FF:345-16C6: Difference between revisions

Latest revision as of 19:10, 4 June 2020

Name:	eyeball, embryo E12
Species:	Mouse (Mus musculus)
Library ID:	CNhs11016
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	eyeball
dev stage	12 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		SAMD00005612

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11016		CAGE		DRX008955		DRR009829

Accession ID Mm9

Library id		BAM		CTSS
CNhs11016		DRZ001254		DRZ002637

Accession ID Mm10

Library id		BAM		CTSS
CNhs11016		DRZ012604		DRZ013987

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

CNhs11016

0	0
1	0.0257
10	0
100	0.1
1000	-0.0355
1001	0.0588
1002	0.354
1003	-0.104
1004	0.654
1005	-0.0978
1006	-0.0752
1007	0.142
1008	0
1009	-0.0469
101	0.158
1010	0
1011	0.0522
1012	0
1013	-0.149
1014	0.267
1015	0.343
1016	0.222
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.0531
1022	-0.0709
1023	0
1024	-0.0367
1025	0
1026	0
1027	0.262
1028	0
1029	0.203
103	-0.0136
1030	0
1031	0.199
1032	-0.141
1033	0.0531
1034	0
1035	0
1036	0.129
1037	0
1038	-0.0941
1039	-0.097
104	0
1040	0.0257
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: CNhs11016

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	1.87475e-5
MA0003.1	MA0003.1	0.108
MA0004.1	MA0004.1	0.908
MA0006.1	MA0006.1	0.282
MA0007.1	MA0007.1	0.334
MA0009.1	MA0009.1	0.221
MA0014.1	MA0014.1	0.196
MA0017.1	MA0017.1	2.45987e-4
MA0018.2	MA0018.2	0.499
MA0019.1	MA0019.1	0.834
MA0024.1	MA0024.1	1.25523e-4
MA0025.1	MA0025.1	0.0127
MA0027.1	MA0027.1	0.12
MA0028.1	MA0028.1	0.184
MA0029.1	MA0029.1	0.623
MA0030.1	MA0030.1	0.0403
MA0031.1	MA0031.1	6.71054e-4
MA0035.2	MA0035.2	0.00205
MA0038.1	MA0038.1	0.00372
MA0039.2	MA0039.2	0.00181
MA0040.1	MA0040.1	0.0347
MA0041.1	MA0041.1	0.198
MA0042.1	MA0042.1	0.329
MA0043.1	MA0043.1	0.122
MA0046.1	MA0046.1	1.3655e-29
MA0047.2	MA0047.2	2.83134e-5
MA0048.1	MA0048.1	0.21
MA0050.1	MA0050.1	2.90774e-7
MA0051.1	MA0051.1	2.32766e-5
MA0052.1	MA0052.1	1.95362e-6
MA0055.1	MA0055.1	0.0769
MA0057.1	MA0057.1	0.076
MA0058.1	MA0058.1	0.705
MA0059.1	MA0059.1	0.314
MA0060.1	MA0060.1	2.5449e-13
MA0061.1	MA0061.1	0.0645
MA0062.2	MA0062.2	0.638
MA0065.2	MA0065.2	1.91768e-5
MA0066.1	MA0066.1	0.312
MA0067.1	MA0067.1	0.53
MA0068.1	MA0068.1	0.367
MA0069.1	MA0069.1	0.102
MA0070.1	MA0070.1	0.781
MA0071.1	MA0071.1	0.532
MA0072.1	MA0072.1	0.364
MA0073.1	MA0073.1	0.166
MA0074.1	MA0074.1	0.597
MA0076.1	MA0076.1	0.117
MA0077.1	MA0077.1	0.00613
MA0078.1	MA0078.1	0.39
MA0079.2	MA0079.2	0.198
MA0080.2	MA0080.2	4.76839e-12
MA0081.1	MA0081.1	0.256
MA0083.1	MA0083.1	0.0336
MA0084.1	MA0084.1	0.757
MA0087.1	MA0087.1	0.285
MA0088.1	MA0088.1	0.514
MA0090.1	MA0090.1	0.42
MA0091.1	MA0091.1	0.456
MA0092.1	MA0092.1	0.324
MA0093.1	MA0093.1	0.869
MA0099.2	MA0099.2	1.12308e-6
MA0100.1	MA0100.1	0.714
MA0101.1	MA0101.1	0.239
MA0102.2	MA0102.2	0.197
MA0103.1	MA0103.1	0.00351
MA0104.2	MA0104.2	0.235
MA0105.1	MA0105.1	0.0347
MA0106.1	MA0106.1	0.485
MA0107.1	MA0107.1	0.101
MA0108.2	MA0108.2	0.613
MA0111.1	MA0111.1	0.549
MA0112.2	MA0112.2	1.426e-4
MA0113.1	MA0113.1	0.431
MA0114.1	MA0114.1	4.1306e-4
MA0115.1	MA0115.1	0.0996
MA0116.1	MA0116.1	0.0346
MA0117.1	MA0117.1	0.36
MA0119.1	MA0119.1	0.00512
MA0122.1	MA0122.1	0.855
MA0124.1	MA0124.1	0.277
MA0125.1	MA0125.1	0.0936
MA0131.1	MA0131.1	0.343
MA0135.1	MA0135.1	0.552
MA0136.1	MA0136.1	2.37768e-8
MA0137.2	MA0137.2	0.156
MA0138.2	MA0138.2	1.61872e-4
MA0139.1	MA0139.1	0.125
MA0140.1	MA0140.1	0.029
MA0141.1	MA0141.1	0.00557
MA0142.1	MA0142.1	0.127
MA0143.1	MA0143.1	2.00473e-4
MA0144.1	MA0144.1	0.0895
MA0145.1	MA0145.1	0.00878
MA0146.1	MA0146.1	0.299
MA0147.1	MA0147.1	0.368
MA0148.1	MA0148.1	9.75145e-6
MA0149.1	MA0149.1	0.0289
MA0150.1	MA0150.1	0.013
MA0152.1	MA0152.1	0.153
MA0153.1	MA0153.1	4.85168e-19
MA0154.1	MA0154.1	0.0015
MA0155.1	MA0155.1	0.755
MA0156.1	MA0156.1	0.00237
MA0157.1	MA0157.1	0.00419
MA0159.1	MA0159.1	0.0318
MA0160.1	MA0160.1	0.0237
MA0162.1	MA0162.1	0.874
MA0163.1	MA0163.1	0.0542
MA0164.1	MA0164.1	0.672
MA0258.1	MA0258.1	0.00477
MA0259.1	MA0259.1	0.501

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: CNhs11016

Novel motif	Logo	P-value
1	1	0.127
10	10	0.378
100	100	0.656
101	101	0.68
102	102	0.68
103	103	0.118
104	104	0.947
105	105	0.129
106	106	0.00682
107	107	0.0688
108	108	0.668
109	109	0.117
11	11	0.113
110	110	0.248
111	111	0.0514
112	112	0.0516
113	113	0.54
114	114	0.0536
115	115	0.822
116	116	0.556
117	117	0.631
118	118	0.875
119	119	0.0425
12	12	0.853
120	120	0.46
121	121	0.808
122	122	0.895
123	123	0.156
124	124	0.142
125	125	0.211
126	126	0.498
127	127	0.12
128	128	0.0981
129	129	0.161
13	13	0.231
130	130	0.903
131	131	0.148
132	132	0.247
133	133	0.773
134	134	0.623
135	135	0.188
136	136	0.783
137	137	0.572
138	138	0.583
139	139	0.0207
14	14	0.347
140	140	0.188
141	141	0.0303
142	142	0.312
143	143	0.467
144	144	0.983
145	145	0.299
146	146	0.192
147	147	0.375
148	148	0.297
149	149	0.0437
15	15	0.0806
150	150	0.721
151	151	0.126
152	152	0.0255
153	153	0.637
154	154	0.977
155	155	0.771
156	156	0.47
157	157	0.674
158	158	0.604
159	159	0.872
160	160	0.737
161	161	0.748
162	162	0.802
163	163	0.0855
164	164	0.102
165	165	0.0851
166	166	0.469
167	167	0.914
168	168	0.339
169	169	0.00397
17	17	0.0422
18	18	0.56
19	19	0.183
2	2	0.285
20	20	0.54
21	21	0.639
22	22	0.215
23	23	0.0546
24	24	0.365
25	25	0.472
26	26	0.306
27	27	0.348
28	28	0.373
29	29	0.586
3	3	0.292
30	30	0.527
31	31	0.582
32	32	0.122
33	33	0.806
34	34	0.604
35	35	0.753
36	36	0.294
37	37	0.0638
38	38	0.174
39	39	0.652
4	4	0.333
40	40	0.227
41	41	0.44
42	42	0.644
43	43	0.154
44	44	0.125
45	45	0.308
46	46	0.322
47	47	0.192
48	48	0.179
49	49	0.195
5	5	0.145
50	50	0.889
51	51	0.571
52	52	0.151
53	53	0.489
54	54	0.35
55	55	0.657
56	56	0.305
57	57	0.662
58	58	0.242
59	59	0.0293
6	6	0.529
60	60	0.0487
61	61	0.854
62	62	0.103
63	63	0.0976
64	64	0.464
65	65	0.0789
66	66	0.583
67	67	0.932
68	68	0.0987
69	69	0.643
7	7	0.224
70	70	0.00244
71	71	0.24
72	72	0.217
73	73	0.0504
74	74	0.222
75	75	0.111
76	76	0.68
77	77	0.141
78	78	0.159
79	79	0.108
8	8	0.29
80	80	0.0831
81	81	0.379
82	82	0.0246
83	83	0.682
84	84	0.437
85	85	0.0311
86	86	0.33
87	87	0.329
88	88	0.679
89	89	0.15
9	9	0.277
90	90	0.529
91	91	0.432
92	92	0.0813
93	93	0.661
94	94	0.487
95	95	0.286
96	96	0.319
97	97	0.508
98	98	0.234
99	99	0.623

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: CNhs11016

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011316 mouse eyeball- embryo E12 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)
0000295 (mouse embryonic day 12 sample)
0011316 (mouse eyeball- embryo E12 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@SAMD00005612
+|accession_numbers=CAGE;DRX008955;DRR009829;DRZ001254;DRZ002637;DRZ012604;DRZ013987
 |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!2.49!309.17!Atoh7;;chr18:66098702..66098742,-!p1@Rax!2.12!130.25!Rax;;chr19:19185671..19185693,-!p1@Rorb!2.07!268.44!Rorb;;chr12:74040861..74040875,+!p1@Six6!1.88!74.69!Six6;;chr2:105509045..105509071,+!p1@Pax6!1.81!63.76!Pax6;;chr12:34642510..34642530,+!p1@Twist1!1.76!173.71!Twist1;;chr2:105522662..105522687,+!p2@Pax6!1.62!40.99!Pax6;;chr3:34548909..34548927,+!p1@Sox2!1.60!64.93!Sox2;;chr12:74040895..74040916,+!p2@Six6!1.57!36.43!Six6;;chr2:38206744..38206766,+!p1@Lhx2!1.55!41.38!Lhx2;;chr3:127336052..127336058,+!p1@Neurog2!1.55!34.74!Neurog2;;chr5:35731493..35731531,+!p1@Hmx1!1.55!34.48!Hmx1;;chr2:38206580..38206600,+!p2@Lhx2!1.53!40.21!Lhx2;;chr4:114598669..114598674,-!p1@Foxe3!1.53!33.18!Foxe3;;chr14:49287186..49287225,-!p1@Otx2!1.53!32.79!Otx2;;chr4:154335024..154335039,+!p1@Hes5!1.52!38.65!Hes5;;chr17:86020510..86020589,+!p3@Six3!1.50!30.71!Six3;;chr2:79296783..79296801,-!p1@Neurod1!1.49!29.93!Neurod1;;chr6:83661226..83661282,+!p1@Vax2!1.48!28.89!Vax2;;chr11:21901608..21901634,-!p1@Otx1!1.48!28.89!Otx1;;chr17:86020156..86020183,+!p1@Six3!1.46!28.11!Six3;;chr3:128916868..128916890,+!p1@Pitx2!1.44!35.91!Pitx2;;chr12:85910771..85910785,+!p1@Vsx2!1.44!26.80!Vsx2;;chr6:70906450..70906454,+!p1@Foxi3!1.38!22.90!Foxi3;;chr17:86020115..86020128,+!p2@Six3!1.37!22.38!Six3;;chr1:19199236..19199258,+!p1@Tfap2b!1.36!21.99!Tfap2b;;chr9:91260616..91260653,-!p2@Zic1!1.35!21.34!Zic1;;chr2:105515635..105515661,+!p5@Pax6!1.34!20.69!Pax6;;chr14:122874619..122874634,+!p1@Zic2!1.33!20.30!Zic2;;chr12:3891810..3891829,+!p2@Dnmt3a!1.30!29.15!Dnmt3a;;chr12:28027561..28027591,-!p1@Sox11!1.29!119.97!Sox11;;chrX:58146612..58146615,-!p1@Sox3!1.29!18.35!Sox3;;chr10:119913546..119913583,-!p3@Hmga2!1.28!36.95!Hmga2;;chr9:91260594..91260612,-!p1@Zic1!1.27!17.57!Zic1;;chr10:102491405..102491416,-!p1@Alx1!1.26!17.31!Alx1;;chr17:86087592..86087615,-!p1@Six2!1.25!16.79!Six2;;chr13:99124189..99124205,+!p1@Foxd1!1.24!24.98!Foxd1;;chrX:55283799..55283813,+!p1@Zic3!1.21!15.22!Zic3;;chr10:119913310..119913366,-!p1@Hmga2!1.20!115.55!Hmga2;;chr2:71384802..71384815,-!p1@Dlx2!1.16!16.66!Dlx2;;chr19:46222859..46222876,-!p1@Pitx3!1.16!13.40!Pitx3;;chr1:19199151..19199170,+!p3@Tfap2b!1.14!12.88!Tfap2b;;chr6:14851440..14851497,+!p2@Foxp2!1.12!30.06!Foxp2;;chr10:119914001..119914078,-!p4@Hmga2!1.12!16.79!Hmga2;;chr11:101755669..101755686,-!p1@Meox1!1.11!21.34!Meox1;;chr13:31898767..31898785,+!p4@Foxc1!1.11!14.44!Foxc1;;chr2:105515793..105515808,+!p3@Pax6!1.11!11.84!Pax6;;chr10:119913278..119913298,-!p2@Hmga2!1.08!24.72!Hmga2;;chr13:72101161..72101177,-!p2@Irx1!1.08!15.48!Irx1;;chr2:105515586..105515606,+!p4@Pax6!1.08!11.06!Pax6;;chr5:114723781..114723795,-!p1@Foxn4!1.07!10.80!Foxn4;;chr2:93482464..93482491,+!p1@Alx4!1.07!10.67!Alx4;;chr14:17407970..17408015,-!p2@Rarb!1.06!28.11!Rarb;;chr3:128902837..128902861,+!p3@Pitx2!1.06!10.54!Pitx2;;chr2:146047829..146047847,+!p1@Insm1!1.05!18.35!Insm1;;chr13:72101178..72101203,-!p1@Irx1!1.05!16.13!Irx1;;chr9:98855868..98855895,+!p1@Foxl2!1.05!10.28!Foxl2;;chr1:165243591..165243625,-!p2@Prrx1!1.04!15.35!Prrx1;;chr9:74709695..74709722,+!p1@Onecut1!1.03!9.63!Onecut1;;chr9:98855944..98855971,+!p4@Foxl2!1.03!9.63!Foxl2;;chr18:66098673..66098684,-!p2@Rax!1.03!9.63!Rax;;chr8:123640063..123640077,+!p1@Foxc2!1.02!17.44!Foxc2;;chr8:12395603..12395621,+!p1@Sox1!1.02!9.50!Sox1;;chr2:71367871..71367898,+!p1@Dlx1!1.02!9.37!Dlx1;;chr19:19185697..19185711,-!p2@Rorb!1.01!11.84!Rorb;;chr1:19199221..19199234,+!p6@Tfap2b!1.01!9.24!Tfap2b;;chr2:17976799..17976829,+!p5@Mllt10!1.00!11.19!Mllt10;;chr11:21901587..21901604,-!p2@Otx1!1.00!9.11!Otx1;;chr4:109650609..109650653,+!p1@Dmrta2!1.00!9.11!Dmrta2;;chr6:14851212..14851226,+!p12@Foxp2!1.00!8.98!Foxp2;;chr1:165243379..165243402,-!p3@Prrx1!0.99!13.27!Prrx1;;chr3:107398056..107398082,+!p1@Alx3!0.99!8.85!Alx3;;chr8:94325321..94325366,-!p1@Irx3!0.98!21.08!Irx3;;chr15:103164702..103164778,-!p3@Zfp385a!0.98!10.15!Zfp385a;;chr17:48061584..48061601,-!p2@Foxp4!0.97!55.43!Foxp4;;chr12:74147689..74147711,-!p1@Six1!0.97!18.74!Six1;;chr17:86012772..86012825,+!p4@Six3!0.97!8.33!Six3;;chr3:34548946..34548972,+!p2@Sox2!0.96!8.98!Sox2;;chr3:101814061..101814094,+!p1@Nhlh2!0.96!8.20!Nhlh2;;chr16:25801993..25802014,+!p1@Trp63!0.96!8.20!Trp63;;chr14:34791937..34791977,-!p1@Zfp488!0.96!8.20!Zfp488;;chr12:3891753..3891801,+!p4@Dnmt3a!0.95!13.14!Dnmt3a;;chr3:99057269..99057306,+!p1@Tbx15!0.95!9.63!Tbx15;;chr13:55932591..55932622,-!p1@Pitx1!0.94!9.37!Pitx1;;chr12:74040716..74040745,+!p3@Six6!0.94!7.68!Six6;;chr13:72766250..72766273,+!p1@Irx2!0.93!11.97!Irx2;;chr13:78339476..78339515,-!p1@Nr2f1!0.93!11.84!Nr2f1;;chr7:16465229..16465249,-!p1@Crx!0.93!7.42!Crx;;chr13:31898729..31898761,+!p1@Foxc1!0.92!18.35!Foxc1;;chr14:17407878..17407926,-!p1@Rarb!0.91!16.40!Rarb;;chr8:94325814..94325839,-!p2@Irx3!0.91!15.35!Irx3;;chr6:14851287..14851342,+!p1@Foxp2!0.90!23.55!Foxp2;;chr13:117099847..117099907,-!p1@Isl1!0.90!13.14!Isl1;;chr19:59533221..59533271,+!p1@Emx2!0.90!8.59!Emx2;;chr13:40829137..40829205,-!p1@Tfap2a!0.90!7.94!Tfap2a;;chr8:80960539..80960548,-!p1@Pou4f2!0.90!6.90!Pou4f2;;chr15:35225845..35225867,+!p1@Osr2!0.89!17.57!Osr2;;chr17:86020137..86020149,+!p5@Six3!0.89!6.77!Six3;;chr10:42303385..42303401,-!p1@Nr2e1!0.89!6.77!Nr2e1;;chr1:170361991..170362015,-!p6@Pbx1!0.88!15.22!Pbx1;;chr9:31720843..31720888,-!p1@Barx2!0.88!7.42!Barx2;;chr11:3189683..3189744,+!p2@Patz1!0.87!13.79!Patz1;;chr10:119913792..119913820,-!p5@Hmga2!0.87!11.32!Hmga2;;chr9:71743854..71743909,-!p1@Tcf12!0.86!52.83!Tcf12;;chr14:98568971..98569025,-!p1@Dach1!0.86!50.88!Dach1;;chr13:31898496..31898519,+!p3@Foxc1!0.86!10.41!Foxc1;;chr8:94325847..94325869,-!p3@Irx3!0.86!10.28!Irx3;;chr10:20880698..20880717,-!p3@Myb!0.86!10.15!Myb;;chr14:49284773..49284790,-!p2@Otx2!0.86!6.25!Otx2;;chr1:19202352..19202354,+!p2@Tfap2b!0.86!6.25!Tfap2b;;chr9:106356211..106356242,+!p1@Pcbp4!0.85!126.74!Pcbp4;;chr17:35031460..35031518,+!p1@Zbtb12!0.85!32.53!Zbtb12;;chr19:7342725..7342784,+!p1@Rcor2!0.85!26.67!Rcor2;;chr10:126778916..126778974,-!p1@Gli1!0.85!14.31!Gli1;;chr10:42303452..42303470,-!p2@Nr2e1!0.85!6.12!Nr2e1;;chr2:30700788..30700824,+!p2@Prrx2!0.84!9.24!Prrx2;;chr18:64499706..64499721,+!p2@Onecut2!0.84!8.59!Onecut2;;chr4:150503457..150503498,-!p3@Camta1!0.84!6.77!Camta1;;chr1:136186574..136186592,+!p1@Myog!0.84!5.99!Myog;;chr14:49287107..49287125,-!p3@Otx2!0.84!5.99!Otx2;;chr6:14851403..14851422,+!p8@Foxp2!0.84!5.86!Foxp2;;chr12:12948633..12948651,-!p1@Mycn!0.83!59.73!Mycn;;chr14:98568761..98568814,-!p2@Dach1!0.83!41.90!Dach1;;chr7:144506077..144506128,-!p1@Ebf3!0.83!13.92!Ebf3;;chr10:12810631..12810649,+!p1@Plagl1!0.82!158.62!Plagl1;;chr2:163028808..163028869,+!p1@Tox2!0.82!21.21!Tox2;;chr10:86956396..86956411,-!p1@Ascl1!0.82!8.98!Ascl1;;chr1:170361678..170361689,-!p13@Pbx1!0.82!6.90!Pbx1;;chr10:129717274..129717298,-!p1@Neurod4!0.82!5.60!Neurod4;;chr5:114724042..114724090,-!p2@Foxn4!0.82!5.60!Foxn4;;chr9:24578720..24578735,-!p1@Tbx20!0.82!5.60!Tbx20;;chr2:65683890..65683907,+!p1@Csrnp3!0.81!11.06!Csrnp3;;chr13:31898637..31898653,+!p2@Foxc1!0.81!10.15!Foxc1;;chr13:72766279..72766296,+!p2@Irx2!0.81!8.33!Irx2;;chr6:15135456..15135520,+!p3@Foxp2!0.80!11.97!Foxp2;;chr13:78339428..78339466,-!p2@Nr2f1!0.80!7.42!Nr2f1;;chr8:90483433..90483457,-!p2@Zfp423!0.80!7.29!Zfp423;;chr18:66098752..66098757,-!p3@Rax!0.80!5.33!Rax;;chr1:19199119..19199134,+!p4@Tfap2b!0.80!5.33!Tfap2b;;chr14:52634234..52634281,-!p3@Zfp219!0.79!15.35!Zfp219;;chr8:94881733..94881790,+!p1@Irx5!0.79!10.54!Irx5;;chr12:56700411..56700416,+!p@chr12:56700411..56700416,+!0.79!5.20!Insm2;;chr4:97248473..97248496,+!p16@Nfia!0.79!5.20!Nfia;;chr17:86020468..86020504,+!p6@Six3!0.79!5.20!Six3;;chr3:5218629..5218684,+!p1@Zfhx4!0.77!17.05!Zfhx4;;chr10:20880731..20880775,-!p2@Myb!0.77!10.80!Myb;;chr7:38554763..38554780,-!p1@Zfp536!0.77!9.24!Zfp536;;chr8:94325486..94325510,-!p4@Irx3!0.77!6.64!Irx3;;chr13:72101141..72101158,-!p3@Irx1!0.77!6.25!Irx1;;chr13:78339382..78339420,-!p3@Nr2f1!0.77!5.86!Nr2f1;;chr19:7342786..7342803,+!p2@Rcor2!0.76!6.64!Rcor2;;chr5:24107676..24107722,-!p4@Smarcd3!0.76!6.64!Smarcd3;;chr7:53631837..53631850,+!p1@Myod1!0.76!4.81!Myod1;;chr10:102491237..102491291,-!p2@Alx1!0.76!4.81!Alx1;;chr3:128917187..128917223,+!p2@Pitx2!0.75!5.47!Pitx2;;chrX:55284180..55284195,+!p2@Zic3!0.75!4.68!Zic3;;chr15:75447162..75447217,+!p2@Zfp41!0.74!14.44!Zfp41;;chr6:14851250..14851277,+!p4@Foxp2!0.74!5.99!Foxp2;;chr9:98855847..98855866,+!p3@Foxl2!0.74!4.55!Foxl2;;chr1:173987720..173987729,-!p1@Nhlh1!0.74!4.55!Nhlh1;;chr11:99092233..99092273,-!p2@Smarce1!0.73!23.42!Smarce1;;chr18:65741935..65741964,+!p2@Zfp532!0.73!13.01!Zfp532;;chr13:53568104..53568156,-!p1@Msx2!0.73!6.77!Msx2;;chr1:165243653..165243664,-!p4@Prrx1!0.73!6.38!Prrx1;;chr11:85646303..85646329,+!p1@Tbx2!0.72!31.75!Tbx2;;chr18:65741358..65741415,+!p1@Zfp532!0.72!20.17!Zfp532;;chr18:64499674..64499696,+!p1@Onecut2!0.72!7.81!Onecut2;;chr11:98789140..98789168,+!p5@Rara!0.72!7.29!Rara;;chr7:52471143..52471186,+!p1@Tead2!0.71!49.45!Tead2;;chr2:152223783..152223812,-!p4@Sox12!0.71!10.15!Sox12;;chr15:102087737..102087801,-!p3@Rarg!0.71!7.29!Rarg;;chr3:128902878..128902893,+!p6@Pitx2!0.71!4.16!Pitx2;;chr10:106923133..106923146,-!p1@Myf5!0.71!4.16!Myf5;;chr7:135019147..135019187,-!p3@Zfp668!0.70!9.50!Zfp668;;chr13:31717548..31717596,+!p1@Foxf2!0.70!8.59!Foxf2;;chr11:50700965..50701027,-!p1@Zfp454!0.69!15.35!Zfp454;;chr13:15555670..15555771,+!p2@Gli3!0.69!10.80!Gli3;;chr1:170361826..170361844,-!p9@Pbx1!0.69!9.50!Pbx1;;chr14:13178147..13178185,-!p1@Fezf2!0.69!3.90!Fezf2;;chr10:42303410..42303422,-!p3@Nr2e1!0.69!3.90!Nr2e1;;chr13:22036953..22037009,+!p1@Zfp184!0.68!11.19!Zfp184;;chr11:85646263..85646278,+!p2@Tbx2!0.68!10.67!Tbx2;;chr1:93698030..93698064,+!p1@Twist2!0.68!8.20!Twist2;;chr7:25292331..25292421,+!p1@Zfp428!0.67!30.06!Zfp428;;chr9:87626083..87626108,-!p1@Tbx18!0.67!8.98!Tbx18;;chr17:86020293..86020318,+!p7@Six3!0.67!3.64!Six3;;chr3:5218516..5218544,+!p2@Zfhx4!0.66!5.73!Zfhx4;;chr2:307008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2.21!Zbed3;;chr10:44178521..44178557,-!p1@Prdm1!0.23!1.95!Prdm1;;chr8:72356384..72356434,+!p2@Pbx4!0.23!1.56!Pbx4;;chr4:133801432..133801448,-!p3@Zfp593!0.23!1.56!Zfp593;;chr1:135551736..135551746,-!p3@Zc3h11a!0.23!1.56!Zc3h11a;;chr18:24113207..24113218,+!p3@Zfp397!0.23!1.56!Zfp397;;chr17:15636925..15636940,+!p2@Tbp!0.23!1.56!Tbp;;chr5:138187411..138187422,+!p8@Tsc22d4!0.23!1.56!Tsc22d4;;chr3:8667033..8667046,-!p3@Hey1!0.23!1.30!Hey1;;chr14:67853632..67853674,+!p3@Ebf2!0.23!1.04!Ebf2;;chr5:107003699..107003717,-!p11@Zfp644!0.23!0.91!Zfp644;;chr4:150513630..150513686,-!p4@Camta1!0.23!0.91!Camta1;;chr8:107793737..107793757,+!p2@Hsf4!0.23!0.91!Hsf4;;chr10:116661536..116661555,-!p1@Yeats4!0.22!85.23!Yeats4;;chr11:3189883..3189925,+!p1@Patz1!0.22!19.78!Patz1;;chr17:71199121..71199165,-!p2@Tgif1!0.22!10.02!Tgif1;;chr6:133985993..133986029,+!p2@Etv6!0.22!8.98!Etv6;;chr1:138521528..138521572,+!p1@Zfp281!0.22!8.07!Zfp281;;chr19:12870598..12870636,-!p1@U05342,p1@Zfp91!0.22!6.90!Zfp91;;chr13:67825201..67825277,-!p1@Zfp71-rs1!0.22!6.77!Zfp71-rs1;;chr13:67209482..67209545,-!p1@Zfp708!0.22!6.38!Zfp708;;chr7:6124098..6124133,+!p1@Zfp444!0.22!5.99!Zfp444;;chr6:131338363..131338383,-!p4@Csda!0.22!5.86!Csda;;chr11:62545367..62545412,-!p1@Zfp287!0.22!5.33!Zfp287;;chr7:134169810..134169824,-!p7@Maz!0.22!4.94!Maz;;chr7:7124057..7124084,+!p1@Zfp418!0.22!4.42!Zfp418;;chr15:10400245..10400282,-!p2@Dnajc21!0.22!4.29!Dnajc21;;chr1:135320962..135320981,-!p2@Sox13!0.22!4.29!Sox13;;chr12:110031207..110031224,+!p5@Yy1!0.22!3.64!Yy1;;chr10:80870405..80870428,-!p4@Nfic!0.22!3.25!Nfic;;chr3:94641455..94641486,+!p4@Pogz!0.22!3.12!Pogz;;chr11:87881818..87881834,+!p4@Vezf1!0.22!2.99!Vezf1;;chrX:92906980..92907024,+!p2@Zc3h12b!0.22!2.99!Zc3h12b;;chr10:75384291..75384298,-!p2@Smarcb1!0.22!2.47!Smarcb1;;chr1:120879128..120879183,-!p3@Gli2!0.22!2.08!Gli2;;chr13:58501849..58501853,-!p5@Hnrnpk!0.22!1.82!Hnrnpk;;chr11:106993257..106993268,-!p4@Bptf!0.22!1.82!Bptf;;chr7:134169648..134169657,-!p14@Maz!0.22!1.30!Maz;;chr5:24107903..24107917,-!p6@Smarcd3!0.22!1.04!Smarcd3;;chr2:28477452..28477483,-!p1@Gfi1b!0.22!1.04!Gfi1b;;chr3:30408384..30408431,-!p4@Mecom!0.22!1.04!Mecom;;chr15:81575472..81575481,+!p4@Zc3h7b!0.22!1.04!Zc3h7b;;chr17:51951662..51951670,-!p21@Satb1!0.22!0.65!Satb1;;chr16:95808192..95808202,-!p2@Erg!0.22!0.65!Erg;;chr18:64499879..64499895,+!p3@Onecut2!0.22!0.65!Onecut2;;chr16:25684232..25684285,+!p2@Trp63!0.22!0.65!Trp63;;chr3:17954496..17954515,+!p3@Bhlhe22!0.22!0.65!Bhlhe22;;chr2:79296907..79296918,-!p2@Neurod1!0.22!0.65!Neurod1;;chr3:34549096..34549111,+!p3@Sox2!0.22!0.65!Sox2;;chr3:66785857..66785873,-!p1@Shox2!0.22!0.65!Shox2;;chr4:84321317..84321332,-!p4@Bnc2!0.22!0.65!Bnc2;;chr3:128902434..128902444,+!p13@Pitx2!0.22!0.65!Pitx2;;chr5:106887474..106887489,-!p1@Barhl2!0.22!0.65!Barhl2;;chr3:29911926..29911942,-!p13@Mecom!0.22!0.65!Mecom;;chr3:130813268..130813275,+!p12@Lef1!0.22!0.65!Lef1;;chr4:89354785..89354801,+!p2@Dmrta1!0.22!0.65!Dmrta1;;chr2:103264245..103264268,+!p2@Elf5!0.22!0.65!Elf5;;chr19:59534052..59534083,+!p8@Emx2!0.22!0.65!Emx2;;chr2:105529735..105529744,+!p33@Pax6!0.22!0.65!Pax6;;chr1:179374820..179374831,+!p3@Zfp238!0.22!0.65!Zfp238;;chr2:105514700..105514715,+!p13@Pax6!0.22!0.65!Pax6;;chr1:78193407..78193420,-!p2@Pax3!0.22!0.65!Pax3;;chr2:146911200..146911219,-!p1@Nkx2-4!0.22!0.65!Nkx2-4;;chr5:148000254..148000260,+!p1@Gsx1!0.22!0.65!Gsx1;;chr6:120314480..120314487,+!p6@Kdm5a!0.22!0.65!Kdm5a;;chr5:114724254..114724278,-!p4@Foxn4!0.22!0.65!Foxn4;;chr9:99776566..99776612,-!p1@Sox14!0.22!0.65!Sox14;;chr8:94881902..94881910,+!p6@Irx5!0.22!0.65!Irx5;;chr9:87625971..87625992,-!p2@Tbx18!0.22!0.65!Tbx18;;chr8:12395629..12395644,+!p6@Sox1!0.22!0.65!Sox1;;chr9:31720903..31720918,-!p2@Barx2!0.22!0.65!Barx2;;chr9:31720746..31720762,-!p4@Barx2!0.22!0.65!Barx2;;
@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011316
 |is_obsolete=
+|library_id=CNhs11016
+|library_id_phase_based=2:CNhs11016
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;345
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;345
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E12.CNhs11016.345-16C6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E12.CNhs11016.345-16C6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E12.CNhs11016.345-16C6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E12.CNhs11016.345-16C6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E12.CNhs11016.345-16C6.mm9.nobarcode.rdna.fa.gz
 |name=eyeball, embryo E12
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11016,LSID731,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.126615583616395,0,0,0,0,0,0.291326212740146,0,0.195896321191404,0,0,0.47225376160198,0,0,0,0,0,0,0.278194555113027,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.149937703791285,0,0,0,0,0.0133873515429207,0.00696602584331645,0.0466845949806989,-0.078056493546129,0.170282148512222,0.331405676217561,0,0,0,0,0,0,0,0,0,0,0,0,0.0344480177361022,0,0,0,0,0,0,0.0265623655145556,0.0531247310291112,0.181981218013818,0.0181672437846385,0.0325806060372074,0.11935433733114,0.092505241893384,0.10422137153797,0,0,0.000717380677445867,0,0,0,0.0751996061911507,-0.0292716307999891,-0.0891329176012576,0.0216219704596351,0,0,0,0,0,0,-0.0714021262265012,0.213325708097009,-0.0038923455921537,0,0,0,0,0
 |rna_box=16
 |rna_catalog_number=
@@ Line 61: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:345-16C6;search_select_hide=table117:345-16C6
 }}

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FF:345-16C6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:10, 4 June 2020

CNhs11016

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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