FF:11722-123D3: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Neurons - raphe, donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs12631
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	RNARAP2
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005499

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12631		CAGE		DRX008840		DRR009712

Accession ID Mm9

Library id		BAM		CTSS
CNhs12631		DRZ001137		DRZ002522

Accession ID Mm10

Library id		BAM		CTSS
CNhs12631		DRZ012487		DRZ013872

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

CNhs12631

0	0
1	0.733
10	0
100	0
1000	0
1001	0
1002	-0.0941
1003	-0.0029
1004	0
1005	0
1006	0.693
1007	-0.198
1008	0
1009	-0.2
101	-0.246
1010	0
1011	0.19
1012	0
1013	0.407
1014	-0.0851
1015	-0.212
1016	0.0537
1017	0
1018	0
1019	0
102	0
1020	0.322
1021	-0.0487
1022	-0.0704
1023	0
1024	-0.0899
1025	0
1026	0
1027	0.416
1028	0
1029	-0.148
103	-0.0848
1030	0
1031	-0.46
1032	0.638
1033	0.247
1034	0
1035	0
1036	-0.328
1037	0
1038	-0.194
1039	3.171674e-4
104	0
1040	-0.268
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: CNhs12631

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.074
MA0003.1	MA0003.1	0.371
MA0004.1	MA0004.1	0.455
MA0006.1	MA0006.1	0.166
MA0007.1	MA0007.1	0.339
MA0009.1	MA0009.1	0.771
MA0014.1	MA0014.1	0.727
MA0017.1	MA0017.1	2.18456e-5
MA0018.2	MA0018.2	0.0071
MA0019.1	MA0019.1	0.406
MA0024.1	MA0024.1	0.00277
MA0025.1	MA0025.1	0.00113
MA0027.1	MA0027.1	0.129
MA0028.1	MA0028.1	0.00447
MA0029.1	MA0029.1	0.851
MA0030.1	MA0030.1	0.977
MA0031.1	MA0031.1	0.223
MA0035.2	MA0035.2	0.0723
MA0038.1	MA0038.1	0.569
MA0039.2	MA0039.2	0.00433
MA0040.1	MA0040.1	0.741
MA0041.1	MA0041.1	0.188
MA0042.1	MA0042.1	0.395
MA0043.1	MA0043.1	0.0848
MA0046.1	MA0046.1	3.37696e-6
MA0047.2	MA0047.2	0.00303
MA0048.1	MA0048.1	0.0136
MA0050.1	MA0050.1	1.7241e-8
MA0051.1	MA0051.1	1.99282e-6
MA0052.1	MA0052.1	0.525
MA0055.1	MA0055.1	4.46814e-4
MA0057.1	MA0057.1	0.388
MA0058.1	MA0058.1	0.471
MA0059.1	MA0059.1	0.324
MA0060.1	MA0060.1	0.0853
MA0061.1	MA0061.1	0.0276
MA0062.2	MA0062.2	2.18002e-6
MA0065.2	MA0065.2	3.99705e-5
MA0066.1	MA0066.1	0.162
MA0067.1	MA0067.1	0.653
MA0068.1	MA0068.1	0.288
MA0069.1	MA0069.1	0.11
MA0070.1	MA0070.1	0.179
MA0071.1	MA0071.1	0.437
MA0072.1	MA0072.1	0.618
MA0073.1	MA0073.1	0.553
MA0074.1	MA0074.1	0.278
MA0076.1	MA0076.1	0.00989
MA0077.1	MA0077.1	0.118
MA0078.1	MA0078.1	0.429
MA0079.2	MA0079.2	0.631
MA0080.2	MA0080.2	1.10516e-9
MA0081.1	MA0081.1	0.171
MA0083.1	MA0083.1	7.51594e-4
MA0084.1	MA0084.1	0.351
MA0087.1	MA0087.1	0.0793
MA0088.1	MA0088.1	0.312
MA0090.1	MA0090.1	0.177
MA0091.1	MA0091.1	0.465
MA0092.1	MA0092.1	0.0956
MA0093.1	MA0093.1	0.482
MA0099.2	MA0099.2	0.0109
MA0100.1	MA0100.1	0.216
MA0101.1	MA0101.1	0.00431
MA0102.2	MA0102.2	0.5
MA0103.1	MA0103.1	0.582
MA0104.2	MA0104.2	0.959
MA0105.1	MA0105.1	0.021
MA0106.1	MA0106.1	0.0675
MA0107.1	MA0107.1	0.0119
MA0108.2	MA0108.2	2.26836e-4
MA0111.1	MA0111.1	0.715
MA0112.2	MA0112.2	0.00518
MA0113.1	MA0113.1	0.525
MA0114.1	MA0114.1	2.50348e-5
MA0115.1	MA0115.1	0.00154
MA0116.1	MA0116.1	0.139
MA0117.1	MA0117.1	0.982
MA0119.1	MA0119.1	0.174
MA0122.1	MA0122.1	0.883
MA0124.1	MA0124.1	0.716
MA0125.1	MA0125.1	0.252
MA0131.1	MA0131.1	0.247
MA0135.1	MA0135.1	0.806
MA0136.1	MA0136.1	1.15751e-11
MA0137.2	MA0137.2	0.153
MA0138.2	MA0138.2	5.96329e-6
MA0139.1	MA0139.1	0.783
MA0140.1	MA0140.1	0.00185
MA0141.1	MA0141.1	0.211
MA0142.1	MA0142.1	0.0174
MA0143.1	MA0143.1	0.442
MA0144.1	MA0144.1	0.0461
MA0145.1	MA0145.1	0.178
MA0146.1	MA0146.1	0.0436
MA0147.1	MA0147.1	0.877
MA0148.1	MA0148.1	0.0103
MA0149.1	MA0149.1	0.753
MA0150.1	MA0150.1	0.344
MA0152.1	MA0152.1	0.0234
MA0153.1	MA0153.1	5.60953e-7
MA0154.1	MA0154.1	0.0667
MA0155.1	MA0155.1	0.535
MA0156.1	MA0156.1	5.96345e-12
MA0157.1	MA0157.1	0.158
MA0159.1	MA0159.1	0.0511
MA0160.1	MA0160.1	0.175
MA0162.1	MA0162.1	0.305
MA0163.1	MA0163.1	0.00338
MA0164.1	MA0164.1	0.846
MA0258.1	MA0258.1	0.094
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: CNhs12631

Novel motif	Logo	P-value
1	1	0.346
10	10	0.0723
100	100	0.243
101	101	0.391
102	102	0.62
103	103	0.295
104	104	0.975
105	105	0.494
106	106	0.0607
107	107	0.361
108	108	0.41
109	109	0.0158
11	11	0.272
110	110	0.0732
111	111	0.725
112	112	0.0229
113	113	0.387
114	114	0.901
115	115	0.644
116	116	0.416
117	117	0.00138
118	118	0.599
119	119	0.375
12	12	0.908
120	120	0.683
121	121	0.489
122	122	0.975
123	123	2.10001e-5
124	124	0.0333
125	125	0.186
126	126	0.076
127	127	0.605
128	128	0.126
129	129	0.371
13	13	4.08607e-10
130	130	0.216
131	131	0.448
132	132	0.618
133	133	0.838
134	134	0.0199
135	135	0.0444
136	136	0.0889
137	137	0.751
138	138	0.645
139	139	0.732
14	14	0.463
140	140	0.366
141	141	0.885
142	142	0.351
143	143	0.797
144	144	0.932
145	145	9.90991e-6
146	146	0.363
147	147	0.112
148	148	0.55
149	149	0.644
15	15	0.405
150	150	0.0457
151	151	0.759
152	152	0.0857
153	153	0.774
154	154	0.435
155	155	0.478
156	156	0.00986
157	157	0.0402
158	158	0.298
159	159	0.62
160	160	0.377
161	161	0.423
162	162	0.366
163	163	0.953
164	164	0.0355
165	165	0.422
166	166	0.351
167	167	0.776
168	168	0.88
169	169	0.00634
17	17	0.108
18	18	0.342
19	19	0.149
2	2	0.352
20	20	0.00368
21	21	0.195
22	22	0.169
23	23	0.893
24	24	0.0291
25	25	0.944
26	26	1.37344e-9
27	27	0.113
28	28	0.917
29	29	0.0449
3	3	0.13
30	30	0.796
31	31	0.423
32	32	0.853
33	33	0.0935
34	34	0.993
35	35	0.294
36	36	0.292
37	37	0.0213
38	38	0.635
39	39	0.326
4	4	0.372
40	40	0.0816
41	41	0.88
42	42	0.285
43	43	0.207
44	44	0.952
45	45	0.685
46	46	0.0701
47	47	0.773
48	48	0.573
49	49	0.396
5	5	0.386
50	50	0.173
51	51	0.825
52	52	0.368
53	53	0.361
54	54	0.923
55	55	0.7
56	56	0.605
57	57	0.959
58	58	0.465
59	59	0.395
6	6	0.968
60	60	0.0466
61	61	0.0409
62	62	0.37
63	63	0.264
64	64	0.924
65	65	0.552
66	66	0.751
67	67	0.86
68	68	0.878
69	69	0.71
7	7	0.0186
70	70	0.384
71	71	0.00167
72	72	0.521
73	73	0.0325
74	74	0.911
75	75	0.0701
76	76	0.249
77	77	0.765
78	78	0.00144
79	79	0.0635
8	8	0.138
80	80	0.659
81	81	0.415
82	82	0.458
83	83	0.35
84	84	0.569
85	85	0.455
86	86	0.196
87	87	0.436
88	88	0.516
89	89	0.85
9	9	0.547
90	90	0.506
91	91	0.142
92	92	0.893
93	93	0.256
94	94	0.956
95	95	0.0323
96	96	0.66
97	97	0.747
98	98	0.689
99	99	0.633

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: CNhs12631

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
-|DRA_sample_Accession=CAGE@DRS008730
+|DRA_sample_Accession=CAGE@SAMD00005499
-|accession_numbers=CAGE;DRX008840;DRR009712;DRZ001137;DRZ002522
+|accession_numbers=CAGE;DRX008840;DRR009712;DRZ001137;DRZ002522;DRZ012487;DRZ013872
 |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
@@ 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!2.55!404.13!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.94!158.57!Tsc22d4;;chr17:48015839..48015915,-!p3@Foxp4!1.77!68.27!Foxp4;;chr16:91225808..91225824,+!p1@Olig2!1.69!48.45!Olig2;;chr9:91260616..91260653,-!p2@Zic1!1.69!48.45!Zic1;;chr15:76353005..76353021,-!p2@Scrt1!1.62!40.74!Scrt1;;chrX:34442872..34442899,-!p1@Nkrf!1.56!45.15!Nkrf;;chr18:36441119..36441158,+!p2@Pura!1.54!80.38!Pura;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.51!39.64!Pou3f3;;chr7:116154364..116154444,+!p1@Tub!1.49!50.65!Tub;;chr2:163051181..163051205,+!p2@Tox2!1.49!29.73!Tox2;;chr19:55969923..55969944,+!p6@Tcf7l2!1.49!29.73!Tcf7l2;;chr16:91270091..91270143,+!p2@Olig1!1.47!28.63!Olig1;;chr17:25707623..25707639,-!p1@Sox8!1.44!109.01!Sox8;;chr3:95032091..95032183,-!p1@Mllt11!1.39!196.01!Mllt11;;chr7:148008023..148008092,-!p1@Zfp941!1.38!53.96!Zfp941;;chr12:30219426..30219506,+!p2@Myt1l!1.38!23.12!Myt1l;;chr15:76352677..76352737,-!p3@Scrt1!1.38!23.12!Scrt1;;chr4:58956447..58956510,+!p1@Zkscan16!1.36!47.35!Zkscan16;;chr4:150482563..150482655,-!p2@Camta1!1.35!74.88!Camta1;;chr19:19185671..19185693,-!p1@Rorb!1.34!49.55!Rorb;;chr10:67375368..67375433,-!p1@Zfp365!1.32!35.24!Zfp365;;chrX:108009761..108009788,+!p1@Pou3f4!1.32!19.82!Pou3f4;;chr4:150513630..150513686,-!p4@Camta1!1.31!22.02!Camta1;;chr9:91260594..91260612,-!p1@Zic1!1.29!18.72!Zic1;;chr12:54349410..54349461,+!p1@Npas3!1.27!20.92!Npas3;;chrX:137083127..137083138,-!p9@Tsc22d3!1.27!17.62!Tsc22d3;;chr2:65683890..65683907,+!p1@Csrnp3!1.25!31.93!Csrnp3;;chr8:24780125..24780143,+!p1@Zmat4!1.25!24.23!Zmat4;;chr11:98636531..98636559,-!p1@Nr1d1!1.22!86.99!Nr1d1;;chr1:6477388..6477419,+!p3@St18!1.22!15.42!St18;;chr10:67375146..67375208,-!p2@Zfp365!1.19!22.02!Zfp365;;chr7:52960888..52960902,+!p7@Dbp!1.19!14.32!Dbp;;chr19:26681865..26681900,+!p6@Smarca2!1.15!38.54!Smarca2;;chr8:112603658..112603674,+!p2@Zfp612!1.15!24.23!Zfp612;;chr3:95032197..95032208,-!p3@Mllt11!1.15!16.52!Mllt11;;chr2:168427068..168427115,-!p3@Nfatc2!1.15!13.21!Nfatc2;;chr2:163030164..163030178,+!p6@Tox2!1.15!13.21!Tox2;;chr7:17062114..17062141,-!p1@Npas1!1.15!13.21!Npas1;;chr8:107793688..107793736,+!p1@Hsf4!1.11!15.42!Hsf4;;chr11:90252223..90252240,-!p1@Hlf!1.10!95.80!Hlf;;chr3:95032184..95032195,-!p4@Mllt11!1.10!14.32!Mllt11;;chr1:140739014..140739032,-!p1@Lhx9!1.09!14.32!Lhx9;;chr1:91827756..91827773,-!p1@Gbx2!1.08!11.01!Gbx2;;chr10:84218800..84218829,+!p2@Rfx4!1.08!11.01!Rfx4;;chrX:90531838..90531861,+!p1@Arx!1.06!13.21!Arx;;chr7:52960555..52960662,+!p1@Dbp!1.05!88.09!Dbp;;chr6:145813905..145813932,-!p2@Bhlhe41!1.05!19.82!Bhlhe41;;chr3:95032558..95032641,-!p2@Mllt11!1.04!56.16!Mllt11;;chr8:12395603..12395621,+!p1@Sox1!1.04!9.91!Sox1;;chr12:87762578..87762612,+!p1@Esrrb!1.04!9.91!Esrrb;;chr11:96685444..96685473,-!p5@Nfe2l1!1.04!9.91!Nfe2l1;;chr10:67375342..67375365,-!p3@Zfp365!1.04!9.91!Zfp365;;chr14:19071466..19071550,-!p1@Nr1d2!1.02!66.07!Nr1d2;;chr13:44936126..44936164,+!p6@Jarid2!1.02!11.01!Jarid2;;chr15:103170533..103170556,-!p1@Zfp385a!1.01!35.24!Zfp385a;;chr3:95032213..95032226,-!p6@Mllt11!1.01!11.01!Mllt11;;chr15:103170516..103170531,-!p2@Zfp385a!1.00!22.02!Zfp385a;;chr6:134780163..134780197,+!p2@Crebl2!0.99!20.92!Crebl2;;chr7:17200403..17200416,-!p5@Grlf1!0.99!14.32!Grlf1;;chr12:3806003..3806031,+!p11@Dnmt3a!0.99!8.81!Dnmt3a;;chr14:34791937..34791977,-!p1@Zfp488!0.99!8.81!Zfp488;;chr14:122874619..122874634,+!p1@Zic2!0.99!8.81!Zic2;;chr15:76352434..76352488,-!p4@Scrt1!0.99!8.81!Scrt1;;chr16:91225654..91225671,+!p2@Olig2!0.99!8.81!Olig2;;chr11:90252071..90252093,-!p7@Hlf!0.99!8.81!Hlf;;chr7:52960663..52960677,+!p6@Dbp!0.99!8.81!Dbp;;chr7:25292141..25292158,+!p2@Zfp428!0.98!30.83!Zfp428;;chr12:72149325..72149343,+!p2@Arid4a!0.98!12.11!Arid4a;;chr6:145813964..145813994,-!p3@Bhlhe41!0.98!11.01!Bhlhe41;;chr17:87153028..87153049,+!p2@Epas1!0.97!175.08!Epas1;;chr3:95032515..95032553,-!p5@Mllt11!0.96!9.91!Mllt11;;chr15:78994907..78994926,-!p1@Sox10!0.95!20.92!Sox10;;chr7:52960700..52960719,+!p2@Dbp!0.95!9.91!Dbp;;chr8:79423672..79423727,+!p2@Nr3c2!0.94!9.91!Nr3c2;;chr15:82742573..82742620,-!p2@Tcf20!0.94!7.71!Tcf20;;chr12:30213247..30213333,+!p1@Myt1l!0.94!7.71!Myt1l;;chr2:163030186..163030204,+!p4@Tox2!0.94!7.71!Tox2;;chr1:122498955..122498968,+!p1@En1!0.94!7.71!En1;;chr5:28492230..28492257,+!p1@En2!0.94!7.71!En2;;chrX:55283799..55283813,+!p1@Zic3!0.94!7.71!Zic3;;chr19:10315179..10315241,-!p1@Gm98!0.92!80.38!Gm98;;chr9:69137716..69137744,+!p1@Rora!0.91!46.25!Rora;;chr2:127347067..127347093,-!p1@Kcnip3!0.91!12.11!Kcnip3;;chr4:154335024..154335039,+!p1@Hes5!0.91!8.81!Hes5;;chr7:25292160..25292213,+!p3@Zfp428!0.89!17.62!Zfp428;;chr14:52935860..52935874,-!p3@Sall2!0.89!9.91!Sall2;;chr6:145814003..145814056,-!p1@Bhlhe41!0.88!19.82!Bhlhe41;;chr7:146768691..146768707,-!p1@Nkx6-2!0.88!6.61!Nkx6-2;;chr8:12395892..12395919,+!p4@Sox1!0.88!6.61!Sox1;;chr19:55969946..55969973,+!p8@Tcf7l2!0.88!6.61!Tcf7l2;;chr2:163030219..163030258,+!p5@Tox2!0.88!6.61!Tox2;;chr19:55967842..55967878,+!p13@Tcf7l2!0.88!6.61!Tcf7l2;;chr2:81893535..81893548,+!p1@Zfp804a!0.88!6.61!Zfp804a;;chr11:21901608..21901634,-!p1@Otx1!0.88!6.61!Otx1;;chrX:137077716..137077734,-!p1@Tsc22d3!0.87!48.45!Tsc22d3;;chr2:25562263..25562314,+!p2@Bmyc!0.86!25.33!Bmyc;;chr1:189821714..189821761,+!p1@Esrrg!0.86!12.11!Esrrg;;chr9:106356278..106356292,+!p3@Pcbp4!0.86!11.01!Pcbp4;;chr7:6683123..6683142,-!p1@Peg3!0.85!334.75!Peg3;;chr17:33766353..33766393,+!p2@Zfp414!0.85!17.62!Zfp414;;chr4:129118044..129118067,-!p1@Zbtb8b!0.85!7.71!Zbtb8b;;chr17:48015645..48015689,-!p9@Foxp4!0.84!7.71!Foxp4;;chr13:99124189..99124205,+!p1@Foxd1!0.82!8.81!Foxd1;;chr18:36441100..36441113,+!p3@Pura!0.82!6.61!Pura;;chr10:80893711..80893784,-!p3@Nfic!0.81!30.83!Nfic;;chr2:9800207..9800234,-!p1@Gata3!0.81!17.62!Gata3;;chr7:30094448..30094481,+!p4@Dpf1!0.81!6.61!Dpf1;;chr15:103164702..103164778,-!p3@Zfp385a!0.81!6.61!Zfp385a;;chr12:86939997..86940040,+!p4@Jdp2!0.81!5.51!Jdp2;;chr2:77541432..77541474,-!p5@Zfp385b!0.81!5.51!Zfp385b;;chr4:150482353..150482386,-!p6@Camta1!0.81!5.51!Camta1;;chrX:34442842..34442866,-!p3@Nkrf!0.81!5.51!Nkrf;;chrX:95345005..95345053,+!p1@Ar!0.81!5.51!Ar;;chr11:84339016..84339044,-!p1@Lhx1!0.81!5.51!Lhx1;;chr10:84218895..84218909,+!p1@Rfx4!0.81!5.51!Rfx4;;chr11:98190918..98190951,-!p1@Neurod2!0.81!5.51!Neurod2;;chr19:55969687..55969714,+!p16@Tcf7l2!0.81!5.51!Tcf7l2;;chr19:55968967..55968991,+!p7@Tcf7l2!0.81!5.51!Tcf7l2;;chr2:168427120..168427138,-!p4@Nfatc2!0.81!5.51!Nfatc2;;chr19:55970072..55970081,+!p38@Tcf7l2!0.81!5.51!Tcf7l2;;chr19:55967803..55967834,+!p12@Tcf7l2!0.81!5.51!Tcf7l2;;chr19:55970060..55970071,+!p25@Tcf7l2!0.81!5.51!Tcf7l2;;chr19:55972767..55972779,+!p20@Tcf7l2!0.81!5.51!Tcf7l2;;chr2:147012101..147012118,-!p3@Nkx2-2!0.81!5.51!Nkx2-2;;chr9:69137672..69137702,+!p2@Rora!0.80!24.23!Rora;;chr7:91558392..91558434,-!p1@Arnt2!0.80!15.42!Arnt2;;chr7:91558472..91558512,-!p2@Arnt2!0.80!7.71!Arnt2;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.79!58.36!Camta2;;chrX:137077151..137077227,-!p2@Tsc22d3!0.79!39.64!Tsc22d3;;chr2:127347094..127347111,-!p2@Kcnip3!0.79!8.81!Kcnip3;;chr15:103170561..103170572,-!p4@Zfp385a!0.79!7.71!Zfp385a;;chr10:13685980..13686007,+!p6@Hivep2!0.79!6.61!Hivep2;;chr14:76903992..76904056,+!p6@Tsc22d1!0.78!11.01!Tsc22d1;;chr3:34548909..34548927,+!p1@Sox2!0.78!8.81!Sox2;;chr13:72766279..72766296,+!p2@Irx2!0.78!7.71!Irx2;;chr7:17200307..17200370,-!p2@Grlf1!0.77!39.64!Grlf1;;chr7:144506077..144506128,-!p1@Ebf3!0.77!12.11!Ebf3;;chr7:30092993..30093076,+!p1@Dpf1!0.77!8.81!Dpf1;;chr6:117813087..117813121,+!p1@Zfp239!0.76!19.82!Zfp239;;chr15:81633165..81633188,+!p2@Tef!0.75!41.84!Tef;;chr1:191994550..191994623,-!p1@Prox1!0.75!35.24!Prox1;;chr8:112603610..112603656,+!p1@Zfp612!0.75!23.12!Zfp612;;chr7:38554763..38554780,-!p1@Zfp536!0.75!8.81!Zfp536;;chr19:23215554..23215567,+!p5@Klf9!0.75!6.61!Klf9;;chr7:38557752..38557793,-!p3@Zfp536!0.75!5.51!Zfp536;;chr14:55711198..55711258,-!p1@Zfhx2!0.74!28.63!Zfhx2;;chr5:125342568..125342602,+!p2@Zfp664!0.74!7.71!Zfp664;;chr7:25292118..25292129,+!p8@Zfp428!0.74!5.51!Zfp428;;chr1:38684414..38684427,-!p7@Aff3!0.74!5.51!Aff3;;chr19:6996294..6996324,-!p2@Esrra!0.73!31.93!Esrra;;chr11:90250944..90250982,-!p2@Hlf!0.73!7.71!Hlf;;chr11:96685487..96685512,-!p7@Nfe2l1!0.73!4.40!Nfe2l1;;chr4:44717334..44717367,-!p5@Pax5!0.73!4.40!Pax5;;chr4:13678482..13678505,+!p9@Runx1t1!0.73!4.40!Runx1t1;;chr15:95485240..95485257,-!p1@Dbx2!0.73!4.40!Dbx2;;chr1:140743964..140743976,-!p3@Lhx9!0.73!4.40!Lhx9;;chr19:55972441..55972456,+!p18@Tcf7l2!0.73!4.40!Tcf7l2;;chr2:65768149..65768173,+!p4@Csrnp3!0.73!4.40!Csrnp3;;chr2:181501710..181501742,+!p2@Myt1!0.73!4.40!Myt1;;chr2:162769220..162769252,+!p1@L3mbtl1!0.73!4.40!L3mbtl1;;chr8:12395874..12395885,+!p2@Sox1!0.73!4.40!Sox1;;chr7:91520922..91520956,-!p5@Arnt2!0.73!4.40!Arnt2;;chr9:99776566..99776612,-!p1@Sox14!0.73!4.40!Sox14;;chr7:130644017..130644092,-!p1@Zkscan2!0.72!8.81!Zkscan2;;chr13:78338076..78338104,-!p4@Nr2f1!0.72!5.51!Nr2f1;;chr15:81641878..81641921,+!p1@Tef!0.71!120.03!Tef;;chr11:98603119..98603130,+!p2@Thra!0.71!39.64!Thra;;chr17:34169016..34169068,+!p2@Rxrb!0.71!34.14!Rxrb;;chr15:81633203..81633215,+!p3@Tef!0.70!6.61!Tef;;chr13:72766250..72766273,+!p1@Irx2!0.70!6.61!Irx2;;chr3:54559463..54559493,+!p3@Smad9!0.69!7.71!Smad9;;chr18:35721821..35721828,+!p4@Matr3!0.69!7.71!Matr3;;chr8:79423144..79423178,+!p3@Nr3c2!0.68!5.51!Nr3c2;;chr8:107793737..107793757,+!p2@Hsf4!0.68!4.40!Hsf4;;chr13:78338288..78338309,-!p7@Nr2f1!0.68!4.40!Nr2f1;;chr2:25562241..25562250,+!p4@Bmyc!0.68!4.40!Bmyc;;chr6:90412556..90412581,+!p3@Klf15!0.67!8.81!Klf15;;chr5:3648045..3648074,-!p2@Gatad1!0.67!6.61!Gatad1;;chr15:81633139..81633152,+!p4@Tef!0.67!6.61!Tef;;chr7:52963269..52963305,+!p4@Dbp!0.67!5.51!Dbp;;chr14:104867201..104867258,-!p1@Pou4f1!0.67!5.51!Pou4f1;;chr14:52935876..52935928,-!p1@Sall2!0.66!34.14!Sall2;;chr9:20385868..20385902,+!p3@Zfp846!0.66!5.51!Zfp846;;chr7:144505980..144506010,-!p3@Ebf3!0.66!4.40!Ebf3;;chr9:106356211..106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cx;;chr6:85463580..85463585,-!p1@Egr4!0.32!1.10!Egr4;;chr7:135019127..135019137,-!p6@Zfp668!0.32!1.10!Zfp668;;chr7:116093986..116093999,+!p4@Tub!0.32!1.10!Tub;;chr5:120881900..120881914,+!p1@Lhx5!0.32!1.10!Lhx5;;chr5:125523164..125523188,-!p8@Ncor2!0.32!1.10!Ncor2;;chr7:30088957..30088966,+!p6@Dpf1!0.32!1.10!Dpf1;;chr9:69608731..69608742,-!p2@Foxb1!0.32!1.10!Foxb1;;chr7:38554684..38554696,-!p10@Zfp536!0.32!1.10!Zfp536;;chr7:38554745..38554756,-!p7@Zfp536!0.32!1.10!Zfp536;;chr9:87625971..87625992,-!p2@Tbx18!0.32!1.10!Tbx18;;chr9:71959508..71959519,-!p15@Tcf12!0.32!1.10!Tcf12;;chr9:91256933..91256954,+!p4@Zic4!0.32!1.10!Zic4;;chr8:94881902..94881910,+!p6@Irx5!0.32!1.10!Irx5;;chr7:28516631..28516640,+!p4@Zfp60!0.32!1.10!Zfp60;;chr9:21992581..21992593,+!p1@Zfp872!0.32!1.10!Zfp872;;chr9:69608672..69608686,-!p1@Foxb1!0.32!1.10!Foxb1;;chr9:96632593..96632620,-!p12@Zbtb38!0.32!1.10!Zbtb38;;chrX:108009602..108009615,+!p4@Pou3f4!0.32!1.10!Pou3f4;;chr9:99776617..99776631,-!p2@Sox14!0.32!1.10!Sox14;;chr8:12395629..12395644,+!p6@Sox1!0.32!1.10!Sox1;;chr7:52252978..52252989,+!p5@Irf3!0.32!1.10!Irf3;;chr7:91521166..91521194,-!p11@Arnt2!0.32!1.10!Arnt2;;chr8:91568074..91568094,-!p1@Sall1!0.32!1.10!Sall1;;chr8:87502423..87502439,-!p4@Junb!0.32!1.10!Junb;;chr9:91263649..91263666,+!p3@Zic4!0.32!1.10!Zic4;;chrX:70656436..70656464,+!p1@Zfp92!0.32!1.10!Zfp92;;chrX:55284180..55284195,+!p2@Zic3!0.32!1.10!Zic3;;chr13:95645608..95645616,+!p2@Otp!0.32!1.10!Otp;;chr13:95645555..95645566,+!p3@Otp!0.32!1.10!Otp;;chr12:39510042..39510069,+!p8@Etv1!0.32!1.10!Etv1;;chr13:78339241..78339273,-!p9@Nr2f1!0.32!1.10!Nr2f1;;chr12:87762732..87762747,+!p9@Esrrb!0.32!1.10!Esrrb;;chr13:78338032..78338049,-!p8@Nr2f1!0.32!1.10!Nr2f1;;chr14:76815156..76815181,+!p16@Tsc22d1!0.32!1.10!Tsc22d1;;chr12:28027256..28027282,-!p2@Sox11!0.32!1.10!Sox11;;chr14:34791987..34791998,-!p2@Zfp488!0.32!1.10!Zfp488;;chr14:52640336..52640341,-!p20@Zfp219!0.32!1.10!Zfp219;;chr13:44936055..44936066,+!p20@Jarid2!0.32!1.10!Jarid2;;chr15:102197405..102197454,-!p1@Sp7!0.32!1.10!Sp7;;chr12:87762625..87762637,+!p7@Esrrb!0.32!1.10!Esrrb;;chr15:102821007..102821021,+!p2@Hoxc8!0.32!1.10!Hoxc8;;chr12:34613267..34613272,+!p1@Ferd3l!0.32!1.10!Ferd3l;;chr12:39510260..39510271,+!p10@Etv1!0.32!1.10!Etv1;;chr14:49284773..49284790,-!p2@Otx2!0.32!1.10!Otx2;;chr14:118636238..118636257,-!p2@Sox21!0.32!1.10!Sox21;;chr14:52948033..52948045,-!p12@Sall2!0.32!1.10!Sall2;;chr12:57714257..57714278,-!p1@Nkx2-9!0.32!1.10!Nkx2-9;;chr14:122874593..122874610,+!p2@Zic2!0.32!1.10!Zic2;;chr14:122874718..122874729,+!p3@Zic2!0.32!1.10!Zic2;;chr14:52948124..52948148,-!p7@Sall2!0.32!1.10!Sall2;;chr14:17408022..17408043,-!p6@Rarb!0.32!1.10!Rarb;;chr13:99124236..99124243,+!p2@Foxd1!0.32!1.10!Foxd1;;chr14:70477113..70477173,+!p1@Egr3!0.32!1.10!Egr3;;chr2:24331085..24331100,-!p1@Pax8!0.32!1.10!Pax8;;chr19:55967883..55967888,+!p57@Tcf7l2!0.32!1.10!Tcf7l2;;chr2:24331116..24331125,-!p2@Pax8!0.32!1.10!Pax8;;chr19:59532915..59532940,+!p5@Emx2!0.32!1.10!Emx2;;chr2:56967316..56967327,-!p3@Nr4a2!0.32!1.10!Nr4a2;;chr2:105515586..105515606,+!p4@Pax6!0.32!1.10!Pax6;;chr1:6477452..6477459,+!p8@St18!0.32!1.10!St18;;chr2:181501988..181502026,+!p3@Myt1!0.32!1.10!Myt1;;chr2:56967381..56967386,-!p8@Nr4a2!0.32!1.10!Nr4a2;;chr2:164829847..164829859,-!p5@Ncoa5!0.32!1.10!Ncoa5;;chr2:38194778..38194798,+!p3@Lhx2!0.32!1.10!Lhx2;;chr2:147871948..147871977,-!p3@Foxa2!0.32!1.10!Foxa2;;chr2:166885917..166885930,-!p9@Znfx1!0.32!1.10!Znfx1;;chr2:147019977..147019985,-!p2@Nkx2-2!0.32!1.10!Nkx2-2;;chr2:105522662..105522687,+!p2@Pax6!0.32!1.10!Pax6;;chr19:55969646..55969665,+!p26@Tcf7l2!0.32!1.10!Tcf7l2;;chr2:169458593..169458603,+!p13@Tshz2!0.32!1.10!Tshz2;;chr19:55969404..55969417,+!p43@Tcf7l2!0.32!1.10!Tcf7l2;;chr2:151906844..151906873,+!p3@Scrt2!0.32!1.10!Scrt2;;chr19:55969438..55969450,+!p53@Tcf7l2!0.32!1.10!Tcf7l2;;chr1:122499088..122499099,+!p2@En1!0.32!1.10!En1;;chr19:59533595..59533628,+!p6@Emx2!0.32!1.10!Emx2;;chr1:19199193..19199207,+!p11@Tfap2b!0.32!1.10!Tfap2b;;chr1:91827728..91827743,-!p2@Gbx2!0.32!1.10!Gbx2;;chr1:19199119..19199134,+!p4@Tfap2b!0.32!1.10!Tfap2b;;chr19:55969096..55969105,+!p52@Tcf7l2!0.32!1.10!Tcf7l2;;chr1:19199095..19199114,+!p5@Tfap2b!0.32!1.10!Tfap2b;;chr2:105509045..105509071,+!p1@Pax6!0.32!1.10!Pax6;;chr19:55968998..55969011,+!p39@Tcf7l2!0.32!1.10!Tcf7l2;;chr19:55969635..55969644,+!p47@Tcf7l2!0.32!1.10!Tcf7l2;;chr1:19093112..19093124,+!p1@Tfap2d!0.32!1.10!Tfap2d;;chr1:19199021..19199048,+!p8@Tfap2b!0.32!1.10!Tfap2b;;chr1:169528433..169528456,+!p10@Rxrg!0.32!1.10!Rxrg;;chr1:19199079..19199092,+!p7@Tfap2b!0.32!1.10!Tfap2b;;chr2:151907368..151907379,+!p8@Scrt2!0.32!1.10!Scrt2;;chr2:9809374..9809396,-!p4@Gata3!0.32!1.10!Gata3;;chr2:9809579..9809627,-!p7@Gata3!0.32!1.10!Gata3;;chr2:77541309..77541322,-!p14@Zfp385b!0.32!1.10!Zfp385b;;chr4:150503544..150503561,-!p8@Camta1!0.32!1.10!Camta1;;chr2:91077026..91077029,-!p5@Ddb2!0.32!1.10!Ddb2;;chr2:77654767..77654784,-!p12@Zfp385b!0.32!1.10!Zfp385b;;chr2:77654737..77654748,-!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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs12631
-|library_id_phase_based=1:CNhs12631
+|library_id_phase_based=2:CNhs12631
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11722
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11722
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520raphe%252c%2520donor1.CNhs12631.11722-123D3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520raphe%252c%2520donor1.CNhs12631.11722-123D3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520raphe%252c%2520donor1.CNhs12631.11722-123D3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520raphe%252c%2520donor1.CNhs12631.11722-123D3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520raphe%252c%2520donor1.CNhs12631.11722-123D3.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - raphe, donor1
 |namespace=FANTOM5
@@ Line 51: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12631,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,0.0453778322370008,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.130565527652598,0,0,0,0,0,0,0,0,0,0,0,0,0.683292908668817,-0.558422792324031,0,0,0,0,0,-0.209322725495826,0.140726333599994,0.00288809005897117,0.56154000156278,0.543431672952463,0.813300310962814,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0428469550828748,0,0,0,0,0,-0.117389802908326,-0.310650657339386,0.574675345876916,-0.0411569821573493,0,-0.0780086007519514,0.0767984415917926,0.289631290656891,0,0,0.0839458279617681,0.312832216705562,1.33190735261962,-0.0788315948399074,0,0,0,0,0,0,0.416635315644637,-0.00201809862833047,0.257809631360187,0,0,0.505464404962115,0.242448038640363,0
@@ 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=table111:11722-123D3;search_select_hide=table117:11722-123D3
 }}

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FF:11722-123D3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12631

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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