;FOX{D1,D2}:-1.34007939062;FOXO1,3,4:-1.37745527526;DMAP1_NCOR{1,2}_SMARC:-1.39290122054;NFATC1..3:-1.41199898885;IRF7:-1.49320407843;PDX1:-1.54148164806;SRF:-1.562931927;IRF1,2:-1.6546577304;NR6A1:-1.71818812591;STAT2,4,6:-1.94453750418
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11646-122D8;search_select_hide=table117:11646-122D8
 }}

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FF:11646-122D8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:13, 4 June 2020

CNhs12111

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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