FF:399-16E2: Difference between revisions

Latest revision as of 19:15, 4 June 2020

Name:	eyeball, embryo E14
Species:	Mouse (Mus musculus)
Library ID:	CNhs10521
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	eyeball
dev stage	14 days embryo
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		SAMD00005492

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10521		CAGE		DRX008956		DRR009830

Accession ID Mm9

Library id		BAM		CTSS
CNhs10521		DRZ001255		DRZ002638

Accession ID Mm10

Library id		BAM		CTSS
CNhs10521		DRZ012605		DRZ013988

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

CNhs10521

0	0
1	0.0536
10	0
100	0.0899
1000	-0.0355
1001	-0.0749
1002	0.208
1003	-0.121
1004	0.503
1005	-0.169
1006	0.0161
1007	0.0466
1008	0
1009	-0.0572
101	0.0814
1010	0
1011	-0.0358
1012	0
1013	-0.147
1014	0.283
1015	0.322
1016	0.207
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.116
1022	-0.0842
1023	0
1024	0
1025	-0.0611
1026	0
1027	0.486
1028	0
1029	-0.129
103	0.0605
1030	0
1031	0.209
1032	-0.0175
1033	0.0466
1034	0
1035	0
1036	0.1
1037	0
1038	-0.122
1039	-0.121
104	0
1040	-0.0678
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: CNhs10521

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	9.20287e-4
MA0003.1	MA0003.1	0.452
MA0004.1	MA0004.1	0.857
MA0006.1	MA0006.1	0.313
MA0007.1	MA0007.1	0.319
MA0009.1	MA0009.1	0.254
MA0014.1	MA0014.1	0.463
MA0017.1	MA0017.1	3.6258e-6
MA0018.2	MA0018.2	0.0197
MA0019.1	MA0019.1	0.981
MA0024.1	MA0024.1	8.99982e-4
MA0025.1	MA0025.1	0.622
MA0027.1	MA0027.1	0.132
MA0028.1	MA0028.1	0.305
MA0029.1	MA0029.1	0.99
MA0030.1	MA0030.1	0.178
MA0031.1	MA0031.1	0.0546
MA0035.2	MA0035.2	0.0726
MA0038.1	MA0038.1	0.00411
MA0039.2	MA0039.2	0.465
MA0040.1	MA0040.1	0.201
MA0041.1	MA0041.1	0.135
MA0042.1	MA0042.1	0.756
MA0043.1	MA0043.1	0.00611
MA0046.1	MA0046.1	1.10616e-18
MA0047.2	MA0047.2	0.00133
MA0048.1	MA0048.1	0.934
MA0050.1	MA0050.1	1.34247e-6
MA0051.1	MA0051.1	2.05267e-4
MA0052.1	MA0052.1	0.315
MA0055.1	MA0055.1	0.241
MA0057.1	MA0057.1	0.107
MA0058.1	MA0058.1	0.934
MA0059.1	MA0059.1	0.983
MA0060.1	MA0060.1	1.6461e-20
MA0061.1	MA0061.1	0.0366
MA0062.2	MA0062.2	0.629
MA0065.2	MA0065.2	5.52949e-6
MA0066.1	MA0066.1	0.168
MA0067.1	MA0067.1	0.901
MA0068.1	MA0068.1	0.102
MA0069.1	MA0069.1	0.0587
MA0070.1	MA0070.1	0.137
MA0071.1	MA0071.1	0.623
MA0072.1	MA0072.1	0.583
MA0073.1	MA0073.1	0.952
MA0074.1	MA0074.1	0.433
MA0076.1	MA0076.1	0.094
MA0077.1	MA0077.1	4.98087e-4
MA0078.1	MA0078.1	0.105
MA0079.2	MA0079.2	0.629
MA0080.2	MA0080.2	3.64073e-11
MA0081.1	MA0081.1	0.198
MA0083.1	MA0083.1	0.493
MA0084.1	MA0084.1	0.107
MA0087.1	MA0087.1	0.124
MA0088.1	MA0088.1	0.659
MA0090.1	MA0090.1	0.91
MA0091.1	MA0091.1	0.421
MA0092.1	MA0092.1	0.383
MA0093.1	MA0093.1	0.898
MA0099.2	MA0099.2	6.51738e-4
MA0100.1	MA0100.1	0.861
MA0101.1	MA0101.1	0.21
MA0102.2	MA0102.2	0.156
MA0103.1	MA0103.1	0.00287
MA0104.2	MA0104.2	0.487
MA0105.1	MA0105.1	0.00242
MA0106.1	MA0106.1	0.267
MA0107.1	MA0107.1	0.0679
MA0108.2	MA0108.2	8.71863e-6
MA0111.1	MA0111.1	0.408
MA0112.2	MA0112.2	3.02324e-6
MA0113.1	MA0113.1	0.332
MA0114.1	MA0114.1	3.53403e-5
MA0115.1	MA0115.1	0.0104
MA0116.1	MA0116.1	0.0107
MA0117.1	MA0117.1	0.598
MA0119.1	MA0119.1	0.00217
MA0122.1	MA0122.1	0.855
MA0124.1	MA0124.1	0.747
MA0125.1	MA0125.1	0.0294
MA0131.1	MA0131.1	0.546
MA0135.1	MA0135.1	0.0276
MA0136.1	MA0136.1	5.09481e-6
MA0137.2	MA0137.2	0.177
MA0138.2	MA0138.2	0.113
MA0139.1	MA0139.1	0.0835
MA0140.1	MA0140.1	0.00979
MA0141.1	MA0141.1	0.00589
MA0142.1	MA0142.1	0.139
MA0143.1	MA0143.1	0.00335
MA0144.1	MA0144.1	0.0962
MA0145.1	MA0145.1	0.0288
MA0146.1	MA0146.1	0.177
MA0147.1	MA0147.1	0.712
MA0148.1	MA0148.1	3.08044e-5
MA0149.1	MA0149.1	0.0553
MA0150.1	MA0150.1	0.14
MA0152.1	MA0152.1	0.961
MA0153.1	MA0153.1	8.69294e-16
MA0154.1	MA0154.1	8.84398e-4
MA0155.1	MA0155.1	0.664
MA0156.1	MA0156.1	0.0132
MA0157.1	MA0157.1	0.0776
MA0159.1	MA0159.1	0.0261
MA0160.1	MA0160.1	0.0498
MA0162.1	MA0162.1	0.684
MA0163.1	MA0163.1	7.86216e-4
MA0164.1	MA0164.1	0.831
MA0258.1	MA0258.1	0.00166
MA0259.1	MA0259.1	0.687

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: CNhs10521

Novel motif	Logo	P-value
1	1	0.0588
10	10	0.107
100	100	0.817
101	101	0.59
102	102	0.583
103	103	0.0532
104	104	0.983
105	105	0.358
106	106	0.00725
107	107	0.0499
108	108	0.844
109	109	0.14
11	11	0.106
110	110	0.081
111	111	6.61576e-4
112	112	0.0147
113	113	0.705
114	114	0.0188
115	115	0.887
116	116	0.51
117	117	0.131
118	118	0.495
119	119	0.0451
12	12	0.541
120	120	0.41
121	121	0.797
122	122	0.945
123	123	0.754
124	124	0.455
125	125	0.115
126	126	0.329
127	127	0.0711
128	128	0.0378
129	129	0.169
13	13	0.0202
130	130	0.756
131	131	0.903
132	132	0.296
133	133	0.0723
134	134	0.921
135	135	0.0532
136	136	0.728
137	137	0.411
138	138	0.4
139	139	0.00759
14	14	0.547
140	140	0.00977
141	141	0.0636
142	142	0.418
143	143	0.59
144	144	0.986
145	145	0.0996
146	146	0.577
147	147	0.395
148	148	0.109
149	149	0.214
15	15	0.0829
150	150	0.472
151	151	0.221
152	152	0.0741
153	153	0.461
154	154	0.362
155	155	0.478
156	156	4.20124e-4
157	157	0.811
158	158	0.209
159	159	0.00926
160	160	0.311
161	161	0.475
162	162	0.695
163	163	0.51
164	164	0.0272
165	165	0.108
166	166	0.751
167	167	0.249
168	168	0.652
169	169	0.00106
17	17	0.0232
18	18	0.689
19	19	0.12
2	2	0.482
20	20	0.957
21	21	0.831
22	22	0.224
23	23	0.069
24	24	0.563
25	25	0.673
26	26	0.0487
27	27	0.457
28	28	0.298
29	29	0.22
3	3	0.101
30	30	0.766
31	31	0.568
32	32	0.12
33	33	0.656
34	34	0.938
35	35	0.417
36	36	0.313
37	37	0.046
38	38	0.36
39	39	0.355
4	4	0.485
40	40	0.618
41	41	0.981
42	42	0.325
43	43	0.112
44	44	0.157
45	45	0.482
46	46	0.122
47	47	0.139
48	48	0.129
49	49	0.12
5	5	0.0846
50	50	0.889
51	51	0.564
52	52	0.201
53	53	0.69
54	54	0.56
55	55	0.806
56	56	0.315
57	57	0.429
58	58	0.283
59	59	0.0833
6	6	0.563
60	60	0.0305
61	61	0.574
62	62	0.0794
63	63	0.107
64	64	0.589
65	65	0.138
66	66	0.226
67	67	0.729
68	68	0.039
69	69	0.562
7	7	0.135
70	70	0.0178
71	71	0.062
72	72	0.547
73	73	0.0959
74	74	0.346
75	75	0.0386
76	76	0.69
77	77	0.165
78	78	0.15
79	79	0.155
8	8	0.122
80	80	0.2
81	81	0.416
82	82	0.00982
83	83	0.895
84	84	0.702
85	85	0.00811
86	86	0.187
87	87	0.252
88	88	0.826
89	89	0.164
9	9	0.341
90	90	0.077
91	91	0.428
92	92	0.0591
93	93	0.0958
94	94	0.375
95	95	0.2
96	96	0.32
97	97	0.735
98	98	0.363
99	99	0.693

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: CNhs10521

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011335 mouse eyeball- embryo E14 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)
0000922 (embryo)
0000970 (eye)
0000019 (camera-type eye)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0001032 (sensory system)
0010317 (germ layer / neural crest derived structure)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002104 (visual system)
0004456 (entire sense organ system)
0001456 (face)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000296 (mouse embryonic day 14 sample)
0011335 (mouse eyeball- embryo E14 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:0003056 (pre-chordal neural plate)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005492
+|accession_numbers=CAGE;DRX008956;DRR009830;DRZ001255;DRZ002638;DRZ012605;DRZ013988
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000970,UBERON:0000019,UBERON:0000033,UBERON:0000479,UBERON:0004121,UBERON:0010314,UBERON:0000047,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0001444,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0001032,UBERON:0010317,UBERON:0004088,UBERON:0000153,UBERON:0007811,UBERON:0002104,UBERON:0004456,UBERON:0001456
 |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=chr10:62562530..62562540,+!p1@Atoh7!2.83!671.31!Atoh7;;chr18:66098702..66098742,-!p1@Rax!2.22!166.45!Rax;;chr4:154335024..154335039,+!p1@Hes5!2.07!138.63!Hes5;;chr19:19185671..19185693,-!p1@Rorb!2.05!254.96!Rorb;;chr3:127336052..127336058,+!p1@Neurog2!2.04!108.51!Neurog2;;chr12:74040861..74040875,+!p1@Six6!1.83!66.67!Six6;;chr2:105509045..105509071,+!p1@Pax6!1.81!63.91!Pax6;;chr2:79296783..79296801,-!p1@Neurod1!1.72!51.96!Neurod1;;chr2:38206744..38206766,+!p1@Lhx2!1.60!46.90!Lhx2;;chr12:85910771..85910785,+!p1@Vsx2!1.59!37.47!Vsx2;;chr6:83661226..83661282,+!p1@Vax2!1.59!37.47!Vax2;;chr5:35731493..35731531,+!p1@Hmx1!1.54!33.34!Hmx1;;chr12:74040895..74040916,+!p2@Six6!1.50!30.35!Six6;;chr14:49287186..49287225,-!p1@Otx2!1.50!30.35!Otx2;;chr12:34642510..34642530,+!p1@Twist1!1.49!93.11!Twist1;;chr2:105522662..105522687,+!p2@Pax6!1.49!29.66!Pax6;;chr4:114598669..114598674,-!p1@Foxe3!1.47!28.74!Foxe3;;chr17:86020156..86020183,+!p1@Six3!1.46!28.05!Six3;;chr3:34548909..34548927,+!p1@Sox2!1.42!41.84!Sox2;;chr10:86956396..86956411,-!p1@Ascl1!1.41!37.93!Ascl1;;chr17:86020115..86020128,+!p2@Six3!1.40!24.37!Six3;;chr10:129717274..129717298,-!p1@Neurod4!1.39!23.45!Neurod4;;chr7:16465229..16465249,-!p1@Crx!1.39!23.45!Crx;;chr2:38206580..38206600,+!p2@Lhx2!1.38!28.51!Lhx2;;chr3:128916868..128916890,+!p1@Pitx2!1.37!30.58!Pitx2;;chr3:101814061..101814094,+!p1@Nhlh2!1.35!21.15!Nhlh2;;chr13:117099847..117099907,-!p1@Isl1!1.34!38.39!Isl1;;chr2:19367259..19367278,+!p1@Ptf1a!1.33!20.23!Ptf1a;;chr10:102491405..102491416,-!p1@Alx1!1.31!19.54!Alx1;;chr2:146047829..146047847,+!p1@Insm1!1.30!33.57!Insm1;;chr2:71384802..71384815,-!p1@Dlx2!1.28!22.07!Dlx2;;chr10:42303385..42303401,-!p1@Nr2e1!1.27!17.47!Nr2e1;;chr17:86020510..86020589,+!p3@Six3!1.26!17.01!Six3;;chr14:49284773..49284790,-!p2@Otx2!1.23!16.09!Otx2;;chr8:80960539..80960548,-!p1@Pou4f2!1.20!14.71!Pou4f2;;chr11:101755669..101755686,-!p1@Meox1!1.19!25.75!Meox1;;chr12:28027561..28027591,-!p1@Sox11!1.18!91.96!Sox11;;chr5:114723781..114723795,-!p1@Foxn4!1.18!14.25!Foxn4;;chrX:58146612..58146615,-!p1@Sox3!1.17!13.79!Sox3;;chr12:56700411..56700416,+!p@chr12:56700411..56700416,+!1.16!13.56!Insm2;;chr2:105515635..105515661,+!p5@Pax6!1.16!13.56!Pax6;;chr2:151907546..151907561,+!p1@Scrt2!1.16!13.33!Scrt2;;chr19:46222859..46222876,-!p1@Pitx3!1.13!12.41!Pitx3;;chr9:91260594..91260612,-!p1@Zic1!1.11!11.95!Zic1;;chr9:74709695..74709722,+!p1@Onecut1!1.11!11.95!Onecut1;;chr2:105515586..105515606,+!p4@Pax6!1.11!11.95!Pax6;;chr14:18814020..18814023,+!p3@Thrb!1.10!11.50!Thrb;;chr12:3891810..3891829,+!p2@Dnmt3a!1.09!17.47!Dnmt3a;;chr1:19199236..19199258,+!p1@Tfap2b!1.09!11.27!Tfap2b;;chr17:86012772..86012825,+!p4@Six3!1.09!11.27!Six3;;chr14:122874619..122874634,+!p1@Zic2!1.08!11.04!Zic2;;chr19:19185697..19185711,-!p2@Rorb!1.07!13.79!Rorb;;chr9:91260616..91260653,-!p2@Zic1!1.07!10.81!Zic1;;chr4:21612929..21612952,-!p1@Prdm13!1.07!10.81!Prdm13;;chr14:104867201..104867258,-!p1@Pou4f1!1.06!14.71!Pou4f1;;chr6:70906450..70906454,+!p1@Foxi3!1.06!10.58!Foxi3;;chr8:12395603..12395621,+!p1@Sox1!1.05!10.12!Sox1;;chr17:86087592..86087615,-!p1@Six2!1.05!10.12!Six2;;chr13:72766250..72766273,+!p1@Irx2!1.04!15.40!Irx2;;chr18:66098673..66098684,-!p2@Rax!1.04!9.89!Rax;;chr1:136186574..136186592,+!p1@Myog!1.04!9.89!Myog;;chr2:163028808..163028869,+!p1@Tox2!1.02!34.49!Tox2;;chr4:150503457..150503498,-!p3@Camta1!1.02!10.81!Camta1;;chr2:71367871..71367898,+!p1@Dlx1!1.02!9.43!Dlx1;;chr10:67364011..67364018,-!p5@Zfp365!1.02!9.43!Zfp365;;chr11:21901608..21901634,-!p1@Otx1!1.02!9.43!Otx1;;chr15:35225845..35225867,+!p1@Osr2!1.01!23.91!Osr2;;chr13:99124189..99124205,+!p1@Foxd1!1.00!14.02!Foxd1;;chr13:72766279..72766296,+!p2@Irx2!0.99!13.10!Irx2;;chr7:144506077..144506128,-!p1@Ebf3!0.96!19.08!Ebf3;;chr1:179374784..179374800,+!p2@Zfp238!0.96!9.66!Zfp238;;chr9:106356211..106356242,+!p1@Pcbp4!0.95!159.09!Pcbp4;;chr3:95032091..95032183,-!p1@Mllt11!0.95!69.89!Mllt11;;chrX:55283799..55283813,+!p1@Zic3!0.95!7.82!Zic3;;chr10:12810631..12810649,+!p1@Plagl1!0.94!208.29!Plagl1;;chr19:7342725..7342784,+!p1@Rcor2!0.94!32.88!Rcor2;;chr16:91225808..91225824,+!p1@Olig2!0.93!7.59!Olig2;;chr1:93698030..93698064,+!p1@Twist2!0.92!14.94!Twist2;;chr10:20880698..20880717,-!p3@Myb!0.92!11.73!Myb;;chr10:42303452..42303470,-!p2@Nr2e1!0.92!7.36!Nr2e1;;chr4:109650609..109650653,+!p1@Dmrta2!0.92!7.36!Dmrta2;;chr10:126778916..126778974,-!p1@Gli1!0.91!16.55!Gli1;;chr18:64499706..64499721,+!p2@Onecut2!0.91!10.12!Onecut2;;chr4:124334894..124334899,+!p1@Pou3f1!0.91!9.43!Pou3f1;;chr5:114724042..114724090,-!p2@Foxn4!0.91!7.13!Foxn4;;chr12:74040716..74040745,+!p3@Six6!0.91!7.13!Six6;;chr10:20880629..20880683,-!p1@Myb!0.90!20.92!Myb;;chr10:42303410..42303422,-!p3@Nr2e1!0.90!6.90!Nr2e1;;chr14:34791937..34791977,-!p1@Zfp488!0.90!6.90!Zfp488;;chr12:12948633..12948651,-!p1@Mycn!0.88!66.90!Mycn;;chr9:31720843..31720888,-!p1@Barx2!0.88!7.36!Barx2;;chr7:116154364..116154444,+!p1@Tub!0.87!11.27!Tub;;chr7:144505957..144505972,-!p2@Ebf3!0.87!8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chr4:32325445..32325468,+!p4@Bach2!0.34!2.07!Bach2;;chr18:14131020..14131033,-!p4@Zfp521!0.34!1.84!Zfp521;;chr9:48644284..48644305,-!p4@Zbtb16!0.34!1.84!Zbtb16;;chr2:156666435..156666476,+!p4@Tgif2!0.34!1.61!Tgif2;;chr8:94325446..94325459,-!p8@Irx3!0.34!1.38!Irx3;;chr1:170362040..170362113,-!p2@Pbx1!0.33!14.71!Pbx1;;chr13:15555079..15555136,+!p3@Gli3!0.33!5.52!Gli3;;chr2:153475210..153475252,+!p2@Dnmt3b!0.33!4.60!Dnmt3b;;chr1:120950098..120950132,-!p2@Gli2!0.33!3.68!Gli2;;chr11:62602947..62602980,-!p2@Zfp286!0.33!2.99!Zfp286;;chr4:114581524..114581551,-!p1@Foxd2!0.33!2.07!Foxd2;;chr2:156666727..156666753,+!p2@Tgif2!0.33!2.07!Tgif2;;chr5:108494765..108494786,+!p2@Mtf2!0.33!1.84!Mtf2;;chr2:152223762..152223777,-!p8@Sox12!0.33!1.38!Sox12;;chr14:18493480..18493494,+!p2@Thrb!0.33!1.38!Thrb;;chr13:78338288..78338309,-!p7@Nr2f1!0.33!1.38!Nr2f1;;chr15:35225873..35225889,+!p2@Osr2!0.33!1.15!Osr2;;chr14:98568502..98568516,-!p7@Dach1!0.33!1.15!Dach1;;chr13:78338032..78338049,-!p8@Nr2f1!0.33!1.15!Nr2f1;;chr13:99124236..99124243,+!p2@Foxd1!0.33!1.15!Foxd1;;chr2:154395524..154395535,-!p5@E2f1!0.33!1.15!E2f1;;chr10:12844757..12844771,+!p2@Plagl1!0.33!1.15!Plagl1;;chr10:106931775..106931798,-!p1@Myf6!0.33!1.15!Myf6;;chr10:126778639..126778670,-!p3@Gli1!0.33!1.15!Gli1;;chr4:122676078..122676090,+!p5@Mycl1!0.33!1.15!Mycl1;;chr4:114581497..114581519,-!p2@Foxd2!0.33!1.15!Foxd2;;chr4:150503544..150503561,-!p8@Camta1!0.33!1.15!Camta1;;chr4:82351639..82351658,-!p14@Nfib!0.33!1.15!Nfib;;chr9:106355745..106355766,+!p7@Pcbp4!0.33!1.15!Pcbp4;;chr7:38557887..38557910,-!p5@Zfp536!0.33!1.15!Zfp536;;chr8:94881639..94881650,+!p5@Irx5!0.33!1.15!Irx5;;chr9:96159133..96159145,+!p9@Tfdp2!0.33!1.15!Tfdp2;;chr13:56804721..56804792,+!p2@Smad5!0.32!9.20!Smad5;;chr13:64254457..64254497,-!p1@Zfp367!0.32!7.82!Zfp367;;chr4:13670499..13670526,+!p2@Runx1t1!0.32!3.45!Runx1t1;;chr4:13712228..13712267,+!p3@Runx1t1!0.32!2.53!Runx1t1;;chr15:100382267..100382287,-!p3@Tfcp2!0.32!2.30!Tfcp2;;chr12:119540395..119540415,-!p5@Sp4!0.32!2.07!Sp4;;chr3:8667033..8667046,-!p3@Hey1!0.32!1.84!Hey1;;chrX:45245621..45245632,-!p3@Smarca1!0.32!1.84!Smarca1;;chr13:78338076..78338104,-!p4@Nr2f1!0.32!1.61!Nr2f1;;chr8:108939219..108939296,+!p1@Zfp90!0.31!19.31!Zfp90;;chr7:28516417..28516460,+!p1@Zfp60!0.31!15.17!Zfp60;;chr4:6917606..6917681,-!p1@Tox!0.31!7.13!Tox;;chr18:83080305..83080335,+!p2@Zfp516!0.31!5.06!Zfp516;;chr13:67182439..67182491,-!p2@Zfp708!0.31!3.91!Zfp708;;chr2:34227446..34227511,-!p1@Pbx3!0.31!3.45!Pbx3;;chr14:56443698..56443726,+!p2@Nfatc4!0.31!2.76!Nfatc4;;chr18:55149986..55150009,-!p7@Zfp608!0.31!2.76!Zfp608;;chr1:170361777..170361797,-!p10@Pbx1!0.31!2.53!Pbx1;;chr2:154395552..154395561,-!p3@E2f1!0.31!1.84!E2f1;;chr13:78339382..78339420,-!p3@Nr2f1!0.31!1.38!Nr2f1;;chr8:73905967..73905978,-!p4@Nr2f6!0.31!1.38!Nr2f6;;chr15:81702313..81702346,-!p1@Phf5a!0.30!53.80!Phf5a;;chr3:30993974..30994045,+!p1@Skil!0.30!50.58!Skil;;chr5:138558139..138558214,+!p1@Zscan21!0.30!48.97!Zscan21;;chr6:98978245..98978289,-!p1@Foxp1!0.30!25.98!Foxp1;;chr4:133801453..133801492,-!p1@Zfp593!0.30!14.25!Zfp593;;chr13:30077847..30077906,-!p1@E2f3!0.30!13.56!E2f3;;chr13:21454695..21454752,+!p1@Zscan12!0.30!9.66!Zscan12;;chrX:132420442..132420482,+!p2@Bhlhb9!0.30!8.74!Bhlhb9;;chr5:139060892..139060911,-!p2@Zfp68!0.30!8.05!Zfp68;;chrX:53599567..53599592,+!p1@Zfp449!0.30!6.90!Zfp449;;chr6:118405493..118405536,-!p1@Zfp248!0.30!6.21!Zfp248;;chr13:15555035..15555073,+!p4@Gli3!0.30!4.14!Gli3;;chr18:79306577..79306592,-!p3@Setbp1!0.30!2.76!Setbp1;;chr11:99092002..99092018,-!p6@Smarce1!0.30!2.07!Smarce1;;chr13:15555555..15555574,+!p5@Gli3!0.30!1.61!Gli3;;chr6:72185179..72185196,-!p4@Atoh8!0.30!1.61!Atoh8;;chr6:14851344..14851364,+!p6@Foxp2!0.30!1.38!Foxp2;;chr1:182499095..182499141,+!p2@Parp1!0.29!30.12!Parp1;;chr18:24179250..24179314,-!p1@Zfp191!0.29!28.28!Zfp191;;chr12:84828663..84828679,-!p1@Dpf3!0.29!12.87!Dpf3;;chr2:126501197..126501245,-!p1@Gabpb1!0.29!12.87!Gabpb1;;chr2:37278526..37278575,-!p2@Rc3h2!0.29!6.67!Rc3h2;;chr11:102179074..102179099,-!p4@Ubtf!0.29!4.60!Ubtf;;chr17:71200558..71200572,-!p4@Tgif1!0.29!3.68!Tgif1;;chr18:76401789..76401814,+!p4@Smad2!0.29!3.22!Smad2;;chr1:170361826..170361844,-!p9@Pbx1!0.29!3.22!Pbx1;;chr17:28487603..28487626,-!p2@Tead3!0.29!2.99!Tead3;;chr17:37140628..37140631,+!p2@Zfp57!0.29!2.76!Zfp57;;chr2:91864449..91864492,-!p3@Creb3l1!0.29!2.07!Creb3l1;;chr2:44965761..44965785,-!p13@Zeb2!0.29!1.84!Zeb2;;chr7:134592574..134592591,-!p2@Zfp689!0.29!1.84!Zfp689;;chr19:5423800..5423821,-!p5@Drap1!0.29!1.84!Drap1;;chr3:54611659..54611668,-!p4@Rfxap!0.29!1.61!Rfxap;;chr2:168427252..168427273,-!p2@Nfatc2!0.29!1.38!Nfatc2;;chr13:40826150..40826167,-!p3@Tfap2a!0.29!1.15!Tfap2a;;chr10:79896360..79896400,-!p1@Tcf3!0.28!69.89!Tcf3;;chr18:14131126..14131211,-!p1@Zfp521!0.28!35.63!Zfp521;;chr5:34163344..34163484,+!p1@Whsc1!0.28!26.44!Whsc1;;chr6:72739185..72739232,-!p1@Tcf7l1!0.28!17.24!Tcf7l1;;chr13:21622917..21622952,-!p1@Zfp192!0.28!10.81!Zfp192;;chrX:132420399..132420436,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37498,-!p6@Crem!0.18!1.84!Crem;;chr11:44430989..44431015,+!p4@Ebf1!0.18!1.61!Ebf1;;chr15:76755821..76755835,-!p2@Zfp647!0.18!0.92!Zfp647;;chr18:35721940..35721951,+!p5@Matr3!0.18!0.92!Matr3;;chr17:48015645..48015689,-!p9@Foxp4!0.18!0.92!Foxp4;;chr9:71743910..71743915,-!p7@Tcf12!0.18!0.69!Tcf12;;chr10:67375223..67375240,-!p4@Zfp365!0.18!0.69!Zfp365;;chr4:135728282..135728310,+!p4@E2f2!0.18!0.69!E2f2;;chr13:58503837..58503885,-!p1@Hnrnpk!0.17!379.80!Hnrnpk;;chr6:86476158..86476181,-!p1@Pcbp1!0.17!174.27!Pcbp1;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.17!62.53!Hmga1;;chr4:149611320..149611348,+!p1@Eno1,p1@Gm5506,p1@LOC100045967,p1@LOC100503183!0.17!57.25!Eno1;;chr7:135056024..135056042,+!p1@Myst1!0.17!37.47!Myst1;;chr18:24113169..24113205,+!p1@Zfp397!0.17!34.95!Zfp397;;chr1:173341436..173341468,+!p1@Usf1!0.17!32.19!Usf1;;chr18:76401546..76401613,+!p1@Smad2!0.17!27.82!Smad2;;chr19:5424768..5424811,-!p2@Drap1!0.17!24.83!Drap1;;chr17:35653725..35653780,-!p1@Tcf19!0.17!21.84!Tcf19;;chr6:64992801..64992894,+!p2@Smarcad1!0.17!19.08!Smarcad1;;chr7:24993112..24993158,-!p1@Zfp111!0.17!13.10!Zfp111;;chr11:90252223..90252240,-!p1@Hlf!0.17!10.35!Hlf;;chr7:5003117..5003159,+!p1@Zfp580!0.17!9.43!Zfp580;;chr17:34784132..34784161,+!p1@Atf6b!0.17!6.90!Atf6b;;chr19:12870598..12870636,-!p1@U05342,p1@Zfp91!0.17!5.98!Zfp91;;chr16:55966525..55966543,+!p5@Rpl24,p5@Zbtb11!0.17!3.91!Zbtb11;;chr9:65675474..65675503,-!p3@Zfp609!0.17!3.22!Zfp609;;chr19:28086084..28086124,-!p6@Rfx3!0.17!2.99!Rfx3;;chr14:100684075..100684098,-!p3@Klf12!0.17!2.53!Klf12;;chr11:44430788..44430804,+!p3@Ebf1!0.17!2.53!Ebf1;;chr4:118846454..118846506,-!p2@Zfp691!0.17!2.30!Zfp691;;chr4:154010409..154010466,-!p2@Prdm16!0.17!2.30!Prdm16;;chr3:90097275..90097302,+!p2@Gatad2b!0.17!2.30!Gatad2b;;chr6:72739234..72739256,-!p2@Tcf7l1!0.17!2.30!Tcf7l1;;chr6:47827547..47827568,+!p4@Zfp282!0.17!2.30!Zfp282;;chr17:27693746..27693759,+!p6@Hmga1-rs1,p7@Hmga1!0.17!1.84!Hmga1;;chr17:27693865..27693877,+!p8@Hmga1-rs1,p9@Hmga1!0.17!1.38!Hmga1;;chr15:88582079..88582091,+!p1@Gm15583,p1@Zbed4!0.17!1.38!Zbed4;;chr5:125342568..125342602,+!p2@Zfp664!0.17!1.38!Zfp664;;chr4:133310214..133310231,-!p11@Arid1a!0.17!1.38!Arid1a;;chr7:4947625..4947634,-!p6@Zfp579!0.17!1.38!Zfp579;;chr13:37870281..37870293,+!p10@Rreb1!0.17!1.38!Rreb1;;chr12:85534937..85534948,-!p10@C130039O16Rik!0.17!0.92!C130039O16Rik;;chr17:44873258..44873281,-!p5@Runx2!0.17!0.92!Runx2;;chr1:64167889..64167898,-!p8@Klf7!0.17!0.92!Klf7;;chr1:64168030..64168037,-!p9@Klf7!0.17!0.92!Klf7;;chr11:23978229..23978268,+!p8@Bcl11a!0.17!0.69!Bcl11a;;chr7:52253119..52253130,+!p4@Irf3!0.17!0.69!Irf3;;chr7:17642018..17642045,-!p4@Hif3a!0.17!0.69!Hif3a;;chr3:30993641..30993651,+!p7@Skil!0.17!0.69!Skil;;chr4:13670661..13670681,+!p12@Runx1t1!0.17!0.69!Runx1t1;;chr12:117285924..117286018,+!p1@Zfp386!0.16!36.55!Zfp386;;chr9:56266612..56266654,+!p1@Hmg20a!0.16!36.09!Hmg20a;;chr7:4966247..4966286,-!p1@Fiz1!0.16!25.06!Fiz1;;chrX:45947560..45947670,-!p1@Zfp280c!0.16!23.91!Zfp280c;;chr16:4594740..4594759,+!p1@Glis2!0.16!14.25!Glis2;;chrX:35542957..35543003,+!p1@Zbtb33!0.16!12.87!Zbtb33;;chr7:134170496..134170539,-!p4@Maz!0.16!10.81!Maz;;chr16:98073403..98073460,-!p1@Prdm15!0.16!9.66!Prdm15;;chr11:87881569..87881633,+!p2@Vezf1!0.16!9.43!Vezf1;;chr17:34169016..34169068,+!p2@Rxrb!0.16!8.74!Rxrb;;chr19:28085628..28085671,-!p1@Rfx3!0.16!8.28!Rfx3;;chr13:67162067..67162114,-!p1@Zfp712!0.16!8.05!Zfp712;;chr7:30644985..30645072,+!p1@Zfp420!0.16!6.90!Zfp420;;chr7:134170038..134170055,-!p8@Maz!0.16!4.83!Maz;;chrX:98449898..98449913,+!p2@Foxo4!0.16!3.45!Foxo4;;chr3:95021799..95021840,-!p4@Gabpb2!0.16!3.22!Gabpb2;;chr17:45570631..45570658,-!p4@Cdc5l!0.16!2.99!Cdc5l;;
@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011335
 |is_obsolete=
+|library_id=CNhs10521
+|library_id_phase_based=2:CNhs10521
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;399
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;399
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E14.CNhs10521.399-16E2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E14.CNhs10521.399-16E2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E14.CNhs10521.399-16E2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E14.CNhs10521.399-16E2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E14.CNhs10521.399-16E2.mm9.nobarcode.rdna.fa.gz
 |name=eyeball, embryo E14
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10521,LSID649,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.0356482906093527,0,0,0,0,0,-0.130187028449593,0,0,0,0,0.143471986349215,0,0,0,0,0,0,0.0359178758631816,0,0,0,0,0,0,0,0,0,0,0,0,0.0449352723065536,-0.330611565578275,0,0,0,0,0,-0.045028114033772,0.0281715987501138,-0.260187232816272,-0.185716210962732,0.62759697198014,0,0,0,0,0,0,0,0,0,0,0,0,0.023864997049667,0,0,0,0,0.0470235895302325,0,0,0,0.0898705446131073,0,-0.0885368073243019,-0.0828394305936301,-0.0682204981579752,-0.0241873895767599,0,0,0.0016911847603085,0,0,0,0.00075502825868351,-0.0226084989773752,-0.219445118855975,0.0110389497731999,0,0,0,0,0,0,-0.028374852301906,-0.0259427699499675,-0.0737500831274941,0,0,0,0,0
@@ Line 59: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=16E2
+|rna_tube_id=1.60E+03
 |rna_weight_ug=
 |sample_age=
@@ Line 83: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:399-16E2;search_select_hide=table117:399-16E2
 }}

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FF:399-16E2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:15, 4 June 2020

CNhs10521

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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