FF:11723-123D4: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Neurons - striatal, donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs12134
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	RNAMNS2
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005105

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12134		CAGE		DRX008843		DRR009715

Accession ID Mm9

Library id		BAM		CTSS
CNhs12134		DRZ001140		DRZ002525

Accession ID Mm10

Library id		BAM		CTSS
CNhs12134		DRZ012490		DRZ013875

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

CNhs12134

0	0
1	0.38
10	0
100	0.412
1000	-0.0355
1001	-0.0749
1002	-0.0618
1003	-0.00666
1004	0.0269
1005	-0.166
1006	0.297
1007	-0.0387
1008	0
1009	-0.2
101	-0.189
1010	0
1011	0.117
1012	0
1013	-0.0029
1014	0.0143
1015	0.377
1016	0.314
1017	0
1018	0
1019	0
102	0
1020	0.646
1021	0.053
1022	-0.0704
1023	0
1024	-0.221
1025	-0.016
1026	0
1027	0.223
1028	0
1029	-0.148
103	-0.0848
1030	0
1031	-0.467
1032	0.06
1033	0.0538
1034	0
1035	0
1036	-0.208
1037	0
1038	0.0708
1039	-0.219
104	0
1040	-0.162
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: CNhs12134

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00401
MA0003.1	MA0003.1	0.184
MA0004.1	MA0004.1	0.627
MA0006.1	MA0006.1	0.0938
MA0007.1	MA0007.1	0.152
MA0009.1	MA0009.1	0.915
MA0014.1	MA0014.1	0.412
MA0017.1	MA0017.1	4.29699e-5
MA0018.2	MA0018.2	0.0103
MA0019.1	MA0019.1	0.314
MA0024.1	MA0024.1	0.896
MA0025.1	MA0025.1	0.697
MA0027.1	MA0027.1	0.619
MA0028.1	MA0028.1	0.504
MA0029.1	MA0029.1	0.505
MA0030.1	MA0030.1	0.326
MA0031.1	MA0031.1	0.0816
MA0035.2	MA0035.2	0.156
MA0038.1	MA0038.1	0.252
MA0039.2	MA0039.2	0.0235
MA0040.1	MA0040.1	0.785
MA0041.1	MA0041.1	0.23
MA0042.1	MA0042.1	0.561
MA0043.1	MA0043.1	0.0541
MA0046.1	MA0046.1	2.23386e-7
MA0047.2	MA0047.2	0.0022
MA0048.1	MA0048.1	0.346
MA0050.1	MA0050.1	2.95862e-9
MA0051.1	MA0051.1	2.92578e-4
MA0052.1	MA0052.1	0.0985
MA0055.1	MA0055.1	0.362
MA0057.1	MA0057.1	0.0881
MA0058.1	MA0058.1	0.581
MA0059.1	MA0059.1	0.408
MA0060.1	MA0060.1	0.00105
MA0061.1	MA0061.1	0.0474
MA0062.2	MA0062.2	0.146
MA0065.2	MA0065.2	2.791e-5
MA0066.1	MA0066.1	0.147
MA0067.1	MA0067.1	0.888
MA0068.1	MA0068.1	0.821
MA0069.1	MA0069.1	0.0918
MA0070.1	MA0070.1	0.357
MA0071.1	MA0071.1	0.253
MA0072.1	MA0072.1	0.222
MA0073.1	MA0073.1	0.936
MA0074.1	MA0074.1	0.37
MA0076.1	MA0076.1	0.807
MA0077.1	MA0077.1	0.00881
MA0078.1	MA0078.1	0.0557
MA0079.2	MA0079.2	0.622
MA0080.2	MA0080.2	8.0982e-10
MA0081.1	MA0081.1	0.353
MA0083.1	MA0083.1	0.00623
MA0084.1	MA0084.1	0.653
MA0087.1	MA0087.1	0.406
MA0088.1	MA0088.1	0.188
MA0090.1	MA0090.1	0.00821
MA0091.1	MA0091.1	0.216
MA0092.1	MA0092.1	0.135
MA0093.1	MA0093.1	0.632
MA0099.2	MA0099.2	1.66632e-4
MA0100.1	MA0100.1	0.943
MA0101.1	MA0101.1	0.054
MA0102.2	MA0102.2	0.914
MA0103.1	MA0103.1	0.168
MA0104.2	MA0104.2	0.618
MA0105.1	MA0105.1	0.0312
MA0106.1	MA0106.1	0.108
MA0107.1	MA0107.1	0.048
MA0108.2	MA0108.2	0.107
MA0111.1	MA0111.1	0.995
MA0112.2	MA0112.2	1.27478e-4
MA0113.1	MA0113.1	0.236
MA0114.1	MA0114.1	1.1707e-4
MA0115.1	MA0115.1	0.00722
MA0116.1	MA0116.1	0.0636
MA0117.1	MA0117.1	0.738
MA0119.1	MA0119.1	0.0437
MA0122.1	MA0122.1	0.556
MA0124.1	MA0124.1	0.866
MA0125.1	MA0125.1	0.151
MA0131.1	MA0131.1	0.879
MA0135.1	MA0135.1	0.15
MA0136.1	MA0136.1	1.29154e-7
MA0137.2	MA0137.2	0.00749
MA0138.2	MA0138.2	0.224
MA0139.1	MA0139.1	0.261
MA0140.1	MA0140.1	0.00484
MA0141.1	MA0141.1	0.0112
MA0142.1	MA0142.1	0.0218
MA0143.1	MA0143.1	0.00618
MA0144.1	MA0144.1	0.0192
MA0145.1	MA0145.1	0.0565
MA0146.1	MA0146.1	0.0514
MA0147.1	MA0147.1	0.686
MA0148.1	MA0148.1	1.64095e-5
MA0149.1	MA0149.1	0.0816
MA0150.1	MA0150.1	0.0342
MA0152.1	MA0152.1	0.152
MA0153.1	MA0153.1	5.91923e-7
MA0154.1	MA0154.1	0.0154
MA0155.1	MA0155.1	0.639
MA0156.1	MA0156.1	4.83295e-5
MA0157.1	MA0157.1	0.0566
MA0159.1	MA0159.1	0.0034
MA0160.1	MA0160.1	0.0723
MA0162.1	MA0162.1	0.294
MA0163.1	MA0163.1	0.0023
MA0164.1	MA0164.1	0.908
MA0258.1	MA0258.1	0.0121
MA0259.1	MA0259.1	0.554

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: CNhs12134

Novel motif	Logo	P-value
1	1	0.145
10	10	0.09
100	100	0.758
101	101	0.977
102	102	0.894
103	103	0.0893
104	104	0.97
105	105	0.155
106	106	0.00713
107	107	0.0454
108	108	0.53
109	109	0.00372
11	11	0.0839
110	110	0.0912
111	111	0.0951
112	112	0.00627
113	113	0.962
114	114	0.305
115	115	0.564
116	116	0.492
117	117	0.0474
118	118	0.428
119	119	0.142
12	12	0.682
120	120	0.878
121	121	0.448
122	122	0.782
123	123	0.181
124	124	0.642
125	125	0.384
126	126	0.233
127	127	0.134
128	128	0.0216
129	129	0.279
13	13	5.77667e-6
130	130	0.359
131	131	0.384
132	132	0.946
133	133	0.231
134	134	0.364
135	135	0.638
136	136	0.204
137	137	0.223
138	138	0.646
139	139	0.105
14	14	0.674
140	140	0.0429
141	141	0.261
142	142	0.0179
143	143	0.536
144	144	0.995
145	145	0.0126
146	146	0.406
147	147	0.789
148	148	0.409
149	149	0.116
15	15	0.18
150	150	0.132
151	151	0.457
152	152	0.0521
153	153	0.522
154	154	0.703
155	155	0.663
156	156	0.00879
157	157	0.111
158	158	0.22
159	159	0.124
160	160	0.198
161	161	0.444
162	162	0.74
163	163	0.37
164	164	0.0175
165	165	0.0411
166	166	0.69
167	167	0.948
168	168	0.443
169	169	0.00382
17	17	0.0216
18	18	0.727
19	19	0.054
2	2	0.913
20	20	0.481
21	21	0.459
22	22	0.0852
23	23	0.236
24	24	0.0361
25	25	0.694
26	26	6.93915e-4
27	27	0.868
28	28	0.379
29	29	0.11
3	3	0.0712
30	30	0.676
31	31	0.912
32	32	0.385
33	33	0.167
34	34	0.551
35	35	0.505
36	36	0.36
37	37	0.00999
38	38	0.268
39	39	0.162
4	4	0.56
40	40	0.294
41	41	0.904
42	42	0.223
43	43	0.13
44	44	0.624
45	45	0.517
46	46	0.132
47	47	0.174
48	48	0.116
49	49	0.147
5	5	0.138
50	50	0.234
51	51	0.532
52	52	0.103
53	53	0.681
54	54	0.662
55	55	0.831
56	56	0.391
57	57	0.571
58	58	0.215
59	59	0.0717
6	6	0.512
60	60	0.0115
61	61	0.152
62	62	0.114
63	63	0.101
64	64	0.892
65	65	0.226
66	66	0.698
67	67	0.796
68	68	0.281
69	69	0.611
7	7	0.0167
70	70	0.0212
71	71	0.0139
72	72	0.345
73	73	0.026
74	74	0.35
75	75	0.119
76	76	0.709
77	77	0.239
78	78	0.0152
79	79	0.468
8	8	0.131
80	80	0.864
81	81	0.501
82	82	0.0862
83	83	0.174
84	84	0.816
85	85	0.0995
86	86	0.287
87	87	0.316
88	88	0.277
89	89	0.287
9	9	0.317
90	90	0.132
91	91	0.238
92	92	0.288
93	93	0.0452
94	94	0.765
95	95	0.0464
96	96	0.344
97	97	0.85
98	98	0.787
99	99	0.321

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: CNhs12134

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@SAMD00005105
-|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;DRX008843;DRR009715;DRZ001140;DRZ002525;DRZ012490;DRZ013875
+|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!2.37!235.02!Tcf7l2;;chr9:91260594..91260612,-!p1@Zic1!2.17!147.98!Zic1;;chr19:55969946..55969973,+!p8@Tcf7l2!2.11!127.01!Tcf7l2;;chr19:55968967..55968991,+!p7@Tcf7l2!2.10!125.03!Tcf7l2;;chr9:91260616..91260653,-!p2@Zic1!2.04!108.54!Zic1;;chr3:127336052..127336058,+!p1@Neurog2!2.00!98.91!Neurog2;;chr19:55969887..55969904,+!p9@Tcf7l2!1.92!81.90!Tcf7l2;;chr1:140739014..140739032,-!p1@Lhx9!1.90!97.46!Lhx9;;chr3:34548909..34548927,+!p1@Sox2!1.88!124.63!Sox2;;chr7:116154364..116154444,+!p1@Tub!1.87!123.84!Tub;;chrX:90531838..90531861,+!p1@Arx!1.84!85.46!Arx;;chr12:28027561..28027591,-!p1@Sox11!1.83!411.22!Sox11;;chr3:95032091..95032183,-!p1@Mllt11!1.79!484.81!Mllt11;;chr3:101814061..101814094,+!p1@Nhlh2!1.79!60.14!Nhlh2;;chr14:122874619..122874634,+!p1@Zic2!1.78!59.35!Zic2;;chr19:55967803..55967834,+!p12@Tcf7l2!1.73!52.49!Tcf7l2;;chrX:108009761..108009788,+!p1@Pou3f4!1.69!48.01!Pou3f4;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.68!59.22!Pou3f3;;chrX:55283799..55283813,+!p1@Zic3!1.68!46.82!Zic3;;chr17:48015839..48015915,-!p3@Foxp4!1.67!53.41!Foxp4;;chr16:91270004..91270023,+!p1@Olig1!1.66!50.64!Olig1;;chr11:84339016..84339044,-!p1@Lhx1!1.66!44.97!Lhx1;;chr4:107353376..107353452,-!p3@Dmrtb1!1.62!41.15!Dmrtb1;;chr1:91827728..91827743,-!p2@Gbx2!1.62!40.88!Gbx2;;chr2:71384802..71384815,-!p1@Dlx2!1.60!47.08!Dlx2;;chr2:71367871..71367898,+!p1@Dlx1!1.59!37.98!Dlx1;;chr7:30088977..30089002,+!p2@Dpf1!1.57!49.72!Dpf1;;chr1:91827756..91827773,-!p1@Gbx2!1.54!33.63!Gbx2;;chr12:54349410..54349461,+!p1@Npas3!1.53!38.91!Npas3;;chr19:55967842..55967878,+!p13@Tcf7l2!1.53!32.58!Tcf7l2;;chr8:12395603..12395621,+!p1@Sox1!1.52!32.31!Sox1;;chr7:56892217..56892221,-!p1@Dbx1!1.52!32.18!Dbx1;;chr15:76352832..76352900,-!p1@Scrt1!1.50!30.73!Scrt1;;chr12:30213247..30213333,+!p1@Myt1l!1.50!30.47!Myt1l;;chr2:38206580..38206600,+!p2@Lhx2!1.45!33.10!Lhx2;;chr4:107353508..107353547,-!p4@Dmrtb1!1.44!26.77!Dmrtb1;;chr2:73110004..73110016,+!p2@Sp9!1.44!26.64!Sp9;;chr7:25292331..25292421,+!p1@Zfp428!1.42!174.49!Zfp428;;chr7:30092993..30093076,+!p1@Dpf1!1.42!42.73!Dpf1;;chr7:91558472..91558512,-!p2@Arnt2!1.42!35.87!Arnt2;;chr9:91263879..91263911,+!p1@Zic4!1.42!25.45!Zic4;;chr16:91225808..91225824,+!p1@Olig2!1.42!25.19!Olig2;;chr4:154335024..154335039,+!p1@Hes5!1.41!29.67!Hes5;;chr14:49287186..49287225,-!p1@Otx2!1.41!24.93!Otx2;;chr2:146047829..146047847,+!p1@Insm1!1.39!41.94!Insm1;;chr3:34548946..34548972,+!p2@Sox2!1.39!26.25!Sox2;;chr2:65683890..65683907,+!p1@Csrnp3!1.38!42.86!Csrnp3;;chr13:44936126..44936164,+!p6@Jarid2!1.38!26.25!Jarid2;;chr2:71367142..71367167,+!p2@Dlx1!1.33!20.18!Dlx1;;chr2:38206744..38206766,+!p1@Lhx2!1.32!23.74!Lhx2;;chr10:86956396..86956411,-!p1@Ascl1!1.31!29.41!Ascl1;;chr13:48356475..48356492,+!p1@Id4!1.30!396.32!Id4;;chr13:117099847..117099907,-!p1@Isl1!1.30!34.29!Isl1;;chr19:55969687..55969714,+!p16@Tcf7l2!1.30!19.12!Tcf7l2;;chr5:120881900..120881914,+!p1@Lhx5!1.30!18.99!Lhx5;;chr13:95645580..95645598,+!p1@Otp!1.29!18.46!Otp;;chrX:58146612..58146615,-!p1@Sox3!1.29!18.46!Sox3;;chr2:73109983..73109996,+!p1@Sp9!1.28!17.94!Sp9;;chr14:122874593..122874610,+!p2@Zic2!1.27!17.67!Zic2;;chr2:147012125..147012149,-!p1@Nkx2-2!1.27!17.41!Nkx2-2;;chr13:72766250..72766273,+!p1@Irx2!1.25!26.11!Irx2;;chr2:65768174..65768247,+!p2@Csrnp3!1.25!16.75!Csrnp3;;chr4:107353563..107353590,-!p6@Dmrtb1!1.25!16.75!Dmrtb1;;chr2:56967334..56967366,-!p1@Nr4a2!1.23!32.18!Nr4a2;;chr11:21901608..21901634,-!p1@Otx1!1.23!15.96!Otx1;;chr4:13670499..13670526,+!p2@Runx1t1!1.22!34.55!Runx1t1;;chr2:79296783..79296801,-!p1@Neurod1!1.22!15.56!Neurod1;;chr7:91558392..91558434,-!p1@Arnt2!1.21!41.94!Arnt2;;chr13:78339382..78339420,-!p3@Nr2f1!1.20!17.54!Nr2f1;;chr2:146911200..146911219,-!p1@Nkx2-4!1.20!14.90!Nkx2-4;;chr4:107353455..107353476,-!p8@Dmrtb1!1.20!14.90!Dmrtb1;;chr5:140019865..140019886,+!p1@Uncx!1.20!14.77!Uncx;;chr5:106887474..106887489,-!p1@Barhl2!1.19!14.64!Barhl2;;chr17:86020156..86020183,+!p1@Six3!1.19!14.38!Six3;;chr3:66785857..66785873,-!p1@Shox2!1.18!14.24!Shox2;;chr19:55816546..55816556,+!p3@Tcf7l2!1.17!52.75!Tcf7l2;;chr1:140739042..140739054,-!p2@Lhx9!1.17!13.85!Lhx9;;chr9:99776566..99776612,-!p1@Sox14!1.17!13.85!Sox14;;chr5:24104751..24104773,-!p5@Smarcd3!1.17!13.72!Smarcd3;;chr5:98609885..98609900,+!p1@Prdm8!1.17!13.72!Prdm8;;chr1:189821714..189821761,+!p1@Esrrg!1.16!24.93!Esrrg;;chr6:6831950..6831985,-!p2@Dlx5!1.16!15.04!Dlx5;;chr17:86020115..86020128,+!p2@Six3!1.15!13.06!Six3;;chr17:86020510..86020589,+!p3@Six3!1.15!13.06!Six3;;chr12:30219426..30219506,+!p2@Myt1l!1.14!12.66!Myt1l;;chr13:78339428..78339466,-!p2@Nr2f1!1.11!16.35!Nr2f1;;chr19:55968937..55968951,+!p21@Tcf7l2!1.11!12.00!Tcf7l2;;chr4:22415443..22415506,-!p1@Pou3f2!1.11!12.00!Pou3f2;;chr15:76352740..76352781,-!p5@Scrt1!1.11!11.87!Scrt1;;chr2:181501745..181501778,+!p1@Myt1!1.11!11.74!Myt1;;chr17:37139472..37139514,+!p1@Zfp57!1.10!79.00!Zfp57;;chr14:104867201..104867258,-!p1@Pou4f1!1.10!16.35!Pou4f1;;chr10:84218895..84218909,+!p1@Rfx4!1.10!11.47!Rfx4;;chr4:107353346..107353375,-!p5@Dmrtb1!1.09!11.34!Dmrtb1;;chr4:150503457..150503498,-!p3@Camta1!1.08!12.40!Camta1;;chr9:69608672..69608686,-!p1@Foxb1!1.08!11.08!Foxb1;;chr7:135019147..135019187,-!p3@Zfp668!1.07!23.61!Zfp668;;chr3:95032197..95032208,-!p3@Mllt11!1.07!13.58!Mllt11;;chr15:76352677..76352737,-!p3@Scrt1!1.07!10.81!Scrt1;;chr9:74709695..74709722,+!p1@Onecut1!1.07!10.68!Onecut1;;chr19:55972441..55972456,+!p18@Tcf7l2!1.07!10.68!Tcf7l2;;chr4:150482563..150482655,-!p2@Camta1!1.06!37.32!Camta1;;chr6:55631042..55631102,-!p1@Neurod6!1.06!10.42!Neurod6;;chr4:122673278..122673336,+!p1@Mycl1!1.05!32.84!Mycl1;;chr17:35031589..35031630,+!p2@Zbtb12!1.05!18.86!Zbtb12;;chr13:78339476..78339515,-!p1@Nr2f1!1.05!15.69!Nr2f1;;chr5:24107676..24107722,-!p4@Smarcd3!1.05!13.98!Smarcd3;;chr4:13678723..13678739,+!p10@Runx1t1!1.05!10.16!Runx1t1;;chr19:55967419..55967424,+!p19@Tcf7l2!1.04!9.89!Tcf7l2;;chr6:6831928..6831949,-!p3@Dlx5!1.04!9.89!Dlx5;;chr19:55969646..55969665,+!p26@Tcf7l2!1.04!9.89!Tcf7l2;;chr15:76353005..76353021,-!p2@Scrt1!1.04!9.89!Scrt1;;chr7:130644017..130644092,-!p1@Zkscan2!1.03!19.26!Zkscan2;;chr2:105509045..105509071,+!p1@Pax6!1.03!9.63!Pax6;;chr1:173987720..173987729,-!p1@Nhlh1!1.03!9.63!Nhlh1;;chr14:55711114..55711159,-!p2@Zfhx2!1.02!21.37!Zfhx2;;chr13:72101178..72101203,-!p1@Irx1!1.02!14.77!Irx1;;chr4:107353480..107353492,-!p9@Dmrtb1!1.02!9.50!Dmrtb1;;chr5:140019843..140019858,+!p2@Uncx!1.02!9.50!Uncx;;chr7:144505957..144505972,-!p2@Ebf3!1.00!11.34!Ebf3;;chr2:181501710..181501742,+!p2@Myt1!1.00!9.10!Myt1;;chr19:55968827..55968868,+!p29@Tcf7l2!1.00!9.10!Tcf7l2;;chr13:29045559..29045574,-!p1@Sox4!0.99!734.74!Sox4;;chr13:72766279..72766296,+!p2@Irx2!0.99!13.19!Irx2;;chr13:72101141..72101158,-!p3@Irx1!0.99!11.08!Irx1;;chr6:6832076..6832092,-!p1@Dlx5!0.99!10.42!Dlx5;;chr9:91263173..91263220,+!p2@Zic4!0.99!8.70!Zic4;;chr13:56353536..56353542,-!p1@Neurog1!0.99!8.70!Neurog1;;chr2:71366660..71366702,+!p3@Dlx1!0.99!8.70!Dlx1;;chr4:13670571..13670625,+!p1@Runx1t1!0.98!23.87!Runx1t1;;chr2:152223783..152223812,-!p4@Sox12!0.98!20.05!Sox12;;chr3:128916868..128916890,+!p1@Pitx2!0.98!11.87!Pitx2;;chrX:55283827..55283838,+!p3@Zic3!0.98!8.57!Zic3;;chr7:25292160..25292213,+!p3@Zfp428!0.97!21.10!Zfp428;;chr14:118636214..118636235,-!p1@Sox21!0.97!10.16!Sox21;;chr1:191994550..191994623,-!p1@Prox1!0.96!57.24!Prox1;;chr7:144506077..144506128,-!p1@Ebf3!0.96!19.26!Ebf3;;chr4:129118044..129118067,-!p1@Zbtb8b!0.96!10.29!Zbtb8b;;chr2:151907546..151907561,+!p1@Scrt2!0.96!8.18!Scrt2;;chr4:109650609..109650653,+!p1@Dmrta2!0.96!8.05!Dmrta2;;chr11:21901587..21901604,-!p2@Otx1!0.96!8.05!Otx1;;chr7:30089006..30089022,+!p3@Dpf1!0.96!8.05!Dpf1;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.95!21.89!Zfhx3;;chr7:144505980..144506010,-!p3@Ebf3!0.95!9.76!Ebf3;;chr5:148000254..148000260,+!p1@Gsx1!0.95!7.91!Gsx1;;chr1:140744193..140744208,-!p4@Lhx9!0.95!7.91!Lhx9;;chr10:84218800..84218829,+!p2@Rfx4!0.95!7.91!Rfx4;;chr11:98190918..98190951,-!p1@Neurod2!0.95!7.91!Neurod2;;chr15:75447162..75447217,+!p2@Zfp41!0.94!23.48!Zfp41;;chr9:18278055..18278126,-!p1@Zfp558!0.94!22.55!Zfp558;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.94!13.98!Zfhx3;;chr11:116196664..116196679,-!p1@Foxj1!0.94!12.00!Foxj1;;chr13:72101161..72101177,-!p2@Irx1!0.94!10.68!Irx1;;chr3:95032184..95032195,-!p4@Mllt11!0.94!9.76!Mllt11;;chr2:152223734..152223756,-!p6@Sox12!0.94!9.10!Sox12;;chr2:31495237..31495243,+!p1@Prdm12!0.94!7.78!Prdm12;;chr12:87762578..87762612,+!p1@Esrrb!0.94!7.78!Esrrb;;chr4:22415290..22415307,-!p2@Pou3f2!0.94!7.78!Pou3f2;;chr2:151907338..151907360,+!p2@Scrt2!0.94!7.65!Scrt2;;chr2:65768149..65768173,+!p4@Csrnp3!0.94!7.65!Csrnp3;;chr13:44936077..44936096,+!p9@Jarid2!0.94!7.65!Jarid2;;chr2:163028808..163028869,+!p1@Tox2!0.93!27.83!Tox2;;chr17:37140628..37140631,+!p2@Zfp57!0.93!15.30!Zfp57;;chr6:38204214..38204267,-!p4@D630045J12Rik!0.93!14.38!D630045J12Rik;;chr18:64499706..64499721,+!p2@Onecut2!0.93!10.81!Onecut2;;chr4:13678482..13678505,+!p9@Runx1t1!0.93!7.52!Runx1t1;;chrX:108009734..108009752,+!p2@Pou3f4!0.93!7.52!Pou3f4;;chr2:71384458..71384526,-!p2@Dlx2!0.92!7.39!Dlx2;;chr19:55969998..55970001,+!p40@Tcf7l2!0.92!7.25!Tcf7l2;;chr13:78339241..78339273,-!p9@Nr2f1!0.92!7.25!Nr2f1;;chr7:148008023..148008092,-!p1@Zfp941!0.91!17.94!Zfp941;;chr4:124334894..124334899,+!p1@Pou3f1!0.91!9.36!Pou3f1;;chr14:118636238..118636257,-!p2@Sox21!0.91!7.12!Sox21;;chr10:79957600..79957618,+!p1@Onecut3!0.91!7.12!Onecut3;;chr8:90483459..90483475,-!p1@Zfp423!0.90!19.91!Zfp423;;chr1:170361991..170362015,-!p6@Pbx1!0.90!16.22!Pbx1;;chr19:55969980..55969987,+!p37@Tcf7l2!0.90!6.99!Tcf7l2;;chr4:13669922..13669957,+!p13@Runx1t1!0.90!6.86!Runx1t1;;chr9:40682064..40682081,+!p1@Bsx!0.90!6.86!Bsx;;chr2:35959541..35959548,-!p2@Lhx6!0.89!6.73!Lhx6;;chr6:23198371..23198390,-!p1@Fezf1!0.89!6.73!Fezf1;;chrX:55284180..55284195,+!p2@Zic3!0.89!6.73!Zic3;;chr3:95032558..95032641,-!p2@Mllt11!0.88!38.51!Mllt11;;chr7:25372631..25372684,-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8032,+!p3@Nr4a3!0.28!2.11!Nr4a3;;chr8:72356384..72356434,+!p2@Pbx4!0.28!1.85!Pbx4;;chr13:29045131..29045159,-!p3@Sox4!0.28!1.71!Sox4;;chr1:64168030..64168037,-!p9@Klf7!0.28!1.45!Klf7;;chr7:38558544..38558566,-!p4@Zfp536!0.28!1.19!Zfp536;;chr7:52252978..52252989,+!p5@Irf3!0.28!0.92!Irf3;;chr7:52071279..52071296,-!p9@Atf5!0.28!0.92!Atf5;;chr1:19199021..19199048,+!p8@Tfap2b!0.28!0.92!Tfap2b;;chr1:169528581..169528607,+!p7@Rxrg!0.28!0.92!Rxrg;;chr2:163030219..163030258,+!p5@Tox2!0.28!0.92!Tox2;;chr2:147871627..147871641,-!p1@Foxa2!0.28!0.92!Foxa2;;chr3:130813268..130813275,+!p12@Lef1!0.28!0.92!Lef1;;chr4:97248652..97248671,+!p19@Nfia!0.28!0.92!Nfia;;chr4:82145196..82145229,-!p7@Nfib!0.28!0.92!Nfib;;chr2:79296907..79296918,-!p2@Neurod1!0.28!0.92!Neurod1;;chr2:81893447..81893468,+!p2@Zfp804a!0.28!0.92!Zfp804a;;chr5:75471615..75471622,+!p1@Gsx2!0.28!0.92!Gsx2;;chr5:24032551..24032557,-!p@chr5:24032551..24032557,-!0.28!0.92!Gbx1;;chr12:57636034..57636087,-!p1@Nkx2-1!0.28!0.92!Nkx2-1;;chr12:50483639..50483654,+!p1@Foxg1!0.28!0.92!Foxg1;;chr14:118636183..118636192,-!p4@Sox21!0.28!0.92!Sox21;;chr14:122874356..122874371,+!p4@Zic2!0.28!0.92!Zic2;;chr13:78335738..78335747,-!p24@Nr2f1!0.28!0.92!Nr2f1;;chr17:48015925..48015934,-!p13@Foxp4!0.28!0.92!Foxp4;;chr11:98601909..98601922,+!p11@Thra!0.28!0.92!Thra;;chr11:44431115..44431132,+!p9@Ebf1!0.28!0.92!Ebf1;;chr7:4966247..4966286,-!p1@Fiz1!0.27!32.31!Fiz1;;chr13:53076396..53076452,-!p1@Nfil3!0.27!30.07!Nfil3;;chr11:115891618..115891699,+!p1@Unk!0.27!20.44!Unk;;chr10:127984778..127984824,-!p1@Zc3h10!0.27!18.33!Zc3h10;;chr17:46520674..46520741,+!p1@Zfp318!0.27!13.45!Zfp318;;chr19:26679615..26679646,+!p3@Smarca2!0.27!11.08!Smarca2;;chr14:22319053..22319105,+!p2@Myst4!0.27!4.88!Myst4;;chr16:17531086..17531109,-!p3@Thap7!0.27!4.48!Thap7;;chr7:30875490..30875555,-!p1@Zfp566,p1@Zfp82!0.27!4.09!Zfp566;;chr11:95170871..95170900,-!p2@Myst2!0.27!3.69!Myst2;;chr11:44430788..44430804,+!p3@Ebf1!0.27!3.43!Ebf1;;chr11:87881818..87881834,+!p4@Vezf1!0.27!3.43!Vezf1;;chr18:55150248..55150308,-!p6@Zfp608!0.27!3.30!Zfp608;;chr4:58956447..58956510,+!p1@Zkscan16!0.27!2.90!Zkscan16;;chr14:100684036..100684068,-!p5@Klf12!0.27!2.11!Klf12;;chr7:148513548..148513560,-!p7@Deaf1!0.27!1.85!Deaf1;;chr14:67853457..67853482,+!p2@Ebf2!0.27!1.58!Ebf2;;chr10:62328079..62328093,-!p5@Tet1!0.27!1.58!Tet1;;chr6:47998938..47998955,-!p2@Zfp777!0.27!1.45!Zfp777;;chr1:64168228..64168250,-!p7@Klf7!0.27!1.45!Klf7;;chr7:123182248..123182264,-!p3@Sox6!0.27!1.19!Sox6;;chr15:76181733..76181767,+!p1@Maf1!0.26!46.42!Maf1;;chr11:74644437..74644507,+!p1@Mnt!0.26!42.47!Mnt;;chr1:95651138..95651255,-!p1@Thap4!0.26!23.34!Thap4;;chr15:75771454..75771521,+!p1@Zfp623!0.26!14.51!Zfp623;;chr8:108160490..108160512,+!p2@Ctcf!0.26!12.92!Ctcf;;chr16:87699149..87699204,+!p2@Bach1!0.26!12.79!Bach1;;chr4:118967125..118967143,-!p2@Ybx1!0.26!9.76!Ybx1;;chr14:76814601..76814630,+!p5@Tsc22d1!0.26!9.23!Tsc22d1;;chr2:92886297..92886329,-!p1@Prdm11!0.26!6.86!Prdm11;;chr19:28085586..28085622,-!p3@Rfx3!0.26!6.33!Rfx3;;chrX:132420525..132420558,+!p3@Bhlhb9!0.26!6.33!Bhlhb9;;chr11:50700965..50701027,-!p1@Zfp454!0.26!5.01!Zfp454;;chr11:87881803..87881817,+!p3@Vezf1!0.26!4.62!Vezf1;;chr6:38204087..38204108,-!p2@D630045J12Rik!0.26!4.09!D630045J12Rik;;chr9:21875812..21875860,-!p1@Zfp653!0.26!3.96!Zfp653;;chr9:113840082..113840105,+!p3@Ubp1!0.26!3.96!Ubp1;;chr7:50817661..50817687,+!p2@LOC100505180,p2@Zfp658!0.26!2.90!Zfp658;;chr2:34227524..34227547,-!p2@Pbx3!0.26!2.37!Pbx3;;chr17:69733108..69733129,+!p3@Zfp161!0.26!1.98!Zfp161;;chr8:81923366..81923371,-!p5@Smad1!0.26!1.85!Smad1;;chr14:65568567..65568588,-!p3@Hmbox1!0.26!1.71!Hmbox1;;chr4:63071779..63071791,-!p3@Akna!0.26!1.58!Akna;;chr11:87881881..87881887,+!p5@Vezf1!0.26!1.58!Vezf1;;chr4:32325955..32325971,+!p3@Bach2!0.26!1.32!Bach2;;chr13:29045274..29045293,-!p6@Sox4!0.26!1.19!Sox4;;chr2:180377386..180377462,-!p1@Tcfl5!0.26!1.19!Tcfl5;;chrX:110411840..110411860,+!p1@Dach2!0.26!1.19!Dach2;;chr8:26951227..26951266,-!p1@Ash2l!0.25!64.49!Ash2l;;
+|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:11723-123D4
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000209
+|is_a=EFO:0002091;;FF:0000209
+|is_obsolete=
+|library_id=CNhs12134
+|library_id_phase_based=2:CNhs12134
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11723
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11723
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor1.CNhs12134.11723-123D4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor1.CNhs12134.11723-123D4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor1.CNhs12134.11723-123D4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor1.CNhs12134.11723-123D4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor1.CNhs12134.11723-123D4.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - striatal, donor1
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12134,LSID839,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.00879071544957335,0,0,0,0,0,-0.323158993728681,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.0902244241744751,0,0,0,0,0,0,0,0,0,0,0,0,0.541748320011178,-0.558422792324031,0,0,0,0,0,-0.158488262141776,0.247548903756559,-0.0509587096191635,-0.0277997438738161,0.826140828130639,0.412063108447055,0,0,0,0,0,0,0,0,0,0,0.0538027986792206,-0.0660055475634404,0,0,0,0,0.0109558435963458,0,-0.0386995374972728,0,0,0,-0.175541021357569,-0.310650657339386,-0.104288244091862,-0.12999678246003,0,-0.0780086007519514,0.180214321839731,0.0538027986792206,0,0,0.0912840964987233,0.154163215137704,0.292051103236913,-0.0788315948399074,0,0,0,0,0,0,0.131835742200018,-0.00994288813459132,-0.015753025062634,0,0,0,0.549496382922405,0
 |rna_box=123
 |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
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+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11723-123D4;search_select_hide=table117:11723-123D4
 }}

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FF:11723-123D4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12134

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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