FF:20-12F2: Difference between revisions

Latest revision as of 19:09, 4 June 2020

Name:	diencephalon, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10482
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	diencephalon
dev stage	adult
sex	male
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		SAMD00005882

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10482		CAGE		DRX008949		DRR009823

Accession ID Mm9

Library id		BAM		CTSS
CNhs10482		DRZ001248		DRZ002631

Accession ID Mm10

Library id		BAM		CTSS
CNhs10482		DRZ012598		DRZ013981

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

CNhs10482

0	0
1	0.771
10	0
100	0
1000	0
1001	0.124
1002	-0.0751
1003	0.132
1004	0.082
1005	0.0345
1006	0.579
1007	-0.103
1008	0
1009	-0.19
101	-0.0855
1010	0
1011	0.549
1012	0.151
1013	0.272
1014	-0.0851
1015	-0.0251
1016	-0.00199
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.0347
1023	0
1024	0.0114
1025	0
1026	0
1027	0.425
1028	0
1029	0.0344
103	-0.0861
1030	0.082
1031	-0.336
1032	0.395
1033	-0.0665
1034	0
1035	0
1036	-0.133
1037	0
1038	-0.0167
1039	0.129
104	0
1040	-0.189
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: CNhs10482

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00127
MA0003.1	MA0003.1	0.341
MA0004.1	MA0004.1	0.466
MA0006.1	MA0006.1	0.195
MA0007.1	MA0007.1	0.297
MA0009.1	MA0009.1	0.754
MA0014.1	MA0014.1	0.744
MA0017.1	MA0017.1	1.60245e-6
MA0018.2	MA0018.2	0.00956
MA0019.1	MA0019.1	0.617
MA0024.1	MA0024.1	0.0519
MA0025.1	MA0025.1	0.00199
MA0027.1	MA0027.1	0.0852
MA0028.1	MA0028.1	0.0554
MA0029.1	MA0029.1	0.896
MA0030.1	MA0030.1	0.842
MA0031.1	MA0031.1	0.287
MA0035.2	MA0035.2	0.0206
MA0038.1	MA0038.1	0.599
MA0039.2	MA0039.2	0.0341
MA0040.1	MA0040.1	0.39
MA0041.1	MA0041.1	0.0369
MA0042.1	MA0042.1	0.252
MA0043.1	MA0043.1	0.0792
MA0046.1	MA0046.1	1.97573e-10
MA0047.2	MA0047.2	7.2676e-4
MA0048.1	MA0048.1	0.0226
MA0050.1	MA0050.1	4.72246e-5
MA0051.1	MA0051.1	0.00274
MA0052.1	MA0052.1	0.741
MA0055.1	MA0055.1	0.00489
MA0057.1	MA0057.1	0.334
MA0058.1	MA0058.1	0.488
MA0059.1	MA0059.1	0.158
MA0060.1	MA0060.1	0.84
MA0061.1	MA0061.1	0.0263
MA0062.2	MA0062.2	5.19664e-4
MA0065.2	MA0065.2	1.69034e-6
MA0066.1	MA0066.1	0.049
MA0067.1	MA0067.1	0.489
MA0068.1	MA0068.1	0.625
MA0069.1	MA0069.1	0.0504
MA0070.1	MA0070.1	0.493
MA0071.1	MA0071.1	0.147
MA0072.1	MA0072.1	0.809
MA0073.1	MA0073.1	0.981
MA0074.1	MA0074.1	0.178
MA0076.1	MA0076.1	0.134
MA0077.1	MA0077.1	0.416
MA0078.1	MA0078.1	0.891
MA0079.2	MA0079.2	0.327
MA0080.2	MA0080.2	5.88263e-10
MA0081.1	MA0081.1	0.27
MA0083.1	MA0083.1	0.00883
MA0084.1	MA0084.1	0.815
MA0087.1	MA0087.1	0.138
MA0088.1	MA0088.1	0.233
MA0090.1	MA0090.1	0.125
MA0091.1	MA0091.1	0.188
MA0092.1	MA0092.1	0.142
MA0093.1	MA0093.1	0.527
MA0099.2	MA0099.2	0.00499
MA0100.1	MA0100.1	0.253
MA0101.1	MA0101.1	0.0107
MA0102.2	MA0102.2	0.482
MA0103.1	MA0103.1	0.211
MA0104.2	MA0104.2	0.804
MA0105.1	MA0105.1	0.0056
MA0106.1	MA0106.1	0.0354
MA0107.1	MA0107.1	0.0259
MA0108.2	MA0108.2	0.0017
MA0111.1	MA0111.1	0.944
MA0112.2	MA0112.2	8.2926e-4
MA0113.1	MA0113.1	0.515
MA0114.1	MA0114.1	6.47116e-6
MA0115.1	MA0115.1	1.60724e-5
MA0116.1	MA0116.1	0.0922
MA0117.1	MA0117.1	0.934
MA0119.1	MA0119.1	0.153
MA0122.1	MA0122.1	0.702
MA0124.1	MA0124.1	0.379
MA0125.1	MA0125.1	0.0304
MA0131.1	MA0131.1	0.642
MA0135.1	MA0135.1	0.352
MA0136.1	MA0136.1	1.76918e-12
MA0137.2	MA0137.2	0.182
MA0138.2	MA0138.2	2.3374e-5
MA0139.1	MA0139.1	0.639
MA0140.1	MA0140.1	6.45205e-5
MA0141.1	MA0141.1	0.00946
MA0142.1	MA0142.1	0.162
MA0143.1	MA0143.1	0.654
MA0144.1	MA0144.1	0.0721
MA0145.1	MA0145.1	0.162
MA0146.1	MA0146.1	0.0344
MA0147.1	MA0147.1	0.647
MA0148.1	MA0148.1	7.7385e-4
MA0149.1	MA0149.1	0.0797
MA0150.1	MA0150.1	0.271
MA0152.1	MA0152.1	0.156
MA0153.1	MA0153.1	2.11423e-10
MA0154.1	MA0154.1	0.0526
MA0155.1	MA0155.1	0.401
MA0156.1	MA0156.1	1.65051e-8
MA0157.1	MA0157.1	0.129
MA0159.1	MA0159.1	0.00323
MA0160.1	MA0160.1	0.0148
MA0162.1	MA0162.1	0.207
MA0163.1	MA0163.1	4.89598e-4
MA0164.1	MA0164.1	0.871
MA0258.1	MA0258.1	0.0189
MA0259.1	MA0259.1	0.767

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: CNhs10482

Novel motif	Logo	P-value
1	1	0.207
10	10	0.0395
100	100	0.342
101	101	0.757
102	102	0.984
103	103	0.0761
104	104	0.873
105	105	0.551
106	106	0.0575
107	107	0.158
108	108	0.528
109	109	0.0141
11	11	0.0926
110	110	0.0469
111	111	0.234
112	112	0.00717
113	113	0.473
114	114	0.444
115	115	0.889
116	116	0.221
117	117	0.00294
118	118	0.359
119	119	0.218
12	12	0.997
120	120	0.838
121	121	0.72
122	122	0.638
123	123	5.5466e-4
124	124	0.038
125	125	0.197
126	126	0.0317
127	127	0.222
128	128	0.0528
129	129	0.343
13	13	8.83796e-8
130	130	0.226
131	131	0.546
132	132	0.748
133	133	0.613
134	134	0.0915
135	135	0.117
136	136	0.0788
137	137	0.797
138	138	0.892
139	139	0.239
14	14	0.805
140	140	0.0713
141	141	0.97
142	142	0.817
143	143	0.299
144	144	0.706
145	145	1.5917e-4
146	146	0.351
147	147	0.25
148	148	0.878
149	149	0.971
15	15	0.205
150	150	0.0639
151	151	0.988
152	152	0.137
153	153	0.796
154	154	0.788
155	155	0.318
156	156	0.00597
157	157	0.127
158	158	0.31
159	159	0.937
160	160	0.206
161	161	0.149
162	162	0.649
163	163	0.69
164	164	0.0382
165	165	0.219
166	166	0.598
167	167	0.686
168	168	0.573
169	169	0.00302
17	17	0.0709
18	18	0.919
19	19	0.114
2	2	0.63
20	20	0.0214
21	21	0.192
22	22	0.167
23	23	0.78
24	24	0.0657
25	25	0.729
26	26	2.05798e-8
27	27	0.398
28	28	0.795
29	29	0.0307
3	3	0.069
30	30	0.738
31	31	0.666
32	32	0.597
33	33	0.154
34	34	0.757
35	35	0.699
36	36	0.179
37	37	0.0327
38	38	0.495
39	39	0.348
4	4	0.222
40	40	0.0896
41	41	0.523
42	42	0.161
43	43	0.122
44	44	0.502
45	45	0.78
46	46	0.0817
47	47	0.464
48	48	0.325
49	49	0.176
5	5	0.156
50	50	0.271
51	51	0.795
52	52	0.396
53	53	0.386
54	54	0.959
55	55	0.807
56	56	0.554
57	57	0.478
58	58	0.331
59	59	0.143
6	6	0.894
60	60	0.058
61	61	0.0452
62	62	0.233
63	63	0.201
64	64	0.76
65	65	0.445
66	66	0.951
67	67	0.856
68	68	0.465
69	69	0.502
7	7	0.0177
70	70	0.128
71	71	0.00258
72	72	0.502
73	73	0.0517
74	74	0.996
75	75	0.0484
76	76	0.315
77	77	0.489
78	78	0.00195
79	79	0.318
8	8	0.0599
80	80	0.62
81	81	0.769
82	82	0.333
83	83	0.245
84	84	0.849
85	85	0.321
86	86	0.145
87	87	0.334
88	88	0.516
89	89	0.803
9	9	0.519
90	90	0.126
91	91	0.0939
92	92	0.329
93	93	0.164
94	94	0.814
95	95	0.0519
96	96	0.301
97	97	0.971
98	98	0.752
99	99	0.505

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: CNhs10482

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
FF:0010193 human diencephalon - adult 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)
0007023 (adult 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)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010193 (human diencephalon - adult 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)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005882
+|accession_numbers=CAGE;DRX008949;DRR009823;DRZ001248;DRZ002631;DRZ012598;DRZ013981
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,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 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!2.46!326.02!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!2.00!179.11!Tsc22d4;;chr9:91260616..91260653,-!p2@Zic1!1.94!85.82!Zic1;;chr9:91260594..91260612,-!p1@Zic1!1.72!51.12!Zic1;;chr12:30219426..30219506,+!p2@Myt1l!1.65!43.43!Myt1l;;chr16:91225808..91225824,+!p1@Olig2!1.65!43.22!Olig2;;chr19:19185671..19185693,-!p1@Rorb!1.61!92.47!Rorb;;chr17:48015839..48015915,-!p3@Foxp4!1.61!46.13!Foxp4;;chr8:24780125..24780143,+!p1@Zmat4!1.59!53.61!Zmat4;;chr2:163051181..163051205,+!p2@Tox2!1.57!35.95!Tox2;;chr7:116154364..116154444,+!p1@Tub!1.56!60.26!Tub;;chr15:76353005..76353021,-!p2@Scrt1!1.52!31.79!Scrt1;;chrX:34442872..34442899,-!p1@Nkrf!1.51!40.73!Nkrf;;chr2:127347067..127347093,-!p1@Kcnip3!1.47!47.17!Kcnip3;;chr2:65683890..65683907,+!p1@Csrnp3!1.43!48.62!Csrnp3;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.43!32.62!Pou3f3;;chr10:67375146..67375208,-!p2@Zfp365!1.42!38.03!Zfp365;;chr15:76352677..76352737,-!p3@Scrt1!1.42!25.35!Scrt1;;chr18:36441119..36441158,+!p2@Pura!1.41!58.60!Pura;;chr10:67375368..67375433,-!p1@Zfp365!1.37!39.48!Zfp365;;chr3:95032091..95032183,-!p1@Mllt11!1.36!182.65!Mllt11;;chr4:58956447..58956510,+!p1@Zkscan16!1.35!45.92!Zkscan16;;chr15:76352434..76352488,-!p4@Scrt1!1.35!21.19!Scrt1;;chr7:146768691..146768707,-!p1@Nkx6-2!1.35!21.19!Nkx6-2;;chr15:78994907..78994926,-!p1@Sox10!1.34!52.78!Sox10;;chr17:25707623..25707639,-!p1@Sox8!1.30!79.38!Sox8;;chr4:150482563..150482655,-!p2@Camta1!1.28!63.58!Camta1;;chr7:148008023..148008092,-!p1@Zfp941!1.25!40.31!Zfp941;;chr8:12395603..12395621,+!p1@Sox1!1.25!16.83!Sox1;;chr19:55969923..55969944,+!p6@Tcf7l2!1.25!16.62!Tcf7l2;;chr16:91270091..91270143,+!p2@Olig1!1.21!15.38!Olig1;;chr10:84218800..84218829,+!p2@Rfx4!1.20!14.96!Rfx4;;chr4:150513630..150513686,-!p4@Camta1!1.19!16.42!Camta1;;chrX:108009761..108009788,+!p1@Pou3f4!1.18!14.13!Pou3f4;;chr1:6477388..6477419,+!p3@St18!1.18!14.13!St18;;chr1:91827756..91827773,-!p1@Gbx2!1.18!14.13!Gbx2;;chr3:34548909..34548927,+!p1@Sox2!1.17!23.06!Sox2;;chr2:127347094..127347111,-!p2@Kcnip3!1.17!22.86!Kcnip3;;chrX:55283799..55283813,+!p1@Zic3!1.16!13.30!Zic3;;chr14:122874619..122874634,+!p1@Zic2!1.14!12.68!Zic2;;chrX:137083127..137083138,-!p9@Tsc22d3!1.13!12.47!Tsc22d3;;chr15:103170533..103170556,-!p1@Zfp385a!1.12!44.88!Zfp385a;;chr19:19185697..19185711,-!p2@Rorb!1.12!15.58!Rorb;;chr11:90252223..90252240,-!p1@Hlf!1.11!99.53!Hlf;;chr11:98636531..98636559,-!p1@Nr1d1!1.10!65.66!Nr1d1;;chr1:140739014..140739032,-!p1@Lhx9!1.09!14.34!Lhx9;;chr2:127347042..127347058,-!p3@Kcnip3!1.09!11.43!Kcnip3;;chr9:69137716..69137744,+!p1@Rora!1.08!68.99!Rora;;chr12:54349410..54349461,+!p1@Npas3!1.08!13.30!Npas3;;chr3:34548946..34548972,+!p2@Sox2!1.07!12.05!Sox2;;chr19:55969946..55969973,+!p8@Tcf7l2!1.06!10.60!Tcf7l2;;chr19:55968967..55968991,+!p7@Tcf7l2!1.06!10.60!Tcf7l2;;chr2:168427068..168427115,-!p3@Nfatc2!1.06!10.39!Nfatc2;;chr11:90250944..90250982,-!p2@Hlf!1.05!17.45!Hlf;;chr2:163030219..163030258,+!p5@Tox2!1.05!10.18!Tox2;;chr8:107793688..107793736,+!p1@Hsf4!1.04!13.09!Hsf4;;chr6:85463580..85463585,-!p1@Egr4!1.04!9.97!Egr4;;chrX:34442842..34442866,-!p3@Nkrf!1.04!9.97!Nkrf;;chr19:10315179..10315241,-!p1@Gm98!1.02!99.95!Gm98;;chr16:91225654..91225671,+!p2@Olig2!1.02!9.56!Olig2;;chr10:67375342..67375365,-!p3@Zfp365!1.02!9.56!Zfp365;;chr2:77541432..77541474,-!p5@Zfp385b!1.02!9.56!Zfp385b;;chr15:103170516..103170531,-!p2@Zfp385a!1.01!22.44!Zfp385a;;chr11:116196664..116196679,-!p1@Foxj1!1.01!14.34!Foxj1;;chr4:154335024..154335039,+!p1@Hes5!1.01!11.22!Hes5;;chr2:38206744..38206766,+!p1@Lhx2!1.01!11.22!Lhx2;;chr14:49287186..49287225,-!p1@Otx2!1.01!9.35!Otx2;;chr11:96685444..96685473,-!p5@Nfe2l1!1.01!9.14!Nfe2l1;;chr5:122499831..122499891,-!p1@Cux2!0.99!13.51!Cux2;;chrX:90531838..90531861,+!p1@Arx!0.99!11.22!Arx;;chr3:95032515..95032553,-!p5@Mllt11!0.99!10.60!Mllt11;;chr2:163030186..163030204,+!p4@Tox2!0.99!8.73!Tox2;;chr12:72149325..72149343,+!p2@Arid4a!0.97!11.84!Arid4a;;chr12:30213247..30213333,+!p1@Myt1l!0.97!8.31!Myt1l;;chr6:145813905..145813932,-!p2@Bhlhe41!0.96!15.79!Bhlhe41;;chr19:55972767..55972779,+!p20@Tcf7l2!0.95!7.90!Tcf7l2;;chr2:81893447..81893468,+!p2@Zfp804a!0.95!7.90!Zfp804a;;chr7:91558392..91558434,-!p1@Arnt2!0.94!22.03!Arnt2;;chr2:163030164..163030178,+!p6@Tox2!0.93!7.48!Tox2;;chr17:86020156..86020183,+!p1@Six3!0.93!7.48!Six3;;chr2:81893535..81893548,+!p1@Zfp804a!0.92!7.27!Zfp804a;;chrX:95345005..95345053,+!p1@Ar!0.92!7.27!Ar;;chr10:84218895..84218909,+!p1@Rfx4!0.92!7.27!Rfx4;;chr3:95032558..95032641,-!p2@Mllt11!0.91!41.56!Mllt11;;chr8:87297878..87297935,-!p3@Nfix!0.91!16.21!Nfix;;chr7:38554763..38554780,-!p1@Zfp536!0.91!13.30!Zfp536;;chr11:90250894..90250916,-!p5@Hlf!0.91!7.06!Hlf;;chr2:71367142..71367167,+!p2@Dlx1!0.91!7.06!Dlx1;;chr3:101814061..101814094,+!p1@Nhlh2!0.91!7.06!Nhlh2;;chr2:25562263..25562314,+!p2@Bmyc!0.90!28.47!Bmyc;;chr15:103170561..103170572,-!p4@Zfp385a!0.90!10.39!Zfp385a;;chr11:90251852..90251855,-!p4@Hlf!0.90!8.52!Hlf;;chr12:30220074..30220102,+!p3@Myt1l!0.90!6.86!Myt1l;;chr9:69137672..69137702,+!p2@Rora!0.88!29.30!Rora;;chr1:189821714..189821761,+!p1@Esrrg!0.88!12.68!Esrrg;;chr14:122874593..122874610,+!p2@Zic2!0.88!6.65!Zic2;;chr6:117813087..117813121,+!p1@Zfp239!0.87!25.56!Zfp239;;chr13:72766250..72766273,+!p1@Irx2!0.87!10.18!Irx2;;chr7:52960888..52960902,+!p7@Dbp!0.87!6.44!Dbp;;chr19:26681865..26681900,+!p6@Smarca2!0.86!19.32!Smarca2;;chr3:95032197..95032208,-!p3@Mllt11!0.86!7.90!Mllt11;;chr3:95032213..95032226,-!p6@Mllt11!0.86!7.48!Mllt11;;chr3:66785201..66785226,-!p3@Shox2!0.86!6.23!Shox2;;chr13:44936126..44936164,+!p6@Jarid2!0.85!7.06!Jarid2;;chr10:67375223..67375240,-!p4@Zfp365!0.85!6.86!Zfp365;;chr11:90252071..90252093,-!p7@Hlf!0.85!6.03!Hlf;;chr3:66785181..66785199,-!p2@Shox2!0.85!6.03!Shox2;;chr4:150482353..150482386,-!p6@Camta1!0.85!6.03!Camta1;;chr4:22415443..22415506,-!p1@Pou3f2!0.85!6.03!Pou3f2;;chr7:17062114..17062141,-!p1@Npas1!0.85!6.03!Npas1;;chr2:151907546..151907561,+!p1@Scrt2!0.85!6.03!Scrt2;;chr14:34791937..34791977,-!p1@Zfp488!0.85!6.03!Zfp488;;chr6:145814003..145814056,-!p1@Bhlhe41!0.84!18.08!Bhlhe41;;chr8:112603658..112603674,+!p2@Zfp612!0.84!11.22!Zfp612;;chr7:91558472..91558512,-!p2@Arnt2!0.84!8.73!Arnt2;;chr3:95032184..95032195,-!p4@Mllt11!0.84!7.48!Mllt11;;chr6:134780163..134780197,+!p2@Crebl2!0.83!13.92!Crebl2;;chr14:104867201..104867258,-!p1@Pou4f1!0.83!8.31!Pou4f1;;chr11:96685487..96685512,-!p7@Nfe2l1!0.83!5.82!Nfe2l1;;chr8:12395892..12395919,+!p4@Sox1!0.83!5.82!Sox1;;chr3:130813200..130813252,+!p1@Lef1!0.82!27.01!Lef1;;chr19:23216132..23216157,+!p3@Klf9!0.82!8.93!Klf9;;chr17:86020510..86020589,+!p3@Six3!0.82!5.61!Six3;;chr6:55631042..55631102,-!p1@Neurod6!0.82!5.61!Neurod6;;chr19:55972403..55972421,+!p22@Tcf7l2!0.82!5.61!Tcf7l2;;chr14:19071466..19071550,-!p1@Nr1d2!0.81!40.31!Nr1d2;;chr11:21901608..21901634,-!p1@Otx1!0.81!5.40!Otx1;;chr15:82742573..82742620,-!p2@Tcf20!0.81!5.40!Tcf20;;chr17:86020115..86020128,+!p2@Six3!0.81!5.40!Six3;;chr17:27693525..27693538,+!p5@Hmga1!0.79!18.91!Hmga1;;chr14:52935860..52935874,-!p3@Sall2!0.79!7.69!Sall2;;chr19:4989964..4989972,-!p1@Npas4!0.79!5.19!Npas4;;chr9:91263879..91263911,+!p1@Zic4!0.79!5.19!Zic4;;chr8:12395874..12395885,+!p2@Sox1!0.78!4.99!Sox1;;chr12:86939997..86940040,+!p4@Jdp2!0.78!4.99!Jdp2;;chr2:181501745..181501778,+!p1@Myt1!0.78!4.99!Myt1;;chr2:79296783..79296801,-!p1@Neurod1!0.78!4.99!Neurod1;;chr7:30092993..30093076,+!p1@Dpf1!0.77!8.93!Dpf1;;chr2:115890294..115890334,-!p9@Meis2!0.77!6.86!Meis2;;chr2:151907338..151907360,+!p2@Scrt2!0.76!4.78!Scrt2;;chr11:90252108..90252134,-!p6@Hlf!0.76!4.78!Hlf;;chr15:103164702..103164778,-!p3@Zfp385a!0.75!5.61!Zfp385a;;chr19:55970060..55970071,+!p25@Tcf7l2!0.75!4.57!Tcf7l2;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.74!51.53!Camta2;;chr4:124334894..124334899,+!p1@Pou3f1!0.74!6.03!Pou3f1;;chr6:6831950..6831985,-!p2@Dlx5!0.74!4.99!Dlx5;;chr7:52960555..52960662,+!p1@Dbp!0.73!41.97!Dbp;;chr9:69137648..69137656,+!p5@Rora!0.73!6.23!Rora;;chr7:91558537..91558558,-!p4@Arnt2!0.73!5.40!Arnt2;;chr14:118636214..118636235,-!p1@Sox21!0.73!5.40!Sox21;;chrX:108009734..108009752,+!p2@Pou3f4!0.73!4.36!Pou3f4;;chr11:98190918..98190951,-!p1@Neurod2!0.73!4.36!Neurod2;;chr2:65768174..65768247,+!p2@Csrnp3!0.73!4.36!Csrnp3;;chr8:79423672..79423727,+!p2@Nr3c2!0.72!5.61!Nr3c2;;chr2:77654815..77654872,-!p2@Zfp385b!0.72!5.40!Zfp385b;;chr9:68501522..68501538,+!p4@Rora!0.71!8.31!Rora;;chr8:12395670..12395682,+!p3@Sox1!0.71!4.16!Sox1;;chr9:99776566..99776612,-!p1@Sox14!0.71!4.16!Sox14;;chr2:31495237..31495243,+!p1@Prdm12!0.71!4.16!Prdm12;;chr2:65768149..65768173,+!p4@Csrnp3!0.71!4.16!Csrnp3;;chr19:55967842..55967878,+!p13@Tcf7l2!0.71!4.16!Tcf7l2;;chr11:84339016..84339044,-!p1@Lhx1!0.71!4.16!Lhx1;;chr4:22415290..22415307,-!p2@Pou3f2!0.71!4.16!Pou3f2;;chr2:71367871..71367898,+!p1@Dlx1!0.71!4.16!Dlx1;;chr13:72766279..72766296,+!p2@Irx2!0.70!6.23!Irx2;;chrX:108810678..108810736,-!p1@Hdx!0.69!14.75!Hdx;;chr9:106356278..106356292,+!p3@Pcbp4!0.69!7.06!Pcbp4;;chr19:55972441..55972456,+!p18@Tcf7l2!0.69!3.95!Tcf7l2;;chr2:147012125..147012149,-!p1@Nkx2-2!0.69!3.95!Nkx2-2;;chr19:55967803..55967834,+!p12@Tcf7l2!0.69!3.95!Tcf7l2;;chr16:91269972..91269978,+!p3@Olig1!0.69!3.95!Olig1;;chr3:66785857..66785873,-!p1@Shox2!0.69!3.95!Shox2;;chr14:100683672..100683717,-!p1@Klf12!0.68!20.16!Klf12;;chr11:98636575..98636607,-!p2@Nr1d1!0.68!15.58!Nr1d1;;chr7:122968213..122968266,-!p4@Sox6!0.68!4.57!Sox6;;chr6:6813269..6813272,+!p2@Dlx6!0.68!3.74!Dlx6;;chr2:162769220..162769252,+!p1@L3mbtl1!0.68!3.74!L3mbtl1;;chr2:181501710..181501742,+!p2@Myt1!0.68!3.74!Myt1;;chr13:44936077..44936096,+!p9@Jarid2!0.68!3.74!Jarid2;;chr15:81633139..81633152,+!p4@Tef!0.67!6.65!Tef;;chr7:30088977..30089002,+!p2@Dpf1!0.67!5.40!Dpf1;;chr6:6832076..6832092,-!p1@Dlx5!0.67!4.36!Dlx5;;chr7:17200307..17200370,-!p2@Grlf1!0.66!30.13!Grlf1;;chr14:55711198..55711258,-!p1@Zfhx2!0.66!23.48!Zfhx2;;chr19:55816398..55816409,+!p5@Tcf7l2!0.66!19.32!Tcf7l2;;chr2:56967334..56967366,-!p1@Nr4a2!0.66!8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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0006222,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 44: @@
 |is_a=FF:0010193
 |is_obsolete=
+|library_id=CNhs10482
+|library_id_phase_based=2:CNhs10482
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;20
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;20
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/diencephalon%252c%2520adult.CNhs10482.20-12F2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/diencephalon%252c%2520adult.CNhs10482.20-12F2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/diencephalon%252c%2520adult.CNhs10482.20-12F2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/diencephalon%252c%2520adult.CNhs10482.20-12F2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/diencephalon%252c%2520adult.CNhs10482.20-12F2.mm9.nobarcode.rdna.fa.gz
 |name=diencephalon, adult
 |namespace=
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10482,LSID647,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0948332550708915,0,0,0,0,0,-0.07037316090974,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.117511142531851,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.249018298909606,0,0,0,0,0.0352173353880723,-0.0286481431196036,0.105203803839404,-0.233038617959035,0.593033158502813,0.601787726676272,0,0,0.0819907263755358,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0.0819907263755358,0,0.0428386874750523,-0.159717439098214,0.38516430139836,0.0453980173786823,0,0,0.118047427097309,0.183835157817696,0.0819907263755358,0,0.101247450320599,0.114334855382306,-0.10766313425957,-0.0788315948399074,0,0,0,0,0,0,-0.0651338284953167,-0.353179759190555,-0.0629741741487032,0,0,0.488251746481,0,0
 |rna_box=12
 |rna_catalog_number=
@@ Line 60: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 80: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:20-12F2;search_select_hide=table117:20-12F2
 }}

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FF:20-12F2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:09, 4 June 2020

CNhs10482

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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