FF:11643-122D5: Difference between revisions

Latest revision as of 18:13, 4 June 2020

Name:	Mouse Neurons - dorsal spinal cord, donor3
Species:	Mouse (Mus musculus)
Library ID:	CNhs12618
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	RNADOR3
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		SAMD00005340

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12618		CAGE		DRX008836		DRR009708

Accession ID Mm9

Library id		BAM		CTSS
CNhs12618		DRZ001133		DRZ002518

Accession ID Mm10

Library id		BAM		CTSS
CNhs12618		DRZ012483		DRZ013868

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

CNhs12618

0	0
1	0.535
10	0
100	0.0867
1000	0
1001	-0.0668
1002	0.00807
1003	0.00203
1004	0
1005	0.0491
1006	0.605
1007	-0.25
1008	0
1009	-0.103
101	-0.244
1010	0
1011	0.298
1012	0
1013	0.25
1014	-6.860561e-4
1015	0.263
1016	0.12
1017	0
1018	0
1019	0
102	0
1020	0.588
1021	0.0867
1022	0
1023	0
1024	0.0514
1025	0.06
1026	0.0572
1027	0.406
1028	0
1029	-0.176
103	0.0635
1030	0
1031	-0.127
1032	0.408
1033	0
1034	0
1035	0
1036	-0.179
1037	0
1038	-0.0644
1039	0.0535
104	0
1040	-0.256
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: CNhs12618

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00558
MA0003.1	MA0003.1	0.583
MA0004.1	MA0004.1	0.449
MA0006.1	MA0006.1	0.228
MA0007.1	MA0007.1	0.221
MA0009.1	MA0009.1	0.893
MA0014.1	MA0014.1	0.556
MA0017.1	MA0017.1	2.34405e-6
MA0018.2	MA0018.2	0.046
MA0019.1	MA0019.1	0.972
MA0024.1	MA0024.1	0.61
MA0025.1	MA0025.1	0.757
MA0027.1	MA0027.1	0.616
MA0028.1	MA0028.1	0.0369
MA0029.1	MA0029.1	0.916
MA0030.1	MA0030.1	0.473
MA0031.1	MA0031.1	0.0895
MA0035.2	MA0035.2	0.0673
MA0038.1	MA0038.1	0.405
MA0039.2	MA0039.2	0.169
MA0040.1	MA0040.1	0.54
MA0041.1	MA0041.1	0.204
MA0042.1	MA0042.1	0.535
MA0043.1	MA0043.1	0.285
MA0046.1	MA0046.1	4.18402e-7
MA0047.2	MA0047.2	2.70993e-4
MA0048.1	MA0048.1	0.0435
MA0050.1	MA0050.1	1.47572e-6
MA0051.1	MA0051.1	7.46617e-5
MA0052.1	MA0052.1	0.475
MA0055.1	MA0055.1	0.0295
MA0057.1	MA0057.1	0.474
MA0058.1	MA0058.1	0.517
MA0059.1	MA0059.1	0.204
MA0060.1	MA0060.1	0.0843
MA0061.1	MA0061.1	0.0608
MA0062.2	MA0062.2	2.36859e-4
MA0065.2	MA0065.2	9.72105e-5
MA0066.1	MA0066.1	0.0605
MA0067.1	MA0067.1	0.891
MA0068.1	MA0068.1	0.619
MA0069.1	MA0069.1	0.0573
MA0070.1	MA0070.1	0.239
MA0071.1	MA0071.1	0.156
MA0072.1	MA0072.1	0.127
MA0073.1	MA0073.1	0.9
MA0074.1	MA0074.1	0.235
MA0076.1	MA0076.1	0.0936
MA0077.1	MA0077.1	0.0655
MA0078.1	MA0078.1	0.825
MA0079.2	MA0079.2	0.117
MA0080.2	MA0080.2	2.39885e-9
MA0081.1	MA0081.1	0.29
MA0083.1	MA0083.1	0.14
MA0084.1	MA0084.1	0.268
MA0087.1	MA0087.1	0.306
MA0088.1	MA0088.1	0.178
MA0090.1	MA0090.1	0.0913
MA0091.1	MA0091.1	0.303
MA0092.1	MA0092.1	0.254
MA0093.1	MA0093.1	0.494
MA0099.2	MA0099.2	0.00463
MA0100.1	MA0100.1	0.0823
MA0101.1	MA0101.1	0.0321
MA0102.2	MA0102.2	0.48
MA0103.1	MA0103.1	0.152
MA0104.2	MA0104.2	0.925
MA0105.1	MA0105.1	0.0216
MA0106.1	MA0106.1	0.0526
MA0107.1	MA0107.1	0.0538
MA0108.2	MA0108.2	0.672
MA0111.1	MA0111.1	0.997
MA0112.2	MA0112.2	4.12756e-4
MA0113.1	MA0113.1	0.231
MA0114.1	MA0114.1	1.13147e-5
MA0115.1	MA0115.1	1.29803e-4
MA0116.1	MA0116.1	0.102
MA0117.1	MA0117.1	0.467
MA0119.1	MA0119.1	0.197
MA0122.1	MA0122.1	0.849
MA0124.1	MA0124.1	0.562
MA0125.1	MA0125.1	0.172
MA0131.1	MA0131.1	0.555
MA0135.1	MA0135.1	0.0302
MA0136.1	MA0136.1	4.85043e-11
MA0137.2	MA0137.2	0.00728
MA0138.2	MA0138.2	0.0107
MA0139.1	MA0139.1	0.552
MA0140.1	MA0140.1	2.16179e-4
MA0141.1	MA0141.1	0.0598
MA0142.1	MA0142.1	0.792
MA0143.1	MA0143.1	0.796
MA0144.1	MA0144.1	0.0209
MA0145.1	MA0145.1	0.114
MA0146.1	MA0146.1	0.0459
MA0147.1	MA0147.1	0.79
MA0148.1	MA0148.1	4.88007e-5
MA0149.1	MA0149.1	0.145
MA0150.1	MA0150.1	0.016
MA0152.1	MA0152.1	0.0304
MA0153.1	MA0153.1	9.59236e-7
MA0154.1	MA0154.1	0.0389
MA0155.1	MA0155.1	0.92
MA0156.1	MA0156.1	2.07301e-8
MA0157.1	MA0157.1	0.0679
MA0159.1	MA0159.1	0.00238
MA0160.1	MA0160.1	0.0385
MA0162.1	MA0162.1	0.315
MA0163.1	MA0163.1	0.00238
MA0164.1	MA0164.1	0.885
MA0258.1	MA0258.1	0.021
MA0259.1	MA0259.1	0.824

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: CNhs12618

Novel motif	Logo	P-value
1	1	0.114
10	10	0.0371
100	100	0.489
101	101	0.751
102	102	0.873
103	103	0.0766
104	104	0.601
105	105	0.64
106	106	0.0757
107	107	0.156
108	108	0.319
109	109	0.0159
11	11	0.105
110	110	0.0277
111	111	0.0414
112	112	0.00146
113	113	0.764
114	114	0.147
115	115	0.981
116	116	0.949
117	117	0.00221
118	118	0.219
119	119	0.141
12	12	0.936
120	120	0.677
121	121	0.179
122	122	0.773
123	123	0.00923
124	124	0.131
125	125	0.389
126	126	0.0545
127	127	0.121
128	128	0.0772
129	129	0.329
13	13	1.34149e-6
130	130	0.355
131	131	0.817
132	132	0.584
133	133	0.737
134	134	0.278
135	135	0.154
136	136	0.429
137	137	0.34
138	138	0.894
139	139	0.266
14	14	0.968
140	140	0.0385
141	141	0.391
142	142	0.046
143	143	0.528
144	144	0.977
145	145	0.00106
146	146	0.589
147	147	0.558
148	148	0.627
149	149	0.942
15	15	0.0989
150	150	0.0831
151	151	0.705
152	152	0.163
153	153	0.309
154	154	0.488
155	155	0.993
156	156	0.00501
157	157	0.154
158	158	0.0273
159	159	0.0568
160	160	0.244
161	161	0.223
162	162	0.728
163	163	0.431
164	164	0.00537
165	165	0.303
166	166	0.743
167	167	0.61
168	168	0.706
169	169	0.00222
17	17	0.0729
18	18	0.968
19	19	0.14
2	2	0.441
20	20	0.0305
21	21	0.488
22	22	0.214
23	23	0.587
24	24	0.13
25	25	0.727
26	26	4.35304e-8
27	27	0.378
28	28	0.497
29	29	0.0242
3	3	0.0586
30	30	0.606
31	31	0.754
32	32	0.969
33	33	0.14
34	34	0.683
35	35	0.874
36	36	0.439
37	37	0.0267
38	38	0.484
39	39	0.438
4	4	0.49
40	40	0.593
41	41	0.568
42	42	0.144
43	43	0.12
44	44	0.937
45	45	0.87
46	46	0.0289
47	47	0.305
48	48	0.188
49	49	0.104
5	5	0.0848
50	50	0.394
51	51	0.738
52	52	0.646
53	53	0.641
54	54	0.924
55	55	0.93
56	56	0.578
57	57	0.501
58	58	0.27
59	59	0.316
6	6	0.86
60	60	0.0547
61	61	0.0584
62	62	0.149
63	63	0.211
64	64	0.808
65	65	0.398
66	66	0.822
67	67	0.784
68	68	0.69
69	69	0.849
7	7	0.014
70	70	0.0583
71	71	0.00537
72	72	0.619
73	73	0.0348
74	74	0.33
75	75	0.038
76	76	0.278
77	77	0.638
78	78	0.00736
79	79	0.566
8	8	0.0771
80	80	0.715
81	81	0.736
82	82	0.306
83	83	0.51
84	84	0.82
85	85	0.183
86	86	0.107
87	87	0.764
88	88	0.142
89	89	0.508
9	9	0.53
90	90	0.0478
91	91	0.253
92	92	0.413
93	93	0.0333
94	94	0.326
95	95	0.0882
96	96	0.167
97	97	0.96
98	98	0.695
99	99	0.778

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: CNhs12618

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:0000468,UBERON:0000922,UBERON:0002240,UBERON:0002100,UBERON:0000483,UBERON:0000479,UBERON:0002346,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:0000467,UBERON:0001062,UBERON:0000119,UBERON:0003103,UBERON:0005291,UBERON:0005174,UBERON:0000489,UBERON:0005177,UBERON:0001948,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0002256,UBERON:0001016,UBERON:0000924,UBERON:0005743,UBERON:0001137,UBERON:0002315,UBERON:0003075,UBERON:0001049,UBERON:0006601,UBERON:0005068,UBERON:0006241,UBERON:0003076,UBERON:0007284,UBERON:0003057,UBERON:0007135
+|DRA_sample_Accession=CAGE@SAMD00005340
-|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:0002611,CL:0000133,CL:0000337
+|accession_numbers=CAGE;DRX008836;DRR009708;DRZ001133;DRZ002518;DRZ012483;DRZ013868
+|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=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.58!426.94!Olig1;;chr11:96143666..96143725,+!p1@Hoxb8!2.28!217.78!Hoxb8;;chr5:138199361..138199441,+!p2@Tsc22d4!2.15!254.00!Tsc22d4;;chr16:91225808..91225824,+!p1@Olig2!1.93!83.93!Olig2;;chr3:95032091..95032183,-!p1@Mllt11!1.68!383.65!Mllt11;;chr11:96143962..96144035,+!p2@Hoxb8!1.67!45.50!Hoxb8;;chr9:91260594..91260612,-!p1@Zic1!1.65!43.51!Zic1;;chr2:74529970..74529997,+!p1@Hoxd10!1.62!40.42!Hoxd10;;chr2:74550015..74550057,+!p2@Hoxd3!1.61!39.76!Hoxd3;;chr6:52176164..52176195,-!p1@Hoxa9!1.60!47.71!Hoxa9;;chr9:91260616..91260653,-!p2@Zic1!1.55!34.23!Zic1;;chr16:91270091..91270143,+!p2@Olig1!1.54!33.35!Olig1;;chr14:33412570..33412586,+!p1@Prrxl1!1.54!33.35!Prrxl1;;chr7:116154364..116154444,+!p1@Tub!1.51!52.79!Tub;;chr17:25707623..25707639,-!p1@Sox8!1.50!125.23!Sox8;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.47!36.22!Pou3f3;;chr11:96143843..96143868,+!p3@Hoxb8!1.45!27.17!Hoxb8;;chr6:52167459..52167492,-!p1@Hoxa7!1.44!31.58!Hoxa7;;chr11:96147952..96147967,+!p1@Hoxb7!1.39!29.60!Hoxb7;;chr12:54349410..54349461,+!p1@Npas3!1.39!28.05!Npas3;;chr3:34548909..34548927,+!p1@Sox2!1.36!36.89!Sox2;;chr17:48015839..48015915,-!p3@Foxp4!1.35!25.18!Foxp4;;chr11:96160426..96160443,+!p2@Hoxb6!1.35!21.42!Hoxb6;;chr15:76352677..76352737,-!p3@Scrt1!1.33!20.54!Scrt1;;chr11:96160360..96160397,+!p3@Hoxb6!1.32!19.66!Hoxb6;;chr3:34548946..34548972,+!p2@Sox2!1.30!20.76!Sox2;;chr7:144505980..144506010,-!p3@Ebf3!1.29!22.53!Ebf3;;chr15:78994907..78994926,-!p1@Sox10!1.28!46.16!Sox10;;chr2:127347067..127347093,-!p1@Kcnip3!1.28!29.82!Kcnip3;;chr10:84218895..84218909,+!p1@Rfx4!1.28!18.11!Rfx4;;chr7:30088977..30089002,+!p2@Dpf1!1.26!23.63!Dpf1;;chr11:84339016..84339044,-!p1@Lhx1!1.26!17.23!Lhx1;;chr6:52190467..52190500,-!p1@Hoxa10!1.24!16.34!Hoxa10;;chr6:52184901..52184959,-!p2@Hoxa10!1.23!15.90!Hoxa10;;chr14:104867201..104867258,-!p1@Pou4f1!1.22!21.65!Pou4f1;;chr3:95032184..95032195,-!p4@Mllt11!1.22!19.22!Mllt11;;chr15:102797288..102797302,+!p1@Hoxc10!1.22!15.46!Hoxc10;;chr3:95032197..95032208,-!p3@Mllt11!1.21!19.22!Mllt11;;chr11:44431016..44431045,+!p5@Ebf1!1.19!20.54!Ebf1;;chr11:96143728..96143745,+!p4@Hoxb8!1.19!14.58!Hoxb8;;chr14:34791937..34791977,-!p1@Zfp488!1.18!14.14!Zfp488;;chr6:55631042..55631102,-!p1@Neurod6!1.17!13.69!Neurod6;;chr2:74549968..74549996,+!p1@Hoxd3!1.16!17.01!Hoxd3;;chr7:25292331..25292421,+!p1@Zfp428!1.15!92.54!Zfp428;;chr4:150482563..150482655,-!p2@Camta1!1.15!46.16!Camta1;;chr11:96153767..96153822,+!p1@Hoxb6!1.15!20.10!Hoxb6;;chr7:144505957..144505972,-!p2@Ebf3!1.14!15.90!Ebf3;;chr4:154335024..154335039,+!p1@Hes5!1.14!15.46!Hes5;;chr15:75578748..75578752,-!p1@Mafa!1.13!12.37!Mafa;;chr12:3806003..3806031,+!p11@Dnmt3a!1.13!12.37!Dnmt3a;;chrX:108009761..108009788,+!p1@Pou3f4!1.12!12.15!Pou3f4;;chr11:96160403..96160416,+!p4@Hoxb6!1.11!11.93!Hoxb6;;chr11:33103563..33103583,-!p1@Tlx3!1.10!11.71!Tlx3;;chr11:98190918..98190951,-!p1@Neurod2!1.10!11.49!Neurod2;;chr5:24032551..24032557,-!p@chr5:24032551..24032557,-!1.10!11.49!Gbx1;;chr6:52163319..52163342,-!p1@Hoxa3!1.08!16.12!Hoxa3;;chr19:19185671..19185693,-!p1@Rorb!1.07!25.62!Rorb;;chr15:76352832..76352900,-!p1@Scrt1!1.06!10.60!Scrt1;;chr12:30219426..30219506,+!p2@Myt1l!1.06!10.38!Myt1l;;chr15:76353005..76353021,-!p2@Scrt1!1.06!10.38!Scrt1;;chr15:76352740..76352781,-!p5@Scrt1!1.05!10.16!Scrt1;;chr2:162769220..162769252,+!p1@L3mbtl1!1.05!10.16!L3mbtl1;;chr15:102828658..102828678,+!p1@Hoxc6!1.04!9.94!Hoxc6;;chr2:65683890..65683907,+!p1@Csrnp3!1.02!18.33!Csrnp3;;chr2:74542918..74542971,+!p1@Hoxd8!1.02!14.58!Hoxd8;;chr2:147019977..147019985,-!p2@Nkx2-2!1.02!9.50!Nkx2-2;;chr6:52176144..52176161,-!p2@Hoxa9!1.02!9.50!Hoxa9;;chr14:118636238..118636257,-!p2@Sox21!1.01!9.28!Sox21;;chrX:34442872..34442899,-!p1@Nkrf!1.00!11.71!Nkrf;;chr15:102820964..102821006,+!p1@Hoxc8!1.00!9.06!Hoxc8;;chr11:96145450..96145517,+!p2@Hoxb7!0.98!13.03!Hoxb7;;chr4:124334894..124334899,+!p1@Pou3f1!0.98!11.26!Pou3f1;;chr4:99322820..99322845,+!p1@Foxd3!0.97!10.60!Foxd3;;chr15:102821007..102821021,+!p2@Hoxc8!0.97!8.39!Hoxc8;;chr1:19199236..19199258,+!p1@Tfap2b!0.97!8.39!Tfap2b;;chr14:118636214..118636235,-!p1@Sox21!0.96!9.94!Sox21;;chr5:98609885..98609900,+!p1@Prdm8!0.96!8.17!Prdm8;;chr7:144506077..144506128,-!p1@Ebf3!0.95!18.77!Ebf3;;chr15:102820946..102820961,+!p3@Hoxc8!0.95!7.95!Hoxc8;;chr15:95485240..95485257,-!p1@Dbx2!0.95!7.95!Dbx2;;chr2:147012125..147012149,-!p1@Nkx2-2!0.95!7.95!Nkx2-2;;chr5:77524250..77524300,-!p1@Hopx!0.94!163.00!Hopx;;chr6:52167434..52167450,-!p3@Hoxa7!0.94!7.73!Hoxa7;;chr13:48356475..48356492,+!p1@Id4!0.93!171.17!Id4;;chr11:96160119..96160135,+!p7@Hoxb6!0.93!7.51!Hoxb6;;chr11:23978291..23978323,+!p7@Bcl11a!0.92!7.29!Bcl11a;;chr5:120881900..120881914,+!p1@Lhx5!0.92!7.29!Lhx5;;chr2:74536026..74536039,+!p1@Hoxd9!0.92!7.29!Hoxd9;;chr15:102839948..102839975,+!p3@Hoxc6!0.92!7.29!Hoxc6;;chr15:102797225..102797243,+!p2@Hoxc10!0.91!7.07!Hoxc10;;chr14:122874619..122874634,+!p1@Zic2!0.91!7.07!Zic2;;chr4:150482353..150482386,-!p6@Camta1!0.91!7.07!Camta1;;chr11:44430989..44431015,+!p4@Ebf1!0.90!12.81!Ebf1;;chr8:24780125..24780143,+!p1@Zmat4!0.90!10.16!Zmat4;;chr10:86956396..86956411,-!p1@Ascl1!0.89!10.60!Ascl1;;chr7:91558472..91558512,-!p2@Arnt2!0.89!9.72!Arnt2;;chr14:67853632..67853674,+!p3@Ebf2!0.89!8.39!Ebf2;;chr2:74529998..74530020,+!p2@Hoxd10!0.89!6.85!Hoxd10;;chrX:58146612..58146615,-!p1@Sox3!0.89!6.85!Sox3;;chr2:127347042..127347058,-!p3@Kcnip3!0.89!6.85!Kcnip3;;chr18:81183755..81183761,-!p1@Sall3!0.89!6.85!Sall3;;chr6:52167513..52167549,-!p2@Hoxa7!0.88!9.50!Hoxa7;;chr2:24331085..24331100,-!p1@Pax8!0.88!6.63!Pax8;;chr7:91558392..91558434,-!p1@Arnt2!0.87!18.33!Arnt2;;chr18:36441119..36441158,+!p2@Pura!0.86!15.90!Pura;;chr11:96144050..96144065,+!p5@Hoxb8!0.86!6.18!Hoxb8;;chr3:95032558..95032641,-!p2@Mllt11!0.85!36.22!Mllt11;;chr7:130644017..130644092,-!p1@Zkscan2!0.85!12.15!Zkscan2;;chr13:78339428..78339466,-!p2@Nr2f1!0.85!8.61!Nr2f1;;chr11:98603185..98603208,+!p1@Thra!0.84!381.44!Thra;;chr11:101646566..101646603,-!p1@Etv4!0.84!20.10!Etv4;;chr13:44936126..44936164,+!p6@Jarid2!0.84!6.85!Jarid2;;chr13:95645580..95645598,+!p1@Otp!0.84!5.96!Otp;;chr5:138199481..138199491,+!p16@Tsc22d4!0.84!5.96!Tsc22d4;;chr4:22415443..22415506,-!p1@Pou3f2!0.84!5.96!Pou3f2;;chr10:67000609..67000625,+!p1@Egr2!0.83!13.91!Egr2;;chr1:189821714..189821761,+!p1@Esrrg!0.83!11.04!Esrrg;;chr10:67375368..67375433,-!p1@Zfp365!0.83!10.60!Zfp365;;chr11:96132767..96132796,+!p2@Hoxb9!0.83!5.74!Hoxb9;;chr10:84218800..84218829,+!p2@Rfx4!0.83!5.74!Rfx4;;chrX:55284180..55284195,+!p2@Zic3!0.83!5.74!Zic3;;chr9:106356278..106356292,+!p3@Pcbp4!0.82!9.94!Pcbp4;;chr3:95032213..95032226,-!p6@Mllt11!0.82!6.85!Mllt11;;chr11:116196664..116196679,-!p1@Foxj1!0.81!8.61!Foxj1;;chr10:67375146..67375208,-!p2@Zfp365!0.81!8.61!Zfp365;;chr3:34549096..34549111,+!p3@Sox2!0.81!5.52!Sox2;;chr8:125897750..125897758,+!p2@Tcf25!0.80!38.43!Tcf25;;chr7:148513409..148513455,-!p2@Deaf1!0.80!26.50!Deaf1;;chr10:30562571..30562597,-!p1@Hey2!0.80!13.25!Hey2;;chr7:30092993..30093076,+!p1@Dpf1!0.80!9.50!Dpf1;;chr3:101814061..101814094,+!p1@Nhlh2!0.80!5.30!Nhlh2;;chr2:168427068..168427115,-!p3@Nfatc2!0.80!5.30!Nfatc2;;chr11:98603160..98603171,+!p3@Thra!0.79!26.28!Thra;;chr2:127347094..127347111,-!p2@Kcnip3!0.78!8.61!Kcnip3;;chr1:173987720..173987729,-!p1@Nhlh1!0.78!5.08!Nhlh1;;chr15:102839976..102839989,+!p4@Hoxc6!0.78!5.08!Hoxc6;;chr12:30213247..30213333,+!p1@Myt1l!0.78!5.08!Myt1l;;chr7:146768691..146768707,-!p1@Nkx6-2!0.78!5.08!Nkx6-2;;chr5:24104751..24104773,-!p5@Smarcd3!0.78!5.08!Smarcd3;;chr6:52161666..52161711,-!p1@Hoxa6!0.78!5.08!Hoxa6;;chr12:87762578..87762612,+!p1@Esrrb!0.77!4.86!Esrrb;;chr11:96132637..96132652,+!p1@Hoxb9!0.77!4.86!Hoxb9;;chr2:25562315..25562344,+!p3@Bmyc!0.76!17.23!Bmyc;;chr5:122499831..122499891,-!p1@Cux2!0.76!7.73!Cux2;;chr4:129118044..129118067,-!p1@Zbtb8b!0.75!5.96!Zbtb8b;;chr2:74517725..74517738,+!p5@Hoxd11!0.75!4.64!Hoxd11;;chr1:91827756..91827773,-!p1@Gbx2!0.75!4.64!Gbx2;;chr7:25292160..25292213,+!p3@Zfp428!0.74!12.15!Zfp428;;chr5:77524231..77524245,-!p3@Hopx!0.74!12.15!Hopx;;chr11:23978229..23978268,+!p8@Bcl11a!0.73!5.08!Bcl11a;;chr11:44431115..44431132,+!p9@Ebf1!0.73!4.42!Ebf1;;chr11:96145393..96145407,+!p3@Hoxb7!0.73!4.42!Hoxb7;;chr16:91225654..91225671,+!p2@Olig2!0.73!4.42!Olig2;;chr15:95485210..95485225,-!p2@Dbx2!0.73!4.42!Dbx2;;chrX:137077151..137077227,-!p2@Tsc22d3!0.72!33.13!Tsc22d3;;chr8:72356532..72356611,+!p1@Pbx4!0.72!19.22!Pbx4;;chr7:148008023..148008092,-!p1@Zfp941!0.72!11.26!Zfp941;;chr13:78339476..78339515,-!p1@Nr2f1!0.72!6.85!Nr2f1;;chr6:52195795..52195825,-!p1@Hoxa11!0.72!4.20!Hoxa11;;chr16:91269972..91269978,+!p3@Olig1!0.72!4.20!Olig1;;chr4:150513630..150513686,-!p4@Camta1!0.71!4.86!Camta1;;chr7:122968213..122968266,-!p4@Sox6!0.70!4.86!Sox6;;chr5:140019843..140019858,+!p2@Uncx!0.70!3.98!Uncx;;chr7:108966820..108966835,+!p1@Phox2a!0.70!3.98!Phox2a;;chr2:181501745..181501778,+!p1@Myt1!0.70!3.98!Myt1;;chr2:74517742..74517758,+!p2@Hoxd11!0.70!3.98!Hoxd11;;chr11:23978270..23978290,+!p9@Bcl11a!0.70!3.98!Bcl11a;;chr7:148513456..148513506,-!p1@Deaf1!0.69!70.24!Deaf1;;chr3:54559463..54559493,+!p3@Smad9!0.69!7.73!Smad9;;chr19:10315179..10315241,-!p1@Gm98!0.68!45.06!Gm98;;chr14:52935876..52935928,-!p1@Sall2!0.68!35.56!Sall2;;chr7:25372631..25372684,-!p1@Zfp575!0.68!12.81!Zfp575;;chr13:99124189..99124205,+!p1@Foxd1!0.68!6.18!Foxd1;;chr13:78339382..78339420,-!p3@Nr2f1!0.68!4.64!Nr2f1;;chrX:34442842..34442866,-!p3@Nkrf!0.68!3.75!Nkrf;;chr10:67375342..67375365,-!p3@Zfp365!0.68!3.75!Zfp365;;chr11:33103600..33103611,-!p2@Tlx3!0.68!3.75!Tlx3;;chr18:77094872..77094887,+!p1@Skor2!0.68!3.75!Skor2;;chr5:140019865..140019886,+!p1@Uncx!0.68!3.75!Uncx;;chr5:77543897..77543911,-!p2@Hopx!0.67!7.73!Hopx;;chr7:37483231..37483263,+!p2@Tshz3!0.67!5.96!Tshz3;;chr4:154010228..154010244,-!p4@Prdm16!0.67!5.30!Prdm16;;chr5:107003725..107003746,-!p5@Zfp644!0.67!5.08!Zfp644;;chr6:53018556..53018650,-!p1@Jazf1!0.66!27.83!Jazf1;;chr15:100325682..100325698,-!p1@Csrnp2!0.66!18.77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+|ffid_belonging_in_development=CL:0000133,CL:0000337,CL:0000031,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000206
 |is_obsolete=
+|library_id=CNhs12618
+|library_id_phase_based=2:CNhs12618
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11643
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11643
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520dorsal%2520spinal%2520cord%252c%2520donor3.CNhs12618.11643-122D5.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%2520donor3.CNhs12618.11643-122D5.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%2520donor3.CNhs12618.11643-122D5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520dorsal%2520spinal%2520cord%252c%2520donor3.CNhs12618.11643-122D5.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%2520donor3.CNhs12618.11643-122D5.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - dorsal spinal cord, donor3
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12618,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.52245608637559,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.105224447800046,0,0,0,0,0,0,0,0,0,0,0,0,0.386167211883141,-0.471753889241503,0,0,0,0,0.0139654258736136,-0.122653822413298,0.180377618412022,0.12817432513121,0.134640723503989,0.364913651073313,0.323116468687679,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,-0.130696565450787,0,0,0,-0.20244242069718,-0.310650657339386,0.0626982021610028,-0.140687683267293,0,-0.0780086007519514,0.109782277900125,0.319981196470152,0.0866689030825281,0,0.04288141229005,0.279026303469401,0.187987015772584,-0.0788315948399074,0,0,0,0,0,0,0.149828849151761,0.000193394674404601,0.172926797912399,0,0,0.0866689030825281,0.32315204382486,0
 |rna_box=122
 |rna_catalog_number=custom
@@ Line 59: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 79: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11643-122D5;search_select_hide=table117:11643-122D5
 }}

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FF:11643-122D5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:13, 4 June 2020

CNhs12618

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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