FF:11770-123I6: Difference between revisions

Latest revision as of 18:19, 4 June 2020

Name:	Mouse Neurons - substantia nigra, donor6
Species:	Mouse (Mus musculus)
Library ID:	CNhs12643
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	RNASUB2
catalog number	custom
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005278

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12643		CAGE		DRX008848		DRR009720

Accession ID Mm9

Library id		BAM		CTSS
CNhs12643		DRZ001145		DRZ002530

Accession ID Mm10

Library id		BAM		CTSS
CNhs12643		DRZ012495		DRZ013880

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

CNhs12643

0	0
1	0.712
10	0
100	0
1000	0
1001	0.0932
1002	0
1003	0.118
1004	0
1005	0
1006	0.566
1007	-0.0812
1008	0
1009	-0.128
101	-0.138
1010	0
1011	0.311
1012	0.164
1013	0.186
1014	0.152
1015	-0.0629
1016	-0.056
1017	0
1018	0
1019	0
102	0
1020	0.574
1021	0.0131
1022	0.0688
1023	0
1024	0
1025	6.239854e-4
1026	0
1027	0.427
1028	0
1029	-0.013
103	-0.0709
1030	0
1031	-0.374
1032	0.52
1033	0.0406
1034	0
1035	0
1036	-0.183
1037	0
1038	-0.04
1039	0.134
104	0
1040	-0.258
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: CNhs12643

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	9.93509e-4
MA0003.1	MA0003.1	0.328
MA0004.1	MA0004.1	0.523
MA0006.1	MA0006.1	0.185
MA0007.1	MA0007.1	0.36
MA0009.1	MA0009.1	0.912
MA0014.1	MA0014.1	0.774
MA0017.1	MA0017.1	4.82693e-7
MA0018.2	MA0018.2	0.0315
MA0019.1	MA0019.1	0.521
MA0024.1	MA0024.1	0.0599
MA0025.1	MA0025.1	0.00715
MA0027.1	MA0027.1	0.0473
MA0028.1	MA0028.1	0.0628
MA0029.1	MA0029.1	1
MA0030.1	MA0030.1	0.943
MA0031.1	MA0031.1	0.189
MA0035.2	MA0035.2	0.00967
MA0038.1	MA0038.1	0.831
MA0039.2	MA0039.2	0.0151
MA0040.1	MA0040.1	0.25
MA0041.1	MA0041.1	0.0938
MA0042.1	MA0042.1	0.248
MA0043.1	MA0043.1	0.189
MA0046.1	MA0046.1	6.41334e-11
MA0047.2	MA0047.2	6.07714e-4
MA0048.1	MA0048.1	0.0442
MA0050.1	MA0050.1	7.23053e-5
MA0051.1	MA0051.1	7.21684e-4
MA0052.1	MA0052.1	0.131
MA0055.1	MA0055.1	0.0136
MA0057.1	MA0057.1	0.278
MA0058.1	MA0058.1	0.556
MA0059.1	MA0059.1	0.263
MA0060.1	MA0060.1	0.604
MA0061.1	MA0061.1	0.0246
MA0062.2	MA0062.2	3.65343e-4
MA0065.2	MA0065.2	7.15793e-6
MA0066.1	MA0066.1	0.0469
MA0067.1	MA0067.1	0.348
MA0068.1	MA0068.1	0.654
MA0069.1	MA0069.1	0.108
MA0070.1	MA0070.1	0.499
MA0071.1	MA0071.1	0.088
MA0072.1	MA0072.1	0.294
MA0073.1	MA0073.1	0.926
MA0074.1	MA0074.1	0.135
MA0076.1	MA0076.1	0.151
MA0077.1	MA0077.1	0.278
MA0078.1	MA0078.1	0.802
MA0079.2	MA0079.2	0.362
MA0080.2	MA0080.2	1.06297e-10
MA0081.1	MA0081.1	0.114
MA0083.1	MA0083.1	0.00183
MA0084.1	MA0084.1	0.568
MA0087.1	MA0087.1	0.102
MA0088.1	MA0088.1	0.272
MA0090.1	MA0090.1	0.141
MA0091.1	MA0091.1	0.137
MA0092.1	MA0092.1	0.131
MA0093.1	MA0093.1	0.592
MA0099.2	MA0099.2	5.54619e-4
MA0100.1	MA0100.1	0.232
MA0101.1	MA0101.1	0.0103
MA0102.2	MA0102.2	0.636
MA0103.1	MA0103.1	0.183
MA0104.2	MA0104.2	0.855
MA0105.1	MA0105.1	0.00752
MA0106.1	MA0106.1	0.0675
MA0107.1	MA0107.1	0.0228
MA0108.2	MA0108.2	0.00125
MA0111.1	MA0111.1	0.95
MA0112.2	MA0112.2	5.79976e-4
MA0113.1	MA0113.1	0.254
MA0114.1	MA0114.1	5.57156e-6
MA0115.1	MA0115.1	9.06248e-5
MA0116.1	MA0116.1	0.0911
MA0117.1	MA0117.1	0.926
MA0119.1	MA0119.1	0.109
MA0122.1	MA0122.1	0.805
MA0124.1	MA0124.1	0.602
MA0125.1	MA0125.1	0.0357
MA0131.1	MA0131.1	0.651
MA0135.1	MA0135.1	0.856
MA0136.1	MA0136.1	9.89907e-14
MA0137.2	MA0137.2	0.0805
MA0138.2	MA0138.2	9.90491e-4
MA0139.1	MA0139.1	0.586
MA0140.1	MA0140.1	1.25481e-4
MA0141.1	MA0141.1	0.0119
MA0142.1	MA0142.1	0.404
MA0143.1	MA0143.1	0.879
MA0144.1	MA0144.1	0.0545
MA0145.1	MA0145.1	0.0874
MA0146.1	MA0146.1	0.0367
MA0147.1	MA0147.1	0.734
MA0148.1	MA0148.1	5.12605e-4
MA0149.1	MA0149.1	0.323
MA0150.1	MA0150.1	0.14
MA0152.1	MA0152.1	0.132
MA0153.1	MA0153.1	3.81474e-12
MA0154.1	MA0154.1	0.0467
MA0155.1	MA0155.1	0.526
MA0156.1	MA0156.1	5.23522e-10
MA0157.1	MA0157.1	0.157
MA0159.1	MA0159.1	0.00777
MA0160.1	MA0160.1	0.0166
MA0162.1	MA0162.1	0.241
MA0163.1	MA0163.1	0.00347
MA0164.1	MA0164.1	0.888
MA0258.1	MA0258.1	0.0152
MA0259.1	MA0259.1	0.835

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: CNhs12643

Novel motif	Logo	P-value
1	1	0.206
10	10	0.0606
100	100	0.337
101	101	0.991
102	102	0.915
103	103	0.115
104	104	0.882
105	105	0.358
106	106	0.0466
107	107	0.108
108	108	0.499
109	109	0.0124
11	11	0.0896
110	110	0.0472
111	111	0.331
112	112	0.0093
113	113	0.664
114	114	0.521
115	115	0.675
116	116	0.435
117	117	0.00299
118	118	0.59
119	119	0.194
12	12	0.903
120	120	0.945
121	121	0.18
122	122	0.886
123	123	3.88617e-4
124	124	0.132
125	125	0.155
126	126	0.0504
127	127	0.46
128	128	0.0355
129	129	0.222
13	13	8.80261e-8
130	130	0.115
131	131	0.471
132	132	0.491
133	133	0.599
134	134	0.135
135	135	0.369
136	136	0.183
137	137	0.481
138	138	0.873
139	139	0.505
14	14	0.936
140	140	0.171
141	141	0.752
142	142	0.641
143	143	0.323
144	144	0.634
145	145	2.94738e-4
146	146	0.23
147	147	0.161
148	148	0.964
149	149	0.703
15	15	0.206
150	150	0.0773
151	151	0.881
152	152	0.111
153	153	0.618
154	154	0.652
155	155	0.343
156	156	0.419
157	157	0.101
158	158	0.0954
159	159	0.717
160	160	0.289
161	161	0.176
162	162	0.638
163	163	0.801
164	164	0.0308
165	165	0.276
166	166	0.513
167	167	0.545
168	168	0.533
169	169	0.00218
17	17	0.0594
18	18	0.813
19	19	0.0846
2	2	0.707
20	20	0.0475
21	21	0.229
22	22	0.139
23	23	0.567
24	24	0.069
25	25	0.748
26	26	2.3136e-8
27	27	0.47
28	28	0.721
29	29	0.0382
3	3	0.0909
30	30	0.833
31	31	0.659
32	32	0.821
33	33	0.111
34	34	0.728
35	35	0.714
36	36	0.2
37	37	0.0371
38	38	0.368
39	39	0.431
4	4	0.261
40	40	0.11
41	41	0.431
42	42	0.186
43	43	0.123
44	44	0.982
45	45	0.665
46	46	0.0444
47	47	0.379
48	48	0.25
49	49	0.173
5	5	0.191
50	50	0.247
51	51	0.739
52	52	0.319
53	53	0.641
54	54	0.856
55	55	0.907
56	56	0.503
57	57	0.625
58	58	0.291
59	59	0.179
6	6	0.975
60	60	0.0308
61	61	0.0548
62	62	0.178
63	63	0.152
64	64	0.67
65	65	0.333
66	66	0.708
67	67	0.817
68	68	0.845
69	69	0.586
7	7	0.0136
70	70	0.178
71	71	0.00293
72	72	0.486
73	73	0.0521
74	74	0.956
75	75	0.0487
76	76	0.422
77	77	0.529
78	78	0.00122
79	79	0.0224
8	8	0.0819
80	80	0.965
81	81	0.708
82	82	0.264
83	83	0.0658
84	84	0.865
85	85	0.163
86	86	0.153
87	87	0.282
88	88	0.516
89	89	0.619
9	9	0.345
90	90	0.202
91	91	0.108
92	92	0.413
93	93	0.0143
94	94	0.65
95	95	0.0633
96	96	0.208
97	97	0.889
98	98	0.601
99	99	0.491

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: CNhs12643

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@SAMD00005278
+|accession_numbers=CAGE;DRX008848;DRR009720;DRZ001145;DRZ002530;DRZ012495;DRZ013880
 |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 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.36!257.62!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.90!144.24!Tsc22d4;;chr17:48015839..48015915,-!p3@Foxp4!1.53!38.20!Foxp4;;chr16:91225808..91225824,+!p1@Olig2!1.53!32.85!Olig2;;chr7:116154364..116154444,+!p1@Tub!1.47!47.83!Tub;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.47!35.45!Pou3f3;;chr3:95032091..95032183,-!p1@Mllt11!1.45!225.22!Mllt11;;chr12:30219426..30219506,+!p2@Myt1l!1.39!23.53!Myt1l;;chr4:58956447..58956510,+!p1@Zkscan16!1.38!49.20!Zkscan16;;chr10:67375368..67375433,-!p1@Zfp365!1.36!37.89!Zfp365;;chr18:36441119..36441158,+!p2@Pura!1.35!51.65!Pura;;chrX:34442872..34442899,-!p1@Nkrf!1.34!26.74!Nkrf;;chr7:146768691..146768707,-!p1@Nkx6-2!1.34!20.93!Nkx6-2;;chr15:76353005..76353021,-!p2@Scrt1!1.34!20.63!Scrt1;;chr2:163051181..163051205,+!p2@Tox2!1.32!19.71!Tox2;;chr2:65683890..65683907,+!p1@Csrnp3!1.31!37.13!Csrnp3;;chr4:150482563..150482655,-!p2@Camta1!1.29!64.33!Camta1;;chr17:25707623..25707639,-!p1@Sox8!1.28!75.02!Sox8;;chr19:19185671..19185693,-!p1@Rorb!1.28!42.17!Rorb;;chr7:148008023..148008092,-!p1@Zfp941!1.25!40.34!Zfp941;;chr10:67375146..67375208,-!p2@Zfp365!1.22!23.84!Zfp365;;chr8:24780125..24780143,+!p1@Zmat4!1.22!22.31!Zmat4;;chr11:98190918..98190951,-!p1@Neurod2!1.22!15.43!Neurod2;;chr12:54349410..54349461,+!p1@Npas3!1.20!17.72!Npas3;;chr14:122874619..122874634,+!p1@Zic2!1.20!14.82!Zic2;;chr2:168427068..168427115,-!p3@Nfatc2!1.20!14.67!Nfatc2;;chr16:91270091..91270143,+!p2@Olig1!1.17!13.90!Olig1;;chr15:76352434..76352488,-!p4@Scrt1!1.16!13.60!Scrt1;;chr15:78994907..78994926,-!p1@Sox10!1.15!33.31!Sox10;;chr4:154335024..154335039,+!p1@Hes5!1.14!15.43!Hes5;;chr9:91260594..91260612,-!p1@Zic1!1.14!12.84!Zic1;;chr6:55631042..55631102,-!p1@Neurod6!1.13!12.38!Neurod6;;chr7:52960700..52960719,+!p2@Dbp!1.12!14.97!Dbp;;chr4:150513630..150513686,-!p4@Camta1!1.12!14.06!Camta1;;chr2:127347067..127347093,-!p1@Kcnip3!1.10!19.41!Kcnip3;;chr5:98609885..98609900,+!p1@Prdm8!1.10!11.46!Prdm8;;chr3:95032197..95032208,-!p3@Mllt11!1.08!13.90!Mllt11;;chrX:108009761..108009788,+!p1@Pou3f4!1.08!11.15!Pou3f4;;chr8:107793688..107793736,+!p1@Hsf4!1.07!13.90!Hsf4;;chr1:6477388..6477419,+!p3@St18!1.06!10.39!St18;;chr9:91260616..91260653,-!p2@Zic1!1.05!10.24!Zic1;;chr3:34548909..34548927,+!p1@Sox2!1.03!16.81!Sox2;;chrX:90531838..90531861,+!p1@Arx!1.02!12.07!Arx;;chr10:84218800..84218829,+!p2@Rfx4!1.02!9.47!Rfx4;;chr3:95032184..95032195,-!p4@Mllt11!1.01!11.46!Mllt11;;chr3:95032213..95032226,-!p6@Mllt11!1.01!11.15!Mllt11;;chr2:163030219..163030258,+!p5@Tox2!1.01!9.17!Tox2;;chr7:52960555..52960662,+!p1@Dbp!0.99!76.40!Dbp;;chr6:145814003..145814056,-!p1@Bhlhe41!0.99!25.67!Bhlhe41;;chr16:91225654..91225671,+!p2@Olig2!0.99!8.71!Olig2;;chr11:90251852..90251855,-!p4@Hlf!0.98!10.54!Hlf;;chr11:84339016..84339044,-!p1@Lhx1!0.98!8.56!Lhx1;;chr15:76352677..76352737,-!p3@Scrt1!0.98!8.56!Scrt1;;chr6:145813905..145813932,-!p2@Bhlhe41!0.97!16.04!Bhlhe41;;chr13:72766250..72766273,+!p1@Irx2!0.97!13.14!Irx2;;chr14:34791937..34791977,-!p1@Zfp488!0.97!8.40!Zfp488;;chr6:134780163..134780197,+!p2@Crebl2!0.96!19.56!Crebl2;;chr13:99124189..99124205,+!p1@Foxd1!0.96!12.53!Foxd1;;chr12:72149325..72149343,+!p2@Arid4a!0.96!11.61!Arid4a;;chrX:34442842..34442866,-!p3@Nkrf!0.96!8.10!Nkrf;;chr11:98636531..98636559,-!p1@Nr1d1!0.95!47.06!Nr1d1;;chr7:91558392..91558434,-!p1@Arnt2!0.95!22.61!Arnt2;;chr8:112603658..112603674,+!p2@Zfp612!0.94!14.67!Zfp612;;chr12:30213247..30213333,+!p1@Myt1l!0.92!7.33!Myt1l;;chr4:150482353..150482386,-!p6@Camta1!0.92!7.33!Camta1;;chr3:95032515..95032553,-!p5@Mllt11!0.91!8.56!Mllt11;;chrX:137083127..137083138,-!p9@Tsc22d3!0.91!7.18!Tsc22d3;;chr3:95032558..95032641,-!p2@Mllt11!0.90!40.95!Mllt11;;chr11:96685444..96685473,-!p5@Nfe2l1!0.90!7.03!Nfe2l1;;chr7:91558472..91558512,-!p2@Arnt2!0.89!9.93!Arnt2;;chr15:82742573..82742620,-!p2@Tcf20!0.89!6.72!Tcf20;;chr3:101814061..101814094,+!p1@Nhlh2!0.88!6.57!Nhlh2;;chr2:163030186..163030204,+!p4@Tox2!0.88!6.57!Tox2;;chr11:90252223..90252240,-!p1@Hlf!0.87!55.92!Hlf;;chr11:116196664..116196679,-!p1@Foxj1!0.87!10.24!Foxj1;;chr2:38206744..38206766,+!p1@Lhx2!0.87!7.79!Lhx2;;chr7:52960663..52960677,+!p6@Dbp!0.87!6.42!Dbp;;chr15:103170533..103170556,-!p1@Zfp385a!0.86!24.29!Zfp385a;;chr10:84218895..84218909,+!p1@Rfx4!0.86!6.26!Rfx4;;chr8:12395603..12395621,+!p1@Sox1!0.86!6.26!Sox1;;chr2:25562263..25562314,+!p2@Bmyc!0.85!25.21!Bmyc;;chr2:163030164..163030178,+!p6@Tox2!0.85!6.11!Tox2;;chr5:122499831..122499891,-!p1@Cux2!0.84!9.32!Cux2;;chr10:67375342..67375365,-!p3@Zfp365!0.84!5.96!Zfp365;;chr3:34548946..34548972,+!p2@Sox2!0.83!6.42!Sox2;;chr8:87297878..87297935,-!p3@Nfix!0.82!12.99!Nfix;;chr2:127347094..127347111,-!p2@Kcnip3!0.82!9.63!Kcnip3;;chr19:10315179..10315241,-!p1@Gm98!0.81!60.97!Gm98;;chr1:189821714..189821761,+!p1@Esrrg!0.81!10.70!Esrrg;;chr2:162769220..162769252,+!p1@L3mbtl1!0.81!5.50!L3mbtl1;;chr8:12395892..12395919,+!p4@Sox1!0.81!5.50!Sox1;;chr14:76903992..76904056,+!p6@Tsc22d1!0.80!11.46!Tsc22d1;;chr2:168427120..168427138,-!p4@Nfatc2!0.80!5.35!Nfatc2;;chr2:127347042..127347058,-!p3@Kcnip3!0.80!5.35!Kcnip3;;chr14:19071466..19071550,-!p1@Nr1d2!0.79!38.05!Nr1d2;;chr2:65768174..65768247,+!p2@Csrnp3!0.79!5.20!Csrnp3;;chr4:22415443..22415506,-!p1@Pou3f2!0.79!5.20!Pou3f2;;chr3:128902837..128902861,+!p3@Pitx2!0.79!5.20!Pitx2;;chr5:140019843..140019858,+!p2@Uncx!0.79!5.20!Uncx;;chr7:6683123..6683142,-!p1@Peg3!0.78!288.02!Peg3;;chr7:30092993..30093076,+!p1@Dpf1!0.78!9.17!Dpf1;;chr14:118636214..118636235,-!p1@Sox21!0.78!6.11!Sox21;;chr6:145813964..145813994,-!p3@Bhlhe41!0.77!6.42!Bhlhe41;;chr4:129118044..129118067,-!p1@Zbtb8b!0.77!6.26!Zbtb8b;;chr15:103164702..103164778,-!p3@Zfp385a!0.77!5.96!Zfp385a;;chr2:181501745..181501778,+!p1@Myt1!0.77!4.89!Myt1;;chr9:40682064..40682081,+!p1@Bsx!0.77!4.89!Bsx;;chr11:90250944..90250982,-!p2@Hlf!0.76!8.40!Hlf;;chr13:44936126..44936164,+!p6@Jarid2!0.76!5.65!Jarid2;;chr2:181501710..181501742,+!p2@Myt1!0.76!4.74!Myt1;;chr7:17062114..17062141,-!p1@Npas1!0.76!4.74!Npas1;;chr15:95485240..95485257,-!p1@Dbx2!0.75!4.58!Dbx2;;chr2:163028808..163028869,+!p1@Tox2!0.74!17.57!Tox2;;chr2:25562315..25562344,+!p3@Bmyc!0.74!16.35!Bmyc;;chr19:26681865..26681900,+!p6@Smarca2!0.74!14.21!Smarca2;;chr1:170361991..170362015,-!p6@Pbx1!0.74!10.85!Pbx1;;chr2:56967334..56967366,-!p1@Nr4a2!0.74!9.78!Nr4a2;;chr11:98603185..98603208,+!p1@Thra!0.73!295.66!Thra;;chr11:98603119..98603130,+!p2@Thra!0.73!41.87!Thra;;chr15:103170516..103170531,-!p2@Zfp385a!0.73!11.31!Zfp385a;;chr4:48058129..48058179,+!p2@Nr4a3!0.73!8.86!Nr4a3;;chr7:52960730..52960762,+!p3@Dbp!0.73!5.65!Dbp;;chr12:86939997..86940040,+!p4@Jdp2!0.73!4.43!Jdp2;;chr14:49287186..49287225,-!p1@Otx2!0.73!4.43!Otx2;;chr2:71367871..71367898,+!p1@Dlx1!0.73!4.43!Dlx1;;chr11:98603160..98603171,+!p3@Thra!0.72!22.31!Thra;;chr7:130644017..130644092,-!p1@Zkscan2!0.72!8.86!Zkscan2;;chr3:54559463..54559493,+!p3@Smad9!0.72!8.25!Smad9;;chr5:28492230..28492257,+!p1@En2!0.72!4.28!En2;;chrX:70656436..70656464,+!p1@Zfp92!0.72!4.28!Zfp92;;chr7:38554763..38554780,-!p1@Zfp536!0.71!7.95!Zfp536;;chr5:125342568..125342602,+!p2@Zfp664!0.71!7.18!Zfp664;;chr17:48015645..48015689,-!p9@Foxp4!0.70!5.35!Foxp4;;chr1:122498955..122498968,+!p1@En1!0.70!3.97!En1;;chr11:90252108..90252134,-!p6@Hlf!0.70!3.97!Hlf;;chr13:95645580..95645598,+!p1@Otp!0.70!3.97!Otp;;chrX:137077151..137077227,-!p2@Tsc22d3!0.69!31.02!Tsc22d3;;chr13:72766279..72766296,+!p2@Irx2!0.69!6.11!Irx2;;chr7:91558537..91558558,-!p4@Arnt2!0.69!4.89!Arnt2;;chr7:17200307..17200370,-!p2@Grlf1!0.68!31.48!Grlf1;;chr6:117813087..117813121,+!p1@Zfp239!0.68!16.04!Zfp239;;chr5:120881900..120881914,+!p1@Lhx5!0.68!3.82!Lhx5;;chr10:5636354..5636373,-!p2@Esr1!0.68!3.82!Esr1;;chr11:98190955..98190968,-!p2@Neurod2!0.68!3.82!Neurod2;;chr15:81633165..81633188,+!p2@Tef!0.67!34.53!Tef;;chr8:112603610..112603656,+!p1@Zfp612!0.67!19.10!Zfp612;;chr14:52935860..52935874,-!p3@Sall2!0.67!5.65!Sall2;;chr4:124334894..124334899,+!p1@Pou3f1!0.67!5.04!Pou3f1;;chr9:69608672..69608686,-!p1@Foxb1!0.67!3.67!Foxb1;;chr9:69608731..69608742,-!p2@Foxb1!0.67!3.67!Foxb1;;chr8:12395874..12395885,+!p2@Sox1!0.67!3.67!Sox1;;chr1:179374784..179374800,+!p2@Zfp238!0.66!4.28!Zfp238;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.65!41.87!Camta2;;chr8:125897750..125897758,+!p2@Tcf25!0.65!27.05!Tcf25;;chr8:79423144..79423178,+!p3@Nr3c2!0.65!5.04!Nr3c2;;chr10:5636374..5636421,-!p1@Esr1!0.65!4.58!Esr1;;chr12:30220074..30220102,+!p3@Myt1l!0.65!3.51!Myt1l;;chr18:66098702..66098742,-!p1@Rax!0.65!3.51!Rax;;chr17:27693525..27693538,+!p5@Hmga1!0.64!12.99!Hmga1;;chr19:19185697..19185711,-!p2@Rorb!0.64!4.43!Rorb;;chr8:79423672..79423727,+!p2@Nr3c2!0.64!4.43!Nr3c2;;chr8:107793737..107793757,+!p2@Hsf4!0.64!3.97!Hsf4;;chr11:96685487..96685512,-!p7@Nfe2l1!0.64!3.36!Nfe2l1;;chr4:149862477..149862553,+!p3@Rere!0.63!13.45!Rere;;chr16:43503493..43503570,+!p9@Zbtb20!0.63!5.96!Zbtb20;;chr15:103170561..103170572,-!p4@Zfp385a!0.63!5.04!Zfp385a;;chr13:72101161..72101177,-!p2@Irx1!0.63!4.74!Irx1;;chr12:72149359..72149406,+!p4@Arid4a!0.63!4.58!Arid4a;;chr14:52935876..52935928,-!p1@Sall2!0.62!30.56!Sall2;;chr8:72356532..72356611,+!p1@Pbx4!0.62!15.13!Pbx4;;chrX:108009734..108009752,+!p2@Pou3f4!0.62!3.21!Pou3f4;;chr14:122874593..122874610,+!p2@Zic2!0.62!3.21!Zic2;;chr1:122499088..122499099,+!p2@En1!0.62!3.21!En1;;chr3:17954392..17954407,+!p2@Bhlhe22!0.62!3.21!Bhlhe22;;chr2:81893535..81893548,+!p1@Zfp804a!0.62!3.21!Zfp804a;;chr3:34549096..34549111,+!p3@Sox2!0.62!3.21!Sox2;;chr4:22415290..22415307,-!p2@Pou3f2!0.62!3.21!Pou3f2;;chr2:71384802..71384815,-!p1@Dlx2!0.61!3.97!Dlx2;;chr7:38558574..38558611,-!p2@Zfp536!0.61!3.97!Zfp536;;chr10:67375223..67375240,-!p4@Zfp365!0.61!3.51!Zfp365;;chr11:21901608..21901634,-!p1@Otx1!0.61!3.06!Otx1;;chr11:90252071..90252093,-!p7@Hlf!0.61!3.06!Hlf;;chr7:91520922..91520956,-!p5@Arnt2!0.61!3.06!Arnt2;;chr6:85463580..85463585,-!p1@Egr4!0.61!3.06!Egr4;;chr19:5424822..5424845,-!p3@Drap1!0.60!13.90!Drap1;;chr13:78338076..78338104,-!p4@Nr2f1!0.60!3.97!Nr2f1;;chr11:6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+|ffid_belonging_in_development=CL:0000133,CL:0000337,CL:0000031,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000208
 |is_obsolete=
+|library_id=CNhs12643
+|library_id_phase_based=2:CNhs12643
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11770
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11770
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor6.CNhs12643.11770-123I6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor6.CNhs12643.11770-123I6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor6.CNhs12643.11770-123I6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor6.CNhs12643.11770-123I6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520substantia%2520nigra%252c%2520donor6.CNhs12643.11770-123I6.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - substantia nigra, donor6
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12643,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0401463245787502,0,0,0,0,0,0.291404129280772,0,0,0,0,-0.0843392403965415,0,0,0,0,0.0308766538450896,0,0.0152542130952958,0,0,0,0,0,0.163875090269313,0,0,0,0,0,0,0.43895936184778,-0.394547702054718,0,0,0,0,0.0617533076901792,-0.0454476352265129,0.141134285969146,0.1041311737115,0.525308905420485,0.591350729925745,0.402774059390807,0,0,0,0,0,0,0,0,0,0,0.0617533076901792,-0.0660055475634404,0,0,0,0,-0.025895724905227,0,0.0735898329307735,0,0,0,-0.0286086612182423,-0.310650657339386,0.481550952963431,-0.0135678466607162,0,0,0.118143374211076,0.165176007583219,0.163875090269313,0,0.120990082487726,0.192133439670186,0.355690170635487,-0.0170782871497282,0,0,0,0,0,0,0.207585939426407,0.131216697174555,0.179991823420822,0,0.0617533076901792,0.428261292319165,0.430330893890267,0
 |rna_box=123
 |rna_catalog_number=custom
@@ Line 60: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 80: / Line 97: @@
 |top_motifs=REST:2.72995994701;ZBTB6:2.72328419067;MTF1:2.6944485555;HAND1,2:2.17988972289;OCT4_SOX2{dimer}:2.15497278077;ZFP161:2.0746371218;PAX5:2.07276465092;MYFfamily:2.0537101963;EGR1..3:2.02821693656;KLF4:1.98902224135;LMO2:1.98002097474;ZIC1..3:1.93750145384;FOXD3:1.9318729483;TFAP2B:1.92707956663;NHLH1,2:1.89788510145;ATF2:1.88533844606;BREu{core}:1.83408375499;HIC1:1.8184567119;CUX2:1.79270848982;POU6F1:1.78937845492;MED-1{core}:1.78521382589;NFIL3:1.73747225502;FOXM1:1.69754387668;PAX4:1.67004723949;RFX1:1.6420519687;UFEwm:1.5933856444;PRRX1,2:1.55828628904;MAFB:1.45871941151;AHR_ARNT_ARNT2:1.44685777762;EVI1:1.4382630428;MTE{core}:1.42330519702;POU3F1..4:1.32492806082;NKX2-2,8:1.31770499406;PAX6:1.31398072551;ADNP_IRX_SIX_ZHX:1.20902503815;SMAD1..7,9:1.20746535222;TGIF1:1.19804104424;GTF2I:1.19154275431;VSX1,2:1.18152613104;JUN:1.18112078562;PRDM1:1.18043211308;DBP:1.17486074266;PBX1:1.16384607408;HBP1_HMGB_SSRP1_UBTF:1.15572001273;ZNF423:1.1519528065;GFI1B:1.14747098274;TFDP1:1.13592294267;RFX2..5_RFXANK_RFXAP:1.08996646788;ALX1:1.08648315168;HMGA1,2:1.06067104494;CREB1:1.06063758684;NRF1:1.05837452446;RBPJ:1.04282837435;TFAP2{A,C}:1.0378280276;ATF5_CREB3:1.02083793877;SREBF1,2:1.01228541051;IKZF1:1.01060811935;FOXN1:1.00911497081;PATZ1:0.984832092273;RREB1:0.974352631346;STAT1,3:0.954193389424;GATA4:0.938792622826;MYOD1:0.887027508341;ONECUT1,2:0.885854877612;MZF1:0.876821704892;ZEB1:0.839336499005;MAZ:0.82750857233;HOXA9_MEIS1:0.827043822172;PAX8:0.809994479496;FOX{I1,J2}:0.795590193238;LHX3,4:0.794719363142;NANOG:0.781322840634;GTF2A1,2:0.75984809042;ZNF143:0.756698105151;GZF1:0.756008766818;ARID5B:0.748933787211;HSF1,2:0.734609894229;NKX3-2:0.718989907939;CDC5L:0.707922879766;FOXP3:0.677511127618;SOX2:0.670620437032;PAX2:0.651684443649;HES1:0.643145355983;NFE2L2:0.578773662892;NFE2L1:0.524300270325;NKX6-1,2:0.521075459159;POU5F1:0.49056574372;POU1F1:0.479329671224;YY1:0.442482315113;RORA:0.430636185762;GCM1,2:0.413812482951;SOX{8,9,10}:0.40744173835;GLI1..3:0.372589770604;NR5A1,2:0.36279740663;FOXQ1:0.347069158158;ZNF384:0.321813804935;TEF:0.315914997231;SOX5:0.281558296324;TFAP4:0.277407429042;SP1:0.266030065655;FOX{F1,F2,J1}:0.234273401953;EBF1:0.201701473271;AIRE:0.170272233957;NFE2:0.16936646752;ESRRA:0.149353178471;SPZ1:0.140611055763;MYBL2:0.13989359478;HMX1:0.117488694377;CDX1,2,4:0.0888180333813;PAX1,9:0.0875302344293;ATF4:0.0742860843536;SOX17:0.0523034784133;LEF1_TCF7_TCF7L1,2:0.0393121710219;NR3C1:0.0199761277261;ZNF148:0.00571607936596;T:0.000947388874438;TAL1_TCF{3,4,12}:-0.0519817304704;ATF6:-0.0550609871518;NKX2-3_NKX2-5:-0.0637876232682;PPARG:-0.0879768465041;XCPE1{core}:-0.145774655587;RXR{A,B,G}:-0.156806149219;FOXP1:-0.158823795497;TLX1..3_NFIC{dimer}:-0.163456949753;BPTF:-0.197606670022;TFCP2:-0.203622530782;NFATC1..3:-0.2416693483;EN1,2:-0.252281495183;NKX3-1:-0.268406879496;NKX2-1,4:-0.288698432737;FOXA2:-0.293818425272;AR:-0.301560475845;SNAI1..3:-0.332267303866;bHLH_family:-0.335996899573;HOX{A4,D4}:-0.346304303105;ZBTB16:-0.346580453902;CRX:-0.366758691632;TOPORS:-0.407285661293;HIF1A:-0.409489023245;IRF7:-0.439025048542;TBX4,5:-0.445912570446;EP300:-0.476696155379;HOX{A5,B5}:-0.500982446169;MEF2{A,B,C,D}:-0.50281582151;IKZF2:-0.541824235652;FOSL2:-0.568896107688;FOXO1,3,4:-0.603865024047;ESR1:-0.605647354402;STAT2,4,6:-0.622188823179;PDX1:-0.642459227457;HLF:-0.644630866829;NR1H4:-0.64889220473;MYB:-0.659464177856;ZNF238:-0.684870687888;ELK1,4_GABP{A,B1}:-0.725524401182;NFY{A,B,C}:-0.773807446362;CEBPA,B_DDIT3:-0.779576229517;HNF4A_NR2F1,2:-0.7803186892;FOX{D1,D2}:-0.801824541714;BACH2:-0.804130930573;POU2F1..3:-0.814935715848;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.860192452449;SPI1:-0.882939508996;HNF1A:-0.888597735472;TEAD1:-0.90452335231;GATA6:-0.907710431904;RUNX1..3:-0.924679847491;IRF1,2:-0.939942284759;FOXL1:-0.959223791141;FOS_FOS{B,L1}_JUN{B,D}:-1.01991993625;NR6A1:-1.04809566519;RXRA_VDR{dimer}:-1.12974531219;TP53:-1.17328978537;NFKB1_REL_RELA:-1.218659505;ETS1,2:-1.26503613002;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.28260878481;DMAP1_NCOR{1,2}_SMARC:-1.28797092037;TBP:-1.30967478837;ELF1,2,4:-1.3937463628;SPIB:-1.41462884364;ALX4:-1.53581034488;TLX2:-1.54467290088;GFI1:-1.64162176749;PITX1..3:-1.67777688256;E2F1..5:-1.68316280936;NANOG{mouse}:-1.69116298058;NFIX:-1.72196269328;STAT5{A,B}:-1.81450939937;SRF:-1.81563336477
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11770-123I6;search_select_hide=table117:11770-123I6
 }}

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FF:11770-123I6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:19, 4 June 2020

CNhs12643

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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