FF:11740-123F3: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Neurons - raphe, donor2
Species:	Mouse (Mus musculus)
Library ID:	CNhs12636
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	raphe nuclei
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	RNARAP3
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		SAMD00004769

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12636		CAGE		DRX008841		DRR009713

Accession ID Mm9

Library id		BAM		CTSS
CNhs12636		DRZ001138		DRZ002523

Accession ID Mm10

Library id		BAM		CTSS
CNhs12636		DRZ012488		DRZ013873

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

CNhs12636

0	0
1	0.777
10	0
100	0
1000	0
1001	0.097
1002	0.00416
1003	-0.0108
1004	0
1005	-0.00803
1006	0.624
1007	-0.116
1008	0
1009	-0.0912
101	-0.141
1010	0
1011	0.443
1012	0.141
1013	0.284
1014	-0.0408
1015	-0.0519
1016	-0.016
1017	0
1018	0
1019	0
102	0
1020	0.518
1021	0.0522
1022	0.0169
1023	0
1024	0
1025	0
1026	0
1027	0.356
1028	0
1029	-0.0488
103	-0.0788
1030	0
1031	-0.413
1032	0.459
1033	-0.0665
1034	0
1035	0
1036	-0.24
1037	0
1038	-0.0615
1039	0.117
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: CNhs12636

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	9.96019e-4
MA0003.1	MA0003.1	0.302
MA0004.1	MA0004.1	0.504
MA0006.1	MA0006.1	0.19
MA0007.1	MA0007.1	0.267
MA0009.1	MA0009.1	0.763
MA0014.1	MA0014.1	0.8
MA0017.1	MA0017.1	4.48578e-6
MA0018.2	MA0018.2	0.0118
MA0019.1	MA0019.1	0.528
MA0024.1	MA0024.1	0.0824
MA0025.1	MA0025.1	0.00112
MA0027.1	MA0027.1	0.109
MA0028.1	MA0028.1	0.0838
MA0029.1	MA0029.1	0.874
MA0030.1	MA0030.1	0.912
MA0031.1	MA0031.1	0.198
MA0035.2	MA0035.2	0.0284
MA0038.1	MA0038.1	0.898
MA0039.2	MA0039.2	0.0286
MA0040.1	MA0040.1	0.568
MA0041.1	MA0041.1	0.177
MA0042.1	MA0042.1	0.32
MA0043.1	MA0043.1	0.0543
MA0046.1	MA0046.1	2.67482e-8
MA0047.2	MA0047.2	0.00107
MA0048.1	MA0048.1	0.0531
MA0050.1	MA0050.1	3.45223e-6
MA0051.1	MA0051.1	3.84505e-4
MA0052.1	MA0052.1	0.967
MA0055.1	MA0055.1	0.0155
MA0057.1	MA0057.1	0.355
MA0058.1	MA0058.1	0.501
MA0059.1	MA0059.1	0.187
MA0060.1	MA0060.1	0.859
MA0061.1	MA0061.1	0.025
MA0062.2	MA0062.2	0.00192
MA0065.2	MA0065.2	5.4068e-6
MA0066.1	MA0066.1	0.101
MA0067.1	MA0067.1	0.355
MA0068.1	MA0068.1	0.212
MA0069.1	MA0069.1	0.0458
MA0070.1	MA0070.1	0.573
MA0071.1	MA0071.1	0.219
MA0072.1	MA0072.1	0.841
MA0073.1	MA0073.1	0.943
MA0074.1	MA0074.1	0.133
MA0076.1	MA0076.1	0.218
MA0077.1	MA0077.1	0.255
MA0078.1	MA0078.1	0.932
MA0079.2	MA0079.2	0.324
MA0080.2	MA0080.2	2.37523e-10
MA0081.1	MA0081.1	0.28
MA0083.1	MA0083.1	0.00516
MA0084.1	MA0084.1	0.658
MA0087.1	MA0087.1	0.112
MA0088.1	MA0088.1	0.28
MA0090.1	MA0090.1	0.0807
MA0091.1	MA0091.1	0.188
MA0092.1	MA0092.1	0.14
MA0093.1	MA0093.1	0.551
MA0099.2	MA0099.2	0.00451
MA0100.1	MA0100.1	0.205
MA0101.1	MA0101.1	0.0115
MA0102.2	MA0102.2	0.581
MA0103.1	MA0103.1	0.236
MA0104.2	MA0104.2	0.886
MA0105.1	MA0105.1	0.00408
MA0106.1	MA0106.1	0.062
MA0107.1	MA0107.1	0.0297
MA0108.2	MA0108.2	7.39012e-4
MA0111.1	MA0111.1	0.926
MA0112.2	MA0112.2	8.18438e-4
MA0113.1	MA0113.1	0.378
MA0114.1	MA0114.1	1.41811e-5
MA0115.1	MA0115.1	8.97439e-5
MA0116.1	MA0116.1	0.0637
MA0117.1	MA0117.1	0.906
MA0119.1	MA0119.1	0.104
MA0122.1	MA0122.1	0.752
MA0124.1	MA0124.1	0.663
MA0125.1	MA0125.1	0.0447
MA0131.1	MA0131.1	0.701
MA0135.1	MA0135.1	0.48
MA0136.1	MA0136.1	5.91469e-12
MA0137.2	MA0137.2	0.115
MA0138.2	MA0138.2	1.87678e-4
MA0139.1	MA0139.1	0.45
MA0140.1	MA0140.1	1.58507e-4
MA0141.1	MA0141.1	0.0195
MA0142.1	MA0142.1	0.447
MA0143.1	MA0143.1	0.814
MA0144.1	MA0144.1	0.0735
MA0145.1	MA0145.1	0.116
MA0146.1	MA0146.1	0.0371
MA0147.1	MA0147.1	0.73
MA0148.1	MA0148.1	3.98357e-4
MA0149.1	MA0149.1	0.185
MA0150.1	MA0150.1	0.166
MA0152.1	MA0152.1	0.0565
MA0153.1	MA0153.1	1.09703e-9
MA0154.1	MA0154.1	0.0422
MA0155.1	MA0155.1	0.417
MA0156.1	MA0156.1	1.17721e-8
MA0157.1	MA0157.1	0.142
MA0159.1	MA0159.1	0.00869
MA0160.1	MA0160.1	0.043
MA0162.1	MA0162.1	0.233
MA0163.1	MA0163.1	7.60967e-4
MA0164.1	MA0164.1	0.848
MA0258.1	MA0258.1	0.0208
MA0259.1	MA0259.1	0.855

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: CNhs12636

Novel motif	Logo	P-value
1	1	0.211
10	10	0.0448
100	100	0.278
101	101	0.94
102	102	0.921
103	103	0.0818
104	104	0.927
105	105	0.575
106	106	0.0564
107	107	0.145
108	108	0.493
109	109	0.00718
11	11	0.109
110	110	0.0495
111	111	0.275
112	112	0.00911
113	113	0.647
114	114	0.482
115	115	0.974
116	116	0.379
117	117	0.00421
118	118	0.471
119	119	0.169
12	12	0.835
120	120	0.762
121	121	0.416
122	122	0.832
123	123	2.68192e-4
124	124	0.181
125	125	0.186
126	126	0.0575
127	127	0.517
128	128	0.0562
129	129	0.197
13	13	3.01135e-7
130	130	0.128
131	131	0.297
132	132	0.682
133	133	0.949
134	134	0.0818
135	135	0.296
136	136	0.225
137	137	0.664
138	138	0.657
139	139	0.26
14	14	0.874
140	140	0.227
141	141	0.818
142	142	0.813
143	143	0.349
144	144	0.603
145	145	2.74394e-4
146	146	0.253
147	147	0.254
148	148	0.992
149	149	0.774
15	15	0.205
150	150	0.0736
151	151	0.777
152	152	0.137
153	153	0.432
154	154	0.754
155	155	0.41
156	156	0.00385
157	157	0.155
158	158	0.147
159	159	0.567
160	160	0.237
161	161	0.223
162	162	0.666
163	163	0.947
164	164	0.0442
165	165	0.198
166	166	0.44
167	167	0.681
168	168	0.523
169	169	0.0028
17	17	0.0638
18	18	0.807
19	19	0.103
2	2	0.678
20	20	0.0355
21	21	0.215
22	22	0.148
23	23	0.661
24	24	0.0579
25	25	0.723
26	26	6.88064e-8
27	27	0.38
28	28	0.754
29	29	0.0485
3	3	0.0709
30	30	0.808
31	31	0.718
32	32	0.572
33	33	0.0956
34	34	0.752
35	35	0.716
36	36	0.109
37	37	0.036
38	38	0.426
39	39	0.389
4	4	0.235
40	40	0.0827
41	41	0.568
42	42	0.149
43	43	0.117
44	44	0.944
45	45	0.673
46	46	0.0532
47	47	0.378
48	48	0.296
49	49	0.14
5	5	0.165
50	50	0.256
51	51	0.715
52	52	0.3
53	53	0.574
54	54	0.958
55	55	0.976
56	56	0.478
57	57	0.526
58	58	0.247
59	59	0.179
6	6	0.9
60	60	0.0395
61	61	0.041
62	62	0.169
63	63	0.156
64	64	0.711
65	65	0.366
66	66	0.697
67	67	0.668
68	68	0.8
69	69	0.435
7	7	0.0122
70	70	0.0828
71	71	0.00338
72	72	0.508
73	73	0.0521
74	74	0.969
75	75	0.0517
76	76	0.392
77	77	0.514
78	78	0.00337
79	79	0.0636
8	8	0.0649
80	80	0.718
81	81	0.795
82	82	0.291
83	83	0.142
84	84	0.843
85	85	0.191
86	86	0.135
87	87	0.462
88	88	0.684
89	89	0.617
9	9	0.382
90	90	0.0983
91	91	0.126
92	92	0.349
93	93	0.0471
94	94	0.654
95	95	0.0623
96	96	0.218
97	97	0.743
98	98	0.637
99	99	0.474

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: CNhs12636

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000205 mouse raphe nuclei 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)
0002610 (raphe nuclei neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0004684 (raphe nuclei)
0001016 (nervous system)
0002275 (reticular formation)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000205 (mouse raphe nuclei 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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000033,UBERON:0000479,UBERON:0000073,UBERON:0004121,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000467,UBERON:0002616,UBERON:0001062,UBERON:0005291,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0004684,UBERON:0001016,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0005743,UBERON:0002275,UBERON:0006238,UBERON:0006601
+|DRA_sample_Accession=CAGE@SAMD00004769
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000540,CL:0000055,CL:0000047,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002321,CL:0002371,CL:0002319,CL:0000221,CL:0000117,CL:0000393,CL:0000220,CL:0000004,CL:0000031,CL:0000211,CL:0000404,CL:0000255,CL:0002610,CL:0000133,CL:0000337
+|accession_numbers=CAGE;DRX008841;DRR009713;DRZ001138;DRZ002523;DRZ012488;DRZ013873
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0004684,UBERON:0001016,UBERON:0002275
+|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:0002610
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000203,FF:0000205
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.45!315.90!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.80!112.75!Tsc22d4;;chr9:91260616..91260653,-!p2@Zic1!1.76!55.93!Zic1;;chr15:76353005..76353021,-!p2@Scrt1!1.73!52.99!Scrt1;;chr17:48015839..48015915,-!p3@Foxp4!1.63!48.90!Foxp4;;chr16:91225808..91225824,+!p1@Olig2!1.63!41.63!Olig2;;chr8:24780125..24780143,+!p1@Zmat4!1.62!57.84!Zmat4;;chr19:19185671..19185693,-!p1@Rorb!1.61!91.55!Rorb;;chr9:91260594..91260612,-!p1@Zic1!1.55!34.86!Zic1;;chr10:67375368..67375433,-!p1@Zfp365!1.54!57.84!Zfp365;;chr7:116154364..116154444,+!p1@Tub!1.54!56.95!Tub;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.51!39.58!Pou3f3;;chr15:76352677..76352737,-!p3@Scrt1!1.51!31.16!Scrt1;;chr12:30219426..30219506,+!p2@Myt1l!1.50!30.77!Myt1l;;chr15:76352434..76352488,-!p4@Scrt1!1.50!30.26!Scrt1;;chr3:95032091..95032183,-!p1@Mllt11!1.48!239.80!Mllt11;;chr18:36441119..36441158,+!p2@Pura!1.41!58.35!Pura;;chr10:67375146..67375208,-!p2@Zfp365!1.41!37.67!Zfp365;;chrX:34442872..34442899,-!p1@Nkrf!1.40!30.90!Nkrf;;chr19:55969923..55969944,+!p6@Tcf7l2!1.35!21.32!Tcf7l2;;chr17:25707623..25707639,-!p1@Sox8!1.34!87.85!Sox8;;chr16:91270091..91270143,+!p2@Olig1!1.34!20.69!Olig1;;chr7:146768691..146768707,-!p1@Nkx6-2!1.33!20.56!Nkx6-2;;chr2:163051181..163051205,+!p2@Tox2!1.33!20.30!Tox2;;chr4:150482563..150482655,-!p2@Camta1!1.31!68.57!Camta1;;chr9:69137716..69137744,+!p1@Rora!1.28!109.56!Rora;;chr4:58956447..58956510,+!p1@Zkscan16!1.27!38.43!Zkscan16;;chr2:127347067..127347093,-!p1@Kcnip3!1.27!29.62!Kcnip3;;chr11:90251852..90251855,-!p4@Hlf!1.24!19.79!Hlf;;chr6:55631042..55631102,-!p1@Neurod6!1.24!16.47!Neurod6;;chr19:55969946..55969973,+!p8@Tcf7l2!1.23!16.09!Tcf7l2;;chr11:98636531..98636559,-!p1@Nr1d1!1.22!87.47!Nr1d1;;chr2:65683890..65683907,+!p1@Csrnp3!1.20!28.35!Csrnp3;;chr2:168427068..168427115,-!p3@Nfatc2!1.19!14.56!Nfatc2;;chr7:148008023..148008092,-!p1@Zfp941!1.18!33.84!Zfp941;;chr12:54349410..54349461,+!p1@Npas3!1.16!16.09!Npas3;;chr19:55968967..55968991,+!p7@Tcf7l2!1.15!13.15!Tcf7l2;;chr19:19185697..19185711,-!p2@Rorb!1.14!16.22!Rorb;;chr3:95032213..95032226,-!p6@Mllt11!1.14!15.32!Mllt11;;chr10:67375342..67375365,-!p3@Zfp365!1.14!12.90!Zfp365;;chr11:98190918..98190951,-!p1@Neurod2!1.14!12.90!Neurod2;;chr15:103170533..103170556,-!p1@Zfp385a!1.13!46.73!Zfp385a;;chr15:78994907..78994926,-!p1@Sox10!1.13!32.43!Sox10;;chr2:163030186..163030204,+!p4@Tox2!1.12!12.26!Tox2;;chr2:127347094..127347111,-!p2@Kcnip3!1.11!19.79!Kcnip3;;chr5:98609885..98609900,+!p1@Prdm8!1.11!11.87!Prdm8;;chrX:34442842..34442866,-!p3@Nkrf!1.11!11.87!Nkrf;;chr2:163030219..163030258,+!p5@Tox2!1.10!11.62!Tox2;;chrX:108009761..108009788,+!p1@Pou3f4!1.10!11.62!Pou3f4;;chr3:95032197..95032208,-!p3@Mllt11!1.09!14.30!Mllt11;;chr15:103170516..103170531,-!p2@Zfp385a!1.08!26.43!Zfp385a;;chr6:145813905..145813932,-!p2@Bhlhe41!1.08!21.20!Bhlhe41;;chr14:122874619..122874634,+!p1@Zic2!1.06!10.60!Zic2;;chr8:12395603..12395621,+!p1@Sox1!1.06!10.47!Sox1;;chr3:34548946..34548972,+!p2@Sox2!1.05!11.24!Sox2;;chr11:90252223..90252240,-!p1@Hlf!1.04!83.38!Hlf;;chr8:112603658..112603674,+!p2@Zfp612!1.04!18.51!Zfp612;;chr8:107793688..107793736,+!p1@Hsf4!1.04!13.15!Hsf4;;chr11:96685444..96685473,-!p5@Nfe2l1!1.04!10.09!Nfe2l1;;chr10:84218895..84218909,+!p1@Rfx4!1.03!9.83!Rfx4;;chr2:81893535..81893548,+!p1@Zfp804a!1.02!9.58!Zfp804a;;chr1:91827756..91827773,-!p1@Gbx2!1.02!9.58!Gbx2;;chr3:34548909..34548927,+!p1@Sox2!1.01!15.71!Sox2;;chr1:6477388..6477419,+!p3@St18!1.01!9.19!St18;;chr11:90250944..90250982,-!p2@Hlf!1.00!15.19!Hlf;;chr3:95032184..95032195,-!p4@Mllt11!1.00!11.11!Mllt11;;chr6:145814003..145814056,-!p1@Bhlhe41!0.99!25.67!Bhlhe41;;chr7:91558392..91558434,-!p1@Arnt2!0.99!24.77!Arnt2;;chr6:134780163..134780197,+!p2@Crebl2!0.99!20.81!Crebl2;;chr2:38206744..38206766,+!p1@Lhx2!0.99!10.60!Lhx2;;chr4:150513630..150513686,-!p4@Camta1!0.99!10.21!Camta1;;chr3:66785201..66785226,-!p3@Shox2!0.99!8.81!Shox2;;chr10:84218800..84218829,+!p2@Rfx4!0.99!8.81!Rfx4;;chr3:95032558..95032641,-!p2@Mllt11!0.98!48.39!Mllt11;;chr3:95032515..95032553,-!p5@Mllt11!0.98!10.47!Mllt11;;chr7:17062114..17062141,-!p1@Npas1!0.98!8.56!Npas1;;chr7:52960555..52960662,+!p1@Dbp!0.97!72.40!Dbp;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.96!87.59!Camta2;;chr9:69137672..69137702,+!p2@Rora!0.96!35.37!Rora;;chr5:122499831..122499891,-!p1@Cux2!0.96!12.77!Cux2;;chr1:140739014..140739032,-!p1@Lhx9!0.96!10.34!Lhx9;;chr2:65768174..65768247,+!p2@Csrnp3!0.96!8.17!Csrnp3;;chr4:150482353..150482386,-!p6@Camta1!0.96!8.04!Camta1;;chrX:137083127..137083138,-!p9@Tsc22d3!0.96!8.04!Tsc22d3;;chr7:52960700..52960719,+!p2@Dbp!0.95!9.96!Dbp;;chr4:154335024..154335039,+!p1@Hes5!0.94!9.45!Hes5;;chr1:179374784..179374800,+!p2@Zfp238!0.94!9.19!Zfp238;;chr19:55967803..55967834,+!p12@Tcf7l2!0.94!7.79!Tcf7l2;;chr11:90250894..90250916,-!p5@Hlf!0.94!7.79!Hlf;;chr2:181501710..181501742,+!p2@Myt1!0.94!7.66!Myt1;;chr2:81893447..81893468,+!p2@Zfp804a!0.94!7.66!Zfp804a;;chr19:26681865..26681900,+!p6@Smarca2!0.93!22.73!Smarca2;;chr10:67375223..67375240,-!p4@Zfp365!0.93!8.43!Zfp365;;chrX:55283799..55283813,+!p1@Zic3!0.92!7.28!Zic3;;chr12:30213247..30213333,+!p1@Myt1l!0.92!7.28!Myt1l;;chr19:10315179..10315241,-!p1@Gm98!0.91!77.76!Gm98;;chr16:91225654..91225671,+!p2@Olig2!0.91!7.15!Olig2;;chr7:30092993..30093076,+!p1@Dpf1!0.90!12.39!Dpf1;;chr3:66785181..66785199,-!p2@Shox2!0.90!7.02!Shox2;;chr2:127347042..127347058,-!p3@Kcnip3!0.90!7.02!Kcnip3;;chr2:25562263..25562314,+!p2@Bmyc!0.89!27.58!Bmyc;;chr13:72766250..72766273,+!p1@Irx2!0.89!10.73!Irx2;;chr12:72149325..72149343,+!p2@Arid4a!0.89!9.70!Arid4a;;chr7:91558472..91558512,-!p2@Arnt2!0.88!9.58!Arnt2;;chr7:52960888..52960902,+!p7@Dbp!0.88!6.64!Dbp;;chr2:163030164..163030178,+!p6@Tox2!0.88!6.64!Tox2;;chr2:151907546..151907561,+!p1@Scrt2!0.88!6.64!Scrt2;;chr14:122874593..122874610,+!p2@Zic2!0.88!6.51!Zic2;;chr3:101814061..101814094,+!p1@Nhlh2!0.88!6.51!Nhlh2;;chr9:69137648..69137656,+!p5@Rora!0.87!9.19!Rora;;chr14:19071466..19071550,-!p1@Nr1d2!0.86!44.69!Nr1d2;;chr6:145813964..145813994,-!p3@Bhlhe41!0.86!8.04!Bhlhe41;;chr15:103164702..103164778,-!p3@Zfp385a!0.86!7.53!Zfp385a;;chr11:90252071..90252093,-!p7@Hlf!0.86!6.26!Hlf;;chr11:96685487..96685512,-!p7@Nfe2l1!0.86!6.26!Nfe2l1;;chr14:52935860..52935874,-!p3@Sall2!0.85!9.07!Sall2;;chr2:181501745..181501778,+!p1@Myt1!0.85!6.13!Myt1;;chr14:104867201..104867258,-!p1@Pou4f1!0.84!8.43!Pou4f1;;chr12:30220074..30220102,+!p3@Myt1l!0.84!5.87!Myt1l;;chr19:55972767..55972779,+!p20@Tcf7l2!0.84!5.87!Tcf7l2;;chr11:90252108..90252134,-!p6@Hlf!0.83!5.75!Hlf;;chr3:54559463..54559493,+!p3@Smad9!0.82!10.73!Smad9;;chr15:103170561..103170572,-!p4@Zfp385a!0.82!8.30!Zfp385a;;chr7:17200307..17200370,-!p2@Grlf1!0.81!42.90!Grlf1;;chr19:55816546..55816556,+!p3@Tcf7l2!0.81!22.35!Tcf7l2;;chr19:55970060..55970071,+!p25@Tcf7l2!0.81!5.49!Tcf7l2;;chrX:90531838..90531861,+!p1@Arx!0.80!6.77!Arx;;chr10:80893711..80893784,-!p3@Nfic!0.79!29.24!Nfic;;chr3:130813200..130813252,+!p1@Lef1!0.79!24.77!Lef1;;chr4:124334894..124334899,+!p1@Pou3f1!0.79!6.90!Pou3f1;;chr11:90250999..90251013,-!p8@Hlf!0.79!5.24!Hlf;;chr11:21901608..21901634,-!p1@Otx1!0.79!5.24!Otx1;;chr19:55967842..55967878,+!p13@Tcf7l2!0.79!5.24!Tcf7l2;;chr14:34791937..34791977,-!p1@Zfp488!0.79!5.24!Zfp488;;chr11:98636508..98636524,-!p3@Nr1d1!0.78!6.38!Nr1d1;;chr7:91558537..91558558,-!p4@Arnt2!0.78!6.26!Arnt2;;chr14:49287186..49287225,-!p1@Otx2!0.78!4.98!Otx2;;chr12:86939997..86940040,+!p4@Jdp2!0.78!4.98!Jdp2;;chr19:55969687..55969714,+!p16@Tcf7l2!0.78!4.98!Tcf7l2;;chr2:56967334..56967366,-!p1@Nr4a2!0.77!10.73!Nr4a2;;chr11:116196664..116196679,-!p1@Foxj1!0.77!7.79!Foxj1;;chr8:79423144..79423178,+!p3@Nr3c2!0.77!7.02!Nr3c2;;chr15:82742573..82742620,-!p2@Tcf20!0.77!4.85!Tcf20;;chr4:22415443..22415506,-!p1@Pou3f2!0.77!4.85!Pou3f2;;chr7:6683123..6683142,-!p1@Peg3!0.76!274.66!Peg3;;chrX:137077151..137077227,-!p2@Tsc22d3!0.76!36.14!Tsc22d3;;chr7:52960730..52960762,+!p3@Dbp!0.76!6.26!Dbp;;chr15:76352832..76352900,-!p1@Scrt1!0.76!4.72!Scrt1;;chr8:112603610..112603656,+!p1@Zfp612!0.75!23.49!Zfp612;;chr19:23216132..23216157,+!p3@Klf9!0.75!7.53!Klf9;;chr2:25562315..25562344,+!p3@Bmyc!0.74!16.47!Bmyc;;chr14:76903992..76904056,+!p6@Tsc22d1!0.74!9.96!Tsc22d1;;chr13:44936126..44936164,+!p6@Jarid2!0.74!5.36!Jarid2;;chr14:122874718..122874729,+!p3@Zic2!0.74!4.47!Zic2;;chr7:52960663..52960677,+!p6@Dbp!0.74!4.47!Dbp;;chr2:79296783..79296801,-!p1@Neurod1!0.74!4.47!Neurod1;;chr2:77541432..77541474,-!p5@Zfp385b!0.74!4.47!Zfp385b;;chr2:162769220..162769252,+!p1@L3mbtl1!0.74!4.47!L3mbtl1;;chr1:191994550..191994623,-!p1@Prox1!0.73!33.84!Prox1;;chr1:38684414..38684427,-!p7@Aff3!0.73!5.36!Aff3;;chr3:34549096..34549111,+!p3@Sox2!0.73!4.34!Sox2;;chr8:125897750..125897758,+!p2@Tcf25!0.72!31.79!Tcf25;;chr6:117813087..117813121,+!p1@Zfp239!0.72!17.88!Zfp239;;chr3:66785857..66785873,-!p1@Shox2!0.72!4.21!Shox2;;chr11:98603119..98603130,+!p2@Thra!0.71!39.07!Thra;;chr1:170361991..170362015,-!p6@Pbx1!0.71!10.09!Pbx1;;chr7:38554763..38554780,-!p1@Zfp536!0.71!7.92!Zfp536;;chr9:106356278..106356292,+!p3@Pcbp4!0.71!7.53!Pcbp4;;chr7:91520922..91520956,-!p5@Arnt2!0.71!4.09!Arnt2;;chr19:19185429..19185440,-!p3@Rorb!0.71!4.09!Rorb;;chr2:168427120..168427138,-!p4@Nfatc2!0.71!4.09!Nfatc2;;chr11:69579401..69579427,+!p2@Zbtb4!0.70!17.24!Zbtb4;;chr11:98636575..98636607,-!p2@Nr1d1!0.70!16.47!Nr1d1;;chr5:3648045..3648074,-!p2@Gatad1!0.70!7.15!Gatad1;;chr8:79423672..79423727,+!p2@Nr3c2!0.70!5.24!Nr3c2;;chrX:95345005..95345053,+!p1@Ar!0.70!3.96!Ar;;chr11:69579472..69579529,+!p1@Zbtb4!0.69!22.35!Zbtb4;;chr11:98603160..98603171,+!p3@Thra!0.69!20.81!Thra;;chr5:125342568..125342602,+!p2@Zfp664!0.69!6.77!Zfp664;;chr4:48058129..48058179,+!p2@Nr4a3!0.68!7.66!Nr4a3;;chr11:98190955..98190968,-!p2@Neurod2!0.67!3.70!Neurod2;;chr11:84339016..84339044,-!p1@Lhx1!0.67!3.70!Lhx1;;chr8:12395892..12395919,+!p4@Sox1!0.67!3.70!Sox1;;chr19:55972441..55972456,+!p18@Tcf7l2!0.67!3.70!Tcf7l2;;chr7:25292160..25292213,+!p3@Zfp428!0.66!9.83!Zfp428;;chr15:8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+|ffid_belonging_in_development=CL:0000133,CL:0000337,CL:0000031,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000205
 |is_obsolete=
+|library_id=CNhs12636
+|library_id_phase_based=2:CNhs12636
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11740
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11740
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520raphe%252c%2520donor2.CNhs12636.11740-123F3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520raphe%252c%2520donor2.CNhs12636.11740-123F3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520raphe%252c%2520donor2.CNhs12636.11740-123F3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520raphe%252c%2520donor2.CNhs12636.11740-123F3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520raphe%252c%2520donor2.CNhs12636.11740-123F3.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - raphe, donor2
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12636,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0208727630824404,0,0,0,0,0,0.167018185711737,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.0551278483626942,0,0,0,0,0,0,0,0,0,0,0,0,0.357844959465935,-0.37923037558583,0,0,0,0,0.052188704109448,-0.110549361823474,0.198536726804159,0.0995205967453243,0.367033469159941,0.378252994886138,0.214429664803005,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0.052188704109448,0,0,0,0,0,-0.0602757386480555,0,0,0,-0.150253716587732,-0.310650657339386,0.0211013739671191,-0.0825789127860286,0,0,0.176325569803597,0.313988004206059,0,0,0.133301213310305,0.258901513529305,0.241270483587836,0.0199417688324445,0,0,0,0,0,0,0.0779028251612911,-0.233454908268419,-0.0332451696722931,0,0,0.66041439935041,0.35641990840645,0.026094352054724
 |rna_box=123
 |rna_catalog_number=custom
@@ Line 58: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11740-123F3;search_select_hide=table117:11740-123F3
 }}

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FF:11740-123F3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12636

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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