FF:1388-42B2: Difference between revisions

Latest revision as of 19:05, 4 June 2020

Name:	diencephalon, neonate N30
Species:	Mouse (Mus musculus)
Library ID:	CNhs11201
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	diencephalon
dev stage	30 days neonate
sex	mixture
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

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

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005403

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11201		CAGE		DRX008950		DRR009824

Accession ID Mm9

Library id		BAM		CTSS
CNhs11201		DRZ001249		DRZ002632

Accession ID Mm10

Library id		BAM		CTSS
CNhs11201		DRZ012599		DRZ013982

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

CNhs11201

0	0
1	0.756
10	0
100	0.0653
1000	-0.0106
1001	0.0303
1002	-0.083
1003	-0.0221
1004	0
1005	0.115
1006	0.585
1007	0.0346
1008	0
1009	-0.19
101	-0.0595
1010	0
1011	0.66
1012	0.361
1013	0.174
1014	-0.0874
1015	-0.0603
1016	-0.0945
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0
1023	0
1024	0.118
1025	0
1026	0
1027	0.508
1028	0
1029	0.143
103	-0.0829
1030	0
1031	-0.356
1032	0.402
1033	0
1034	0
1035	0.0532
1036	-0.244
1037	0
1038	0.0308
1039	0.136
104	0
1040	-0.31
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: CNhs11201

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00125
MA0003.1	MA0003.1	0.296
MA0004.1	MA0004.1	0.485
MA0006.1	MA0006.1	0.181
MA0007.1	MA0007.1	0.389
MA0009.1	MA0009.1	0.741
MA0014.1	MA0014.1	0.641
MA0017.1	MA0017.1	1.38324e-6
MA0018.2	MA0018.2	0.0132
MA0019.1	MA0019.1	0.346
MA0024.1	MA0024.1	0.0582
MA0025.1	MA0025.1	0.00457
MA0027.1	MA0027.1	0.0591
MA0028.1	MA0028.1	0.0706
MA0029.1	MA0029.1	0.437
MA0030.1	MA0030.1	0.798
MA0031.1	MA0031.1	0.214
MA0035.2	MA0035.2	0.0133
MA0038.1	MA0038.1	0.285
MA0039.2	MA0039.2	0.0383
MA0040.1	MA0040.1	0.325
MA0041.1	MA0041.1	0.115
MA0042.1	MA0042.1	0.221
MA0043.1	MA0043.1	0.0562
MA0046.1	MA0046.1	1.0205e-11
MA0047.2	MA0047.2	8.53604e-5
MA0048.1	MA0048.1	0.0428
MA0050.1	MA0050.1	1.9755e-5
MA0051.1	MA0051.1	0.00199
MA0052.1	MA0052.1	0.846
MA0055.1	MA0055.1	0.012
MA0057.1	MA0057.1	0.357
MA0058.1	MA0058.1	0.43
MA0059.1	MA0059.1	0.132
MA0060.1	MA0060.1	0.716
MA0061.1	MA0061.1	0.033
MA0062.2	MA0062.2	0.00135
MA0065.2	MA0065.2	1.30554e-6
MA0066.1	MA0066.1	0.03
MA0067.1	MA0067.1	0.562
MA0068.1	MA0068.1	0.4
MA0069.1	MA0069.1	0.0643
MA0070.1	MA0070.1	0.83
MA0071.1	MA0071.1	0.0561
MA0072.1	MA0072.1	0.428
MA0073.1	MA0073.1	0.774
MA0074.1	MA0074.1	0.116
MA0076.1	MA0076.1	0.168
MA0077.1	MA0077.1	0.401
MA0078.1	MA0078.1	0.793
MA0079.2	MA0079.2	0.341
MA0080.2	MA0080.2	3.04834e-10
MA0081.1	MA0081.1	0.237
MA0083.1	MA0083.1	0.00941
MA0084.1	MA0084.1	0.903
MA0087.1	MA0087.1	0.248
MA0088.1	MA0088.1	0.243
MA0090.1	MA0090.1	0.125
MA0091.1	MA0091.1	0.214
MA0092.1	MA0092.1	0.203
MA0093.1	MA0093.1	0.534
MA0099.2	MA0099.2	0.00278
MA0100.1	MA0100.1	0.276
MA0101.1	MA0101.1	0.0169
MA0102.2	MA0102.2	0.481
MA0103.1	MA0103.1	0.197
MA0104.2	MA0104.2	0.83
MA0105.1	MA0105.1	0.00699
MA0106.1	MA0106.1	0.0527
MA0107.1	MA0107.1	0.0423
MA0108.2	MA0108.2	0.00286
MA0111.1	MA0111.1	0.977
MA0112.2	MA0112.2	7.19482e-4
MA0113.1	MA0113.1	0.358
MA0114.1	MA0114.1	5.98976e-6
MA0115.1	MA0115.1	5.89665e-6
MA0116.1	MA0116.1	0.0631
MA0117.1	MA0117.1	0.955
MA0119.1	MA0119.1	0.115
MA0122.1	MA0122.1	0.959
MA0124.1	MA0124.1	0.447
MA0125.1	MA0125.1	0.0186
MA0131.1	MA0131.1	0.713
MA0135.1	MA0135.1	0.581
MA0136.1	MA0136.1	1.41749e-12
MA0137.2	MA0137.2	0.0611
MA0138.2	MA0138.2	1.73492e-4
MA0139.1	MA0139.1	0.493
MA0140.1	MA0140.1	1.97393e-4
MA0141.1	MA0141.1	0.00287
MA0142.1	MA0142.1	0.236
MA0143.1	MA0143.1	0.955
MA0144.1	MA0144.1	0.0446
MA0145.1	MA0145.1	0.145
MA0146.1	MA0146.1	0.0247
MA0147.1	MA0147.1	0.666
MA0148.1	MA0148.1	3.75712e-4
MA0149.1	MA0149.1	0.105
MA0150.1	MA0150.1	0.159
MA0152.1	MA0152.1	0.216
MA0153.1	MA0153.1	4.05514e-11
MA0154.1	MA0154.1	0.045
MA0155.1	MA0155.1	0.406
MA0156.1	MA0156.1	2.8707e-8
MA0157.1	MA0157.1	0.105
MA0159.1	MA0159.1	0.0014
MA0160.1	MA0160.1	0.00444
MA0162.1	MA0162.1	0.148
MA0163.1	MA0163.1	7.54726e-4
MA0164.1	MA0164.1	0.82
MA0258.1	MA0258.1	0.0178
MA0259.1	MA0259.1	0.838

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: CNhs11201

Novel motif	Logo	P-value
1	1	0.202
10	10	0.0477
100	100	0.385
101	101	0.836
102	102	0.955
103	103	0.0617
104	104	0.954
105	105	0.666
106	106	0.0609
107	107	0.179
108	108	0.709
109	109	0.00999
11	11	0.0717
110	110	0.0419
111	111	0.118
112	112	0.00602
113	113	0.498
114	114	0.33
115	115	0.895
116	116	0.197
117	117	0.00361
118	118	0.338
119	119	0.213
12	12	0.949
120	120	0.718
121	121	0.564
122	122	0.61
123	123	8.15991e-4
124	124	0.0544
125	125	0.236
126	126	0.0266
127	127	0.214
128	128	0.0573
129	129	0.371
13	13	4.20859e-7
130	130	0.205
131	131	0.734
132	132	0.668
133	133	0.863
134	134	0.113
135	135	0.265
136	136	0.039
137	137	0.705
138	138	0.912
139	139	0.276
14	14	0.889
140	140	0.0232
141	141	0.63
142	142	0.917
143	143	0.362
144	144	0.799
145	145	2.93122e-4
146	146	0.331
147	147	0.359
148	148	0.722
149	149	0.9
15	15	0.214
150	150	0.0601
151	151	0.839
152	152	0.0993
153	153	0.85
154	154	0.959
155	155	0.29
156	156	0.00655
157	157	0.213
158	158	0.317
159	159	0.612
160	160	0.178
161	161	0.0997
162	162	0.661
163	163	0.657
164	164	0.0402
165	165	0.147
166	166	0.814
167	167	0.644
168	168	0.554
169	169	0.00337
17	17	0.0545
18	18	0.861
19	19	0.102
2	2	0.786
20	20	0.035
21	21	0.213
22	22	0.149
23	23	0.741
24	24	0.0631
25	25	0.698
26	26	9.73217e-8
27	27	0.566
28	28	0.774
29	29	0.0278
3	3	0.0613
30	30	0.767
31	31	0.929
32	32	0.468
33	33	0.136
34	34	0.738
35	35	0.807
36	36	0.215
37	37	0.0261
38	38	0.547
39	39	0.342
4	4	0.257
40	40	0.0987
41	41	0.444
42	42	0.179
43	43	0.127
44	44	0.399
45	45	0.712
46	46	0.101
47	47	0.354
48	48	0.265
49	49	0.193
5	5	0.155
50	50	0.246
51	51	0.747
52	52	0.353
53	53	0.425
54	54	0.943
55	55	0.923
56	56	0.477
57	57	0.582
58	58	0.342
59	59	0.11
6	6	0.814
60	60	0.0454
61	61	0.0463
62	62	0.223
63	63	0.174
64	64	0.642
65	65	0.407
66	66	0.699
67	67	0.63
68	68	0.798
69	69	0.493
7	7	0.0195
70	70	0.0634
71	71	0.00389
72	72	0.459
73	73	0.0355
74	74	0.896
75	75	0.0459
76	76	0.409
77	77	0.407
78	78	0.00187
79	79	0.416
8	8	0.0542
80	80	0.401
81	81	0.783
82	82	0.232
83	83	0.106
84	84	0.807
85	85	0.208
86	86	0.159
87	87	0.119
88	88	0.453
89	89	0.661
9	9	0.469
90	90	0.214
91	91	0.12
92	92	0.222
93	93	0.0722
94	94	0.813
95	95	0.0346
96	96	0.313
97	97	0.977
98	98	0.523
99	99	0.43

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: CNhs11201

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011470 mouse diencephalon- neonate N30 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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0001894 (diencephalon)
0000479 (tissue)
0004121 (ectoderm-derived structure)
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)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001890 (forebrain)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011470 (mouse diencephalon- neonate N30 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
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006222 (future diencephalon)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008813
+|DRA_sample_Accession=CAGE@SAMD00005403
-|accession_numbers=CAGE;DRX008950;DRR009824;DRZ001249;DRZ002632
+|accession_numbers=CAGE;DRX008950;DRR009824;DRZ001249;DRZ002632;DRZ012599;DRZ013982
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0001894,UBERON:0000479,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001890
 |ancestors_in_cell_lineage_facet=
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.32!238.49!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.98!172.95!Tsc22d4;;chr10:67375368..67375433,-!p1@Zfp365!1.75!96.37!Zfp365;;chr16:91225808..91225824,+!p1@Olig2!1.75!55.32!Olig2;;chr12:30219426..30219506,+!p2@Myt1l!1.62!40.24!Myt1l;;chr9:91260616..91260653,-!p2@Zic1!1.61!39.75!Zic1;;chr17:48015839..48015915,-!p3@Foxp4!1.57!42.67!Foxp4;;chr10:67375146..67375208,-!p2@Zfp365!1.53!49.48!Zfp365;;chr7:116154364..116154444,+!p1@Tub!1.52!53.86!Tub;;chr8:24780125..24780143,+!p1@Zmat4!1.52!46.24!Zmat4;;chr2:65683890..65683907,+!p1@Csrnp3!1.49!56.46!Csrnp3;;chr9:91260594..91260612,-!p1@Zic1!1.47!28.72!Zic1;;chr19:19185671..19185693,-!p1@Rorb!1.46!65.06!Rorb;;chr2:127347067..127347093,-!p1@Kcnip3!1.46!45.59!Kcnip3;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.44!33.26!Pou3f3;;chr16:91270091..91270143,+!p2@Olig1!1.43!25.63!Olig1;;chr3:95032091..95032183,-!p1@Mllt11!1.41!203.94!Mllt11;;chr17:25707623..25707639,-!p1@Sox8!1.39!97.34!Sox8;;chr4:58956447..58956510,+!p1@Zkscan16!1.38!49.48!Zkscan16;;chrX:34442872..34442899,-!p1@Nkrf!1.37!29.20!Nkrf;;chr15:76353005..76353021,-!p2@Scrt1!1.35!21.42!Scrt1;;chr15:78994907..78994926,-!p1@Sox10!1.33!51.27!Sox10;;chr7:146768691..146768707,-!p1@Nkx6-2!1.33!20.28!Nkx6-2;;chr15:76352677..76352737,-!p3@Scrt1!1.31!19.63!Scrt1;;chr7:148008023..148008092,-!p1@Zfp941!1.30!45.59!Zfp941;;chr2:163051181..163051205,+!p2@Tox2!1.30!19.14!Tox2;;chr10:67375342..67375365,-!p3@Zfp365!1.30!19.14!Zfp365;;chr6:85463580..85463585,-!p1@Egr4!1.28!17.85!Egr4;;chr18:36441119..36441158,+!p2@Pura!1.27!42.18!Pura;;chr4:150482563..150482655,-!p2@Camta1!1.24!57.60!Camta1;;chrX:108009761..108009788,+!p1@Pou3f4!1.23!16.06!Pou3f4;;chr2:127347042..127347058,-!p3@Kcnip3!1.21!15.09!Kcnip3;;chr2:127347094..127347111,-!p2@Kcnip3!1.20!24.50!Kcnip3;;chr12:30220074..30220102,+!p3@Myt1l!1.19!14.44!Myt1l;;chr6:55631042..55631102,-!p1@Neurod6!1.17!13.95!Neurod6;;chr3:34548909..34548927,+!p1@Sox2!1.15!22.23!Sox2;;chr1:6477388..6477419,+!p3@St18!1.14!12.65!St18;;chr4:154335024..154335039,+!p1@Hes5!1.12!14.93!Hes5;;chr12:30213247..30213333,+!p1@Myt1l!1.11!12.01!Myt1l;;chrX:90531838..90531861,+!p1@Arx!1.10!14.44!Arx;;chr12:54349410..54349461,+!p1@Npas3!1.10!13.95!Npas3;;chr15:76352434..76352488,-!p4@Scrt1!1.10!11.52!Scrt1;;chr2:38206744..38206766,+!p1@Lhx2!1.09!13.79!Lhx2;;chr2:65768174..65768247,+!p2@Csrnp3!1.08!11.03!Csrnp3;;chr14:34791937..34791977,-!p1@Zfp488!1.08!11.03!Zfp488;;chr11:98190918..98190951,-!p1@Neurod2!1.06!10.55!Neurod2;;chr7:38554763..38554780,-!p1@Zfp536!1.04!18.33!Zfp536;;chr15:103170533..103170556,-!p1@Zfp385a!1.01!35.04!Zfp385a;;chr3:95032197..95032208,-!p3@Mllt11!1.01!11.52!Mllt11;;chr6:117813087..117813121,+!p1@Zfp239!1.00!34.56!Zfp239;;chr2:168427068..168427115,-!p3@Nfatc2!1.00!9.09!Nfatc2;;chr10:84218800..84218829,+!p2@Rfx4!1.00!9.09!Rfx4;;chr5:98609885..98609900,+!p1@Prdm8!1.00!8.92!Prdm8;;chr5:122499831..122499891,-!p1@Cux2!0.99!13.79!Cux2;;chr2:115890294..115890334,-!p9@Meis2!0.99!12.17!Meis2;;chr4:150513630..150513686,-!p4@Camta1!0.99!10.22!Camta1;;chr2:81893447..81893468,+!p2@Zfp804a!0.99!8.76!Zfp804a;;chr2:71367142..71367167,+!p2@Dlx1!0.98!8.60!Dlx1;;chr11:96685444..96685473,-!p5@Nfe2l1!0.98!8.60!Nfe2l1;;chr10:84218895..84218909,+!p1@Rfx4!0.98!8.60!Rfx4;;chr2:162769220..162769252,+!p1@L3mbtl1!0.98!8.60!L3mbtl1;;chr11:90252223..90252240,-!p1@Hlf!0.97!71.22!Hlf;;chr8:12395603..12395621,+!p1@Sox1!0.97!8.44!Sox1;;chr19:19185697..19185711,-!p2@Rorb!0.96!10.55!Rorb;;chr2:77541432..77541474,-!p5@Zfp385b!0.96!8.11!Zfp385b;;chr12:109242266..109242295,-!p1@Bcl11b!0.95!68.63!Bcl11b;;chr12:72149325..72149343,+!p2@Arid4a!0.95!11.19!Arid4a;;chr9:69137716..69137744,+!p1@Rora!0.94!49.65!Rora;;chrX:34442842..34442866,-!p3@Nkrf!0.94!7.63!Nkrf;;chr7:30092993..30093076,+!p1@Dpf1!0.93!13.14!Dpf1;;chr2:163030219..163030258,+!p5@Tox2!0.93!7.46!Tox2;;chr2:61642631..61642684,+!p1@Tbr1!0.93!7.46!Tbr1;;chr2:81893535..81893548,+!p1@Zfp804a!0.92!7.30!Zfp804a;;chr3:95032213..95032226,-!p6@Mllt11!0.90!8.27!Mllt11;;chr1:169528520..169528542,+!p2@Rxrg!0.90!6.98!Rxrg;;chr15:103170516..103170531,-!p2@Zfp385a!0.89!16.87!Zfp385a;;chr5:125342568..125342602,+!p2@Zfp664!0.89!11.36!Zfp664;;chr12:30220046..30220070,+!p6@Myt1l!0.89!6.81!Myt1l;;chr1:189821714..189821761,+!p1@Esrrg!0.88!12.49!Esrrg;;chr7:91558472..91558512,-!p2@Arnt2!0.88!9.57!Arnt2;;chr3:34548946..34548972,+!p2@Sox2!0.88!7.30!Sox2;;chr14:122874619..122874634,+!p1@Zic2!0.88!6.65!Zic2;;chr11:96685487..96685512,-!p7@Nfe2l1!0.88!6.65!Nfe2l1;;chr16:91225654..91225671,+!p2@Olig2!0.88!6.65!Olig2;;chr11:90250944..90250982,-!p2@Hlf!0.86!10.87!Hlf;;chr19:4989964..4989972,-!p1@Npas4!0.86!6.33!Npas4;;chr2:71367871..71367898,+!p1@Dlx1!0.86!6.33!Dlx1;;chr8:12395892..12395919,+!p4@Sox1!0.86!6.33!Sox1;;chr2:181501710..181501742,+!p2@Myt1!0.86!6.33!Myt1;;chr19:10315179..10315241,-!p1@Gm98!0.85!67.49!Gm98;;chr2:25562263..25562314,+!p2@Bmyc!0.85!25.31!Bmyc;;chr4:124334894..124334899,+!p1@Pou3f1!0.85!8.11!Pou3f1;;chr6:6832076..6832092,-!p1@Dlx5!0.85!7.14!Dlx5;;chr11:98636531..98636559,-!p1@Nr1d1!0.84!35.86!Nr1d1;;chr2:77654815..77654872,-!p2@Zfp385b!0.84!7.63!Zfp385b;;chrX:95345005..95345053,+!p1@Ar!0.84!5.84!Ar;;chr3:95032558..95032641,-!p2@Mllt11!0.83!34.07!Mllt11;;chr11:116196664..116196679,-!p1@Foxj1!0.83!9.09!Foxj1;;chr19:59533221..59533271,+!p1@Emx2!0.83!7.30!Emx2;;chr12:109241728..109241781,-!p2@Bcl11b!0.83!6.17!Bcl11b;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.82!62.79!Camta2;;chr7:122968213..122968266,-!p4@Sox6!0.82!6.81!Sox6;;chr2:163030186..163030204,+!p4@Tox2!0.82!5.68!Tox2;;chr4:150482353..150482386,-!p6@Camta1!0.82!5.68!Camta1;;chr7:130644017..130644092,-!p1@Zkscan2!0.81!11.19!Zkscan2;;chr19:23216132..23216157,+!p3@Klf9!0.81!8.76!Klf9;;chr8:79423672..79423727,+!p2@Nr3c2!0.81!7.14!Nr3c2;;chr1:169528491..169528505,+!p4@Rxrg!0.81!5.52!Rxrg;;chr1:169528581..169528607,+!p7@Rxrg!0.80!5.35!Rxrg;;chr19:55969946..55969973,+!p8@Tcf7l2!0.80!5.35!Tcf7l2;;chr15:76352832..76352900,-!p1@Scrt1!0.80!5.35!Scrt1;;chrX:55283799..55283813,+!p1@Zic3!0.80!5.35!Zic3;;chr7:71083876..71083932,-!p2@Klf13!0.79!45.10!Klf13;;chr11:23980664..23980706,+!p2@Bcl11a!0.79!24.17!Bcl11a;;chr3:95032184..95032195,-!p4@Mllt11!0.79!6.49!Mllt11;;chr2:71384802..71384815,-!p1@Dlx2!0.79!6.49!Dlx2;;chr2:73109983..73109996,+!p1@Sp9!0.79!5.19!Sp9;;chr2:38206580..38206600,+!p2@Lhx2!0.78!6.33!Lhx2;;chr3:95032515..95032553,-!p5@Mllt11!0.78!6.17!Mllt11;;chr8:12395874..12395885,+!p2@Sox1!0.78!5.03!Sox1;;chr6:145814003..145814056,-!p1@Bhlhe41!0.77!15.25!Bhlhe41;;chr8:87297878..87297935,-!p3@Nfix!0.77!11.52!Nfix;;chr7:52960888..52960902,+!p7@Dbp!0.77!4.87!Dbp;;chr3:34549096..34549111,+!p3@Sox2!0.77!4.87!Sox2;;chr17:86020156..86020183,+!p1@Six3!0.77!4.87!Six3;;chr14:49287186..49287225,-!p1@Otx2!0.77!4.87!Otx2;;chr9:69137672..69137702,+!p2@Rora!0.76!21.90!Rora;;chr16:95923651..95923701,+!p3@Ets2!0.76!8.11!Ets2;;chr14:52935860..52935874,-!p3@Sall2!0.76!7.14!Sall2;;chr12:109242296..109242307,-!p3@Bcl11b!0.76!7.14!Bcl11b;;chr11:90252071..90252093,-!p7@Hlf!0.76!4.70!Hlf;;chr11:90250894..90250916,-!p5@Hlf!0.76!4.70!Hlf;;chr2:181501745..181501778,+!p1@Myt1!0.76!4.70!Myt1;;chr13:44936126..44936164,+!p6@Jarid2!0.75!5.52!Jarid2;;chr14:19071466..19071550,-!p1@Nr1d2!0.74!34.23!Nr1d2;;chr6:134780163..134780197,+!p2@Crebl2!0.74!11.19!Crebl2;;chr14:70476975..70476997,+!p2@Egr3!0.74!4.54!Egr3;;chr11:90252108..90252134,-!p6@Hlf!0.74!4.54!Hlf;;chr19:55969923..55969944,+!p6@Tcf7l2!0.74!4.54!Tcf7l2;;chr2:79296783..79296801,-!p1@Neurod1!0.74!4.54!Neurod1;;chr7:91558392..91558434,-!p1@Arnt2!0.73!12.98!Arnt2;;chr17:86012772..86012825,+!p4@Six3!0.73!4.38!Six3;;chr2:65768149..65768173,+!p4@Csrnp3!0.73!4.38!Csrnp3;;chr13:83663902..83663927,+!p1@Mef2c!0.72!116.33!Mef2c;;chr13:48356475..48356492,+!p1@Id4!0.72!104.65!Id4;;chr8:112603610..112603656,+!p1@Zfp612!0.72!21.90!Zfp612;;chr6:72850124..72850210,-!p7@Kcmf1!0.72!5.84!Kcmf1;;chr1:91827756..91827773,-!p1@Gbx2!0.72!4.22!Gbx2;;chr2:151907338..151907360,+!p2@Scrt2!0.72!4.22!Scrt2;;chr13:83663868..83663894,+!p2@Mef2c!0.71!67.17!Mef2c;;chr1:140739014..140739032,-!p1@Lhx9!0.71!5.35!Lhx9;;chr7:52960555..52960662,+!p1@Dbp!0.70!38.78!Dbp;;chr19:26681865..26681900,+!p6@Smarca2!0.70!12.98!Smarca2;;chr6:145813905..145813932,-!p2@Bhlhe41!0.70!8.11!Bhlhe41;;chr10:67375223..67375240,-!p4@Zfp365!0.70!4.54!Zfp365;;chr17:86020115..86020128,+!p2@Six3!0.70!4.06!Six3;;chr2:168427120..168427138,-!p4@Nfatc2!0.70!4.06!Nfatc2;;chr2:151907546..151907561,+!p1@Scrt2!0.70!4.06!Scrt2;;chr9:68501522..68501538,+!p4@Rora!0.69!7.79!Rora;;chr6:6812962..6812979,+!p1@Dlx6!0.69!3.89!Dlx6;;chrX:58146612..58146615,-!p1@Sox3!0.69!3.89!Sox3;;chr16:43363968..43364001,+!p7@Zbtb20!0.68!7.46!Zbtb20;;chr19:23216166..23216191,+!p6@Klf9!0.68!5.19!Klf9;;chr18:36441100..36441113,+!p3@Pura!0.68!4.54!Pura;;chrX:108009734..108009752,+!p2@Pou3f4!0.68!3.73!Pou3f4;;chr1:169528551..169528569,+!p8@Rxrg!0.68!3.73!Rxrg;;chr7:30094448..30094481,+!p4@Dpf1!0.67!4.54!Dpf1;;chr1:39250584..39250643,+!p1@Npas2!0.66!20.44!Npas2;;chr9:69137648..69137656,+!p5@Rora!0.66!5.19!Rora;;chr7:30088977..30089002,+!p2@Dpf1!0.66!5.19!Dpf1;;chr7:91520922..91520956,-!p5@Arnt2!0.66!3.57!Arnt2;;chr14:122874593..122874610,+!p2@Zic2!0.66!3.57!Zic2;;chr14:70477113..70477173,+!p1@Egr3!0.66!3.57!Egr3;;chr12:3806003..3806031,+!p11@Dnmt3a!0.66!3.57!Dnmt3a;;chr2:65683842..65683856,+!p3@Csrnp3!0.66!3.57!Csrnp3;;chr4:107353376..107353452,-!p3@Dmrtb1!0.66!3.57!Dmrtb1;;chr3:66785181..66785199,-!p2@Shox2!0.66!3.57!Shox2;;chr4:22415443..22415506,-!p1@Pou3f2!0.66!3.57!Pou3f2;;chr11:98603119..98603130,+!p2@Thra!0.65!33.91!Thra;;chr14:55711114..55711159,-!p2@Zfhx2!0.65!8.60!Zfhx2;;chr8:112603658..112603674,+!p2@Zfp612!0.65!6.98!Zfp612;;chr13:99124189..99124205,+!p1@Foxd1!0.65!5.68!Foxd1;;chr1:179374784..179374800,+!p2@Zfp238!0.65!4.22!Zfp238;;chr10:30522690..30522752,-!p2@Ncoa7!0.64!23.52!Ncoa7;;chr8:107793688..107793736,+!p1@Hsf4!0.64!4.54!Hsf4;;chr2:73110004..73110016,+!p2@Sp9!0.64!3.41!Sp9;;chr17:86020510..86020589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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11201
-|library_id_phase_based=1:CNhs11201
+|library_id_phase_based=2:CNhs11201
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1388
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1388
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/diencephalon%252c%2520neonate%2520N30.CNhs11201.1388-42B2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/diencephalon%252c%2520neonate%2520N30.CNhs11201.1388-42B2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/diencephalon%252c%2520neonate%2520N30.CNhs11201.1388-42B2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/diencephalon%252c%2520neonate%2520N30.CNhs11201.1388-42B2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/diencephalon%252c%2520neonate%2520N30.CNhs11201.1388-42B2.mm9.nobarcode.rdna.fa.gz
 |name=diencephalon, neonate N30
 |namespace=FANTOM5
@@ Line 51: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11201,LSID747,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.00918987063051575,0,0,0,0,0,0.190531026533895,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.0660745729321428,0,0.0326481450697549,0,0,0,0,0,0,0,0,0,0,0,-0.228884813758906,0,0,0,0,0.0652962901395099,-0.0396938832685002,0.141303253619427,-0.164780292746105,0.629351318063097,0.604592915390124,0,0,0,0,0,0,0,0,0,0,0,0,-0.000709257423930423,0,0,0,0,0,0,0,0,0.122046233034924,0.0391442429051524,0.0540633756758727,-0.188604424304462,0.666584259397754,0.0854535240380705,0,0,0.133400283225237,0.115780230894074,0.295225594521175,0,0.132373038671474,0.104616715295533,0.0150202482755876,-0.0788315948399074,0,0,0,0,0,0,0.00899034519556102,0.0786348634502962,0.0904486669067544,0,0,0.703809777604454,0,0
@@ Line 88: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1388-42B2;search_select_hide=table117:1388-42B2
 }}

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FF:1388-42B2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:05, 4 June 2020

CNhs11201

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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