FF:11725-123D6: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Neurons - ventral spinal cord, donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs12632
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	RNASPI1
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		SAMD00004838

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12632		CAGE		DRX008849		DRR009721

Accession ID Mm9

Library id		BAM		CTSS
CNhs12632		DRZ001146		DRZ002531

Accession ID Mm10

Library id		BAM		CTSS
CNhs12632		DRZ012496		DRZ013881

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

CNhs12632

0	0
1	0.599
10	0
100	0.112
1000	0
1001	-0.0275
1002	0.175
1003	0.14
1004	0
1005	0
1006	0.503
1007	-0.215
1008	0
1009	-0.148
101	-0.145
1010	0
1011	0.259
1012	0.112
1013	0
1014	0.112
1015	0.133
1016	0.288
1017	0
1018	0
1019	0
102	0
1020	0.563
1021	0
1022	0
1023	0
1024	0
1025	0.112
1026	0.0763
1027	0.507
1028	0
1029	-0.018
103	0.0545
1030	0
1031	-0.139
1032	0.299
1033	-0.0418
1034	0
1035	0.112
1036	-0.189
1037	0
1038	0.063
1039	-0.0102
104	0
1040	-0.216
1041	0

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

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

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

library id: CNhs12632

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	8.35172e-4
MA0003.1	MA0003.1	0.294
MA0004.1	MA0004.1	0.426
MA0006.1	MA0006.1	0.184
MA0007.1	MA0007.1	0.227
MA0009.1	MA0009.1	0.698
MA0014.1	MA0014.1	0.49
MA0017.1	MA0017.1	7.47927e-7
MA0018.2	MA0018.2	0.149
MA0019.1	MA0019.1	0.447
MA0024.1	MA0024.1	0.968
MA0025.1	MA0025.1	0.787
MA0027.1	MA0027.1	0.263
MA0028.1	MA0028.1	0.0232
MA0029.1	MA0029.1	0.896
MA0030.1	MA0030.1	0.212
MA0031.1	MA0031.1	0.0083
MA0035.2	MA0035.2	0.00405
MA0038.1	MA0038.1	0.479
MA0039.2	MA0039.2	0.0226
MA0040.1	MA0040.1	0.357
MA0041.1	MA0041.1	0.272
MA0042.1	MA0042.1	0.481
MA0043.1	MA0043.1	0.766
MA0046.1	MA0046.1	2.50377e-11
MA0047.2	MA0047.2	2.00594e-6
MA0048.1	MA0048.1	0.128
MA0050.1	MA0050.1	1.89313e-6
MA0051.1	MA0051.1	8.13548e-5
MA0052.1	MA0052.1	0.0292
MA0055.1	MA0055.1	0.0318
MA0057.1	MA0057.1	0.277
MA0058.1	MA0058.1	0.355
MA0059.1	MA0059.1	0.228
MA0060.1	MA0060.1	0.384
MA0061.1	MA0061.1	0.0814
MA0062.2	MA0062.2	4.01976e-5
MA0065.2	MA0065.2	4.0135e-6
MA0066.1	MA0066.1	0.0686
MA0067.1	MA0067.1	0.954
MA0068.1	MA0068.1	0.708
MA0069.1	MA0069.1	0.0584
MA0070.1	MA0070.1	0.633
MA0071.1	MA0071.1	0.104
MA0072.1	MA0072.1	0.0849
MA0073.1	MA0073.1	0.966
MA0074.1	MA0074.1	0.129
MA0076.1	MA0076.1	0.0456
MA0077.1	MA0077.1	0.169
MA0078.1	MA0078.1	0.857
MA0079.2	MA0079.2	0.384
MA0080.2	MA0080.2	4.19789e-10
MA0081.1	MA0081.1	0.18
MA0083.1	MA0083.1	0.0654
MA0084.1	MA0084.1	0.722
MA0087.1	MA0087.1	0.345
MA0088.1	MA0088.1	0.13
MA0090.1	MA0090.1	0.0749
MA0091.1	MA0091.1	0.235
MA0092.1	MA0092.1	0.197
MA0093.1	MA0093.1	0.44
MA0099.2	MA0099.2	1.99782e-4
MA0100.1	MA0100.1	0.263
MA0101.1	MA0101.1	0.0354
MA0102.2	MA0102.2	0.735
MA0103.1	MA0103.1	0.101
MA0104.2	MA0104.2	0.84
MA0105.1	MA0105.1	0.0629
MA0106.1	MA0106.1	0.109
MA0107.1	MA0107.1	0.0771
MA0108.2	MA0108.2	0.0255
MA0111.1	MA0111.1	0.938
MA0112.2	MA0112.2	1.85186e-4
MA0113.1	MA0113.1	0.106
MA0114.1	MA0114.1	1.39515e-5
MA0115.1	MA0115.1	1.8405e-4
MA0116.1	MA0116.1	0.0676
MA0117.1	MA0117.1	0.685
MA0119.1	MA0119.1	0.158
MA0122.1	MA0122.1	0.709
MA0124.1	MA0124.1	0.959
MA0125.1	MA0125.1	0.213
MA0131.1	MA0131.1	0.796
MA0135.1	MA0135.1	0.922
MA0136.1	MA0136.1	2.063e-13
MA0137.2	MA0137.2	0.143
MA0138.2	MA0138.2	0.0235
MA0139.1	MA0139.1	0.4
MA0140.1	MA0140.1	2.45483e-4
MA0141.1	MA0141.1	0.00765
MA0142.1	MA0142.1	0.156
MA0143.1	MA0143.1	0.621
MA0144.1	MA0144.1	0.0975
MA0145.1	MA0145.1	0.0589
MA0146.1	MA0146.1	0.0143
MA0147.1	MA0147.1	0.693
MA0148.1	MA0148.1	1.21883e-6
MA0149.1	MA0149.1	0.109
MA0150.1	MA0150.1	0.0178
MA0152.1	MA0152.1	0.0459
MA0153.1	MA0153.1	1.32653e-11
MA0154.1	MA0154.1	0.0369
MA0155.1	MA0155.1	0.615
MA0156.1	MA0156.1	4.40462e-10
MA0157.1	MA0157.1	0.0197
MA0159.1	MA0159.1	0.00388
MA0160.1	MA0160.1	0.027
MA0162.1	MA0162.1	0.281
MA0163.1	MA0163.1	0.00147
MA0164.1	MA0164.1	0.938
MA0258.1	MA0258.1	0.0074
MA0259.1	MA0259.1	0.942

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: CNhs12632

Novel motif	Logo	P-value
1	1	0.14
10	10	0.0828
100	100	0.544
101	101	0.684
102	102	0.784
103	103	0.116
104	104	0.75
105	105	0.258
106	106	0.0547
107	107	0.17
108	108	0.391
109	109	0.00537
11	11	0.0644
110	110	0.0383
111	111	0.0487
112	112	0.00338
113	113	0.768
114	114	0.158
115	115	0.815
116	116	0.69
117	117	0.00484
118	118	0.283
119	119	0.1
12	12	0.856
120	120	0.674
121	121	0.0531
122	122	0.524
123	123	0.00692
124	124	0.19
125	125	0.553
126	126	0.054
127	127	0.131
128	128	0.051
129	129	0.0969
13	13	2.17071e-6
130	130	0.147
131	131	0.374
132	132	0.702
133	133	0.762
134	134	0.217
135	135	0.287
136	136	0.125
137	137	0.935
138	138	0.986
139	139	0.218
14	14	0.755
140	140	0.211
141	141	0.358
142	142	0.278
143	143	0.544
144	144	0.759
145	145	0.00296
146	146	0.261
147	147	0.439
148	148	0.795
149	149	0.474
15	15	0.103
150	150	0.115
151	151	0.478
152	152	0.0871
153	153	0.713
154	154	0.681
155	155	0.518
156	156	4.09073e-4
157	157	0.245
158	158	0.044
159	159	0.422
160	160	0.288
161	161	0.146
162	162	0.684
163	163	0.376
164	164	0.0159
165	165	0.0656
166	166	0.966
167	167	0.81
168	168	0.444
169	169	0.00171
17	17	0.0307
18	18	0.992
19	19	0.112
2	2	0.805
20	20	0.0805
21	21	0.271
22	22	0.111
23	23	0.6
24	24	0.0239
25	25	0.653
26	26	2.52317e-6
27	27	0.617
28	28	0.499
29	29	0.058
3	3	0.0551
30	30	0.981
31	31	0.806
32	32	0.988
33	33	0.124
34	34	0.795
35	35	0.984
36	36	0.305
37	37	0.0177
38	38	0.42
39	39	0.417
4	4	0.534
40	40	0.205
41	41	0.276
42	42	0.158
43	43	0.129
44	44	0.874
45	45	0.619
46	46	0.0596
47	47	0.199
48	48	0.13
49	49	0.145
5	5	0.112
50	50	0.31
51	51	0.617
52	52	0.365
53	53	0.928
54	54	0.732
55	55	0.819
56	56	0.468
57	57	0.678
58	58	0.251
59	59	0.107
6	6	0.896
60	60	0.038
61	61	0.0731
62	62	0.11
63	63	0.115
64	64	0.63
65	65	0.278
66	66	0.772
67	67	0.703
68	68	0.543
69	69	0.461
7	7	0.0204
70	70	0.0157
71	71	0.0105
72	72	0.383
73	73	0.0233
74	74	0.667
75	75	0.0433
76	76	0.513
77	77	0.354
78	78	0.00911
79	79	0.231
8	8	0.0856
80	80	0.595
81	81	0.8
82	82	0.194
83	83	0.103
84	84	0.947
85	85	0.12
86	86	0.162
87	87	0.102
88	88	0.247
89	89	0.236
9	9	0.414
90	90	0.135
91	91	0.448
92	92	0.423
93	93	0.0314
94	94	0.858
95	95	0.0244
96	96	0.174
97	97	0.819
98	98	0.441
99	99	0.663

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: CNhs12632

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000207 mouse neuron of the ventral 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)
0002612 (neuron of the ventral 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)
0002257 (ventral 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)
0000207 (mouse neuron of the ventral 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:0002257,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@SAMD00004838
-|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:0002612,CL:0000133,CL:0000337
+|accession_numbers=CAGE;DRX008849;DRR009721;DRZ001146;DRZ002531;DRZ012496;DRZ013881
+|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:0002257,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:0002612
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000203,FF:0000207
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.44!314.07!Olig1;;chr11:96143666..96143725,+!p1@Hoxb8!2.30!225.10!Hoxb8;;chr11:96143962..96144035,+!p2@Hoxb8!1.82!65.41!Hoxb8;;chr5:138199361..138199441,+!p2@Tsc22d4!1.80!113.14!Tsc22d4;;chr16:91225808..91225824,+!p1@Olig2!1.79!61.28!Olig2;;chr2:74529970..74529997,+!p1@Hoxd10!1.74!53.33!Hoxd10;;chr14:33412570..33412586,+!p1@Prrxl1!1.73!52.15!Prrxl1;;chr3:95032091..95032183,-!p1@Mllt11!1.72!420.73!Mllt11;;chr2:74550015..74550057,+!p2@Hoxd3!1.70!48.91!Hoxd3;;chr12:54349410..54349461,+!p1@Npas3!1.68!56.27!Npas3;;chr9:91260616..91260653,-!p2@Zic1!1.64!42.72!Zic1;;chr9:91260594..91260612,-!p1@Zic1!1.62!40.95!Zic1;;chr7:116154364..116154444,+!p1@Tub!1.59!63.93!Tub;;chr6:52176164..52176195,-!p1@Hoxa9!1.59!47.14!Hoxa9;;chr11:96143843..96143868,+!p3@Hoxb8!1.53!33.00!Hoxb8;;chr11:96147952..96147967,+!p1@Hoxb7!1.51!38.60!Hoxb7;;chr17:48015839..48015915,-!p3@Foxp4!1.51!37.12!Foxp4;;chr15:102797288..102797302,+!p1@Hoxc10!1.51!31.53!Hoxc10;;chr19:19185671..19185693,-!p1@Rorb!1.49!70.42!Rorb;;chr6:52184901..52184959,-!p2@Hoxa10!1.47!28.58!Hoxa10;;chr6:52190467..52190500,-!p1@Hoxa10!1.42!25.04!Hoxa10;;chr2:74549968..74549996,+!p1@Hoxd3!1.40!30.05!Hoxd3;;chr7:144505980..144506010,-!p3@Ebf3!1.39!28.28!Ebf3;;chr12:30219426..30219506,+!p2@Myt1l!1.39!23.28!Myt1l;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.38!28.87!Pou3f3;;chr4:150482563..150482655,-!p2@Camta1!1.37!78.08!Camta1;;chr4:154335024..154335039,+!p1@Hes5!1.36!26.52!Hes5;;chr16:91270091..91270143,+!p2@Olig1!1.35!21.51!Olig1;;chr14:104867201..104867258,-!p1@Pou4f1!1.34!29.46!Pou4f1;;chrX:34442872..34442899,-!p1@Nkrf!1.34!27.11!Nkrf;;chr11:84339016..84339044,-!p1@Lhx1!1.33!20.33!Lhx1;;chr2:65683890..65683907,+!p1@Csrnp3!1.32!37.42!Csrnp3;;chr6:52163319..52163342,-!p1@Hoxa3!1.32!28.87!Hoxa3;;chr6:55631042..55631102,-!p1@Neurod6!1.32!20.03!Neurod6;;chr17:25707623..25707639,-!p1@Sox8!1.30!79.84!Sox8;;chr10:84218895..84218909,+!p1@Rfx4!1.30!19.15!Rfx4;;chr11:96160360..96160397,+!p3@Hoxb6!1.30!18.86!Hoxb6;;chr7:144505957..144505972,-!p2@Ebf3!1.29!22.69!Ebf3;;chr1:19199236..19199258,+!p1@Tfap2b!1.28!17.97!Tfap2b;;chr7:30088977..30089002,+!p2@Dpf1!1.26!23.57!Dpf1;;chr15:76352677..76352737,-!p3@Scrt1!1.26!17.09!Scrt1;;chr12:30213247..30213333,+!p1@Myt1l!1.25!16.79!Myt1l;;chr11:96160426..96160443,+!p2@Hoxb6!1.25!16.79!Hoxb6;;chr3:34548909..34548927,+!p1@Sox2!1.24!27.70!Sox2;;chr11:23978291..23978323,+!p7@Bcl11a!1.23!15.91!Bcl11a;;chr11:96153767..96153822,+!p1@Hoxb6!1.22!24.16!Hoxb6;;chr3:95032184..95032195,-!p4@Mllt11!1.22!19.45!Mllt11;;chr3:34548946..34548972,+!p2@Sox2!1.18!15.62!Sox2;;chr5:98609885..98609900,+!p1@Prdm8!1.18!14.14!Prdm8;;chr3:95032197..95032208,-!p3@Mllt11!1.17!17.09!Mllt11;;chr15:102767247..102767265,+!p1@Hoxc12!1.17!13.85!Hoxc12;;chr15:102797225..102797243,+!p2@Hoxc10!1.17!13.85!Hoxc10;;chr11:98190918..98190951,-!p1@Neurod2!1.17!13.85!Neurod2;;chr6:52167459..52167492,-!p1@Hoxa7!1.16!16.20!Hoxa7;;chr11:33103563..33103583,-!p1@Tlx3!1.16!13.55!Tlx3;;chr7:144506077..144506128,-!p1@Ebf3!1.15!30.05!Ebf3;;chr7:25292331..25292421,+!p1@Zfp428!1.14!90.16!Zfp428;;chr15:76352832..76352900,-!p1@Scrt1!1.14!12.67!Scrt1;;chr11:96143728..96143745,+!p4@Hoxb8!1.13!12.37!Hoxb8;;chr14:122874619..122874634,+!p1@Zic2!1.12!12.08!Zic2;;chr7:148008023..148008092,-!p1@Zfp941!1.10!28.28!Zfp941;;chr11:96132637..96132652,+!p1@Hoxb9!1.10!11.49!Hoxb9;;chr15:76352740..76352781,-!p5@Scrt1!1.08!10.90!Scrt1;;chr2:74529998..74530020,+!p2@Hoxd10!1.08!10.90!Hoxd10;;chr5:24032551..24032557,-!p@chr5:24032551..24032557,-!1.08!10.90!Gbx1;;chr2:24331085..24331100,-!p1@Pax8!1.08!10.90!Pax8;;chr7:91558472..91558512,-!p2@Arnt2!1.07!15.32!Arnt2;;chr15:102828658..102828678,+!p1@Hoxc6!1.06!10.61!Hoxc6;;chr4:150482353..150482386,-!p6@Camta1!1.06!10.61!Camta1;;chr11:44431016..44431045,+!p5@Ebf1!1.05!14.44!Ebf1;;chr4:22415443..22415506,-!p1@Pou3f2!1.05!10.31!Pou3f2;;chrX:108009761..108009788,+!p1@Pou3f4!1.05!10.31!Pou3f4;;chr15:78994907..78994926,-!p1@Sox10!1.04!25.93!Sox10;;chr11:96145450..96145517,+!p2@Hoxb7!1.04!15.03!Hoxb7;;chr11:96132767..96132796,+!p2@Hoxb9!1.04!10.02!Hoxb9;;chr10:84218800..84218829,+!p2@Rfx4!1.04!10.02!Rfx4;;chr15:102751603..102751630,+!p1@Hoxc13!1.04!10.02!Hoxc13;;chr15:76353005..76353021,-!p2@Scrt1!1.04!10.02!Scrt1;;chr7:130644017..130644092,-!p1@Zkscan2!1.03!18.86!Zkscan2;;chr4:13670499..13670526,+!p2@Runx1t1!1.02!21.21!Runx1t1;;chr1:189821714..189821761,+!p1@Esrrg!1.02!17.97!Esrrg;;chr2:127347067..127347093,-!p1@Kcnip3!1.02!16.20!Kcnip3;;chr18:81183755..81183761,-!p1@Sall3!1.02!9.43!Sall3;;chr6:52195795..52195825,-!p1@Hoxa11!1.01!9.13!Hoxa11;;chrX:58146612..58146615,-!p1@Sox3!1.01!9.13!Sox3;;chr15:75578748..75578752,-!p1@Mafa!1.01!9.13!Mafa;;chr13:48356475..48356492,+!p1@Id4!0.99!194.45!Id4;;chr8:24780125..24780143,+!p1@Zmat4!0.98!12.67!Zmat4;;chr2:74520343..74520383,+!p4@Hoxd11!0.98!8.54!Hoxd11;;chr7:37483231..37483263,+!p2@Tshz3!0.97!12.96!Tshz3;;chr15:102767273..102767285,+!p2@Hoxc12!0.97!8.25!Hoxc12;;chr7:91558392..91558434,-!p1@Arnt2!0.96!22.69!Arnt2;;chr11:44430989..44431015,+!p4@Ebf1!0.96!14.73!Ebf1;;chr13:44936126..44936164,+!p6@Jarid2!0.96!9.43!Jarid2;;chr2:74517742..74517758,+!p2@Hoxd11!0.95!7.95!Hoxd11;;chr2:74536026..74536039,+!p1@Hoxd9!0.95!7.95!Hoxd9;;chr14:118636214..118636235,-!p1@Sox21!0.94!9.43!Sox21;;chr2:147012125..147012149,-!p1@Nkx2-2!0.94!7.66!Nkx2-2;;chr6:53018556..53018650,-!p1@Jazf1!0.92!50.68!Jazf1;;chr12:28027561..28027591,-!p1@Sox11!0.92!49.50!Sox11;;chr4:99322820..99322845,+!p1@Foxd3!0.92!9.43!Foxd3;;chr2:151907546..151907561,+!p1@Scrt2!0.92!7.37!Scrt2;;chr13:78339428..78339466,-!p2@Nr2f1!0.91!10.02!Nr2f1;;chr5:120881900..120881914,+!p1@Lhx5!0.91!7.07!Lhx5;;chr6:52167434..52167450,-!p3@Hoxa7!0.91!7.07!Hoxa7;;chr4:150513630..150513686,-!p4@Camta1!0.90!7.95!Camta1;;chr6:53018700..53018759,-!p2@Jazf1!0.89!25.63!Jazf1;;chr10:86956396..86956411,-!p1@Ascl1!0.89!10.61!Ascl1;;chr9:20385868..20385902,+!p3@Zfp846!0.89!10.02!Zfp846;;chr7:108966820..108966835,+!p1@Phox2a!0.89!6.78!Phox2a;;chr15:102821007..102821021,+!p2@Hoxc8!0.89!6.78!Hoxc8;;chr15:102820964..102821006,+!p1@Hoxc8!0.89!6.78!Hoxc8;;chr2:163051181..163051205,+!p2@Tox2!0.89!6.78!Tox2;;chrX:34442842..34442866,-!p3@Nkrf!0.89!6.78!Nkrf;;chr4:13670571..13670625,+!p1@Runx1t1!0.87!18.56!Runx1t1;;chr5:77543897..77543911,-!p2@Hopx!0.87!12.67!Hopx;;chr18:77094872..77094887,+!p1@Skor2!0.87!6.48!Skor2;;chr9:91263879..91263911,+!p1@Zic4!0.87!6.48!Zic4;;chr12:87762578..87762612,+!p1@Esrrb!0.87!6.48!Esrrb;;chr12:3806003..3806031,+!p11@Dnmt3a!0.87!6.48!Dnmt3a;;chr18:36441119..36441158,+!p2@Pura!0.86!15.91!Pura;;chr17:32525943..32525992,-!p4@Wiz!0.86!9.72!Wiz;;chr14:118636238..118636257,-!p2@Sox21!0.86!6.19!Sox21;;chr13:95645580..95645598,+!p1@Otp!0.86!6.19!Otp;;chr6:52176144..52176161,-!p2@Hoxa9!0.86!6.19!Hoxa9;;chr11:96144050..96144065,+!p5@Hoxb8!0.86!6.19!Hoxb8;;chr11:96160403..96160416,+!p4@Hoxb6!0.86!6.19!Hoxb6;;chr5:77524250..77524300,-!p1@Hopx!0.85!130.52!Hopx;;chr7:25292246..25292259,+!p6@Zfp428!0.85!7.66!Zfp428;;chrX:109714331..109714347,+!p1@Zfp711!0.84!25.93!Zfp711;;chr11:101646566..101646603,-!p1@Etv4!0.84!20.03!Etv4;;chr4:58956447..58956510,+!p1@Zkscan16!0.84!13.55!Zkscan16;;chr4:129118044..129118067,-!p1@Zbtb8b!0.84!7.66!Zbtb8b;;chr3:95032213..95032226,-!p6@Mllt11!0.84!7.07!Mllt11;;chr4:150503457..150503498,-!p3@Camta1!0.84!6.78!Camta1;;chr2:81893535..81893548,+!p1@Zfp804a!0.84!5.89!Zfp804a;;chr3:101814061..101814094,+!p1@Nhlh2!0.84!5.89!Nhlh2;;chr15:102820946..102820961,+!p3@Hoxc8!0.84!5.89!Hoxc8;;chr14:122874593..122874610,+!p2@Zic2!0.84!5.89!Zic2;;chrX:55284180..55284195,+!p2@Zic3!0.84!5.89!Zic3;;chr5:24104751..24104773,-!p5@Smarcd3!0.84!5.89!Smarcd3;;chr6:52161666..52161711,-!p1@Hoxa6!0.84!5.89!Hoxa6;;chr7:144506051..144506062,-!p5@Ebf3!0.84!5.89!Ebf3;;chr2:162769220..162769252,+!p1@L3mbtl1!0.84!5.89!L3mbtl1;;chr1:173987720..173987729,-!p1@Nhlh1!0.84!5.89!Nhlh1;;chr10:30562571..30562597,-!p1@Hey2!0.83!14.44!Hey2;;chr14:76814736..76814781,+!p4@Tsc22d1!0.82!34.77!Tsc22d1;;chr3:95032558..95032641,-!p2@Mllt11!0.82!33.88!Mllt11;;chr17:37140628..37140631,+!p2@Zfp57!0.82!11.79!Zfp57;;chr11:116196664..116196679,-!p1@Foxj1!0.82!8.84!Foxj1;;chr4:124334894..124334899,+!p1@Pou3f1!0.82!7.37!Pou3f1;;chr11:96145537..96145556,+!p6@Hoxb7!0.82!5.60!Hoxb7;;chr1:91827756..91827773,-!p1@Gbx2!0.82!5.60!Gbx2;;chr7:30089006..30089022,+!p3@Dpf1!0.82!5.60!Dpf1;;chrX:55283799..55283813,+!p1@Zic3!0.82!5.60!Zic3;;chr7:25372631..25372684,-!p1@Zfp575!0.81!17.68!Zfp575;;chr7:30092993..30093076,+!p1@Dpf1!0.81!9.72!Dpf1;;chr2:74542918..74542971,+!p1@Hoxd8!0.81!8.54!Hoxd8;;chr12:72149325..72149343,+!p2@Arid4a!0.81!7.95!Arid4a;;chr14:67853632..67853674,+!p3@Ebf2!0.81!6.78!Ebf2;;chr11:96145393..96145407,+!p3@Hoxb7!0.80!5.30!Hoxb7;;chr11:96145362..96145389,+!p4@Hoxb7!0.80!5.30!Hoxb7;;chr6:52184880..52184893,-!p6@Hoxa10!0.80!5.30!Hoxa10;;chr11:98603160..98603171,+!p3@Thra!0.79!25.93!Thra;;chr5:77524231..77524245,-!p3@Hopx!0.79!13.55!Hopx;;chr13:78339476..78339515,-!p1@Nr2f1!0.79!8.25!Nr2f1;;chr13:78339382..78339420,-!p3@Nr2f1!0.79!6.19!Nr2f1;;chr17:37139519..37139531,+!p5@Zfp57!0.79!6.19!Zfp57;;chr7:25292141..25292158,+!p2@Zfp428!0.78!19.15!Zfp428;;chr11:98602203..98602266,+!p4@Thra!0.78!8.25!Thra;;chr10:19076364..19076371,+!p1@Olig3!0.78!5.01!Olig3;;chr15:95485240..95485257,-!p1@Dbx2!0.78!5.01!Dbx2;;chr2:168427068..168427115,-!p3@Nfatc2!0.78!5.01!Nfatc2;;chr2:181501745..181501778,+!p1@Myt1!0.78!5.01!Myt1;;chr7:25292310..25292329,+!p5@Zfp428!0.77!7.07!Zfp428;;chr7:25292160..25292213,+!p3@Zfp428!0.76!12.67!Zfp428;;chr19:19185697..19185711,-!p2@Rorb!0.76!6.19!Rorb;;chr11:44431626..44431637,+!p10@Ebf1!0.76!5.60!Ebf1;;chr4:13678482..13678505,+!p9@Runx1t1!0.76!4.71!Runx1t1;;chr14:34791937..34791977,-!p1@Zfp488!0.76!4.71!Zfp488;;chr1:19199119..19199134,+!p4@Tfap2b!0.76!4.71!Tfap2b;;chr2:127347042..127347058,-!p3@Kcnip3!0.76!4.71!Kcnip3;;chr2:147019977..147019985,-!p2@Nkx2-2!0.76!4.71!Nkx2-2;;chr7:5003205..5003234,+!p3@Zfp580!0.75!14.44!Zfp580;;chr2:127347094..127347111,-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8!Zbtb25;;chr4:119960301..119960359,-!p1@Foxo6!0.27!4.71!Foxo6;;chr3:5218629..5218684,+!p1@Zfhx4!0.27!4.71!Zfhx4;;chr13:23460838..23460880,-!p2@Zfp322a!0.27!4.12!Zfp322a;;chr1:13364202..13364263,-!p3@Ncoa2!0.27!4.12!Ncoa2;;chr6:38204087..38204108,-!p2@D630045J12Rik!0.27!4.12!D630045J12Rik;;chr12:86940300..86940312,+!p2@Jdp2!0.27!3.24!Jdp2;;chr17:46520518..46520571,+!p2@Zfp318!0.27!2.95!Zfp318;;chr7:13420092..13420160,+!p2@Zfp110!0.27!2.36!Zfp110;;chr14:100683884..100683908,-!p4@Klf12!0.27!2.36!Klf12;;chr7:16760434..16760453,+!p2@LOC100046899,p2@Meis3!0.27!1.47!Meis3;;chr1:38684383..38684394,-!p4@Aff3!0.27!1.47!Aff3;;chr11:18918406..18918431,-!p6@Meis1!0.27!1.47!Meis1;;chr10:127896295..127896304,+!p6@Smarcc2!0.27!1.18!Smarcc2;;chr8:73905967..73905978,-!p4@Nr2f6!0.27!1.18!Nr2f6;;chr1:38684414..38684427,-!p7@Aff3!0.27!1.18!Aff3;;chr2:152223734..152223756,-!p6@Sox12!0.27!1.18!Sox12;;chr11:23978022..23978076,+!p1@Bcl11a!0.26!35.06!Bcl11a;;chr15:76701830..76701883,-!p1@Zfp251!0.26!21.80!Zfp251;;chr7:71083876..71083932,-!p2@Klf13!0.26!12.67!Klf13;;chr11:50872733..50872809,+!p1@Zfp354a!0.26!6.78!Zfp354a;;chr18:69504195..69504213,+!p4@Tcf4!0.26!6.78!Tcf4;;chr19:26681672..26681716,+!p5@Smarca2!0.26!6.19!Smarca2;;chr4:133309531..133309581,-!p4@Arid1a!0.26!6.19!Arid1a;;chr9:48644306..48644364,-!p1@Zbtb16!0.26!5.89!Zbtb16;;chr7:30836380..30836430,-!p1@Zfp14!0.26!5.60!Zfp14;;chr6:118405493..118405536,-!p1@Zfp248!0.26!5.60!Zfp248;;chr17:23004125..23004157,-!p3@Zfp945!0.26!4.42!Zfp945;;chr7:50568466..50568486,-!p2@Zfp715!0.26!3.54!Zfp715;;chr14:17407878..17407926,-!p1@Rarb!0.26!2.95!Rarb;;chr16:43619057..43619078,+!p8@Zbtb20!0.26!2.65!Zbtb20;;chr2:34227524..34227547,-!p2@Pbx3!0.26!2.36!Pbx3;;chr13:112476433..112476448,+!p2@Mier3!0.26!2.36!Mier3;;chr12:3807076..3807086,+!p8@Dnmt3a!0.26!2.06!Dnmt3a;;chr4:135840552..135840567,+!p4@Zfp46!0.26!1.77!Zfp46;;chr7:6238175..6238186,+!p2@Zfp667!0.26!1.77!Zfp667;;chr8:112229401..112229419,+!p3@Zfp821!0.26!1.47!Zfp821;;chr14:52936049..52936057,-!p6@Sall2!0.26!1.18!Sall2;;chr6:14851344..14851364,+!p6@Foxp2!0.26!1.18!Foxp2;;chr9:21420674..21420725,+!p1@Smarca4!0.25!126.98!Smarca4;;chr2:83484681..83484704,+!p1@Zc3h15!0.25!73.07!Zc3h15;;chr4:82151178..82151262,-!p1@Nfib!0.25!64.52!Nfib;;chr7:134170235..134170294,-!p1@Maz!0.25!44.49!Maz;;chr5:67698180..67698216,+!p1@Slc30a9!0.25!41.84!Slc30a9;;chr4:151235807..151235870,-!p1@Camta1!0.25!25.34!Camta1;;chr7:48888915..48888973,+!p1@Zfp788!0.25!19.74!Zfp788;;chr3:8666963..8666978,-!p1@Hey1!0.25!9.72!Hey1;;chr15:40486566..40486600,+!p1@Zfpm2!0.25!8.84!Zfpm2;;chr7:30644985..30645072,+!p1@Zfp420!0.25!8.84!Zfp420;;chr11:70577930..70577985,+!p1@Zfp3!0.25!8.84!Zfp3;;chr4:102787317..102787364,+!p3@Mier1!0.25!8.54!Mier1;;chr2:92886297..92886329,-!p1@Prdm11!0.25!6.78!Prdm11;;chr11:62602904..62602945,-!p1@Zfp286!0.25!6.78!Zfp286;;chr2:127410404..127410439,-!p1@Zfp661!0.25!6.19!Zfp661;;chr2:128769721..128769770,-!p1@Zc3h8!0.25!5.60!Zc3h8;;chr12:119539902..119539931,-!p2@Sp4!0.25!5.30!Sp4;;chr18:79306158..79306249,-!p1@Setbp1!0.25!4.71!Setbp1;;chr15:10400245..10400282,-!p2@Dnajc21!0.25!4.71!Dnajc21;;chr18:84255771..84255795,-!p3@Tshz1!0.25!4.12!Tshz1;;chrX:34443339..34443348,-!p2@Nkrf!0.25!3.54!Nkrf;;chr6:47827547..47827568,+!p4@Zfp282!0.25!2.95!Zfp282;;chr4:119406412..119406439,+!p2@Hivep3!0.25!2.36!Hivep3;;chr7:87171256..87171280,+!p4@Zfp710!0.25!2.36!Zfp710;;chr14:75684203..75684214,+!p4@Zc3h13!0.25!2.06!Zc3h13;;chr6:92041506..92041517,+!p5@Nr2c2!0.25!1.47!Nr2c2;;chr16:18587076..18587106,-!p1@Tbx1!0.25!1.47!Tbx1;;chr8:111227455..111227464,+!p@chr8:111227455..111227464,+!0.25!1.18!Zfhx3;;chr4:133309775..133309784,-!p15@Arid1a!0.25!1.18!Arid1a;;chr2:38206580..38206600,+!p2@Lhx2!0.25!1.18!Lhx2;;chr12:109241728..109241781,-!p2@Bcl11b!0.25!0.88!Bcl11b;;chrX:137077134..137077143,-!p10@Tsc22d3!0.25!0.88!Tsc22d3;;chr10:75384307..75384370,-!p1@Smarcb1!0.24!122.27!Smarcb1;;chr9:72380021..72380078,+!p1@Rfx7!0.24!28.87!Rfx7;;chr2:114027152..114027181,-!p1@Zfp770!0.24!26.81!Zfp770;;chr4:97444297..97444323,+!p2@Nfia!0.24!23.86!Nfia;;
+|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:0000207
 |is_obsolete=
+|library_id=CNhs12632
+|library_id_phase_based=2:CNhs12632
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11725
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11725
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor1.CNhs12632.11725-123D6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor1.CNhs12632.11725-123D6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor1.CNhs12632.11725-123D6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor1.CNhs12632.11725-123D6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor1.CNhs12632.11725-123D6.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - ventral spinal cord, donor1
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12632,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0788290115316775,0,0,0,0,0,0.130513571332721,0,0,0,0,0.0278059516383896,0,0,0,0,0.0560725960174655,0,0.14626707250566,0,0,0,0,0,0,0,0,0,0,0,0,0.549379763110866,-0.165173576579917,0,0,0,0,0.0574171715104187,-0.0526530396266313,0.244738847524333,0.164381522857721,0.943541368082276,0.586691110057492,0.627459510724423,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.0692982369520563,0,-0.0335186795399985,0,0,0,0.142623103624294,-0.310650657339386,0.367864009277708,-0.0333062097308183,0,0,0.165398973834904,0.187539590717448,0,0,0.115793424692746,0.268475955988857,0.567035109969636,0.0333135971950237,0,0,0,0,0,0,0.320560890931152,0.337091641933561,0.110755244060166,0,0,0.338160423388235,0.302292572272633,0
 |rna_box=123
 |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=table111:11725-123D6;search_select_hide=table117:11725-123D6
 }}

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FF:11725-123D6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12632

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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