FF:11648-122E1: Difference between revisions

Latest revision as of 18:13, 4 June 2020

Name:	Mouse Neurons - ventral spinal cord, donor3
Species:	Mouse (Mus musculus)
Library ID:	CNhs12113
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	RNAMSC1
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		SAMD00005498

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12113		CAGE		DRX008851		DRR009723

Accession ID Mm9

Library id		BAM		CTSS
CNhs12113		DRZ001148		DRZ002533

Accession ID Mm10

Library id		BAM		CTSS
CNhs12113		DRZ012498		DRZ013883

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

CNhs12113

0	0
1	0.457
10	0
100	0.286
1000	0
1001	-0.0668
1002	0.0198
1003	0.0753
1004	0.0371
1005	-0.0257
1006	0.422
1007	-0.0517
1008	0
1009	-0.2
101	-0.0956
1010	0
1011	0.26
1012	0
1013	-0.0423
1014	0.0508
1015	0.3
1016	0.253
1017	0
1018	0
1019	0
102	0
1020	0.463
1021	0.0742
1022	-0.0498
1023	0
1024	-0.14
1025	0
1026	0
1027	0.278
1028	0
1029	-0.0452
103	-0.0405
1030	0
1031	-0.224
1032	-0.0389
1033	-0.0665
1034	0
1035	0.0742
1036	-0.139
1037	0
1038	0.106
1039	-0.179
104	0
1040	-0.245
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: CNhs12113

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	2.66653e-4
MA0003.1	MA0003.1	0.189
MA0004.1	MA0004.1	0.703
MA0006.1	MA0006.1	0.144
MA0007.1	MA0007.1	0.13
MA0009.1	MA0009.1	0.919
MA0014.1	MA0014.1	0.55
MA0017.1	MA0017.1	1.68141e-5
MA0018.2	MA0018.2	0.0213
MA0019.1	MA0019.1	0.558
MA0024.1	MA0024.1	0.688
MA0025.1	MA0025.1	0.472
MA0027.1	MA0027.1	0.801
MA0028.1	MA0028.1	0.37
MA0029.1	MA0029.1	0.799
MA0030.1	MA0030.1	0.428
MA0031.1	MA0031.1	0.0431
MA0035.2	MA0035.2	0.0397
MA0038.1	MA0038.1	0.23
MA0039.2	MA0039.2	0.0618
MA0040.1	MA0040.1	0.588
MA0041.1	MA0041.1	0.173
MA0042.1	MA0042.1	0.465
MA0043.1	MA0043.1	0.146
MA0046.1	MA0046.1	1.37939e-8
MA0047.2	MA0047.2	5.44481e-5
MA0048.1	MA0048.1	0.316
MA0050.1	MA0050.1	2.81428e-7
MA0051.1	MA0051.1	1.86522e-4
MA0052.1	MA0052.1	0.0522
MA0055.1	MA0055.1	0.328
MA0057.1	MA0057.1	0.169
MA0058.1	MA0058.1	0.754
MA0059.1	MA0059.1	0.338
MA0060.1	MA0060.1	0.00464
MA0061.1	MA0061.1	0.0555
MA0062.2	MA0062.2	0.0726
MA0065.2	MA0065.2	1.01454e-5
MA0066.1	MA0066.1	0.0518
MA0067.1	MA0067.1	0.571
MA0068.1	MA0068.1	0.459
MA0069.1	MA0069.1	0.0477
MA0070.1	MA0070.1	0.0462
MA0071.1	MA0071.1	0.123
MA0072.1	MA0072.1	0.09
MA0073.1	MA0073.1	0.967
MA0074.1	MA0074.1	0.364
MA0076.1	MA0076.1	0.855
MA0077.1	MA0077.1	0.0437
MA0078.1	MA0078.1	0.431
MA0079.2	MA0079.2	0.411
MA0080.2	MA0080.2	1.36865e-10
MA0081.1	MA0081.1	0.483
MA0083.1	MA0083.1	0.0584
MA0084.1	MA0084.1	0.513
MA0087.1	MA0087.1	0.473
MA0088.1	MA0088.1	0.189
MA0090.1	MA0090.1	0.0607
MA0091.1	MA0091.1	0.154
MA0092.1	MA0092.1	0.158
MA0093.1	MA0093.1	0.756
MA0099.2	MA0099.2	1.82694e-4
MA0100.1	MA0100.1	0.551
MA0101.1	MA0101.1	0.0648
MA0102.2	MA0102.2	0.926
MA0103.1	MA0103.1	0.0984
MA0104.2	MA0104.2	0.849
MA0105.1	MA0105.1	0.0221
MA0106.1	MA0106.1	0.072
MA0107.1	MA0107.1	0.0563
MA0108.2	MA0108.2	0.198
MA0111.1	MA0111.1	0.9
MA0112.2	MA0112.2	6.51549e-5
MA0113.1	MA0113.1	0.156
MA0114.1	MA0114.1	7.49936e-5
MA0115.1	MA0115.1	0.00195
MA0116.1	MA0116.1	0.0544
MA0117.1	MA0117.1	0.749
MA0119.1	MA0119.1	0.0934
MA0122.1	MA0122.1	0.728
MA0124.1	MA0124.1	0.951
MA0125.1	MA0125.1	0.178
MA0131.1	MA0131.1	0.832
MA0135.1	MA0135.1	0.182
MA0136.1	MA0136.1	2.352e-9
MA0137.2	MA0137.2	0.141
MA0138.2	MA0138.2	0.123
MA0139.1	MA0139.1	0.271
MA0140.1	MA0140.1	0.00236
MA0141.1	MA0141.1	0.00693
MA0142.1	MA0142.1	0.121
MA0143.1	MA0143.1	0.203
MA0144.1	MA0144.1	0.0498
MA0145.1	MA0145.1	0.0516
MA0146.1	MA0146.1	0.0239
MA0147.1	MA0147.1	0.992
MA0148.1	MA0148.1	7.62196e-6
MA0149.1	MA0149.1	0.0915
MA0150.1	MA0150.1	0.0402
MA0152.1	MA0152.1	0.0749
MA0153.1	MA0153.1	5.15142e-8
MA0154.1	MA0154.1	0.0155
MA0155.1	MA0155.1	0.51
MA0156.1	MA0156.1	1.47699e-5
MA0157.1	MA0157.1	0.0246
MA0159.1	MA0159.1	0.00412
MA0160.1	MA0160.1	0.0458
MA0162.1	MA0162.1	0.264
MA0163.1	MA0163.1	0.00138
MA0164.1	MA0164.1	0.995
MA0258.1	MA0258.1	0.00462
MA0259.1	MA0259.1	0.779

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: CNhs12113

Novel motif	Logo	P-value
1	1	0.124
10	10	0.0723
100	100	0.755
101	101	0.836
102	102	0.806
103	103	0.0956
104	104	0.747
105	105	0.249
106	106	0.0157
107	107	0.0835
108	108	0.483
109	109	0.00561
11	11	0.0695
110	110	0.0722
111	111	0.0562
112	112	0.0038
113	113	0.898
114	114	0.206
115	115	0.606
116	116	0.493
117	117	0.0229
118	118	0.276
119	119	0.0891
12	12	0.829
120	120	0.727
121	121	0.336
122	122	0.697
123	123	0.156
124	124	0.653
125	125	0.456
126	126	0.233
127	127	0.1
128	128	0.0388
129	129	0.134
13	13	4.26538e-5
130	130	0.321
131	131	0.506
132	132	0.971
133	133	0.672
134	134	0.402
135	135	0.935
136	136	0.168
137	137	0.499
138	138	0.992
139	139	0.132
14	14	0.576
140	140	0.0838
141	141	0.208
142	142	0.142
143	143	0.367
144	144	0.935
145	145	0.0107
146	146	0.418
147	147	0.781
148	148	0.447
149	149	0.195
15	15	0.0866
150	150	0.141
151	151	0.413
152	152	0.0803
153	153	0.541
154	154	0.771
155	155	0.729
156	156	9.41785e-4
157	157	0.279
158	158	0.0926
159	159	0.0562
160	160	0.204
161	161	0.228
162	162	0.782
163	163	0.302
164	164	0.0257
165	165	0.0276
166	166	0.745
167	167	0.903
168	168	0.587
169	169	0.00225
17	17	0.024
18	18	0.976
19	19	0.0709
2	2	0.842
20	20	0.292
21	21	0.408
22	22	0.0945
23	23	0.25
24	24	0.0312
25	25	0.658
26	26	3.31154e-5
27	27	0.884
28	28	0.451
29	29	0.0898
3	3	0.0667
30	30	0.839
31	31	0.909
32	32	0.475
33	33	0.206
34	34	0.646
35	35	0.945
36	36	0.354
37	37	0.0196
38	38	0.318
39	39	0.229
4	4	0.569
40	40	0.302
41	41	0.553
42	42	0.163
43	43	0.117
44	44	0.639
45	45	0.581
46	46	0.0654
47	47	0.185
48	48	0.096
49	49	0.126
5	5	0.0977
50	50	0.321
51	51	0.6
52	52	0.22
53	53	0.809
54	54	0.707
55	55	0.862
56	56	0.337
57	57	0.543
58	58	0.219
59	59	0.0762
6	6	0.722
60	60	0.0211
61	61	0.115
62	62	0.0924
63	63	0.108
64	64	0.723
65	65	0.194
66	66	0.931
67	67	0.577
68	68	0.484
69	69	0.477
7	7	0.0256
70	70	0.0095
71	71	0.0131
72	72	0.383
73	73	0.0289
74	74	0.251
75	75	0.0775
76	76	0.616
77	77	0.257
78	78	0.0311
79	79	0.942
8	8	0.0809
80	80	0.809
81	81	0.672
82	82	0.208
83	83	0.282
84	84	0.749
85	85	0.0556
86	86	0.238
87	87	0.313
88	88	0.225
89	89	0.225
9	9	0.335
90	90	0.0759
91	91	0.293
92	92	0.357
93	93	0.0232
94	94	0.7
95	95	0.0519
96	96	0.321
97	97	0.87
98	98	0.595
99	99	0.335

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: CNhs12113

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: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:0002257,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@SAMD00005498
-|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:0002612
+|accession_numbers=CAGE;DRX008851;DRR009723;DRZ001148;DRZ002533;DRZ012498;DRZ013883
+|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=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:96143666..96143725,+!p1@Hoxb8!2.61!468.05!Hoxb8;;chr11:96143962..96144035,+!p2@Hoxb8!1.91!79.59!Hoxb8;;chr9:91260594..91260612,-!p1@Zic1!1.90!78.66!Zic1;;chr14:33412570..33412586,+!p1@Prrxl1!1.89!77.36!Prrxl1;;chr2:74529970..74529997,+!p1@Hoxd10!1.84!68.41!Hoxd10;;chr15:102797288..102797302,+!p1@Hoxc10!1.83!67.29!Hoxc10;;chr6:52176164..52176195,-!p1@Hoxa9!1.77!71.02!Hoxa9;;chr11:96143843..96143868,+!p3@Hoxb8!1.77!57.22!Hoxb8;;chr16:91270004..91270023,+!p1@Olig1!1.76!64.49!Olig1;;chr3:95032091..95032183,-!p1@Mllt11!1.74!435.99!Mllt11;;chr2:74550015..74550057,+!p2@Hoxd3!1.72!52.01!Hoxd3;;chr14:104867201..104867258,-!p1@Pou4f1!1.68!64.49!Pou4f1;;chr9:91260616..91260653,-!p2@Zic1!1.68!46.79!Zic1;;chr7:116154364..116154444,+!p1@Tub!1.66!75.68!Tub;;chr7:144505957..144505972,-!p2@Ebf3!1.66!54.62!Ebf3;;chr11:96132637..96132652,+!p1@Hoxb9!1.64!42.50!Hoxb9;;chr11:84339016..84339044,-!p1@Lhx1!1.61!39.33!Lhx1;;chr6:52190467..52190500,-!p1@Hoxa10!1.58!37.28!Hoxa10;;chr6:55631042..55631102,-!p1@Neurod6!1.57!36.16!Neurod6;;chr11:98190918..98190951,-!p1@Neurod2!1.57!35.98!Neurod2;;chr11:33103563..33103583,-!p1@Tlx3!1.56!35.60!Tlx3;;chr7:30088977..30089002,+!p2@Dpf1!1.54!45.85!Dpf1;;chr12:30213247..30213333,+!p1@Myt1l!1.54!33.74!Myt1l;;chr11:96160426..96160443,+!p2@Hoxb6!1.53!32.62!Hoxb6;;chr12:28027561..28027591,-!p1@Sox11!1.50!191.06!Sox11;;chr11:96147952..96147967,+!p1@Hoxb7!1.50!38.03!Hoxb7;;chr17:48015839..48015915,-!p3@Foxp4!1.50!35.79!Foxp4;;chr11:96132767..96132796,+!p2@Hoxb9!1.50!30.57!Hoxb9;;chr2:74549968..74549996,+!p1@Hoxd3!1.47!35.23!Hoxd3;;chr7:144505980..144506010,-!p3@Ebf3!1.47!34.67!Ebf3;;chr2:151907546..151907561,+!p1@Scrt2!1.43!25.72!Scrt2;;chr15:102820964..102821006,+!p1@Hoxc8!1.42!25.35!Hoxc8;;chr11:23978291..23978323,+!p7@Bcl11a!1.42!25.35!Bcl11a;;chr11:96153767..96153822,+!p1@Hoxb6!1.41!37.65!Hoxb6;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.41!30.76!Pou3f3;;chr15:102828658..102828678,+!p1@Hoxc6!1.41!24.79!Hoxc6;;chr6:52167459..52167492,-!p1@Hoxa7!1.40!29.08!Hoxa7;;chr3:101814061..101814094,+!p1@Nhlh2!1.40!23.86!Nhlh2;;chr11:96160360..96160397,+!p3@Hoxb6!1.40!23.86!Hoxb6;;chr11:96143728..96143745,+!p4@Hoxb8!1.40!23.86!Hoxb8;;chr12:54349410..54349461,+!p1@Npas3!1.39!28.33!Npas3;;chr5:120881900..120881914,+!p1@Lhx5!1.39!23.49!Lhx5;;chr4:154335024..154335039,+!p1@Hes5!1.38!27.40!Hes5;;chr7:144506077..144506128,-!p1@Ebf3!1.37!51.45!Ebf3;;chr1:19199236..19199258,+!p1@Tfap2b!1.37!22.37!Tfap2b;;chr15:76352832..76352900,-!p1@Scrt1!1.37!22.37!Scrt1;;chr1:189821714..189821761,+!p1@Esrrg!1.36!40.26!Esrrg;;chr16:91225808..91225824,+!p1@Olig2!1.34!20.88!Olig2;;chr7:25292331..25292421,+!p1@Zfp428!1.32!138.68!Zfp428;;chr14:122874619..122874634,+!p1@Zic2!1.32!19.94!Zic2;;chr2:65683890..65683907,+!p1@Csrnp3!1.31!36.72!Csrnp3;;chr15:102767247..102767265,+!p1@Hoxc12!1.28!18.27!Hoxc12;;chr6:52184901..52184959,-!p2@Hoxa10!1.28!17.89!Hoxa10;;chr6:52163319..52163342,-!p1@Hoxa3!1.27!25.72!Hoxa3;;chr13:44936126..44936164,+!p6@Jarid2!1.27!20.32!Jarid2;;chr18:81183755..81183761,-!p1@Sall3!1.27!17.71!Sall3;;chr15:102821007..102821021,+!p2@Hoxc8!1.26!17.34!Hoxc8;;chr7:91558472..91558512,-!p2@Arnt2!1.25!23.67!Arnt2;;chr2:24331085..24331100,-!p1@Pax8!1.25!16.59!Pax8;;chr15:102820946..102820961,+!p3@Hoxc8!1.25!16.59!Hoxc8;;chr3:34548909..34548927,+!p1@Sox2!1.24!27.40!Sox2;;chr5:98609885..98609900,+!p1@Prdm8!1.24!16.40!Prdm8;;chr11:96145450..96145517,+!p2@Hoxb7!1.23!23.86!Hoxb7;;chr15:75578748..75578752,-!p1@Mafa!1.23!16.03!Mafa;;chr4:150482563..150482655,-!p2@Camta1!1.19!50.70!Camta1;;chr2:74529998..74530020,+!p2@Hoxd10!1.19!14.54!Hoxd10;;chr5:24032551..24032557,-!p@chr5:24032551..24032557,-!1.19!14.54!Gbx1;;chr7:37483231..37483263,+!p2@Tshz3!1.18!21.25!Tshz3;;chr10:84218895..84218909,+!p1@Rfx4!1.18!14.17!Rfx4;;chrX:108009761..108009788,+!p1@Pou3f4!1.18!13.98!Pou3f4;;chr15:76352677..76352737,-!p3@Scrt1!1.17!13.79!Scrt1;;chr7:144506051..144506062,-!p5@Ebf3!1.16!13.61!Ebf3;;chr6:52176144..52176161,-!p2@Hoxa9!1.16!13.42!Hoxa9;;chr11:96145393..96145407,+!p3@Hoxb7!1.15!13.23!Hoxb7;;chr11:44431016..44431045,+!p5@Ebf1!1.14!18.08!Ebf1;;chr4:13678723..13678739,+!p10@Runx1t1!1.14!12.86!Runx1t1;;chr11:96132523..96132538,+!p3@Hoxb9!1.14!12.68!Hoxb9;;chr13:95645580..95645598,+!p1@Otp!1.13!12.49!Otp;;chr2:31495237..31495243,+!p1@Prdm12!1.13!12.49!Prdm12;;chr7:30092993..30093076,+!p1@Dpf1!1.12!21.06!Dpf1;;chr12:30219426..30219506,+!p2@Myt1l!1.12!12.30!Myt1l;;chr15:76352740..76352781,-!p5@Scrt1!1.12!12.12!Scrt1;;chr7:91558392..91558434,-!p1@Arnt2!1.10!32.43!Arnt2;;chr7:130644017..130644092,-!p1@Zkscan2!1.10!22.55!Zkscan2;;chr11:96145362..96145389,+!p4@Hoxb7!1.10!11.56!Hoxb7;;chr11:96213183..96213188,+!p@chr11:96213183..96213188,+!1.10!11.56!Hoxb2;;chr15:76353005..76353021,-!p2@Scrt1!1.10!11.56!Scrt1;;chr1:173987720..173987729,-!p1@Nhlh1!1.09!11.37!Nhlh1;;chr17:37140628..37140631,+!p2@Zfp57!1.08!22.00!Zfp57;;chr3:95032197..95032208,-!p3@Mllt11!1.08!13.98!Mllt11;;chr2:79296783..79296801,-!p1@Neurod1!1.07!10.81!Neurod1;;chrX:55283799..55283813,+!p1@Zic3!1.07!10.62!Zic3;;chr15:102797225..102797243,+!p2@Hoxc10!1.07!10.62!Hoxc10;;chr7:148008023..148008092,-!p1@Zfp941!1.06!25.35!Zfp941;;chr13:117099847..117099907,-!p1@Isl1!1.06!19.39!Isl1;;chr3:34548946..34548972,+!p2@Sox2!1.05!11.37!Sox2;;chr2:74536026..74536039,+!p1@Hoxd9!1.05!10.25!Hoxd9;;chr11:33103600..33103611,-!p2@Tlx3!1.05!10.25!Tlx3;;chr19:19185671..19185693,-!p1@Rorb!1.04!24.23!Rorb;;chr4:13670499..13670526,+!p2@Runx1t1!1.04!22.18!Runx1t1;;chr17:37139519..37139531,+!p5@Zfp57!1.04!11.74!Zfp57;;chr7:30089006..30089022,+!p3@Dpf1!1.04!10.07!Dpf1;;chr5:140019843..140019858,+!p2@Uncx!1.04!9.88!Uncx;;chr13:48356475..48356492,+!p1@Id4!1.03!212.68!Id4;;chr3:95032184..95032195,-!p4@Mllt11!1.03!12.12!Mllt11;;chr1:19199119..19199134,+!p4@Tfap2b!1.03!9.69!Tfap2b;;chr11:96160403..96160416,+!p4@Hoxb6!1.03!9.69!Hoxb6;;chr7:108966820..108966835,+!p1@Phox2a!1.02!9.51!Phox2a;;chr2:74520343..74520383,+!p4@Hoxd11!1.02!9.51!Hoxd11;;chr2:81893535..81893548,+!p1@Zfp804a!1.02!9.51!Zfp804a;;chr4:13670571..13670625,+!p1@Runx1t1!1.01!25.72!Runx1t1;;chr7:25292160..25292213,+!p3@Zfp428!1.01!23.67!Zfp428;;chr8:24780125..24780143,+!p1@Zmat4!1.01!13.42!Zmat4;;chr5:140019865..140019886,+!p1@Uncx!1.01!9.13!Uncx;;chr13:44936077..44936096,+!p9@Jarid2!1.01!9.13!Jarid2;;chr9:55388997..55389016,+!p1@Isl2!1.00!8.95!Isl2;;chr2:181501745..181501778,+!p1@Myt1!1.00!8.95!Myt1;;chr11:44430989..44431015,+!p4@Ebf1!0.99!16.03!Ebf1;;chrX:34442872..34442899,-!p1@Nkrf!0.99!11.56!Nkrf;;chr4:129118044..129118067,-!p1@Zbtb8b!0.99!11.18!Zbtb8b;;chr17:37139472..37139514,+!p1@Zfp57!0.98!59.65!Zfp57;;chr6:52167434..52167450,-!p3@Hoxa7!0.98!8.57!Hoxa7;;chr15:102751603..102751630,+!p1@Hoxc13!0.97!8.39!Hoxc13;;chr5:138199361..138199441,+!p2@Tsc22d4!0.95!15.28!Tsc22d4;;chr11:23977742..23977794,+!p6@Bcl11a!0.95!10.07!Bcl11a;;chr4:150503457..150503498,-!p3@Camta1!0.95!8.95!Camta1;;chr9:91263879..91263911,+!p1@Zic4!0.95!8.02!Zic4;;chr7:144505876..144505884,-!p9@Ebf3!0.95!8.02!Ebf3;;chr4:22415443..22415506,-!p1@Pou3f2!0.95!7.83!Pou3f2;;chr11:96132456..96132467,+!p4@Hoxb9!0.95!7.83!Hoxb9;;chr2:34227446..34227511,-!p1@Pbx3!0.94!18.08!Pbx3;;chr11:96144050..96144065,+!p5@Hoxb8!0.93!7.46!Hoxb8;;chr7:144505906..144505913,-!p7@Ebf3!0.93!7.46!Ebf3;;chr4:122673278..122673336,+!p1@Mycl1!0.92!23.86!Mycl1;;chr11:44430877..44430899,+!p6@Ebf1!0.92!9.51!Ebf1;;chr4:13678482..13678505,+!p9@Runx1t1!0.92!7.27!Runx1t1;;chr1:91827756..91827773,-!p1@Gbx2!0.92!7.27!Gbx2;;chr17:35031589..35031630,+!p2@Zbtb12!0.91!13.23!Zbtb12;;chr4:99322820..99322845,+!p1@Foxd3!0.91!9.13!Foxd3;;chr18:77094872..77094887,+!p1@Skor2!0.91!7.08!Skor2;;chr15:102767273..102767285,+!p2@Hoxc12!0.91!7.08!Hoxc12;;chr9:18278055..18278126,-!p1@Zfp558!0.90!20.69!Zfp558;;chr10:86956396..86956411,-!p1@Ascl1!0.90!11.00!Ascl1;;chr7:25292310..25292329,+!p5@Zfp428!0.90!10.07!Zfp428;;chr2:152223783..152223812,-!p4@Sox12!0.89!16.22!Sox12;;chr5:77543897..77543911,-!p2@Hopx!0.89!13.23!Hopx;;chrX:58146612..58146615,-!p1@Sox3!0.89!6.71!Sox3;;chr14:118636238..118636257,-!p2@Sox21!0.89!6.71!Sox21;;chr14:118636214..118636235,-!p1@Sox21!0.88!8.02!Sox21;;chr12:87762578..87762612,+!p1@Esrrb!0.88!6.52!Esrrb;;chr11:96160119..96160135,+!p7@Hoxb6!0.88!6.52!Hoxb6;;chr9:99776566..99776612,-!p1@Sox14!0.88!6.52!Sox14;;chr2:33496386..33496410,-!p1@Lmx1b!0.88!6.52!Lmx1b;;chr12:109242266..109242295,-!p1@Bcl11b!0.87!57.04!Bcl11b;;chr6:52195795..52195825,-!p1@Hoxa11!0.87!6.34!Hoxa11;;chrX:55284180..55284195,+!p2@Zic3!0.87!6.34!Zic3;;chr2:146047829..146047847,+!p1@Insm1!0.86!11.74!Insm1;;chr7:135019147..135019187,-!p3@Zfp668!0.85!13.98!Zfp668;;chr6:52158644..52158677,-!p2@Hoxa6!0.85!6.15!Hoxa6;;chr11:96160068..96160084,+!p6@Hoxb6!0.85!6.15!Hoxb6;;chr15:102797170..102797182,+!p3@Hoxc10!0.85!6.15!Hoxc10;;chr4:13669922..13669957,+!p13@Runx1t1!0.85!6.15!Runx1t1;;chr11:23978229..23978268,+!p8@Bcl11a!0.84!6.90!Bcl11a;;chr11:23978270..23978290,+!p9@Bcl11a!0.84!5.96!Bcl11a;;chr11:96160098..96160112,+!p8@Hoxb6!0.84!5.96!Hoxb6;;chr5:106887474..106887489,-!p1@Barhl2!0.84!5.96!Barhl2;;chr4:82145196..82145229,-!p7@Nfib!0.84!5.96!Nfib;;chr16:91270091..91270143,+!p2@Olig1!0.84!5.96!Olig1;;chr11:23978111..23978134,+!p3@Bcl11a!0.83!12.68!Bcl11a;;chr2:56967334..56967366,-!p1@Nr4a2!0.83!12.30!Nr4a2;;chr2:152223586..152223604,-!p5@Sox12!0.83!8.57!Sox12;;chr2:65768174..65768247,+!p2@Csrnp3!0.83!5.78!Csrnp3;;chr11:96132544..96132553,+!p6@Hoxb9!0.83!5.78!Hoxb9;;chr11:98190955..98190968,-!p2@Neurod2!0.83!5.78!Neurod2;;chr11:33103589..33103599,-!p3@Tlx3!0.83!5.78!Tlx3;;chr18:84255649..84255661,-!p4@Tshz1!0.82!15.47!Tshz1;;chr13:78339382..78339420,-!p3@Nr2f1!0.82!6.71!Nr2f1;;chr5:24104751..24104773,-!p5@Smarcd3!0.82!5.59!Smarcd3;;chrX:34442842..34442866,-!p3@Nkrf!0.82!5.59!Nkrf;;chr2:115891534..115891589,-!p1@Meis2!0.81!82.95!Meis2;;chr17:25707623..25707639,-!p1@Sox8!0.81!25.16!Sox8;;chr9:55785981..55786009,-!p2@Scaper!0.81!15.66!Scaper;;chr2:74542918..74542971,+!p1@Hoxd8!0.81!8.57!Hoxd8;;chr13:40829137..40829205,-!p1@Tfap2a!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:11648-122E1
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000207
+|is_a=EFO:0002091;;FF:0000207
+|is_obsolete=
+|library_id=CNhs12113
+|library_id_phase_based=2:CNhs12113
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11648
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11648
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor3.CNhs12113.11648-122E1.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%2520donor3.CNhs12113.11648-122E1.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%2520donor3.CNhs12113.11648-122E1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520ventral%2520spinal%2520cord%252c%2520donor3.CNhs12113.11648-122E1.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%2520donor3.CNhs12113.11648-122E1.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - ventral spinal cord, donor3
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12113,LSID839,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0452080467040714,0,0,0,0,0,-0.133380731197635,0,0,0,0,0.0532676794741855,0,0,0,0,0,0,0.0941131483315104,0,0,0,0,0,0,0,0,0,0,0,0,0.379520168325414,-0.484191857165363,0,0,0,0,0.0462159258322438,-0.140519265560463,0.229222520918703,-0.0346174416872684,0.359455902695425,0.815920067114044,0.192901363035279,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,0,-0.081470329825696,-0.310650657339386,0.0838531389718853,-0.0593831718178933,0,-0.0780086007519514,0.168985880002793,0.192901363035279,0,0,0.11904012428753,0.183977858107347,0.170972574605164,-0.0788315948399074,0,0,0,0,0,0,0.125014287660718,-0.0206293412310332,-0.0523802298422757,0,0,0.0742309351586685,0.323199110136342,0
 |rna_box=122
 |rna_catalog_number=custom
@@ Line 54: / Line 73: @@
 |rna_rin=
 |rna_sample_type=total RNA
-|rna_tube_id=122E1
+|rna_tube_id=1.22E+03
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=N/A
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=spinal cord
 |top_motifs=BREu{core}:2.62828205902;PAX6:2.6003403454;TFDP1:2.34513993373;ZFP161:2.2929034122;MED-1{core}:2.25630857807;ZIC1..3:2.24886426979;AHR_ARNT_ARNT2:2.17955661188;ZBTB6:2.10574149493;PRRX1,2:2.08490719798;MTE{core}:2.08285508009;ONECUT1,2:2.06366890665;TFAP2B:2.05989429;GFI1B:1.99821864287;ADNP_IRX_SIX_ZHX:1.89937247703;MZF1:1.89333228917;EGR1..3:1.88608532926;VSX1,2:1.8657781174;RREB1:1.80196776528;REST:1.78376730739;DBP:1.75456510575;PAX5:1.75268889085;HIC1:1.74591593091;PATZ1:1.71273101314;ATF2:1.63775594375;FOXD3:1.61991643814;HOXA9_MEIS1:1.61465579267;NRF1:1.60710370287;ALX1:1.59858735897;SOX2:1.59627951172;NKX6-1,2:1.5906734905;PRDM1:1.56351395804;CUX2:1.56256663083;MTF1:1.50579233186;NANOG:1.48851688631;ZNF423:1.48518449759;POU5F1:1.48436163079;LHX3,4:1.46430968087;SOX{8,9,10}:1.45703911184;POU6F1:1.44583362136;LMO2:1.42821069742;OCT4_SOX2{dimer}:1.42607530344;PAX8:1.41449487942;KLF4:1.4023180266;MYFfamily:1.38175020733;NHLH1,2:1.37696627376;FOXQ1:1.34964542559;SMAD1..7,9:1.26149277343;POU3F1..4:1.23745381478;HSF1,2:1.23307587553;NANOG{mouse}:1.22470003987;UFEwm:1.19338572612;NKX2-1,4:1.16115743812;RFX1:1.13921637053;LEF1_TCF7_TCF7L1,2:1.13499738162;EN1,2:1.0813761788;TGIF1:1.05528183354;CDX1,2,4:1.00964012944;GTF2I:0.982130297684;FOX{I1,J2}:0.978296199615;SOX17:0.941846648833;MAZ:0.934635969117;YY1:0.91809821743;FOXL1:0.89754538783;PAX4:0.889322518465;FOXM1:0.878393375887;NKX3-2:0.872892384351;NKX2-3_NKX2-5:0.834844541336;MAFB:0.804365245767;ZNF143:0.792237461847;JUN:0.769450419803;ATF5_CREB3:0.728829389112;NKX3-1:0.696172028823;TFAP2{A,C}:0.658410219814;ZNF384:0.649023262098;PBX1:0.64513610833;GZF1:0.628828889279;HOX{A5,B5}:0.624628990764;TEF:0.609166814224;HBP1_HMGB_SSRP1_UBTF:0.578908095406;RFX2..5_RFXANK_RFXAP:0.534286698706;ATF4:0.516011140386;HMGA1,2:0.507366390809;GATA4:0.496728644538;NFE2L1:0.496210389915;POU2F1..3:0.432913997523;SREBF1,2:0.425591974231;SP1:0.421316145498;NR5A1,2:0.41511463057;ELK1,4_GABP{A,B1}:0.389649545138;HES1:0.389513528122;RORA:0.378301729802;RBPJ:0.364567476759;NR3C1:0.351302930626;RXR{A,B,G}:0.327308092345;SOX5:0.301991325648;CREB1:0.290888083638;EP300:0.267890966375;NFY{A,B,C}:0.256723044237;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.246172175171;IKZF2:0.235402816095;TAL1_TCF{3,4,12}:0.234582064721;ATF6:0.211286863262;BPTF:0.19432348302;HMX1:0.191901389912;FOXN1:0.186647135216;XCPE1{core}:0.185551582576;GTF2A1,2:0.16626041656;PAX2:0.131100947328;ZBTB16:0.106873842485;CDC5L:0.0517950539649;FOXP3:0.0212706866139;EVI1:0.0126416668257;POU1F1:-0.00501908126848;FOXP1:-0.00693389509564;TBX4,5:-0.0114917392479;T:-0.0624284401641;MYOD1:-0.0993728178226;TFAP4:-0.105646677257;HIF1A:-0.133071113505;STAT1,3:-0.140759840713;ZNF238:-0.154200776936;FOX{F1,F2,J1}:-0.161622484261;GLI1..3:-0.219082248422;ARID5B:-0.236795544002;ZEB1:-0.244771341198;PPARG:-0.317858320904;HOX{A4,D4}:-0.320257295609;CEBPA,B_DDIT3:-0.341954212934;CRX:-0.344277028058;GFI1:-0.350148130538;PITX1..3:-0.350853021875;TLX1..3_NFIC{dimer}:-0.354207369511;NFIX:-0.383716422458;IKZF1:-0.38402338266;NFIL3:-0.38666431146;MYB:-0.392532149068;FOXA2:-0.39786052059;HAND1,2:-0.46770327938;ESRRA:-0.504028960171;ZNF148:-0.539683528218;GATA6:-0.565376962367;STAT5{A,B}:-0.566371171246;ESR1:-0.59631956726;RUNX1..3:-0.603102985046;SNAI1..3:-0.609554385324;EBF1:-0.615943033588;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.619075473937;MEF2{A,B,C,D}:-0.62365789274;TOPORS:-0.626410407318;TFCP2:-0.657595187652;TP53:-0.683895087675;HNF1A:-0.684720320404;SPI1:-0.70550653876;bHLH_family:-0.70787389262;HNF4A_NR2F1,2:-0.721478644031;FOSL2:-0.729899996991;E2F1..5:-0.767772754522;SPZ1:-0.785177571649;PAX1,9:-0.799604523155;NFATC1..3:-0.809307638194;TBP:-0.877164836679;NFE2L2:-0.879420075122;NFKB1_REL_RELA:-0.897340384761;TEAD1:-0.94842036094;GCM1,2:-1.0148651802;SPIB:-1.02197100221;NFE2:-1.02561474036;HLF:-1.03173085322;BACH2:-1.10913419534;AR:-1.12104733309;STAT2,4,6:-1.12415832824;MYBL2:-1.12608113794;ETS1,2:-1.15436550958;AIRE:-1.16866832711;ELF1,2,4:-1.23245642468;NR1H4:-1.32050843288;SRF:-1.38229990355;IRF7:-1.40458809543;PDX1:-1.42896622818;DMAP1_NCOR{1,2}_SMARC:-1.43225862826;RXRA_VDR{dimer}:-1.46031882334;FOX{D1,D2}:-1.54491282025;FOS_FOS{B,L1}_JUN{B,D}:-1.54524305286;NR6A1:-1.56359128722;ALX4:-1.65032337649;IRF1,2:-1.67662646731;TLX2:-1.72114966581;NKX2-2,8:-1.8636901693;FOXO1,3,4:-2.08005899665
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11648-122E1;search_select_hide=table117:11648-122E1
 }}

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FF:11648-122E1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:13, 4 June 2020

CNhs12113

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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