FF:11490-119E5: Difference between revisions

Latest revision as of 18:04, 4 June 2020

Name:	Mouse Neurons - substantia nigra, donor5
Species:	Mouse (Mus musculus)
Library ID:	CNhs12614,CNhs12923
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	substantia nigra
dev stage	NA
sex	NA
age	NA
cell type	NA
cell line	NA
company	Sciencell/3H
collaboration	NA
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	RNASUB1
catalog number	custom
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004762

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12614		CAGE		DRX008847		DRR009719
CNhs12923		CAGE		DRX023599		DRR025994

Accession ID Mm9

Library id		BAM		CTSS
CNhs12614		DRZ001144		DRZ002529
CNhs12923		DRZ005246		DRZ006036

Accession ID Mm10

Library id		BAM		CTSS
CNhs12614		DRZ012494		DRZ013879
CNhs12923		DRZ009987		DRZ010651

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

CNhs12614

0	0
1	0.694
10	0
100	0
1000	-0.0355
1001	-0.0305
1002	-0.032
1003	-0.0249
1004	0
1005	0
1006	0.687
1007	-0.114
1008	0
1009	-0.19
101	-0.174
1010	0
1011	0.304
1012	0
1013	0.355
1014	0.0653
1015	0.0246
1016	-0.0127
1017	0
1018	0
1019	0
102	0
1020	0.387
1021	0
1022	0.2
1023	0
1024	0
1025	-0.0611
1026	0
1027	0.533
1028	0
1029	-0.176
103	-0.0665
1030	0
1031	-0.27
1032	0.465
1033	0
1034	0
1035	0
1036	-0.184
1037	0
1038	-0.105
1039	0.183
104	0
1040	-0.278
1041	0

CNhs12923

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: CNhs12614

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00537
MA0003.1	MA0003.1	0.435
MA0004.1	MA0004.1	0.487
MA0006.1	MA0006.1	0.161
MA0007.1	MA0007.1	0.292
MA0009.1	MA0009.1	0.846
MA0014.1	MA0014.1	0.867
MA0017.1	MA0017.1	8.3748e-7
MA0018.2	MA0018.2	0.00835
MA0019.1	MA0019.1	0.497
MA0024.1	MA0024.1	0.0109
MA0025.1	MA0025.1	0.00112
MA0027.1	MA0027.1	0.0768
MA0028.1	MA0028.1	0.118
MA0029.1	MA0029.1	0.778
MA0030.1	MA0030.1	0.585
MA0031.1	MA0031.1	0.249
MA0035.2	MA0035.2	0.0213
MA0038.1	MA0038.1	0.877
MA0039.2	MA0039.2	0.0142
MA0040.1	MA0040.1	0.294
MA0041.1	MA0041.1	0.0966
MA0042.1	MA0042.1	0.29
MA0043.1	MA0043.1	0.0835
MA0046.1	MA0046.1	1.477e-10
MA0047.2	MA0047.2	3.39584e-4
MA0048.1	MA0048.1	0.0298
MA0050.1	MA0050.1	7.6571e-6
MA0051.1	MA0051.1	9.39236e-5
MA0052.1	MA0052.1	0.612
MA0055.1	MA0055.1	0.00803
MA0057.1	MA0057.1	0.354
MA0058.1	MA0058.1	0.593
MA0059.1	MA0059.1	0.325
MA0060.1	MA0060.1	0.624
MA0061.1	MA0061.1	0.0137
MA0062.2	MA0062.2	0.00217
MA0065.2	MA0065.2	1.74653e-5
MA0066.1	MA0066.1	0.0807
MA0067.1	MA0067.1	0.368
MA0068.1	MA0068.1	0.531
MA0069.1	MA0069.1	0.0499
MA0070.1	MA0070.1	0.404
MA0071.1	MA0071.1	0.21
MA0072.1	MA0072.1	0.215
MA0073.1	MA0073.1	0.891
MA0074.1	MA0074.1	0.168
MA0076.1	MA0076.1	0.306
MA0077.1	MA0077.1	0.386
MA0078.1	MA0078.1	0.891
MA0079.2	MA0079.2	0.41
MA0080.2	MA0080.2	2.24086e-10
MA0081.1	MA0081.1	0.164
MA0083.1	MA0083.1	4.15671e-4
MA0084.1	MA0084.1	0.273
MA0087.1	MA0087.1	0.132
MA0088.1	MA0088.1	0.336
MA0090.1	MA0090.1	0.228
MA0091.1	MA0091.1	0.121
MA0092.1	MA0092.1	0.136
MA0093.1	MA0093.1	0.539
MA0099.2	MA0099.2	8.06354e-4
MA0100.1	MA0100.1	0.317
MA0101.1	MA0101.1	0.00305
MA0102.2	MA0102.2	0.524
MA0103.1	MA0103.1	0.233
MA0104.2	MA0104.2	0.976
MA0105.1	MA0105.1	0.0111
MA0106.1	MA0106.1	0.055
MA0107.1	MA0107.1	0.00368
MA0108.2	MA0108.2	0.00166
MA0111.1	MA0111.1	0.749
MA0112.2	MA0112.2	0.002
MA0113.1	MA0113.1	0.329
MA0114.1	MA0114.1	4.33709e-6
MA0115.1	MA0115.1	1.02712e-4
MA0116.1	MA0116.1	0.167
MA0117.1	MA0117.1	0.884
MA0119.1	MA0119.1	0.0709
MA0122.1	MA0122.1	0.713
MA0124.1	MA0124.1	0.419
MA0125.1	MA0125.1	0.0356
MA0131.1	MA0131.1	0.546
MA0135.1	MA0135.1	0.371
MA0136.1	MA0136.1	5.3253e-12
MA0137.2	MA0137.2	0.102
MA0138.2	MA0138.2	1.6088e-4
MA0139.1	MA0139.1	0.719
MA0140.1	MA0140.1	2.10689e-4
MA0141.1	MA0141.1	0.0683
MA0142.1	MA0142.1	0.0275
MA0143.1	MA0143.1	0.543
MA0144.1	MA0144.1	0.0309
MA0145.1	MA0145.1	0.0914
MA0146.1	MA0146.1	0.0391
MA0147.1	MA0147.1	0.869
MA0148.1	MA0148.1	0.0012
MA0149.1	MA0149.1	0.465
MA0150.1	MA0150.1	0.238
MA0152.1	MA0152.1	0.162
MA0153.1	MA0153.1	4.75483e-10
MA0154.1	MA0154.1	0.0566
MA0155.1	MA0155.1	0.658
MA0156.1	MA0156.1	2.72807e-9
MA0157.1	MA0157.1	0.409
MA0159.1	MA0159.1	0.04
MA0160.1	MA0160.1	0.0485
MA0162.1	MA0162.1	0.374
MA0163.1	MA0163.1	0.0066
MA0164.1	MA0164.1	0.831
MA0258.1	MA0258.1	0.0376
MA0259.1	MA0259.1	0.895

library id: CNhs12923This sample isn't target for the analysis

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: CNhs12614

Novel motif	Logo	P-value
1	1	0.253
10	10	0.0705
100	100	0.44
101	101	0.837
102	102	0.659
103	103	0.278
104	104	0.771
105	105	0.489
106	106	0.0163
107	107	0.0631
108	108	0.564
109	109	0.0261
11	11	0.186
110	110	0.0556
111	111	0.541
112	112	0.0237
113	113	0.539
114	114	0.623
115	115	0.749
116	116	0.433
117	117	0.00284
118	118	0.578
119	119	0.176
12	12	0.945
120	120	0.895
121	121	0.136
122	122	0.722
123	123	0.00123
124	124	0.0775
125	125	0.0952
126	126	0.0445
127	127	0.224
128	128	0.0362
129	129	0.235
13	13	3.01285e-8
130	130	0.0778
131	131	0.583
132	132	0.655
133	133	0.791
134	134	0.222
135	135	0.3
136	136	0.265
137	137	0.373
138	138	0.732
139	139	0.508
14	14	0.688
140	140	0.2
141	141	0.832
142	142	0.552
143	143	0.662
144	144	0.602
145	145	1.35458e-4
146	146	0.261
147	147	0.189
148	148	0.905
149	149	0.93
15	15	0.247
150	150	0.0655
151	151	0.977
152	152	0.113
153	153	0.552
154	154	0.727
155	155	0.417
156	156	0.0641
157	157	0.0858
158	158	0.0748
159	159	0.0871
160	160	0.343
161	161	0.26
162	162	0.675
163	163	0.663
164	164	0.0329
165	165	0.275
166	166	0.396
167	167	0.378
168	168	0.97
169	169	0.00231
17	17	0.0595
18	18	0.729
19	19	0.0852
2	2	0.64
20	20	0.0233
21	21	0.267
22	22	0.134
23	23	0.469
24	24	0.0839
25	25	0.82
26	26	1.77003e-9
27	27	0.3
28	28	0.72
29	29	0.0182
3	3	0.127
30	30	0.824
31	31	0.56
32	32	0.907
33	33	0.159
34	34	0.847
35	35	0.463
36	36	0.52
37	37	0.0329
38	38	0.379
39	39	0.243
4	4	0.303
40	40	0.245
41	41	0.653
42	42	0.207
43	43	0.0991
44	44	0.857
45	45	0.636
46	46	0.0558
47	47	0.521
48	48	0.354
49	49	0.169
5	5	0.156
50	50	0.18
51	51	0.829
52	52	0.272
53	53	0.433
54	54	0.785
55	55	0.746
56	56	0.562
57	57	0.663
58	58	0.366
59	59	0.268
6	6	0.869
60	60	0.0213
61	61	0.048
62	62	0.24
63	63	0.141
64	64	0.769
65	65	0.301
66	66	0.837
67	67	0.749
68	68	0.961
69	69	0.693
7	7	0.0144
70	70	0.312
71	71	0.00249
72	72	0.608
73	73	0.0432
74	74	0.985
75	75	0.0607
76	76	0.43
77	77	0.468
78	78	3.77131e-4
79	79	0.054
8	8	0.135
80	80	0.982
81	81	0.659
82	82	0.368
83	83	0.128
84	84	0.894
85	85	0.14
86	86	0.14
87	87	0.97
88	88	0.451
89	89	0.709
9	9	0.306
90	90	0.227
91	91	0.0848
92	92	0.648
93	93	0.0175
94	94	0.779
95	95	0.0503
96	96	0.262
97	97	0.86
98	98	0.588
99	99	0.544

library id: CNhs12923This sample isn't target for the analysis

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: CNhs12614
library id: CNhs12923

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000208 mouse neuron of the substantia nigra 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)
0002614 (neuron of the substantia nigra)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002038 (substantia nigra)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009663 (telencephalic nucleus)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0009661 (midbrain nucleus)
0000125 (neural nucleus)
0002950 (regional part of midbrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0002308 (nucleus of brain)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0001891 (midbrain)
0010011 (collection of basal ganglia)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000208 (mouse neuron of the substantia nigra 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
-|DRA_sample_Accession=CAGE@DRS008737
+|DRA_sample_Accession=CAGE@SAMD00004762
-|accession_numbers=CAGE;DRX008847;DRR009719;DRZ001144;DRZ002529
+|accession_numbers=CAGE;DRX008847;DRR009719;DRZ001144;DRZ002529;DRZ012494;DRZ013879!CAGE;DRX023599;DRR025994;DRZ005246;DRZ006036;DRZ009987;DRZ010651
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0002038,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009663,UBERON:0002420,UBERON:0002616,UBERON:0002780,UBERON:0009661,UBERON:0000125,UBERON:0002950,UBERON:0002020,UBERON:0007245,UBERON:0010317,UBERON:0002308,UBERON:0010009,UBERON:0001017,UBERON:0001016,UBERON:0001893,UBERON:0001890,UBERON:0001891,UBERON:0010011,UBERON:0000454
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0002614
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.28!216.10!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.95!162.08!Tsc22d4;;chr17:48015839..48015915,-!p3@Foxp4!1.53!38.83!Foxp4;;chr7:116154364..116154444,+!p1@Tub!1.52!54.03!Tub;;chr3:95032091..95032183,-!p1@Mllt11!1.44!215.54!Mllt11;;chr16:91225808..91225824,+!p1@Olig2!1.43!25.89!Olig2;;chr18:36441119..36441158,+!p2@Pura!1.40!57.96!Pura;;chr2:65683890..65683907,+!p1@Csrnp3!1.38!43.33!Csrnp3;;chrX:34442872..34442899,-!p1@Nkrf!1.37!28.70!Nkrf;;chr2:163051181..163051205,+!p2@Tox2!1.37!22.51!Tox2;;chr15:76353005..76353021,-!p2@Scrt1!1.37!22.51!Scrt1;;chr4:58956447..58956510,+!p1@Zkscan16!1.34!45.02!Zkscan16;;chr7:146768691..146768707,-!p1@Nkx6-2!1.34!20.82!Nkx6-2;;chr4:150482563..150482655,-!p2@Camta1!1.28!63.59!Camta1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.28!22.51!Pou3f3;;chr7:148008023..148008092,-!p1@Zfp941!1.26!41.08!Zfp941;;chr4:154335024..154335039,+!p1@Hes5!1.24!19.70!Hes5;;chr16:91270091..91270143,+!p2@Olig1!1.24!16.32!Olig1;;chr10:67375368..67375433,-!p1@Zfp365!1.23!28.14!Zfp365;;chr3:95032197..95032208,-!p3@Mllt11!1.20!18.57!Mllt11;;chr4:150513630..150513686,-!p4@Camta1!1.20!16.88!Camta1;;chr19:19185671..19185693,-!p1@Rorb!1.19!34.89!Rorb;;chr3:34548909..34548927,+!p1@Sox2!1.19!24.76!Sox2;;chr17:25707623..25707639,-!p1@Sox8!1.18!60.78!Sox8;;chr8:24780125..24780143,+!p1@Zmat4!1.18!20.26!Zmat4;;chr12:30219426..30219506,+!p2@Myt1l!1.18!14.07!Myt1l;;chr10:67375146..67375208,-!p2@Zfp365!1.17!20.82!Zfp365;;chr8:107793688..107793736,+!p1@Hsf4!1.14!16.88!Hsf4;;chrX:108009761..108009788,+!p1@Pou3f4!1.14!12.94!Pou3f4;;chr12:54349410..54349461,+!p1@Npas3!1.12!14.63!Npas3;;chr3:101814061..101814094,+!p1@Nhlh2!1.11!11.82!Nhlh2;;chr3:95032213..95032226,-!p6@Mllt11!1.09!13.51!Mllt11;;chr2:168427068..168427115,-!p3@Nfatc2!1.09!11.26!Nfatc2;;chr12:72149325..72149343,+!p2@Arid4a!1.06!14.63!Arid4a;;chr2:163030219..163030258,+!p5@Tox2!1.05!10.13!Tox2;;chr9:91260594..91260612,-!p1@Zic1!1.05!10.13!Zic1;;chr9:40682064..40682081,+!p1@Bsx!1.05!10.13!Bsx;;chr11:84339016..84339044,-!p1@Lhx1!1.05!10.13!Lhx1;;chr10:84218800..84218829,+!p2@Rfx4!1.02!9.57!Rfx4;;chr15:76352677..76352737,-!p3@Scrt1!1.02!9.57!Scrt1;;chr7:52960555..52960662,+!p1@Dbp!1.01!80.48!Dbp;;chr3:95032558..95032641,-!p2@Mllt11!1.00!51.77!Mllt11;;chr3:128902837..128902861,+!p3@Pitx2!1.00!9.00!Pitx2;;chr7:91558392..91558434,-!p1@Arnt2!0.98!24.20!Arnt2;;chr3:95032184..95032195,-!p4@Mllt11!0.98!10.69!Mllt11;;chrX:34442842..34442866,-!p3@Nkrf!0.98!8.44!Nkrf;;chr8:112603658..112603674,+!p2@Zfp612!0.96!15.19!Zfp612;;chr13:44936126..44936164,+!p6@Jarid2!0.96!9.57!Jarid2;;chr2:127347067..127347093,-!p1@Kcnip3!0.95!13.51!Kcnip3;;chr7:52960700..52960719,+!p2@Dbp!0.94!9.57!Dbp;;chr3:95032515..95032553,-!p5@Mllt11!0.93!9.00!Mllt11;;chr14:19071466..19071550,-!p1@Nr1d2!0.92!52.34!Nr1d2;;chr13:99124189..99124205,+!p1@Foxd1!0.92!11.26!Foxd1;;chr12:30213247..30213333,+!p1@Myt1l!0.92!7.32!Myt1l;;chr2:163030186..163030204,+!p4@Tox2!0.92!7.32!Tox2;;chr11:98636531..98636559,-!p1@Nr1d1!0.91!42.21!Nr1d1;;chr5:122499831..122499891,-!p1@Cux2!0.91!11.26!Cux2;;chr15:78994907..78994926,-!p1@Sox10!0.90!18.57!Sox10;;chr6:134780163..134780197,+!p2@Crebl2!0.90!16.88!Crebl2;;chr1:6477388..6477419,+!p3@St18!0.89!6.75!St18;;chr2:71367871..71367898,+!p1@Dlx1!0.89!6.75!Dlx1;;chrX:95345005..95345053,+!p1@Ar!0.89!6.75!Ar;;chr7:52960888..52960902,+!p7@Dbp!0.89!6.75!Dbp;;chrX:90531838..90531861,+!p1@Arx!0.88!8.44!Arx;;chr6:145813964..145813994,-!p3@Bhlhe41!0.88!8.44!Bhlhe41;;chr7:130644017..130644092,-!p1@Zkscan2!0.87!12.94!Zkscan2;;chr3:128916868..128916890,+!p1@Pitx2!0.87!9.00!Pitx2;;chr8:107793737..107793757,+!p2@Hsf4!0.87!7.32!Hsf4;;chr9:69608731..69608742,-!p2@Foxb1!0.86!6.19!Foxb1;;chrX:137083127..137083138,-!p9@Tsc22d3!0.86!6.19!Tsc22d3;;chr4:150482353..150482386,-!p6@Camta1!0.86!6.19!Camta1;;chr2:163028808..163028869,+!p1@Tox2!0.85!23.07!Tox2;;chr7:52960730..52960762,+!p3@Dbp!0.85!7.88!Dbp;;chr3:34548946..34548972,+!p2@Sox2!0.85!6.75!Sox2;;chr6:145814003..145814056,-!p1@Bhlhe41!0.84!18.01!Bhlhe41;;chr7:38554763..38554780,-!p1@Zfp536!0.84!11.26!Zfp536;;chr2:25562263..25562314,+!p2@Bmyc!0.83!23.64!Bmyc;;chr6:117813087..117813121,+!p1@Zfp239!0.83!23.07!Zfp239;;chr4:129118044..129118067,-!p1@Zbtb8b!0.83!7.32!Zbtb8b;;chr6:145813905..145813932,-!p2@Bhlhe41!0.82!11.26!Bhlhe41;;chr2:163030164..163030178,+!p6@Tox2!0.82!5.63!Tox2;;chr2:127347042..127347058,-!p3@Kcnip3!0.82!5.63!Kcnip3;;chr2:181501710..181501742,+!p2@Myt1!0.82!5.63!Myt1;;chr8:12395892..12395919,+!p4@Sox1!0.82!5.63!Sox1;;chr18:66098702..66098742,-!p1@Rax!0.82!5.63!Rax;;chr10:84218895..84218909,+!p1@Rfx4!0.82!5.63!Rfx4;;chr14:122874619..122874634,+!p1@Zic2!0.82!5.63!Zic2;;chr14:118636238..118636257,-!p2@Sox21!0.82!5.63!Sox21;;chr7:6683123..6683142,-!p1@Peg3!0.81!304.45!Peg3;;chr8:72356532..72356611,+!p1@Pbx4!0.78!22.51!Pbx4;;chr1:170361991..170362015,-!p6@Pbx1!0.78!11.82!Pbx1;;chr7:91558472..91558512,-!p2@Arnt2!0.78!7.32!Arnt2;;chr14:118636214..118636235,-!p1@Sox21!0.78!6.19!Sox21;;chr15:76352434..76352488,-!p4@Scrt1!0.78!5.06!Scrt1;;chr2:162769220..162769252,+!p1@L3mbtl1!0.78!5.06!L3mbtl1;;chr2:168427120..168427138,-!p4@Nfatc2!0.78!5.06!Nfatc2;;chr5:120881900..120881914,+!p1@Lhx5!0.78!5.06!Lhx5;;chr5:140019843..140019858,+!p2@Uncx!0.78!5.06!Uncx;;chrX:70656436..70656464,+!p1@Zfp92!0.78!5.06!Zfp92;;chr14:76903992..76904056,+!p6@Tsc22d1!0.77!10.69!Tsc22d1;;chr11:116196664..116196679,-!p1@Foxj1!0.77!7.88!Foxj1;;chr14:52935860..52935874,-!p3@Sall2!0.77!7.32!Sall2;;chr8:79423672..79423727,+!p2@Nr3c2!0.76!6.19!Nr3c2;;chr15:103170533..103170556,-!p1@Zfp385a!0.75!18.57!Zfp385a;;chr2:56967334..56967366,-!p1@Nr4a2!0.75!10.13!Nr4a2;;chr7:30092993..30093076,+!p1@Dpf1!0.75!8.44!Dpf1;;chr15:103164702..103164778,-!p3@Zfp385a!0.75!5.63!Zfp385a;;chr2:25562315..25562344,+!p3@Bmyc!0.74!16.32!Bmyc;;chr9:69608672..69608686,-!p1@Foxb1!0.74!4.50!Foxb1;;chr9:91260616..91260653,-!p2@Zic1!0.74!4.50!Zic1;;chr5:138199481..138199491,+!p16@Tsc22d4!0.74!4.50!Tsc22d4;;chr5:140019816..140019825,+!p3@Uncx!0.74!4.50!Uncx;;chr5:106887496..106887515,-!p2@Barhl2!0.74!4.50!Barhl2;;chr5:106887474..106887489,-!p1@Barhl2!0.74!4.50!Barhl2;;chr12:30220074..30220102,+!p3@Myt1l!0.74!4.50!Myt1l;;chr12:86939997..86940040,+!p4@Jdp2!0.74!4.50!Jdp2;;chr11:96685444..96685473,-!p5@Nfe2l1!0.74!4.50!Nfe2l1;;chr16:91225654..91225671,+!p2@Olig2!0.74!4.50!Olig2;;chr15:82742573..82742620,-!p2@Tcf20!0.74!4.50!Tcf20;;chr7:17200307..17200370,-!p2@Grlf1!0.73!36.02!Grlf1;;chr14:76904356..76904367,+!p3@Tsc22d1!0.72!34.89!Tsc22d1;;chr19:26681865..26681900,+!p6@Smarca2!0.72!13.51!Smarca2;;chr5:125342568..125342602,+!p2@Zfp664!0.72!7.32!Zfp664;;chr17:48015645..48015689,-!p9@Foxp4!0.72!5.63!Foxp4;;chr11:90252223..90252240,-!p1@Hlf!0.71!38.83!Hlf;;chr3:5218546..5218561,+!p4@Zfhx4!0.71!6.75!Zfhx4;;chr15:98126545..98126588,-!p1@Zfp641!0.70!9.57!Zfp641;;chr3:54559463..54559493,+!p3@Smad9!0.70!7.88!Smad9;;chr7:38558574..38558611,-!p2@Zfp536!0.69!5.06!Zfp536;;chr8:12395603..12395621,+!p1@Sox1!0.69!3.94!Sox1;;chr3:34549096..34549111,+!p3@Sox2!0.69!3.94!Sox2;;chr10:67375342..67375365,-!p3@Zfp365!0.69!3.94!Zfp365;;chr2:127347094..127347111,-!p2@Kcnip3!0.68!6.75!Kcnip3;;chr5:3648045..3648074,-!p2@Gatad1!0.68!6.75!Gatad1;;chr9:20385868..20385902,+!p3@Zfp846!0.67!5.63!Zfp846;;chr15:103170561..103170572,-!p4@Zfp385a!0.67!5.63!Zfp385a;;chr7:52960780..52960793,+!p5@Dbp!0.67!4.50!Dbp;;chr11:98603119..98603130,+!p2@Thra!0.66!34.89!Thra;;chr8:112603610..112603656,+!p1@Zfp612!0.66!18.57!Zfp612;;chr2:38206744..38206766,+!p1@Lhx2!0.66!4.50!Lhx2;;chr17:33766353..33766393,+!p2@Zfp414!0.65!10.69!Zfp414;;chr6:90412556..90412581,+!p3@Klf15!0.65!8.44!Klf15;;chr9:106355684..106355744,+!p5@Pcbp4!0.65!5.63!Pcbp4;;chr15:81633165..81633188,+!p2@Tef!0.64!32.64!Tef;;chr17:27693525..27693538,+!p5@Hmga1!0.64!12.94!Hmga1;;chr19:19185697..19185711,-!p2@Rorb!0.64!4.50!Rorb;;chr7:38557887..38557910,-!p5@Zfp536!0.64!3.38!Zfp536;;chr7:91520922..91520956,-!p5@Arnt2!0.64!3.38!Arnt2;;chr7:52960663..52960677,+!p6@Dbp!0.64!3.38!Dbp;;chr11:90250894..90250916,-!p5@Hlf!0.64!3.38!Hlf;;chr11:90252108..90252134,-!p6@Hlf!0.64!3.38!Hlf;;chr10:5636354..5636373,-!p2@Esr1!0.64!3.38!Esr1;;chr11:21901608..21901634,-!p1@Otx1!0.64!3.38!Otx1;;chr14:34791937..34791977,-!p1@Zfp488!0.64!3.38!Zfp488;;chr13:95645555..95645566,+!p3@Otp!0.64!3.38!Otp;;chr7:17062114..17062141,-!p1@Npas1!0.64!3.38!Npas1;;chr1:122499088..122499099,+!p2@En1!0.64!3.38!En1;;chr2:65768174..65768247,+!p2@Csrnp3!0.64!3.38!Csrnp3;;chr2:65768149..65768173,+!p4@Csrnp3!0.64!3.38!Csrnp3;;chr5:106886962..106886973,-!p3@Barhl2!0.64!3.38!Barhl2;;chr11:98603185..98603208,+!p1@Thra!0.63!232.98!Thra;;chr7:25372631..25372684,-!p1@Zfp575!0.63!11.26!Zfp575;;chr19:10315179..10315241,-!p1@Gm98!0.61!38.83!Gm98;;chr15:81633139..81633152,+!p4@Tef!0.61!5.63!Tef;;chr18:35721834..35721851,+!p2@Matr3!0.60!18.57!Matr3;;chr11:69579472..69579529,+!p1@Zbtb4!0.60!18.01!Zbtb4;;chr9:87626083..87626108,-!p1@Tbx18!0.60!7.32!Tbx18;;chr7:25292331..25292421,+!p1@Zfp428!0.59!24.76!Zfp428;;chr5:107003699..107003717,-!p11@Zfp644!0.59!3.38!Zfp644;;chr17:87153028..87153049,+!p2@Epas1!0.58!70.35!Epas1;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.58!35.45!Camta2;;chr5:122500142..122500167,-!p2@Cux2!0.58!6.75!Cux2;;chr1:38684431..38684450,-!p3@Aff3!0.58!5.06!Aff3;;chr6:72850124..72850210,-!p7@Kcmf1!0.58!3.94!Kcmf1;;chr5:140019865..140019886,+!p1@Uncx!0.58!2.81!Uncx;;chr15:95485240..95485257,-!p1@Dbx2!0.58!2.81!Dbx2;;chr4:109650609..109650653,+!p1@Dmrta2!0.58!2.81!Dmrta2;;chr2:71367142..71367167,+!p2@Dlx1!0.58!2.81!Dlx1;;chr3:128902878..128902893,+!p6@Pitx2!0.58!2.81!Pitx2;;chr9:8900459..8900489,+!p1@Pgr!0.58!2.81!Pgr;;chrX:55284180..55284195,+!p2@Zic3!0.58!2.81!Zic3;;chr2:147019977..147019985,-!p2@Nkx2-2!0.58!2.81!Nkx2-2;;chr2:147012101..147012118,-!p3@Nkx2-2!0.58!2.81!Nkx2-2;;chr2:28771380..28771413,-!p2@Barhl1!0.58!2.81!Barhl1;;chr1:42752654..42752665,+!p@chr1:42752654..42752665,+!0.58!2.81!Pou3f3;;chr12:57636220..57636236,-!p3@Nkx2-1!0.58!2.81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ox5;;chr6:6831928..6831949,-!p3@Dlx5!0.19!0.56!Dlx5;;chr6:6813269..6813272,+!p2@Dlx6!0.19!0.56!Dlx6;;chr6:85137505..85137517,+!p2@Emx1!0.19!0.56!Emx1;;chr6:6812962..6812979,+!p1@Dlx6!0.19!0.56!Dlx6;;chr6:144157968..144157989,-!p7@Sox5!0.19!0.56!Sox5;;chr6:85463580..85463585,-!p1@Egr4!0.19!0.56!Egr4;;chr6:88148324..88148328,+!p3@Gata2!0.19!0.56!Gata2;;chr4:107353508..107353547,-!p4@Dmrtb1!0.19!0.56!Dmrtb1;;chr4:97248607..97248649,+!p15@Nfia!0.19!0.56!Nfia;;chr2:9809374..9809396,-!p4@Gata3!0.19!0.56!Gata3;;chr3:130813254..130813263,+!p4@Lef1!0.19!0.56!Lef1;;chr4:150503544..150503561,-!p8@Camta1!0.19!0.56!Camta1;;chr4:84321280..84321298,-!p5@Bnc2!0.19!0.56!Bnc2;;chr4:89354729..89354776,+!p1@Dmrta1!0.19!0.56!Dmrta1;;chr4:13678723..13678739,+!p10@Runx1t1!0.19!0.56!Runx1t1;;chr3:17954258..17954267,+!p7@Bhlhe22!0.19!0.56!Bhlhe22;;chr4:97248473..97248496,+!p16@Nfia!0.19!0.56!Nfia;;chr2:71367855..71367864,+!p6@Dlx1!0.19!0.56!Dlx1;;chr4:13669922..13669957,+!p13@Runx1t1!0.19!0.56!Runx1t1;;chr2:9809402..9809422,-!p5@Gata3!0.19!0.56!Gata3;;chr4:32325910..32325921,+!p8@Bach2!0.19!0.56!Bach2;;chr4:97248379..97248387,+!p29@Nfia!0.19!0.56!Nfia;;chr3:95032254..95032261,-!p8@Mllt11!0.19!0.56!Mllt11;;chr3:130813756..130813767,+!p8@Lef1!0.19!0.56!Lef1;;chr3:95032802..95032830,-!p7@Mllt11!0.19!0.56!Mllt11;;chr4:107353563..107353590,-!p6@Dmrtb1!0.19!0.56!Dmrtb1;;chr3:66785857..66785873,-!p1@Shox2!0.19!0.56!Shox2;;chr2:79296907..79296918,-!p2@Neurod1!0.19!0.56!Neurod1;;chr2:79296783..79296801,-!p1@Neurod1!0.19!0.56!Neurod1;;chr4:114581497..114581519,-!p2@Foxd2!0.19!0.56!Foxd2;;chr4:114729957..114730012,+!p3@Tal1!0.19!0.56!Tal1;;chr4:119486980..119486993,+!p6@Hivep3!0.19!0.56!Hivep3;;chr4:118967319..118967330,-!p6@Ybx1!0.19!0.56!Ybx1;;chr2:77541309..77541322,-!p14@Zfp385b!0.19!0.56!Zfp385b;;chr2:77541432..77541474,-!p5@Zfp385b!0.19!0.56!Zfp385b;;chr4:82145232..82145259,-!p9@Nfib!0.19!0.56!Nfib;;chr4:44717308..44717321,-!p6@Pax5!0.19!0.56!Pax5;;chr2:77654793..77654805,-!p7@Zfp385b!0.19!0.56!Zfp385b;;chrX:58146612..58146615,-!p1@Sox3!0.19!0.56!Sox3;;chrX:7156792..7156811,+!p1@Foxp3!0.19!0.56!Foxp3;;chrX:55283827..55283838,+!p3@Zic3!0.19!0.56!Zic3;;chr17:51951370..51951382,-!p27@Satb1!0.19!0.56!Satb1;;chr18:66098752..66098757,-!p3@Rax!0.19!0.56!Rax;;chr19:23215616..23215627,+!p9@Klf9!0.19!0.56!Klf9;;chr18:69752864..69752875,+!p25@Tcf4!0.19!0.56!Tcf4;;chr17:71201050..71201078,-!p9@Tgif1!0.19!0.56!Tgif1;;chr19:28085572..28085579,-!p9@Rfx3!0.19!0.56!Rfx3;;chr16:25865862..25865871,+!p8@Trp63!0.19!0.56!Trp63;;chr15:96117679..96117696,+!p6@Arid2!0.19!0.56!Arid2;;chr17:86020293..86020318,+!p7@Six3!0.19!0.56!Six3;;chr17:86020137..86020149,+!p5@Six3!0.19!0.56!Six3;;chr18:5593880..5593898,+!p13@Zeb1!0.19!0.56!Zeb1;;chr18:5594197..5594228,+!p7@Zeb1!0.19!0.56!Zeb1;;chr19:46222859..46222876,-!p1@Pitx3!0.19!0.56!Pitx3;;chr16:43364258..43364270,+!p27@Zbtb20!0.19!0.56!Zbtb20;;chr17:71201572..71201601,-!p10@Tgif1!0.19!0.56!Tgif1;;chr16:25684232..25684285,+!p2@Trp63!0.19!0.56!Trp63;;chr19:4989964..4989972,-!p1@Npas4!0.19!0.56!Npas4;;chr16:94085471..94085495,+!p1@Sim2!0.19!0.56!Sim2;;chr17:86020115..86020128,+!p2@Six3!0.19!0.56!Six3;;chr10:75384163..75384185,-!p3@Smarcb1!0.19!0.56!Smarcb1;;chr10:67599527..67599530,-!p9@Arid5b!0.19!0.56!Arid5b;;chr11:52095821..52095836,-!p3@Tcf7!0.19!0.56!Tcf7;;chr10:79957600..79957618,+!p1@Onecut3!0.19!0.56!Onecut3;;chr11:96880072..96880079,+!p1@Sp6!0.19!0.56!Sp6;;chr12:109241804..109241823,-!p5@Bcl11b!0.19!0.56!Bcl11b;;chr10:12844757..12844771,+!p2@Plagl1!0.19!0.56!Plagl1;;chr10:5636336..5636347,-!p9@Esr1!0.19!0.56!Esr1;;chr11:101645980..101645989,-!p16@Etv4!0.19!0.56!Etv4;;chr11:98190955..98190968,-!p2@Neurod2!0.19!0.56!Neurod2;;chr11:23670827..23670846,-!p3@Rel!0.19!0.56!Rel;;chr19:59533139..59533152,+!p2@Emx2!0.19!0.56!Emx2;;chr19:59533206..59533217,+!p9@Emx2!0.19!0.56!Emx2;;chr2:105509045..105509071,+!p1@Pax6!0.19!0.56!Pax6;;chr2:105515772..105515780,+!p9@Pax6!0.19!0.56!Pax6;;chr2:105515793..105515808,+!p3@Pax6!0.19!0.56!Pax6;;chr2:105515586..105515606,+!p4@Pax6!0.19!0.56!Pax6;;chr19:59533163..59533185,+!p3@Emx2!0.19!0.56!Emx2;;chr2:105515826..105515837,+!p7@Pax6!0.19!0.56!Pax6;;chr2:168781014..168781025,-!p4@LOC100502777,p4@Zfp64!0.19!0.56!Zfp64;;chr1:168168856..168168893,-!p1@Mael!0.19!0.56!Mael;;chr1:169528457..169528482,+!p3@Rxrg!0.19!0.56!Rxrg;;chr1:6724908..6724955,+!p2@St18!0.19!0.56!St18;;chr1:91827728..91827743,-!p2@Gbx2!0.19!0.56!Gbx2;;chr2:61642631..61642684,+!p1@Tbr1!0.19!0.56!Tbr1;;chr1:6720186..6720198,+!p5@St18!0.19!0.56!St18;;chr1:6477452..6477459,+!p8@St18!0.19!0.56!St18;;chr1:122498982..122498991,+!p3@En1!0.19!0.56!En1;;chr19:55969923..55969944,+!p6@Tcf7l2!0.19!0.56!Tcf7l2;;chr2:24331085..24331100,-!p1@Pax8!0.19!0.56!Pax8;;chr1:189432881..189432903,+!p2@Esrrg!0.19!0.56!Esrrg;;chr1:173987720..173987729,-!p1@Nhlh1!0.19!0.56!Nhlh1;;chr19:55970072..55970081,+!p38@Tcf7l2!0.19!0.56!Tcf7l2;;chr2:56967381..56967386,-!p8@Nr4a2!0.19!0.56!Nr4a2;;chr2:163028876..163028885,+!p7@Tox2!0.19!0.56!Tox2;;chr1:781936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@@ Line 43: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000208
 |is_obsolete=
-|library_id=CNhs12614
+|library_id=CNhs12614!CNhs12923
-|library_ids=CNhs12614
+|library_id_phase_based=2:CNhs12923
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11490
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11490
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Neurons%2520-%2520substantia%2520nigra%252c%2520donor5%252c%2520tech_rep2.CNhs12923.11490-119E5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Neurons%2520-%2520substantia%2520nigra%252c%2520donor5%252c%2520tech_rep2.CNhs12923.11490-119E5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Neurons%2520-%2520substantia%2520nigra%252c%2520donor5%252c%2520tech_rep2.CNhs12923.11490-119E5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Neurons%2520-%2520substantia%2520nigra%252c%2520donor5%252c%2520tech_rep2.CNhs12923.11490-119E5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Neurons%2520-%2520substantia%2520nigra%252c%2520donor5%252c%2520tech_rep2.CNhs12923.11490-119E5.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - substantia nigra, donor5
 |namespace=FANTOM5
@@ Line 50: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12614 & CNhs12923,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0459375348506807,0,0,0,0,0,0.05591297648005,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.535305103370291,-0.364529780385038,0,0,0,0,0,-0.112376219526329,0.121109573262774,0.0563200476069179,0.488558142355031,0.242155069627506,0.193893011938994,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,0,-0.105495914727683,-0.310650657339386,0.535577727034941,-0.140687683267293,0,0,0.0793159455339409,0.267915894396217,0,0,0.0737427530379917,0.162381258139449,0.893008186991139,-0.0788315948399074,0,0,0,0,0,0,0.431870466913689,0.312032538056503,0.276888551832071,0,0,0.581359400489082,0.327466262382121,0
@@ Line 63: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=119E5
+|rna_tube_id=1.19E+07
 |rna_weight_ug=10
 |sample_age=
@@ Line 87: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11490-119E5;search_select_hide=table117:11490-119E5
 }}

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FF:11490-119E5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:04, 4 June 2020

CNhs12614

CNhs12923

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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