FF:11738-123F1: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Neurons - dorsal spinal cord, donor2
Species:	Mouse (Mus musculus)
Library ID:	CNhs12635
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	spinal cord
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	RNADOR2
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		SAMD00004921

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12635		CAGE		DRX008835		DRR009707

Accession ID Mm9

Library id		BAM		CTSS
CNhs12635		DRZ001132		DRZ002517

Accession ID Mm10

Library id		BAM		CTSS
CNhs12635		DRZ012482		DRZ013867

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

CNhs12635

0	0
1	0.554
10	0
100	0.0887
1000	0
1001	-0.0749
1002	0.0151
1003	0.0575
1004	0
1005	0
1006	0.667
1007	-0.223
1008	0
1009	-0.151
101	-0.281
1010	0
1011	0.319
1012	0
1013	0.136
1014	-0.0851
1015	0.214
1016	0.216
1017	0
1018	0
1019	0
102	0
1020	0.452
1021	0.109
1022	-0.0554
1023	0
1024	0
1025	0.048
1026	0
1027	0.269
1028	0
1029	-0.176
103	0
1030	0
1031	-0.222
1032	0.508
1033	-0.0665
1034	0
1035	0
1036	-0.173
1037	0
1038	0.0327
1039	0.112
104	0
1040	-0.293
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: CNhs12635

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00516
MA0003.1	MA0003.1	0.548
MA0004.1	MA0004.1	0.484
MA0006.1	MA0006.1	0.223
MA0007.1	MA0007.1	0.218
MA0009.1	MA0009.1	0.829
MA0014.1	MA0014.1	0.548
MA0017.1	MA0017.1	5.10269e-6
MA0018.2	MA0018.2	0.0543
MA0019.1	MA0019.1	0.841
MA0024.1	MA0024.1	0.511
MA0025.1	MA0025.1	0.818
MA0027.1	MA0027.1	0.262
MA0028.1	MA0028.1	0.0371
MA0029.1	MA0029.1	0.767
MA0030.1	MA0030.1	0.575
MA0031.1	MA0031.1	0.0823
MA0035.2	MA0035.2	0.0795
MA0038.1	MA0038.1	0.429
MA0039.2	MA0039.2	0.148
MA0040.1	MA0040.1	0.804
MA0041.1	MA0041.1	0.172
MA0042.1	MA0042.1	0.44
MA0043.1	MA0043.1	0.589
MA0046.1	MA0046.1	1.16136e-5
MA0047.2	MA0047.2	8.60336e-4
MA0048.1	MA0048.1	0.0797
MA0050.1	MA0050.1	3.63345e-7
MA0051.1	MA0051.1	3.17976e-5
MA0052.1	MA0052.1	0.543
MA0055.1	MA0055.1	0.0539
MA0057.1	MA0057.1	0.431
MA0058.1	MA0058.1	0.519
MA0059.1	MA0059.1	0.21
MA0060.1	MA0060.1	0.0715
MA0061.1	MA0061.1	0.0526
MA0062.2	MA0062.2	1.60251e-4
MA0065.2	MA0065.2	6.16213e-5
MA0066.1	MA0066.1	0.0465
MA0067.1	MA0067.1	0.898
MA0068.1	MA0068.1	0.882
MA0069.1	MA0069.1	0.0609
MA0070.1	MA0070.1	0.111
MA0071.1	MA0071.1	0.196
MA0072.1	MA0072.1	0.201
MA0073.1	MA0073.1	0.878
MA0074.1	MA0074.1	0.221
MA0076.1	MA0076.1	0.0888
MA0077.1	MA0077.1	0.0815
MA0078.1	MA0078.1	0.866
MA0079.2	MA0079.2	0.138
MA0080.2	MA0080.2	2.23842e-9
MA0081.1	MA0081.1	0.276
MA0083.1	MA0083.1	0.0673
MA0084.1	MA0084.1	0.396
MA0087.1	MA0087.1	0.385
MA0088.1	MA0088.1	0.122
MA0090.1	MA0090.1	0.085
MA0091.1	MA0091.1	0.259
MA0092.1	MA0092.1	0.203
MA0093.1	MA0093.1	0.531
MA0099.2	MA0099.2	0.00684
MA0100.1	MA0100.1	0.14
MA0101.1	MA0101.1	0.0246
MA0102.2	MA0102.2	0.427
MA0103.1	MA0103.1	0.198
MA0104.2	MA0104.2	0.926
MA0105.1	MA0105.1	0.0138
MA0106.1	MA0106.1	0.0615
MA0107.1	MA0107.1	0.0488
MA0108.2	MA0108.2	0.697
MA0111.1	MA0111.1	0.996
MA0112.2	MA0112.2	4.27394e-4
MA0113.1	MA0113.1	0.235
MA0114.1	MA0114.1	1.98411e-5
MA0115.1	MA0115.1	2.03282e-4
MA0116.1	MA0116.1	0.0788
MA0117.1	MA0117.1	0.586
MA0119.1	MA0119.1	0.192
MA0122.1	MA0122.1	0.688
MA0124.1	MA0124.1	0.7
MA0125.1	MA0125.1	0.285
MA0131.1	MA0131.1	0.534
MA0135.1	MA0135.1	0.0794
MA0136.1	MA0136.1	1.40206e-11
MA0137.2	MA0137.2	0.00956
MA0138.2	MA0138.2	0.00888
MA0139.1	MA0139.1	0.519
MA0140.1	MA0140.1	2.44548e-4
MA0141.1	MA0141.1	0.0859
MA0142.1	MA0142.1	0.593
MA0143.1	MA0143.1	0.789
MA0144.1	MA0144.1	0.0155
MA0145.1	MA0145.1	0.101
MA0146.1	MA0146.1	0.0402
MA0147.1	MA0147.1	0.808
MA0148.1	MA0148.1	8.97309e-5
MA0149.1	MA0149.1	0.169
MA0150.1	MA0150.1	0.0288
MA0152.1	MA0152.1	0.024
MA0153.1	MA0153.1	2.87169e-6
MA0154.1	MA0154.1	0.0359
MA0155.1	MA0155.1	0.943
MA0156.1	MA0156.1	4.68132e-9
MA0157.1	MA0157.1	0.065
MA0159.1	MA0159.1	0.00489
MA0160.1	MA0160.1	0.0572
MA0162.1	MA0162.1	0.328
MA0163.1	MA0163.1	0.00177
MA0164.1	MA0164.1	0.904
MA0258.1	MA0258.1	0.0244
MA0259.1	MA0259.1	0.889

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: CNhs12635

Novel motif	Logo	P-value
1	1	0.145
10	10	0.0292
100	100	0.451
101	101	0.832
102	102	0.967
103	103	0.0756
104	104	0.649
105	105	0.552
106	106	0.0849
107	107	0.153
108	108	0.366
109	109	0.0162
11	11	0.111
110	110	0.0338
111	111	0.0495
112	112	0.00179
113	113	0.771
114	114	0.187
115	115	0.51
116	116	0.886
117	117	0.00257
118	118	0.262
119	119	0.093
12	12	0.947
120	120	0.842
121	121	0.339
122	122	0.849
123	123	0.00842
124	124	0.121
125	125	0.514
126	126	0.0732
127	127	0.166
128	128	0.0781
129	129	0.221
13	13	1.89587e-6
130	130	0.266
131	131	0.544
132	132	0.485
133	133	0.763
134	134	0.172
135	135	0.268
136	136	0.459
137	137	0.384
138	138	0.857
139	139	0.252
14	14	0.977
140	140	0.058
141	141	0.357
142	142	0.0835
143	143	0.555
144	144	0.974
145	145	0.00142
146	146	0.504
147	147	0.517
148	148	0.734
149	149	0.709
15	15	0.0826
150	150	0.123
151	151	0.705
152	152	0.148
153	153	0.351
154	154	0.527
155	155	0.999
156	156	0.00829
157	157	0.255
158	158	0.0326
159	159	0.0814
160	160	0.229
161	161	0.172
162	162	0.825
163	163	0.293
164	164	0.0115
165	165	0.122
166	166	0.691
167	167	0.521
168	168	0.5
169	169	0.00177
17	17	0.0687
18	18	0.914
19	19	0.15
2	2	0.522
20	20	0.0426
21	21	0.446
22	22	0.184
23	23	0.576
24	24	0.104
25	25	0.661
26	26	2.42206e-8
27	27	0.43
28	28	0.527
29	29	0.0238
3	3	0.0571
30	30	0.688
31	31	0.756
32	32	0.972
33	33	0.0753
34	34	0.74
35	35	0.987
36	36	0.25
37	37	0.0286
38	38	0.466
39	39	0.402
4	4	0.671
40	40	0.501
41	41	0.57
42	42	0.138
43	43	0.106
44	44	0.93
45	45	0.876
46	46	0.02
47	47	0.241
48	48	0.198
49	49	0.107
5	5	0.0879
50	50	0.375
51	51	0.644
52	52	0.552
53	53	0.706
54	54	0.797
55	55	0.969
56	56	0.559
57	57	0.481
58	58	0.21
59	59	0.259
6	6	0.813
60	60	0.0481
61	61	0.0649
62	62	0.104
63	63	0.204
64	64	0.845
65	65	0.381
66	66	0.981
67	67	0.777
68	68	0.935
69	69	0.9
7	7	0.0105
70	70	0.0797
71	71	0.00439
72	72	0.535
73	73	0.0412
74	74	0.542
75	75	0.0439
76	76	0.374
77	77	0.58
78	78	0.00967
79	79	0.353
8	8	0.108
80	80	0.599
81	81	0.795
82	82	0.212
83	83	0.454
84	84	0.793
85	85	0.198
86	86	0.114
87	87	0.929
88	88	0.202
89	89	0.457
9	9	0.518
90	90	0.0405
91	91	0.337
92	92	0.422
93	93	0.0314
94	94	0.429
95	95	0.0922
96	96	0.179
97	97	0.918
98	98	0.722
99	99	0.684

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: CNhs12635

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000206 mouse neuron of the dorsal spinal cord 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)
0002611 (neuron of the dorsal spinal cord)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002240 (spinal cord)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0000489 (cavitated compound organ)
0005174 (dorsal region element)
0001948 (regional part of spinal cord)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002256 (dorsal horn of spinal cord)
0001016 (nervous system)
0001137 (dorsum)
0002315 (gray matter of spinal cord)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000206 (mouse neuron of the dorsal spinal cord 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:0000025,UBERON:0000061,UBERON:0000062,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000489,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001137,UBERON:0001948,UBERON:0002020,UBERON:0002050,UBERON:0002100,UBERON:0002240,UBERON:0002256,UBERON:0002315,UBERON:0002346,UBERON:0002532,UBERON:0003057,UBERON:0003075,UBERON:0003076,UBERON:0003103,UBERON:0004121,UBERON:0005068,UBERON:0005174,UBERON:0005177,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007135,UBERON:0007284
+|DRA_sample_Accession=CAGE@SAMD00004921
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000031,CL:0000034,CL:0000047,CL:0000048,CL:0000055,CL:0000117,CL:0000133,CL:0000144,CL:0000211,CL:0000220,CL:0000221,CL:0000255,CL:0000337,CL:0000393,CL:0000404,CL:0000540,CL:0000548,CL:0000723,CL:0002319,CL:0002321,CL:0002371,CL:0002611
+|accession_numbers=CAGE;DRX008835;DRR009707;DRZ001132;DRZ002517;DRZ012482;DRZ013867
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002240,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0000489,UBERON:0005174,UBERON:0001948,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0002256,UBERON:0001016,UBERON:0001137,UBERON:0002315
+|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:0002611
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000203,FF:0000206
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.65!501.03!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!2.16!260.51!Tsc22d4;;chr11:96143666..96143725,+!p1@Hoxb8!2.14!156.54!Hoxb8;;chr16:91225808..91225824,+!p1@Olig2!1.92!82.84!Olig2;;chr3:95032091..95032183,-!p1@Mllt11!1.71!411.05!Mllt11;;chr16:91270091..91270143,+!p2@Olig1!1.66!45.13!Olig1;;chr6:52176164..52176195,-!p1@Hoxa9!1.58!45.42!Hoxa9;;chr11:96143962..96144035,+!p2@Hoxb8!1.58!36.85!Hoxb8;;chr2:74529970..74529997,+!p1@Hoxd10!1.57!36.56!Hoxd10;;chr17:25707623..25707639,-!p1@Sox8!1.52!131.40!Sox8;;chr12:54349410..54349461,+!p1@Npas3!1.51!37.42!Npas3;;chr9:91260594..91260612,-!p1@Zic1!1.50!30.56!Zic1;;chr7:116154364..116154444,+!p1@Tub!1.46!47.70!Tub;;chr17:48015839..48015915,-!p3@Foxp4!1.46!32.56!Foxp4;;chr2:74550015..74550057,+!p2@Hoxd3!1.46!27.99!Hoxd3;;chr15:102797288..102797302,+!p1@Hoxc10!1.46!27.71!Hoxc10;;chr11:96143843..96143868,+!p3@Hoxb8!1.44!26.28!Hoxb8;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.42!31.71!Pou3f3;;chr9:91260616..91260653,-!p2@Zic1!1.38!23.14!Zic1;;chr14:33412570..33412586,+!p1@Prrxl1!1.38!22.85!Prrxl1;;chr3:34548946..34548972,+!p2@Sox2!1.35!23.71!Sox2;;chr6:52190467..52190500,-!p1@Hoxa10!1.35!21.42!Hoxa10;;chr3:34548909..34548927,+!p1@Sox2!1.34!35.14!Sox2;;chr15:78994907..78994926,-!p1@Sox10!1.33!51.70!Sox10;;chr7:30088977..30089002,+!p2@Dpf1!1.33!27.99!Dpf1;;chr11:84339016..84339044,-!p1@Lhx1!1.32!20.00!Lhx1;;chr11:96147952..96147967,+!p1@Hoxb7!1.31!23.99!Hoxb7;;chr15:76352677..76352737,-!p3@Scrt1!1.31!19.42!Scrt1;;chr11:96160426..96160443,+!p2@Hoxb6!1.29!18.57!Hoxb6;;chr3:95032197..95032208,-!p3@Mllt11!1.28!22.57!Mllt11;;chr10:84218895..84218909,+!p1@Rfx4!1.27!17.71!Rfx4;;chr11:96160360..96160397,+!p3@Hoxb6!1.25!16.85!Hoxb6;;chr7:144505980..144506010,-!p3@Ebf3!1.21!18.57!Ebf3;;chr3:95032184..95032195,-!p4@Mllt11!1.19!18.00!Mllt11;;chr4:150482563..150482655,-!p2@Camta1!1.18!49.99!Camta1;;chr2:127347067..127347093,-!p1@Kcnip3!1.18!23.42!Kcnip3;;chr14:34791937..34791977,-!p1@Zfp488!1.18!14.28!Zfp488;;chr6:52184901..52184959,-!p2@Hoxa10!1.18!14.28!Hoxa10;;chr7:25292331..25292421,+!p1@Zfp428!1.16!96.26!Zfp428;;chr6:52167459..52167492,-!p1@Hoxa7!1.16!16.00!Hoxa7;;chr7:146768691..146768707,-!p1@Nkx6-2!1.16!13.43!Nkx6-2;;chr6:52163319..52163342,-!p1@Hoxa3!1.14!18.85!Hoxa3;;chr14:104867201..104867258,-!p1@Pou4f1!1.14!18.00!Pou4f1;;chr11:33103563..33103583,-!p1@Tlx3!1.14!12.85!Tlx3;;chr15:76352832..76352900,-!p1@Scrt1!1.13!12.57!Scrt1;;chr15:75578748..75578752,-!p1@Mafa!1.13!12.57!Mafa;;chrX:34442872..34442899,-!p1@Nkrf!1.12!16.00!Nkrf;;chrX:58146612..58146615,-!p1@Sox3!1.11!12.00!Sox3;;chr11:116196664..116196679,-!p1@Foxj1!1.10!18.00!Foxj1;;chr4:154335024..154335039,+!p1@Hes5!1.10!14.00!Hes5;;chr2:74542918..74542971,+!p1@Hoxd8!1.09!17.14!Hoxd8;;chr15:76353005..76353021,-!p2@Scrt1!1.09!11.43!Scrt1;;chr6:52176144..52176161,-!p2@Hoxa9!1.09!11.43!Hoxa9;;chr19:19185671..19185693,-!p1@Rorb!1.08!26.28!Rorb;;chr12:3806003..3806031,+!p11@Dnmt3a!1.08!11.14!Dnmt3a;;chr6:55631042..55631102,-!p1@Neurod6!1.07!10.85!Neurod6;;chr11:96143728..96143745,+!p4@Hoxb8!1.07!10.85!Hoxb8;;chr5:138199481..138199491,+!p16@Tsc22d4!1.06!10.57!Tsc22d4;;chr2:74549968..74549996,+!p1@Hoxd3!1.05!12.85!Hoxd3;;chr11:98190918..98190951,-!p1@Neurod2!1.05!10.28!Neurod2;;chr2:65683890..65683907,+!p1@Csrnp3!1.04!19.14!Csrnp3;;chr2:147012125..147012149,-!p1@Nkx2-2!1.04!10.00!Nkx2-2;;chr14:122874619..122874634,+!p1@Zic2!1.04!10.00!Zic2;;chr11:23978291..23978323,+!p7@Bcl11a!1.04!10.00!Bcl11a;;chr11:96145450..96145517,+!p2@Hoxb7!1.03!14.85!Hoxb7;;chr2:162769220..162769252,+!p1@L3mbtl1!1.03!9.71!L3mbtl1;;chr14:118636238..118636257,-!p2@Sox21!1.03!9.71!Sox21;;chr15:102797225..102797243,+!p2@Hoxc10!1.03!9.71!Hoxc10;;chr2:74536026..74536039,+!p1@Hoxd9!1.02!9.43!Hoxd9;;chr3:34549096..34549111,+!p3@Sox2!1.01!9.14!Sox2;;chr15:102767247..102767265,+!p1@Hoxc12!1.01!9.14!Hoxc12;;chr11:96153767..96153822,+!p1@Hoxb6!1.00!14.00!Hoxb6;;chr7:144505957..144505972,-!p2@Ebf3!1.00!11.14!Ebf3;;chr2:74529998..74530020,+!p2@Hoxd10!0.98!8.57!Hoxd10;;chr11:96132767..96132796,+!p2@Hoxb9!0.97!8.28!Hoxb9;;chr12:87762578..87762612,+!p1@Esrrb!0.97!8.28!Esrrb;;chr13:48356475..48356492,+!p1@Id4!0.95!176.25!Id4;;chr15:102828658..102828678,+!p1@Hoxc6!0.95!8.00!Hoxc6;;chrX:108009761..108009788,+!p1@Pou3f4!0.95!8.00!Pou3f4;;chr7:148513409..148513455,-!p2@Deaf1!0.94!37.13!Deaf1;;chr15:102821007..102821021,+!p2@Hoxc8!0.94!7.71!Hoxc8;;chr15:102820964..102821006,+!p1@Hoxc8!0.94!7.71!Hoxc8;;chr7:91558472..91558512,-!p2@Arnt2!0.93!10.85!Arnt2;;chr15:102820946..102820961,+!p3@Hoxc8!0.93!7.43!Hoxc8;;chr18:81183755..81183761,-!p1@Sall3!0.93!7.43!Sall3;;chr11:101646566..101646603,-!p1@Etv4!0.92!24.28!Etv4;;chr10:67375368..67375433,-!p1@Zfp365!0.92!13.14!Zfp365;;chr11:44431016..44431045,+!p5@Ebf1!0.92!10.57!Ebf1;;chr5:120881900..120881914,+!p1@Lhx5!0.91!7.14!Lhx5;;chr12:30219426..30219506,+!p2@Myt1l!0.91!7.14!Myt1l;;chr18:36441119..36441158,+!p2@Pura!0.90!17.71!Pura;;chr1:189821714..1898217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fp536;;chr5:3648045..3648074,-!p2@Gatad1!0.34!2.57!Gatad1;;chr4:135700687..135700719,+!p2@Id3!0.34!2.29!Id3;;chr7:52960730..52960762,+!p3@Dbp!0.34!1.71!Dbp;;chr8:123640090..123640101,+!p2@Foxc2!0.34!1.43!Foxc2;;chr10:30522881..30522960,-!p1@Ncoa7!0.33!22.57!Ncoa7;;chr7:17199897..17199955,-!p1@Grlf1!0.33!21.42!Grlf1;;chr7:26067619..26067702,+!p2@Cic!0.33!10.28!Cic;;chr7:6124098..6124133,+!p1@Zfp444!0.33!8.00!Zfp444;;chr4:133309531..133309581,-!p4@Arid1a!0.33!7.43!Arid1a;;chr7:6282837..6282892,-!p1@Zfp583!0.33!7.14!Zfp583;;chr4:148178559..148178603,+!p1@Casz1!0.33!4.86!Casz1;;chr4:13670571..13670625,+!p1@Runx1t1!0.33!4.57!Runx1t1;;chr4:45024965..45025031,-!p3@Zbtb5!0.33!4.00!Zbtb5;;chr15:76181718..76181729,+!p3@Maf1!0.33!4.00!Maf1;;chr6:38204214..38204267,-!p4@D630045J12Rik!0.33!2.86!D630045J12Rik;;chr19:5424878..5424890,-!p7@Drap1!0.33!2.29!Drap1;;chr15:40486427..40486437,+!p5@Zfpm2!0.33!1.71!Zfpm2;;chr2:115891680..115891701,-!p12@Meis2!0.33!1.71!Meis2;;chr8:107793688..107793736,+!p1@Hsf4!0.33!1.71!Hsf4;;chr11:44430877..44430899,+!p6@Ebf1!0.33!1.71!Ebf1;;chr11:96685487..96685512,-!p7@Nfe2l1!0.33!1.14!Nfe2l1;;chr11:23977965..23977974,+!p11@Bcl11a!0.33!1.14!Bcl11a;;chr1:122498955..122498968,+!p1@En1!0.33!1.14!En1;;chr1:19199079..19199092,+!p7@Tfap2b!0.33!1.14!Tfap2b;;chr2:105515635..105515661,+!p5@Pax6!0.33!1.14!Pax6;;chr2:105515586..105515606,+!p4@Pax6!0.33!1.14!Pax6;;chr2:151907604..151907629,+!p4@Scrt2!0.33!1.14!Scrt2;;chr1:191994700..191994711,-!p4@Prox1!0.33!1.14!Prox1;;chr17:48015995..48016037,-!p12@Foxp4!0.33!1.14!Foxp4;;chr17:51965860..51965876,-!p14@Satb1!0.33!1.14!Satb1;;chr18:84256138..84256150,-!p7@Tshz1!0.33!1.14!Tshz1;;chr5:140019865..140019886,+!p1@Uncx!0.33!1.14!Uncx;;chr5:77524199..77524210,-!p10@Hopx!0.33!1.14!Hopx;;chr6:52195747..52195762,-!p3@Hoxa11!0.33!1.14!Hoxa11;;chr12:87762625..87762637,+!p7@Esrrb!0.33!1.14!Esrrb;;chr12:87762732..87762747,+!p9@Esrrb!0.33!1.14!Esrrb;;chr13:31717614..31717628,+!p3@Foxf2!0.33!1.14!Foxf2;;chr14:33413108..33413118,+!p3@Prrxl1!0.33!1.14!Prrxl1;;chr13:40825465..40825469,-!p2@Tfap2a!0.33!1.14!Tfap2a;;chr14:34791987..34791998,-!p2@Zfp488!0.33!1.14!Zfp488;;chr13:42147117..42147142,+!p3@Hivep1!0.33!1.14!Hivep1;;chr9:96632593..96632620,-!p12@Zbtb38!0.33!1.14!Zbtb38;;chr9:69608731..69608742,-!p2@Foxb1!0.33!1.14!Foxb1;;chr9:91263173..91263220,+!p2@Zic4!0.33!1.14!Zic4;;chr9:99776617..99776631,-!p2@Sox14!0.33!1.14!Sox14;;chr2:74520343..74520383,+!p4@Hoxd11!0.33!1.14!Hoxd11;;chr4:119487109..119487131,+!p4@Hivep3!0.33!1.14!Hivep3;;chr3:17954233..17954249,+!p1@Bhlhe22!0.33!1.14!Bhlhe22;;chr2:77541362..77541382,-!p8@Zfp385b!0.33!1.14!Zfp385b;;chr4:13678482..13678505,+!p9@Runx1t1!0.33!1.14!Runx1t1;;chr3:34549144..34549155,+!p5@Sox2!0.33!1.14!Sox2;;chr3:54611692..54611726,-!p1@Rfxap!0.32!43.13!Rfxap;;chr16:22439681..22439698,-!p1@Etv5!0.32!32.56!Etv5;;chr2:181327438..181327495,-!p1@Znf512b!0.32!24.57!Znf512b;;chr10:22451142..22451191,-!p2@Tbpl1!0.32!18.28!Tbpl1;;chr8:112229478..112229536,+!p1@Zfp821!0.32!16.00!Zfp821;;chr4:135841976..135842029,+!p2@Zfp46!0.32!13.43!Zfp46;;chr19:26679615..26679646,+!p3@Smarca2!0.32!12.57!Smarca2;;chr2:169458352..169458397,+!p3@Tshz2!0.32!4.00!Tshz2;;chr14:52935788..52935817,-!p2@Sall2!0.32!3.43!Sall2;;chr19:26679596..26679607,+!p8@Smarca2!0.32!3.14!Smarca2;;chr18:55149986..55150009,-!p7@Zfp608!0.32!2.86!Zfp608;;chr2:34227524..34227547,-!p2@Pbx3!0.32!2.86!Pbx3;;chr10:22451100..22451111,-!p5@Tbpl1!0.32!2.57!Tbpl1;;chr19:7342786..7342803,+!p2@Rcor2!0.32!1.71!Rcor2;;chr10:127896295..127896304,+!p6@Smarcc2!0.32!1.43!Smarcc2;;chr14:76904313..76904328,+!p1@Tsc22d1!0.31!361.06!Tsc22d1;;chr4:118967105..118967123,-!p1@Ybx1!0.31!54.56!Ybx1;;chr10:79862175..79862221,-!p1@Mbd3!0.31!25.14!Mbd3;;chr4:128483534..128483613,-!p1@Zfp362!0.31!12.28!Zfp362;;chr11:102180696..102180760,-!p2@Ubtf!0.31!8.57!Ubtf;;chr12:77470372..77470456,-!p1@Zbtb25!0.31!7.43!Zbtb25;;chr6:117813087..117813121,+!p1@Zfp239!0.31!6.28!Zfp239;;chr17:27693546..27693557,+!p6@Hmga1!0.31!6.00!Hmga1;;chr9:21420744..21420755,+!p3@Smarca4!0.31!4.57!Smarca4;;chr6:117791276..117791304,+!p2@Zfp637!0.31!4.57!Zfp637;;chr10:82226613..82226641,-!p4@Nfyb!0.31!4.28!Nfyb;;chr4:62626682..62626705,+!p2@Zfp618!0.31!3.43!Zfp618;;chr7:4947724..4947743,-!p3@Zfp579!0.31!3.43!Zfp579;;chr1:170361730..170361769,-!p7@Pbx1!0.31!3.43!Pbx1;;chr18:75979866..75979890,+!p3@Zbtb7c!0.31!3.14!Zbtb7c;;chr4:133310214..133310231,-!p11@Arid1a!0.31!2.29!Arid1a;;chr14:65568567..65568588,-!p3@Hmbox1!0.31!2.00!Hmbox1;;chr18:69752912..69752928,+!p9@Tcf4!0.31!2.00!Tcf4;;chr2:115890294..115890334,-!p9@Meis2!0.31!1.71!Meis2;;chr6:47998938..47998955,-!p2@Zfp777!0.31!1.71!Zfp777;;chr7:123182248..123182264,-!p3@Sox6!0.31!1.43!Sox6;;chr7:25292118..25292129,+!p8@Zfp428!0.31!1.43!Zfp428;;chr18:14131126..14131211,-!p1@Zfp521!0.30!37.99!Zfp521;;chr17:33766023..33766059,+!p1@Zfp414!0.30!27.14!Zfp414;;chr5:39075982..39076052,-!p1@Zfp518b!0.30!12.28!Zfp518b;;chr8:118230866..118230891,-!p4@Maf!0.30!11.14!Maf;;chr9:48644306..48644364,-!p1@Zbtb16!0.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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:11738-123F1
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000206
+|is_a=EFO:0002091;;FF:0000206
+|is_obsolete=
+|library_id=CNhs12635
+|library_id_phase_based=2:CNhs12635
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11738
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11738
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520dorsal%2520spinal%2520cord%252c%2520donor2.CNhs12635.11738-123F1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520dorsal%2520spinal%2520cord%252c%2520donor2.CNhs12635.11738-123F1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520dorsal%2520spinal%2520cord%252c%2520donor2.CNhs12635.11738-123F1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520dorsal%2520spinal%2520cord%252c%2520donor2.CNhs12635.11738-123F1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520dorsal%2520spinal%2520cord%252c%2520donor2.CNhs12635.11738-123F1.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - dorsal spinal cord, donor2
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12635,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0632340529948655,0,0,0,0,0,-0.361104917602818,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.193400926831458,0,0,0,0,0,0,0,0,0,0,0,0,0.372929002090136,-0.449299705633003,0,0,0,0,0.0360356550279375,-0.100199638804798,0.233028027750616,0.225431782994583,0.238785982644842,0.476018972135158,0.109123086691028,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,-0.0984344453019895,0,0,0,-0.147880877351666,-0.310650657339386,-0.0489679560800542,-0.0679859710142546,0,0,0.155239858324784,0.394423262585803,0.109123086691028,0,0.0797488248363452,0.348029291889141,0.397749702883479,-0.0788315948399074,0,0,0,0,0,0,0.191185921132963,0.0514557211262616,0.272290647408573,0,0,0.268800900821362,0.368747671231146,0
 |rna_box=123
 |rna_catalog_number=custom
@@ Line 57: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=spinal cord
 |top_motifs=ZIC1..3:2.70017856664;ZBTB6:2.69261171684;ZNF423:2.59837563395;MTE{core}:2.45998197333;MTF1:2.40379728751;LMO2:2.36145086782;BREu{core}:2.23401556302;TFAP2B:2.19687068222;TFAP2{A,C}:2.16190772908;REST:2.14646851857;ZFP161:2.1456719835;PAX5:2.14398821412;EGR1..3:2.12643880654;PAX6:2.08899200182;HIC1:2.04893411303;MYFfamily:1.92925473804;MED-1{core}:1.91399540112;PRRX1,2:1.90679800883;HES1:1.86328430629;SMAD1..7,9:1.78602014831;KLF4:1.71653197154;PATZ1:1.68372914121;TFDP1:1.62026356348;FOXM1:1.58218781196;RREB1:1.54982206467;HOXA9_MEIS1:1.48015464389;ADNP_IRX_SIX_ZHX:1.43619292411;NHLH1,2:1.33248792192;TBX4,5:1.32301721681;GTF2I:1.30920097929;MYOD1:1.2915120309;GFI1B:1.25626675911;GTF2A1,2:1.23533967084;MZF1:1.22990340067;UFEwm:1.22500096987;ATF2:1.21195160672;RFX1:1.20705354068;DBP:1.16020834738;EBF1:1.15286403024;PRDM1:1.11156599592;AHR_ARNT_ARNT2:1.09493611901;ONECUT1,2:1.06248698511;VSX1,2:1.06232052467;OCT4_SOX2{dimer}:1.05937395712;SOX{8,9,10}:1.04278797925;POU5F1:1.04050064312;MAZ:0.961423373493;HAND1,2:0.910076200539;JUN:0.907171695779;XCPE1{core}:0.900591673249;NR5A1,2:0.870715946272;FOXD3:0.812410298438;MAFB:0.804435671577;SP1:0.789878244397;PAX8:0.78691832525;RORA:0.784707993488;SOX2:0.782476527099;GLI1..3:0.769671444089;IKZF1:0.760112945615;NRF1:0.742067623997;TFCP2:0.723807350951;POU6F1:0.675435928331;ZNF148:0.636836253463;POU3F1..4:0.616329146958;ESR1:0.605953551772;TGIF1:0.597999836484;RXR{A,B,G}:0.576682908409;CUX2:0.558324519715;YY1:0.530691834402;TEF:0.511414065411;ALX1:0.495437651481;NANOG:0.484628318534;TFAP4:0.46926785143;GZF1:0.448791479532;HMGA1,2:0.439191896943;PBX1:0.436024710096;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.434381319474;POU2F1..3:0.429012240161;RFX2..5_RFXANK_RFXAP:0.400074759879;NKX2-3_NKX2-5:0.345354186209;ZEB1:0.330324106836;EN1,2:0.310361868139;ATF5_CREB3:0.301868118608;HMX1:0.297102745076;HSF1,2:0.288846607439;NKX6-1,2:0.280644498145;FOXL1:0.279570436251;SOX17:0.277659163321;NR3C1:0.276421876278;PAX4:0.261533431783;NFE2L1:0.257688883432;HIF1A:0.242145416695;LHX3,4:0.219214538121;ZNF143:0.210727674262;TLX1..3_NFIC{dimer}:0.19701023799;HOX{A5,B5}:0.183890993862;GATA4:0.150226585777;FOX{F1,F2,J1}:0.127345768434;ESRRA:0.0840404551701;LEF1_TCF7_TCF7L1,2:0.0444661272258;ZNF384:0.0103158991926;PAX2:-0.0444500648135;ATF6:-0.0460932715697;NKX3-2:-0.0465538966291;ATF4:-0.0480950892967;FOXQ1:-0.0494651942682;NFY{A,B,C}:-0.0835119220937;ZNF238:-0.089250890302;NANOG{mouse}:-0.0968492641066;FOXP3:-0.103350977718;SREBF1,2:-0.137320358177;NFIL3:-0.143751580227;NKX2-1,4:-0.151526203169;GCM1,2:-0.153383104197;PPARG:-0.181265787822;NR1H4:-0.20491333421;STAT1,3:-0.228413925451;RBPJ:-0.250040453125;EP300:-0.252208248348;NFE2L2:-0.255032749053;CREB1:-0.26715903669;TOPORS:-0.316660367585;CRX:-0.352768165495;TAL1_TCF{3,4,12}:-0.355675265646;BACH2:-0.375960760174;CDC5L:-0.385879111077;RUNX1..3:-0.391434154555;SOX5:-0.403796976929;SNAI1..3:-0.409728835784;SPZ1:-0.444358219845;PAX1,9:-0.486438661934;TP53:-0.495447576048;FOX{I1,J2}:-0.502947576645;CDX1,2,4:-0.538735770812;NKX2-2,8:-0.557642240914;HBP1_HMGB_SSRP1_UBTF:-0.559495009815;MEF2{A,B,C,D}:-0.570313847319;NFKB1_REL_RELA:-0.577545388241;FOSL2:-0.583841030071;MYB:-0.588795860169;FOXN1:-0.625910754964;NKX3-1:-0.632231353923;FOXA2:-0.64414218142;TBP:-0.653974896884;NFATC1..3:-0.671219510087;HOX{A4,D4}:-0.675072185287;HNF1A:-0.722730164666;HNF4A_NR2F1,2:-0.724044608103;GATA6:-0.765989048105;CEBPA,B_DDIT3:-0.767917419864;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.800001709577;NFE2:-0.803797241329;IKZF2:-0.809789286051;ZBTB16:-0.82788094911;TEAD1:-0.848761449899;ELK1,4_GABP{A,B1}:-0.848847235842;HLF:-0.873424072417;SPI1:-0.873870468291;POU1F1:-0.895289614496;MYBL2:-0.919334828276;RXRA_VDR{dimer}:-0.929583080674;GFI1:-0.945524553423;EVI1:-0.975908716233;T:-0.985783898835;FOS_FOS{B,L1}_JUN{B,D}:-0.992736100569;ARID5B:-1.01224104192;ETS1,2:-1.09413460393;SPIB:-1.10581373288;IRF7:-1.1123121163;E2F1..5:-1.17195586179;BPTF:-1.1725756455;AR:-1.19695985222;FOXP1:-1.21214164882;PITX1..3:-1.24992330077;bHLH_family:-1.25159077244;FOXO1,3,4:-1.26337083459;STAT2,4,6:-1.28210330413;NR6A1:-1.29260896865;ALX4:-1.40531145196;SRF:-1.459520187;NFIX:-1.47449991176;STAT5{A,B}:-1.49633370895;TLX2:-1.5333532763;DMAP1_NCOR{1,2}_SMARC:-1.60607709467;ELF1,2,4:-1.64200092849;FOX{D1,D2}:-1.73551653676;IRF1,2:-1.74498764587;AIRE:-2.04571096606;PDX1:-2.18474739718
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11738-123F1;search_select_hide=table117:11738-123F1
 }}

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FF:11738-123F1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12635

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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