FF:11644-122D6: Difference between revisions

Latest revision as of 18:13, 4 June 2020

Name:	Mouse Neurons - hippocampal, donor3
Species:	Mouse (Mus musculus)
Library ID:	CNhs12110
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	hippocampus
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	RNAMNh3
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		SAMD00005482

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12110		CAGE		DRX008839		DRR009711

Accession ID Mm9

Library id		BAM		CTSS
CNhs12110		DRZ001136		DRZ002521

Accession ID Mm10

Library id		BAM		CTSS
CNhs12110		DRZ012486		DRZ013871

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

CNhs12110

0	0
1	0.277
10	0
100	0.575
1000	-0.0355
1001	-0.0749
1002	0.511
1003	0.191
1004	0
1005	-0.384
1006	0.064
1007	-0.0794
1008	0
1009	-0.2
101	-0.128
1010	0
1011	0.176
1012	0
1013	-0.217
1014	-0.0851
1015	0.396
1016	0.311
1017	0
1018	0
1019	0
102	0
1020	0.922
1021	0.283
1022	-0.124
1023	0
1024	-0.277
1025	-0.0611
1026	0
1027	0.392
1028	0
1029	-0.148
103	-0.0861
1030	0
1031	-0.458
1032	-0.177
1033	0
1034	0
1035	0
1036	-0.0378
1037	0
1038	0.111
1039	-0.338
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: CNhs12110

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0275
MA0003.1	MA0003.1	0.136
MA0004.1	MA0004.1	0.87
MA0006.1	MA0006.1	0.0675
MA0007.1	MA0007.1	0.283
MA0009.1	MA0009.1	0.841
MA0014.1	MA0014.1	0.387
MA0017.1	MA0017.1	5.25118e-5
MA0018.2	MA0018.2	0.0328
MA0019.1	MA0019.1	0.0977
MA0024.1	MA0024.1	0.0834
MA0025.1	MA0025.1	0.272
MA0027.1	MA0027.1	0.797
MA0028.1	MA0028.1	0.67
MA0029.1	MA0029.1	0.91
MA0030.1	MA0030.1	0.054
MA0031.1	MA0031.1	0.0191
MA0035.2	MA0035.2	0.221
MA0038.1	MA0038.1	0.15
MA0039.2	MA0039.2	0.00334
MA0040.1	MA0040.1	0.887
MA0041.1	MA0041.1	0.206
MA0042.1	MA0042.1	0.507
MA0043.1	MA0043.1	0.0735
MA0046.1	MA0046.1	6.09893e-9
MA0047.2	MA0047.2	5.81977e-4
MA0048.1	MA0048.1	0.63
MA0050.1	MA0050.1	1.65737e-10
MA0051.1	MA0051.1	8.18298e-5
MA0052.1	MA0052.1	0.0261
MA0055.1	MA0055.1	0.768
MA0057.1	MA0057.1	0.0774
MA0058.1	MA0058.1	0.762
MA0059.1	MA0059.1	0.954
MA0060.1	MA0060.1	6.24941e-6
MA0061.1	MA0061.1	0.0331
MA0062.2	MA0062.2	0.23
MA0065.2	MA0065.2	1.40217e-4
MA0066.1	MA0066.1	0.387
MA0067.1	MA0067.1	0.879
MA0068.1	MA0068.1	0.375
MA0069.1	MA0069.1	0.119
MA0070.1	MA0070.1	0.446
MA0071.1	MA0071.1	0.539
MA0072.1	MA0072.1	0.234
MA0073.1	MA0073.1	0.813
MA0074.1	MA0074.1	0.768
MA0076.1	MA0076.1	0.645
MA0077.1	MA0077.1	4.06695e-5
MA0078.1	MA0078.1	6.0696e-4
MA0079.2	MA0079.2	0.542
MA0080.2	MA0080.2	1.72666e-10
MA0081.1	MA0081.1	0.347
MA0083.1	MA0083.1	3.89726e-5
MA0084.1	MA0084.1	0.634
MA0087.1	MA0087.1	0.623
MA0088.1	MA0088.1	0.303
MA0090.1	MA0090.1	0.00575
MA0091.1	MA0091.1	0.82
MA0092.1	MA0092.1	0.302
MA0093.1	MA0093.1	0.823
MA0099.2	MA0099.2	8.12468e-5
MA0100.1	MA0100.1	0.605
MA0101.1	MA0101.1	0.0396
MA0102.2	MA0102.2	0.339
MA0103.1	MA0103.1	0.163
MA0104.2	MA0104.2	0.234
MA0105.1	MA0105.1	0.0983
MA0106.1	MA0106.1	0.108
MA0107.1	MA0107.1	0.0232
MA0108.2	MA0108.2	0.00799
MA0111.1	MA0111.1	0.981
MA0112.2	MA0112.2	7.50073e-4
MA0113.1	MA0113.1	0.42
MA0114.1	MA0114.1	9.00665e-5
MA0115.1	MA0115.1	0.0652
MA0116.1	MA0116.1	0.238
MA0117.1	MA0117.1	0.623
MA0119.1	MA0119.1	0.136
MA0122.1	MA0122.1	0.682
MA0124.1	MA0124.1	0.879
MA0125.1	MA0125.1	0.287
MA0131.1	MA0131.1	0.948
MA0135.1	MA0135.1	0.34
MA0136.1	MA0136.1	1.61246e-8
MA0137.2	MA0137.2	0.0216
MA0138.2	MA0138.2	0.227
MA0139.1	MA0139.1	0.38
MA0140.1	MA0140.1	0.0212
MA0141.1	MA0141.1	0.0619
MA0142.1	MA0142.1	1.7405e-4
MA0143.1	MA0143.1	2.0373e-4
MA0144.1	MA0144.1	0.0165
MA0145.1	MA0145.1	0.0282
MA0146.1	MA0146.1	0.0816
MA0147.1	MA0147.1	0.258
MA0148.1	MA0148.1	6.17297e-6
MA0149.1	MA0149.1	0.163
MA0150.1	MA0150.1	0.0678
MA0152.1	MA0152.1	0.411
MA0153.1	MA0153.1	2.66988e-8
MA0154.1	MA0154.1	0.0241
MA0155.1	MA0155.1	0.596
MA0156.1	MA0156.1	7.80708e-7
MA0157.1	MA0157.1	0.0298
MA0159.1	MA0159.1	0.0132
MA0160.1	MA0160.1	0.138
MA0162.1	MA0162.1	0.394
MA0163.1	MA0163.1	0.018
MA0164.1	MA0164.1	0.911
MA0258.1	MA0258.1	0.0261
MA0259.1	MA0259.1	0.264

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: CNhs12110

Novel motif	Logo	P-value
1	1	0.275
10	10	0.147
100	100	0.948
101	101	0.918
102	102	0.963
103	103	0.29
104	104	0.979
105	105	0.136
106	106	0.00435
107	107	0.0208
108	108	0.509
109	109	0.00409
11	11	0.186
110	110	0.176
111	111	0.0462
112	112	0.00166
113	113	0.795
114	114	0.541
115	115	0.153
116	116	0.635
117	117	0.114
118	118	0.467
119	119	0.269
12	12	0.48
120	120	0.848
121	121	0.188
122	122	0.39
123	123	0.343
124	124	0.158
125	125	0.185
126	126	0.0931
127	127	0.127
128	128	0.0306
129	129	0.238
13	13	2.64717e-6
130	130	0.972
131	131	0.517
132	132	0.813
133	133	0.227
134	134	0.316
135	135	0.277
136	136	0.0297
137	137	0.183
138	138	0.486
139	139	0.366
14	14	0.589
140	140	0.998
141	141	0.418
142	142	0.0669
143	143	0.743
144	144	0.835
145	145	0.0699
146	146	0.313
147	147	0.799
148	148	0.478
149	149	0.143
15	15	0.217
150	150	0.172
151	151	0.456
152	152	0.0323
153	153	0.903
154	154	0.979
155	155	0.508
156	156	0.0451
157	157	0.011
158	158	0.545
159	159	0.0801
160	160	0.251
161	161	0.357
162	162	0.975
163	163	0.162
164	164	0.0513
165	165	0.0216
166	166	0.624
167	167	0.672
168	168	0.815
169	169	0.0102
17	17	0.0192
18	18	0.52
19	19	0.0522
2	2	0.536
20	20	0.827
21	21	0.704
22	22	0.0553
23	23	0.285
24	24	0.0522
25	25	0.822
26	26	5.14923e-4
27	27	0.778
28	28	0.345
29	29	0.296
3	3	0.131
30	30	0.45
31	31	0.762
32	32	0.57
33	33	0.276
34	34	0.584
35	35	0.177
36	36	0.971
37	37	0.00809
38	38	0.666
39	39	0.125
4	4	0.742
40	40	0.425
41	41	0.707
42	42	0.521
43	43	0.185
44	44	0.907
45	45	0.37
46	46	0.205
47	47	0.313
48	48	0.231
49	49	0.272
5	5	0.217
50	50	0.158
51	51	0.62
52	52	0.0451
53	53	0.52
54	54	0.674
55	55	0.595
56	56	0.3
57	57	0.864
58	58	0.304
59	59	0.0748
6	6	0.67
60	60	0.00556
61	61	0.532
62	62	0.171
63	63	0.161
64	64	0.573
65	65	0.712
66	66	0.56
67	67	0.743
68	68	0.588
69	69	0.624
7	7	0.0242
70	70	0.0717
71	71	0.0227
72	72	0.383
73	73	0.0116
74	74	0.534
75	75	0.0953
76	76	0.957
77	77	0.167
78	78	0.0304
79	79	0.71
8	8	0.461
80	80	0.79
81	81	0.339
82	82	0.0567
83	83	0.129
84	84	0.452
85	85	0.0465
86	86	0.293
87	87	0.174
88	88	0.27
89	89	0.301
9	9	0.434
90	90	0.416
91	91	0.428
92	92	0.201
93	93	0.134
94	94	0.819
95	95	0.0847
96	96	0.796
97	97	0.965
98	98	0.967
99	99	0.227

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: CNhs12110

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000202 mouse hippocampal neuron 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)
0002609 (neuron of cerebral cortex)
0002608 (hippocampal neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0001954 (Ammon's horn)
0000956 (cerebral cortex)
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)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0003022 (lobe parts of cerebral cortex)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000201 (hippocampal neuron sample)
0000203 (mouse neuron samples)
0000202 (mouse hippocampal neuron 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@SAMD00005482
+|accession_numbers=CAGE;DRX008839;DRR009711;DRZ001136;DRZ002521;DRZ012486;DRZ013871
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0001954,UBERON:0000956,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:0002619,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0003022,UBERON:0010317,UBERON:0001017,UBERON:0002421,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0000349,UBERON:0002600
 |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:0002609,CL:0002608
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chrX:90531838..90531861,+!p1@Arx!2.54!431.11!Arx;;chr2:71384802..71384815,-!p1@Dlx2!2.38!288.63!Dlx2;;chr11:98190918..98190951,-!p1@Neurod2!2.30!199.47!Neurod2;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!2.29!241.75!Pou3f3;;chr6:55631042..55631102,-!p1@Neurod6!2.16!143.40!Neurod6;;chr12:28027561..28027591,-!p1@Sox11!2.04!665.51!Sox11;;chr2:61642631..61642684,+!p1@Tbr1!2.02!104.79!Tbr1;;chr8:12395603..12395621,+!p1@Sox1!1.91!80.89!Sox1;;chr10:86956396..86956411,-!p1@Ascl1!1.87!110.31!Ascl1;;chr2:146047829..146047847,+!p1@Insm1!1.84!120.42!Insm1;;chr1:179374784..179374800,+!p2@Zfp238!1.83!78.13!Zfp238;;chr2:73109983..73109996,+!p1@Sp9!1.83!67.10!Sp9;;chrX:108009761..108009788,+!p1@Pou3f4!1.83!66.18!Pou3f4;;chr2:71367871..71367898,+!p1@Dlx1!1.82!65.26!Dlx1;;chr3:34548909..34548927,+!p1@Sox2!1.77!96.52!Sox2;;chr2:71367142..71367167,+!p2@Dlx1!1.72!51.48!Dlx1;;chr7:30088977..30089002,+!p2@Dpf1!1.69!66.18!Dpf1;;chr6:6832076..6832092,-!p1@Dlx5!1.67!53.31!Dlx5;;chr12:30213247..30213333,+!p1@Myt1l!1.66!45.04!Myt1l;;chr2:71366660..71366702,+!p3@Dlx1!1.61!39.53!Dlx1;;chr3:95032091..95032183,-!p1@Mllt11!1.60!312.53!Mllt11;;chr2:71384458..71384526,-!p2@Dlx2!1.60!38.61!Dlx2;;chr4:154335024..154335039,+!p1@Hes5!1.59!45.96!Hes5;;chr15:76352832..76352900,-!p1@Scrt1!1.57!35.85!Scrt1;;chr5:98609885..98609900,+!p1@Prdm8!1.57!35.85!Prdm8;;chr12:109242266..109242295,-!p1@Bcl11b!1.56!279.44!Bcl11b;;chr2:61642743..61642758,+!p2@Tbr1!1.52!32.17!Tbr1;;chr12:50483639..50483654,+!p1@Foxg1!1.50!30.33!Foxg1;;chr2:38206580..38206600,+!p2@Lhx2!1.47!34.93!Lhx2;;chr16:91225808..91225824,+!p1@Olig2!1.47!28.50!Olig2;;chr2:115891534..115891589,-!p1@Meis2!1.46!375.96!Meis2;;chr13:117099847..117099907,-!p1@Isl1!1.46!50.56!Isl1;;chr7:116154364..116154444,+!p1@Tub!1.46!46.88!Tub;;chr9:118387300..118387317,+!p1@Eomes!1.46!27.58!Eomes;;chrX:58146612..58146615,-!p1@Sox3!1.44!26.66!Sox3;;chr7:91558472..91558512,-!p2@Arnt2!1.43!36.77!Arnt2;;chr2:73110004..73110016,+!p2@Sp9!1.43!25.74!Sp9;;chr17:25707623..25707639,-!p1@Sox8!1.42!104.79!Sox8;;chr2:38206744..38206766,+!p1@Lhx2!1.42!30.33!Lhx2;;chr2:61642558..61642595,+!p3@Tbr1!1.41!24.82!Tbr1;;chr3:127336052..127336058,+!p1@Neurog2!1.41!24.82!Neurog2;;chr7:25292160..25292213,+!p3@Zfp428!1.40!58.83!Zfp428;;chr7:30092993..30093076,+!p1@Dpf1!1.39!39.53!Dpf1;;chr16:91270004..91270023,+!p1@Olig1!1.39!26.66!Olig1;;chr17:86020156..86020183,+!p1@Six3!1.38!22.98!Six3;;chr2:115890953..115890974,-!p6@Meis2!1.36!33.09!Meis2;;chr4:124334894..124334899,+!p1@Pou3f1!1.36!28.50!Pou3f1;;chr4:150503457..150503498,-!p3@Camta1!1.35!23.90!Camta1;;chr4:22415443..22415506,-!p1@Pou3f2!1.35!21.14!Pou3f2;;chr6:6831950..6831985,-!p2@Dlx5!1.34!22.98!Dlx5;;chr2:151907546..151907561,+!p1@Scrt2!1.33!20.22!Scrt2;;chr1:57028125..57028149,-!p2@Satb2!1.31!19.30!Satb2;;chr15:76352740..76352781,-!p5@Scrt1!1.29!18.38!Scrt1;;chr17:37140628..37140631,+!p2@Zfp57!1.28!35.85!Zfp57;;chr17:86020115..86020128,+!p2@Six3!1.27!17.47!Six3;;chr7:25292141..25292158,+!p2@Zfp428!1.26!58.83!Zfp428;;chr17:48015839..48015915,-!p3@Foxp4!1.26!20.22!Foxp4;;chr2:79296783..79296801,-!p1@Neurod1!1.24!16.55!Neurod1;;chr12:109241728..109241781,-!p2@Bcl11b!1.22!16.55!Bcl11b;;chr2:71368786..71368813,+!p5@Dlx1!1.22!15.63!Dlx1;;chr3:17954233..17954249,+!p1@Bhlhe22!1.22!15.63!Bhlhe22;;chr11:23978111..23978134,+!p3@Bcl11a!1.21!31.25!Bcl11a;;chr11:23978229..23978268,+!p8@Bcl11a!1.21!17.47!Bcl11a;;chr13:29045559..29045574,-!p1@Sox4!1.20!1188.55!Sox4;;chr17:86020510..86020589,+!p3@Six3!1.20!14.71!Six3;;chr11:98190955..98190968,-!p2@Neurod2!1.20!14.71!Neurod2;;chr1:57028606..57028625,-!p4@Satb2!1.20!14.71!Satb2;;chr12:54349410..54349461,+!p1@Npas3!1.19!17.47!Npas3;;chr11:23977742..23977794,+!p6@Bcl11a!1.18!17.47!Bcl11a;;chr1:169528457..169528482,+!p3@Rxrg!1.17!13.79!Rxrg;;chr2:71384401..71384424,-!p3@Dlx2!1.17!13.79!Dlx2;;chr6:6831928..6831949,-!p3@Dlx5!1.17!13.79!Dlx5;;chr7:25292331..25292421,+!p1@Zfp428!1.14!91.00!Zfp428;;chr11:23980664..23980706,+!p2@Bcl11a!1.14!55.15!Bcl11a;;chr13:78339428..78339466,-!p2@Nr2f1!1.14!17.47!Nr2f1;;chr9:91260594..91260612,-!p1@Zic1!1.14!12.87!Zic1;;chr8:12395500..12395511,+!p5@Sox1!1.14!12.87!Sox1;;chr2:35959541..35959548,-!p2@Lhx6!1.14!12.87!Lhx6;;chr1:57028157..57028173,-!p3@Satb2!1.14!12.87!Satb2;;chr2:151906844..151906873,+!p3@Scrt2!1.14!12.87!Scrt2;;chr19:7342786..7342803,+!p2@Rcor2!1.13!16.55!Rcor2;;chr6:144157924..144157955,-!p2@Sox5!1.13!15.63!Sox5;;chr13:29045321..29045337,-!p2@Sox4!1.12!16.55!Sox4;;chr19:7342725..7342784,+!p1@Rcor2!1.11!48.72!Rcor2;;chr12:3891810..3891829,+!p2@Dnmt3a!1.11!18.38!Dnmt3a;;chr14:13178361..13178386,-!p2@Fezf2!1.11!11.95!Fezf2;;chr7:30089006..30089022,+!p3@Dpf1!1.11!11.95!Dpf1;;chr2:71368815..71368836,+!p4@Dlx1!1.11!11.95!Dlx1;;chr1:169528520..169528542,+!p2@Rxrg!1.11!11.95!Rxrg;;chr2:181501745..181501778,+!p1@Myt1!1.11!11.95!Myt1;;chr19:19185671..19185693,-!p1@Rorb!1.10!27.58!Rorb;;chr13:78339382..78339420,-!p3@Nr2f1!1.10!13.79!Nr2f1;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!1.09!30.33!Zfhx3;;chr2:65683890..65683907,+!p1@Csrnp3!1.08!21.14!Csrnp3;;chr15:76352677..76352737,-!p3@Scrt1!1.08!11.03!Scrt1;;chr8:12395629..12395644,+!p6@Sox1!1.08!11.03!Sox1;;chr2:71366574..71366587,+!p8@Dlx1!1.08!11.03!Dlx1;;chr2:71384541..71384555,-!p6@Dlx2!1.08!11.03!Dlx2;;chr4:122673278..122673336,+!p1@Mycl1!1.07!34.01!Mycl1;;chr2:56967334..56967366,-!p1@Nr4a2!1.07!22.06!Nr4a2;;chr7:91558392..91558434,-!p1@Arnt2!1.06!29.42!Arnt2;;chr6:38204274..38204327,-!p3@D630045J12Rik!1.06!21.14!D630045J12Rik;;chr13:78338076..78338104,-!p4@Nr2f1!1.05!12.87!Nr2f1;;chr12:30219426..30219506,+!p2@Myt1l!1.05!10.11!Myt1l;;chrX:108009734..108009752,+!p2@Pou3f4!1.05!10.11!Pou3f4;;chr2:71384425..71384456,-!p4@Dlx2!1.05!10.11!Dlx2;;chr5:75471615..75471622,+!p1@Gsx2!1.05!10.11!Gsx2;;chr1:179374820..179374831,+!p3@Zfp238!1.05!10.11!Zfp238;;chr1:179374764..179374776,+!p5@Zfp238!1.05!10.11!Zfp238;;chr1:42752654..42752665,+!p@chr1:42752654..42752665,+!1.05!10.11!Pou3f3;;chr3:34548946..34548972,+!p2@Sox2!1.04!11.03!Sox2;;chr12:12948633..12948651,-!p1@Mycn!1.02!91.92!Mycn;;chr11:23978078..23978096,+!p4@Bcl11a!1.02!29.42!Bcl11a;;chr5:122499831..122499891,-!p1@Cux2!1.02!14.71!Cux2;;chr1:57029281..57029326,-!p1@Satb2!1.02!14.71!Satb2;;chr7:25292118..25292129,+!p8@Zfp428!1.01!11.03!Zfp428;;chr19:59244875..59244895,-!p2@Vax1!1.01!9.19!Vax1;;chr2:151907338..151907360,+!p2@Scrt2!1.01!9.19!Scrt2;;chr2:181501710..181501742,+!p2@Myt1!1.01!9.19!Myt1;;chr1:179374862..179374873,+!p6@Zfp238!1.01!9.19!Zfp238;;chr1:169528581..169528607,+!p7@Rxrg!1.01!9.19!Rxrg;;chr3:101814061..101814094,+!p1@Nhlh2!1.01!9.19!Nhlh2;;chr6:144152648..144152680,-!p5@Sox5!1.01!9.19!Sox5;;chr6:85137520..85137563,+!p1@Emx1!1.01!9.19!Emx1;;chr11:23978270..23978290,+!p9@Bcl11a!1.01!9.19!Bcl11a;;chr12:109242296..109242307,-!p3@Bcl11b!0.99!12.87!Bcl11b;;chr13:44936126..44936164,+!p6@Jarid2!0.99!10.11!Jarid2;;chr6:38204214..38204267,-!p4@D630045J12Rik!0.98!16.55!D630045J12Rik;;chr1:169528491..169528505,+!p4@Rxrg!0.97!8.27!Rxrg;;chr1:179372543..179372557,+!p9@Zfp238!0.97!8.27!Zfp238;;chr14:118636238..118636257,-!p2@Sox21!0.97!8.27!Sox21;;chr2:71384193..71384205,-!p5@Dlx2!0.97!8.27!Dlx2;;chr2:71367979..71367993,+!p7@Dlx1!0.97!8.27!Dlx1;;chr4:128483680..128483715,-!p3@Zfp362!0.94!29.42!Zfp362;;chr13:78339476..78339515,-!p1@Nr2f1!0.94!11.95!Nr2f1;;chr4:119960301..119960359,-!p1@Foxo6!0.93!24.82!Foxo6;;chr2:115891409..115891425,-!p2@Meis2!0.92!22.06!Meis2;;chr2:115891381..115891392,-!p5@Meis2!0.92!14.71!Meis2;;chr9:106356278..106356292,+!p3@Pcbp4!0.92!12.87!Pcbp4;;chr4:54957886..54957907,+!p3@Zfp462!0.92!12.87!Zfp462;;chr13:78339134..78339185,-!p5@Nr2f1!0.92!9.19!Nr2f1;;chr13:78338057..78338069,-!p11@Nr2f1!0.92!7.35!Nr2f1;;chr12:50485973..50486015,+!p2@Foxg1!0.92!7.35!Foxg1;;chr2:172375081..172375105,+!p1@Tfap2c!0.92!7.35!Tfap2c;;chr5:24104751..24104773,-!p5@Smarcd3!0.92!7.35!Smarcd3;;chr6:144158267..144158282,-!p16@Sox5!0.92!7.35!Sox5;;chr5:148000254..148000260,+!p1@Gsx1!0.92!7.35!Gsx1;;chr5:24104540..24104584,-!p7@Smarcd3!0.92!7.35!Smarcd3;;chr4:82145196..82145229,-!p7@Nfib!0.92!7.35!Nfib;;chr11:44431115..44431132,+!p9@Ebf1!0.92!7.35!Ebf1;;chr11:23978291..23978323,+!p7@Bcl11a!0.92!7.35!Bcl11a;;chr10:84218800..84218829,+!p2@Rfx4!0.92!7.35!Rfx4;;chr8:12395670..12395682,+!p3@Sox1!0.92!7.35!Sox1;;chr2:35960919..35960954,-!p1@Lhx6!0.91!13.79!Lhx6;;chr19:19185697..19185711,-!p2@Rorb!0.91!9.19!Rorb;;chr13:48356475..48356492,+!p1@Id4!0.90!159.02!Id4;;chr17:37139472..37139514,+!p1@Zfp57!0.90!48.72!Zfp57;;chr9:18278055..18278126,-!p1@Zfp558!0.89!20.22!Zfp558;;chr8:87297878..87297935,-!p3@Nfix!0.89!15.63!Nfix;;chr2:115891521..115891532,-!p8@Meis2!0.89!10.11!Meis2;;chr18:69753168..69753186,+!p12@Tcf4!0.89!9.19!Tcf4;;chr14:118636214..118636235,-!p1@Sox21!0.89!8.27!Sox21;;chr11:80196900..80196917,+!p3@Zfp207!0.88!22.98!Zfp207;;chr3:95032184..95032195,-!p4@Mllt11!0.88!8.27!Mllt11;;chr3:95032197..95032208,-!p3@Mllt11!0.88!8.27!Mllt11;;chr7:130644017..130644092,-!p1@Zkscan2!0.87!12.87!Zkscan2;;chr11:44431016..44431045,+!p5@Ebf1!0.87!9.19!Ebf1;;chr10:42303385..42303401,-!p1@Nr2e1!0.87!6.43!Nr2e1;;chr12:109241804..109241823,-!p5@Bcl11b!0.87!6.43!Bcl11b;;chr2:71366714..71366725,+!p12@Dlx1!0.87!6.43!Dlx1;;chr4:97248473..97248496,+!p16@Nfia!0.87!6.43!Nfia;;chr2:71367855..71367864,+!p6@Dlx1!0.87!6.43!Dlx1;;chr4:82145232..82145259,-!p9@Nfib!0.87!6.43!Nfib;;chr12:50483663..50483678,+!p3@Foxg1!0.87!6.43!Foxg1;;chr14:13178323..13178347,-!p3@Fezf2!0.87!6.43!Fezf2;;chr12:120085778..120085784,+!p2@Sp8!0.87!6.43!Sp8;;chr1:189821714..189821761,+!p1@Esrrg!0.86!11.95!Esrrg;;chr6:98978245..98978289,-!p1@Foxp1!0.85!96.52!Foxp1;;chr3:95032558..95032641,-!p2@Mllt11!0.85!35.85!Mllt11;;chr15:75447105..75447159,+!p1@Zfp41!0.85!25.74!Zfp41;;chr2:152223783..152223812,-!p4@Sox12!0.85!14.71!Sox12;;chr3:95032213..95032226,-!p6@Mllt11!0.85!7.35!Mllt11;;chr17:32525943..32525992,-!p4@Wiz!0.84!9.19!Wiz;;chr4:13670571..13670625,+!p1@Runx1t1!0.83!16.55!Runx1t1;;chr5:39075982..39076052,-!p1@Zfp518b!0.81!42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omes;;chr8:87297330..87297365,-!p5@Nfix!0.67!3.68!Nfix;;chrX:108009798..108009815,+!p3@Pou3f4!0.67!3.68!Pou3f4;;chr10:84218895..84218909,+!p1@Rfx4!0.67!3.68!Rfx4;;chr18:65742044..65742053,+!p11@Zfp532!0.67!3.68!Zfp532;;chr16:91270091..91270143,+!p2@Olig1!0.67!3.68!Olig1;;chr18:81183755..81183761,-!p1@Sall3!0.67!3.68!Sall3;;chr19:43686789..43686811,+!p1@Nkx2-3!0.67!3.68!Nkx2-3;;chr17:86020137..86020149,+!p5@Six3!0.67!3.68!Six3;;chr6:98978428..98978450,-!p15@Foxp1!0.67!3.68!Foxp1;;chr5:122345353..122345358,-!p5@Cux2!0.67!3.68!Cux2;;chr6:6813269..6813272,+!p2@Dlx6!0.67!3.68!Dlx6;;chr6:6812988..6813002,+!p3@Dlx6!0.67!3.68!Dlx6;;chr12:120085700..120085711,+!p1@Sp8!0.67!3.68!Sp8;;chr1:167865149..167865167,-!p3@Pou2f1!0.67!3.68!Pou2f1;;chr2:151906968..151906988,+!p5@Scrt2!0.67!3.68!Scrt2;;chr1:189821700..189821713,+!p4@Esrrg!0.67!3.68!Esrrg;;chr2:81893535..81893548,+!p1@Zfp804a!0.67!3.68!Zfp804a;;chr3:34548845..34548856,+!p4@Sox2!0.67!3.68!Sox2;;chr4:22415600..22415616,-!p3@Pou3f2!0.67!3.68!Pou3f2;;chr7:88005795..88005858,+!p1@Zscan2!0.66!29.42!Zscan2;;chr17:48061605..48061629,-!p6@Foxp4!0.66!16.55!Foxp4;;chr2:115891427..115891441,-!p4@Meis2!0.66!8.27!Meis2;;chr2:127347067..127347093,-!p1@Kcnip3!0.66!6.43!Kcnip3;;chr19:59533221..59533271,+!p1@Emx2!0.66!4.60!Emx2;;chr3:94641455..94641486,+!p4@Pogz!0.65!10.11!Pogz;;chr14:22807216..22807231,-!p3@Zfp503!0.65!6.43!Zfp503;;chr9:21420812..21420815,+!p6@Smarca4!0.65!5.52!Smarca4;;chr6:38204109..38204155,-!p1@D630045J12Rik!0.64!21.14!D630045J12Rik;;chr18:55149735..55149776,-!p4@Zfp608!0.64!9.19!Zfp608;;chr4:6917971..6918000,-!p3@Tox!0.64!7.35!Tox;;chr14:65568567..65568588,-!p3@Hmbox1!0.64!5.52!Hmbox1;;chr4:6918396..6918411,-!p4@Tox!0.64!4.60!Tox;;chr4:133310175..133310212,-!p5@Arid1a!0.63!11.95!Arid1a;;chr16:8672256..8672279,-!p1@Carhsp1,p1@Gm9791!0.63!8.27!Carhsp1;;chr13:29044875..29044928,-!p4@Sox4!0.63!4.60!Sox4;;chr2:164860270..164860320,-!p1@Ncoa5!0.62!75.38!Ncoa5;;chr19:5424822..5424845,-!p3@Drap1!0.62!14.71!Drap1;;chr6:47827547..47827568,+!p4@Zfp282!0.62!8.27!Zfp282;;chr1:38684383..38684394,-!p4@Aff3!0.62!4.60!Aff3;;chr4:149610794..149610876,+!p2@LOC100045967,p2@LOC100503183,p3@Eno1,p3@Gm5506!0.62!4.60!Eno1;;chr8:108160490..108160512,+!p2@Ctcf!0.61!30.33!Ctcf;;chr14:76814736..76814781,+!p4@Tsc22d1!0.61!21.14!Tsc22d1;;chr17:35031460..35031518,+!p1@Zbtb12!0.61!18.38!Zbtb12;;chr14:76814784..76814803,+!p7@Tsc22d1!0.61!6.43!Tsc22d1;;chr4:133310214..133310231,-!p11@Arid1a!0.61!5.52!Arid1a;;chr1:170362242..170362256,-!p3@Pbx1!0.60!25.74!Pbx1;;chr7:11080671..11080750,-!p1@Zik1!0.60!24.82!Zik1;;chr2:166888481..166888548,-!p3@Znfx1!0.60!9.19!Znfx1;;chr16:43503493..43503570,+!p9@Zbtb20!0.60!5.52!Zbtb20;;chr13:96094769..96094829,+!p4@Zbed3!0.60!4.60!Zbed3;;chr10:127896295..127896304,+!p6@Smarcc2!0.60!3.68!Smarcc2;;chr11:3189883..3189925,+!p1@Patz1!0.59!48.72!Patz1;;chr10:82226649..82226694,-!p2@Nfyb!0.59!22.06!Nfyb;;chr2:44968775..44968795,-!p4@Zeb2!0.59!16.55!Zeb2;;chr16:55966525..55966543,+!p5@Rpl24,p5@Zbtb11!0.59!11.95!Zbtb11;;chr18:65741935..65741964,+!p2@Zfp532!0.59!9.19!Zfp532;;chr11:44430788..44430804,+!p3@Ebf1!0.59!8.27!Ebf1;;chr7:87171256..87171280,+!p4@Zfp710!0.59!6.43!Zfp710;;chr7:91558537..91558558,-!p4@Arnt2!0.59!3.68!Arnt2;;chr15:81575487..81575561,+!p1@Zc3h7b!0.58!74.46!Zc3h7b;;chr1:179372411..179372509,+!p1@Zfp238!0.58!43.20!Zfp238;;chr7:6124135..6124158,+!p2@Zfp444!0.58!12.87!Zfp444;;chr5:143942477..143942493,-!p2@Rbak!0.58!6.43!Rbak;;chr4:122673187..122673201,+!p2@Mycl1!0.58!5.52!Mycl1;;chr7:25292033..25292043,+!p9@Zfp428!0.58!3.68!Zfp428;;chr7:25292223..25292234,+!p7@Zfp428!0.58!3.68!Zfp428;;chr7:148513599..148513636,-!p3@Deaf1!0.57!12.87!Deaf1;;chr6:55631324..55631335,-!p3@Neurod6!0.57!2.76!Neurod6;;chr6:144157968..144157989,-!p7@Sox5!0.57!2.76!Sox5;;chr6:28347999..28348023,-!p3@Zfp800!0.57!2.76!Zfp800;;chr7:135019127..135019137,-!p6@Zfp668!0.57!2.76!Zfp668;;chr7:116093986..116093999,+!p4@Tub!0.57!2.76!Tub;;chr6:6831986..6832007,-!p4@Dlx5!0.57!2.76!Dlx5;;chr6:144158183..144158210,-!p11@Sox5!0.57!2.76!Sox5;;chr6:14851403..14851422,+!p8@Foxp2!0.57!2.76!Foxp2;;chr2:79296907..79296918,-!p2@Neurod1!0.57!2.76!Neurod1;;chr3:17954392..17954407,+!p2@Bhlhe22!0.57!2.76!Bhlhe22;;chr3:34549144..34549155,+!p5@Sox2!0.57!2.76!Sox2;;chr4:119487109..119487131,+!p4@Hivep3!0.57!2.76!Hivep3;;chr4:22415290..22415307,-!p2@Pou3f2!0.57!2.76!Pou3f2;;chr4:150503544..150503561,-!p8@Camta1!0.57!2.76!Camta1;;chr3:34549096..34549111,+!p3@Sox2!0.57!2.76!Sox2;;chr11:23978206..23978219,+!p12@Bcl11a!0.57!2.76!Bcl11a;;chr11:23977965..23977974,+!p11@Bcl11a!0.57!2.76!Bcl11a;;chr12:28027256..28027282,-!p2@Sox11!0.57!2.76!Sox11;;chr12:39510042..39510069,+!p8@Etv1!0.57!2.76!Etv1;;chr15:100430393..100430410,-!p3@Pou6f1!0.57!2.76!Pou6f1;;chrX:55284180..55284195,+!p2@Zic3!0.57!2.76!Zic3;;chr8:12395874..12395885,+!p2@Sox1!0.57!2.76!Sox1;;chr8:47379946..47379955,-!p1@Helt!0.57!2.76!Helt;;chr2:163051181..163051205,+!p2@Tox2!0.57!2.76!Tox2;;chr1:57028182..57028191,-!p11@Satb2!0.57!2.76!Satb2;;chr1:1739877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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000202
 |is_obsolete=
+|library_id=CNhs12110
+|library_id_phase_based=2:CNhs12110
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11644
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11644
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520hippocampal%252c%2520donor3.CNhs12110.11644-122D6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520hippocampal%252c%2520donor3.CNhs12110.11644-122D6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520hippocampal%252c%2520donor3.CNhs12110.11644-122D6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520hippocampal%252c%2520donor3.CNhs12110.11644-122D6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520hippocampal%252c%2520donor3.CNhs12110.11644-122D6.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - hippocampal, donor3
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12110,LSID839,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0.28312448614836,0,0,-0.386200560896736,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.561517561618512,-0.558422792324031,0,0,0,0,0,-0.209322725495826,0.199710508918196,0.0385758257921702,-0.0623298771198322,0.92623844657323,0.747884995716671,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0428469550828748,0,-0.130696565450787,0,0,0,0.0240972528385661,-0.310650657339386,0.125033443377277,-0.140687683267293,0,-0.0780086007519514,0.081028701852325,0,0,0,0.0523585594561709,0.125986371641797,-0.31279039459221,-0.0788315948399074,0,0,0,0,0,0,0,-0.146960869996828,0.0176555282994105,0,0,0,0.574917061061619,0
@@ Line 83: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11644-122D6;search_select_hide=table117:11644-122D6
 }}

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FF:11644-122D6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:13, 4 June 2020

CNhs12110

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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