FF:426-16C9: Difference between revisions

Latest revision as of 19:16, 4 June 2020

Name:	eyeball, embryo E15
Species:	Mouse (Mus musculus)
Library ID:	CNhs10593
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	eyeball
dev stage	15 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		SAMD00004677

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10593		CAGE		DRX008957		DRR009831

Accession ID Mm9

Library id		BAM		CTSS
CNhs10593		DRZ001256		DRZ002639

Accession ID Mm10

Library id		BAM		CTSS
CNhs10593		DRZ012606		DRZ013989

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

CNhs10593

0	0
1	0.0719
10	0
100	0.0719
1000	0
1001	-0.0303
1002	0.269
1003	-0.0539
1004	0.497
1005	-0.0389
1006	0.0416
1007	0.00775
1008	0
1009	0.0584
101	0.0713
1010	0
1011	0.0204
1012	0
1013	-0.147
1014	0.279
1015	0.224
1016	0.3
1017	0
1018	0.0719
1019	0
102	0
1020	0
1021	0.0719
1022	-0.0704
1023	0
1024	-0.0322
1025	0
1026	0
1027	0.41
1028	0
1029	-0.0424
103	0.16
1030	0
1031	0.271
1032	-7.9209e-4
1033	0.0584
1034	0
1035	0
1036	0.0278
1037	0
1038	-0.0217
1039	-0.176
104	0
1040	0.0117
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: CNhs10593

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	6.74939e-5
MA0003.1	MA0003.1	0.354
MA0004.1	MA0004.1	0.623
MA0006.1	MA0006.1	0.323
MA0007.1	MA0007.1	0.276
MA0009.1	MA0009.1	0.27
MA0014.1	MA0014.1	0.188
MA0017.1	MA0017.1	2.62133e-7
MA0018.2	MA0018.2	0.0773
MA0019.1	MA0019.1	0.641
MA0024.1	MA0024.1	0.00207
MA0025.1	MA0025.1	0.229
MA0027.1	MA0027.1	0.462
MA0028.1	MA0028.1	0.928
MA0029.1	MA0029.1	0.913
MA0030.1	MA0030.1	0.363
MA0031.1	MA0031.1	0.0886
MA0035.2	MA0035.2	0.0185
MA0038.1	MA0038.1	9.04169e-4
MA0039.2	MA0039.2	0.355
MA0040.1	MA0040.1	0.0926
MA0041.1	MA0041.1	0.166
MA0042.1	MA0042.1	0.441
MA0043.1	MA0043.1	0.12
MA0046.1	MA0046.1	6.16473e-19
MA0047.2	MA0047.2	7.44076e-4
MA0048.1	MA0048.1	0.612
MA0050.1	MA0050.1	1.0849e-7
MA0051.1	MA0051.1	1.57441e-4
MA0052.1	MA0052.1	0.69
MA0055.1	MA0055.1	0.914
MA0057.1	MA0057.1	0.131
MA0058.1	MA0058.1	0.657
MA0059.1	MA0059.1	0.332
MA0060.1	MA0060.1	7.22073e-17
MA0061.1	MA0061.1	0.0564
MA0062.2	MA0062.2	0.298
MA0065.2	MA0065.2	1.23956e-6
MA0066.1	MA0066.1	0.079
MA0067.1	MA0067.1	0.903
MA0068.1	MA0068.1	0.25
MA0069.1	MA0069.1	0.0602
MA0070.1	MA0070.1	0.307
MA0071.1	MA0071.1	0.265
MA0072.1	MA0072.1	0.686
MA0073.1	MA0073.1	0.922
MA0074.1	MA0074.1	0.228
MA0076.1	MA0076.1	0.51
MA0077.1	MA0077.1	0.00171
MA0078.1	MA0078.1	0.318
MA0079.2	MA0079.2	0.374
MA0080.2	MA0080.2	9.35648e-12
MA0081.1	MA0081.1	0.228
MA0083.1	MA0083.1	0.948
MA0084.1	MA0084.1	0.0642
MA0087.1	MA0087.1	0.0678
MA0088.1	MA0088.1	0.313
MA0090.1	MA0090.1	0.789
MA0091.1	MA0091.1	0.4
MA0092.1	MA0092.1	0.333
MA0093.1	MA0093.1	0.658
MA0099.2	MA0099.2	0.00219
MA0100.1	MA0100.1	0.998
MA0101.1	MA0101.1	0.151
MA0102.2	MA0102.2	0.417
MA0103.1	MA0103.1	0.00367
MA0104.2	MA0104.2	0.901
MA0105.1	MA0105.1	0.00406
MA0106.1	MA0106.1	0.166
MA0107.1	MA0107.1	0.0951
MA0108.2	MA0108.2	1.99412e-7
MA0111.1	MA0111.1	0.491
MA0112.2	MA0112.2	1.20505e-5
MA0113.1	MA0113.1	0.218
MA0114.1	MA0114.1	6.00225e-6
MA0115.1	MA0115.1	3.92795e-4
MA0116.1	MA0116.1	0.00833
MA0117.1	MA0117.1	0.673
MA0119.1	MA0119.1	0.00977
MA0122.1	MA0122.1	0.826
MA0124.1	MA0124.1	0.41
MA0125.1	MA0125.1	0.0023
MA0131.1	MA0131.1	0.566
MA0135.1	MA0135.1	0.0256
MA0136.1	MA0136.1	1.5578e-8
MA0137.2	MA0137.2	0.0445
MA0138.2	MA0138.2	0.179
MA0139.1	MA0139.1	0.0575
MA0140.1	MA0140.1	0.00213
MA0141.1	MA0141.1	1.90697e-4
MA0142.1	MA0142.1	0.119
MA0143.1	MA0143.1	0.0081
MA0144.1	MA0144.1	0.0612
MA0145.1	MA0145.1	0.0566
MA0146.1	MA0146.1	0.154
MA0147.1	MA0147.1	0.863
MA0148.1	MA0148.1	3.33905e-5
MA0149.1	MA0149.1	0.00296
MA0150.1	MA0150.1	0.123
MA0152.1	MA0152.1	0.989
MA0153.1	MA0153.1	2.12946e-18
MA0154.1	MA0154.1	0.00277
MA0155.1	MA0155.1	0.741
MA0156.1	MA0156.1	0.0026
MA0157.1	MA0157.1	0.0944
MA0159.1	MA0159.1	0.00594
MA0160.1	MA0160.1	0.0205
MA0162.1	MA0162.1	0.597
MA0163.1	MA0163.1	3.24484e-4
MA0164.1	MA0164.1	0.95
MA0258.1	MA0258.1	0.00145
MA0259.1	MA0259.1	0.919

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: CNhs10593

Novel motif	Logo	P-value
1	1	0.0631
10	10	0.0639
100	100	0.978
101	101	0.755
102	102	0.667
103	103	0.0262
104	104	0.775
105	105	0.323
106	106	0.0168
107	107	0.0902
108	108	0.893
109	109	0.0323
11	11	0.0435
110	110	0.0598
111	111	3.85463e-4
112	112	0.00918
113	113	0.896
114	114	0.019
115	115	0.881
116	116	0.52
117	117	0.0396
118	118	0.444
119	119	0.0402
12	12	0.708
120	120	0.384
121	121	0.766
122	122	0.893
123	123	0.913
124	124	0.534
125	125	0.0338
126	126	0.231
127	127	0.0801
128	128	0.0652
129	129	0.331
13	13	0.0111
130	130	0.758
131	131	0.729
132	132	0.272
133	133	0.253
134	134	0.672
135	135	0.301
136	136	0.503
137	137	0.69
138	138	0.577
139	139	0.00677
14	14	0.699
140	140	0.0631
141	141	0.0528
142	142	0.68
143	143	0.512
144	144	0.872
145	145	0.0834
146	146	0.544
147	147	0.563
148	148	0.0931
149	149	0.232
15	15	0.0622
150	150	0.344
151	151	0.25
152	152	0.0726
153	153	0.338
154	154	0.467
155	155	0.31
156	156	4.9982e-4
157	157	0.857
158	158	0.189
159	159	0.0228
160	160	0.377
161	161	0.248
162	162	0.761
163	163	0.517
164	164	0.00997
165	165	0.0768
166	166	0.794
167	167	0.177
168	168	0.702
169	169	0.00113
17	17	0.0285
18	18	0.557
19	19	0.175
2	2	0.744
20	20	0.66
21	21	0.646
22	22	0.244
23	23	0.204
24	24	0.318
25	25	0.567
26	26	0.0311
27	27	0.505
28	28	0.373
29	29	0.157
3	3	0.0551
30	30	0.924
31	31	0.545
32	32	0.196
33	33	0.387
34	34	0.96
35	35	0.36
36	36	0.158
37	37	0.0242
38	38	0.23
39	39	0.304
4	4	0.576
40	40	0.328
41	41	0.651
42	42	0.295
43	43	0.117
44	44	0.135
45	45	0.566
46	46	0.145
47	47	0.0905
48	48	0.0814
49	49	0.102
5	5	0.0662
50	50	0.923
51	51	0.543
52	52	0.315
53	53	0.914
54	54	0.567
55	55	0.589
56	56	0.344
57	57	0.366
58	58	0.328
59	59	0.0908
6	6	0.721
60	60	0.0462
61	61	0.477
62	62	0.155
63	63	0.097
64	64	0.507
65	65	0.13
66	66	0.308
67	67	0.918
68	68	0.0409
69	69	0.603
7	7	0.118
70	70	0.00708
71	71	0.0416
72	72	0.443
73	73	0.0384
74	74	0.552
75	75	0.0266
76	76	0.458
77	77	0.169
78	78	0.114
79	79	0.128
8	8	0.0546
80	80	0.457
81	81	0.302
82	82	0.0183
83	83	0.693
84	84	0.961
85	85	0.0208
86	86	0.158
87	87	0.924
88	88	0.697
89	89	0.17
9	9	0.495
90	90	0.0504
91	91	0.557
92	92	0.111
93	93	0.234
94	94	0.514
95	95	0.0678
96	96	0.352
97	97	0.841
98	98	0.315
99	99	0.5

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: CNhs10593

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011344 mouse eyeball- embryo E15 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)
0000298 (mouse embryonic day 15 sample)
0011344 (mouse eyeball- embryo E15 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@SAMD00004677
+|accession_numbers=CAGE;DRX008957;DRR009831;DRZ001256;DRZ002639;DRZ012606;DRZ013989
 |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!2.61!410.00!Atoh7;;chr19:19185671..19185693,-!p1@Rorb!2.34!501.29!Rorb;;chr18:66098702..66098742,-!p1@Rax!2.17!146.93!Rax;;chr3:127336052..127336058,+!p1@Neurog2!2.06!114.34!Neurog2;;chr2:79296783..79296801,-!p1@Neurod1!2.02!102.82!Neurod1;;chr2:105509045..105509071,+!p1@Pax6!1.95!88.95!Pax6;;chr4:154335024..154335039,+!p1@Hes5!1.93!99.75!Hes5;;chr7:16465229..16465249,-!p1@Crx!1.81!64.10!Crx;;chr12:74040861..74040875,+!p1@Six6!1.80!61.58!Six6;;chr10:86956396..86956411,-!p1@Ascl1!1.78!89.31!Ascl1;;chr17:86020115..86020128,+!p2@Six3!1.77!57.80!Six3;;chr17:86020156..86020183,+!p1@Six3!1.76!56.00!Six3;;chr10:129717274..129717298,-!p1@Neurod4!1.71!50.24!Neurod4;;chr2:38206744..38206766,+!p1@Lhx2!1.66!53.48!Lhx2;;chr12:85910771..85910785,+!p1@Vsx2!1.62!40.69!Vsx2;;chr14:49287186..49287225,-!p1@Otx2!1.61!39.97!Otx2;;chr4:114598669..114598674,-!p1@Foxe3!1.59!38.35!Foxe3;;chr6:83661226..83661282,+!p1@Vax2!1.57!36.01!Vax2;;chr2:38206580..38206600,+!p2@Lhx2!1.54!41.59!Lhx2;;chr12:74040895..74040916,+!p2@Six6!1.54!33.67!Six6;;chr3:34548909..34548927,+!p1@Sox2!1.52!54.02!Sox2;;chr3:101814061..101814094,+!p1@Nhlh2!1.52!32.23!Nhlh2;;chr17:86020510..86020589,+!p3@Six3!1.48!29.17!Six3;;chr9:74709695..74709722,+!p1@Onecut1!1.47!28.81!Onecut1;;chr2:19367259..19367278,+!p1@Ptf1a!1.45!27.19!Ptf1a;;chr14:49284773..49284790,-!p2@Otx2!1.44!26.65!Otx2;;chr2:105522662..105522687,+!p2@Pax6!1.43!25.93!Pax6;;chr14:18814020..18814023,+!p3@Thrb!1.42!25.57!Thrb;;chr5:35731493..35731531,+!p1@Hmx1!1.41!24.67!Hmx1;;chr12:34642510..34642530,+!p1@Twist1!1.38!72.02!Twist1;;chr1:19199236..19199258,+!p1@Tfap2b!1.37!22.33!Tfap2b;;chr13:117099847..117099907,-!p1@Isl1!1.33!36.91!Isl1;;chr2:146047829..146047847,+!p1@Insm1!1.33!36.01!Insm1;;chr2:105515635..105515661,+!p5@Pax6!1.33!20.35!Pax6;;chr14:104867201..104867258,-!p1@Pou4f1!1.32!27.91!Pou4f1;;chr5:114723781..114723795,-!p1@Foxn4!1.32!19.99!Foxn4;;chr2:71384802..71384815,-!p1@Dlx2!1.30!23.41!Dlx2;;chr8:12395603..12395621,+!p1@Sox1!1.29!18.37!Sox1;;chr12:28027561..28027591,-!p1@Sox11!1.27!113.98!Sox11;;chr3:128916868..128916890,+!p1@Pitx2!1.27!24.31!Pitx2;;chr4:21612929..21612952,-!p1@Prdm13!1.25!16.93!Prdm13;;chr2:151907546..151907561,+!p1@Scrt2!1.25!16.93!Scrt2;;chr19:19185697..19185711,-!p2@Rorb!1.23!20.35!Rorb;;chr17:86012772..86012825,+!p4@Six3!1.23!15.85!Six3;;chr3:99057269..99057306,+!p1@Tbx15!1.22!18.91!Tbx15;;chr2:105515586..105515606,+!p4@Pax6!1.22!15.67!Pax6;;chr10:42303385..42303401,-!p1@Nr2e1!1.21!15.31!Nr2e1;;chr11:101755669..101755686,-!p1@Meox1!1.19!25.93!Meox1;;chr8:80960539..80960548,-!p1@Pou4f2!1.18!14.22!Pou4f2;;chr13:72766250..72766273,+!p1@Irx2!1.16!20.71!Irx2;;chr11:21901608..21901634,-!p1@Otx1!1.16!13.32!Otx1;;chr10:76285563..76285576,-!p2@Pcbp3!1.16!13.32!Pcbp3;;chr16:91225808..91225824,+!p1@Olig2!1.15!13.14!Olig2;;chr9:91260616..91260653,-!p2@Zic1!1.14!12.78!Zic1;;chr2:71367871..71367898,+!p1@Dlx1!1.13!12.60!Dlx1;;chr10:20880698..20880717,-!p3@Myb!1.10!18.19!Myb;;chr19:46222859..46222876,-!p1@Pitx3!1.10!11.70!Pitx3;;chr18:66098673..66098684,-!p2@Rax!1.10!11.52!Rax;;chr10:20880731..20880775,-!p2@Myb!1.09!23.95!Myb;;chr15:35225845..35225867,+!p1@Osr2!1.08!27.91!Osr2;;chr10:67364011..67364018,-!p5@Zfp365!1.07!10.80!Zfp365;;chr14:122874619..122874634,+!p1@Zic2!1.07!10.62!Zic2;;chr9:91260594..91260612,-!p1@Zic1!1.07!10.62!Zic1;;chr2:163028808..163028869,+!p1@Tox2!1.06!38.35!Tox2;;chr1:136186574..136186592,+!p1@Myog!1.06!10.44!Myog;;chr3:95032091..95032183,-!p1@Mllt11!1.05!87.69!Mllt11;;chr1:19199151..19199170,+!p3@Tfap2b!1.04!10.08!Tfap2b;;chr9:55388997..55389016,+!p1@Isl2!1.04!9.90!Isl2;;chr17:86020137..86020149,+!p5@Six3!1.04!9.90!Six3;;chr10:12810631..12810649,+!p1@Plagl1!1.03!256.95!Plagl1;;chr10:20880629..20880683,-!p1@Myb!1.03!28.27!Myb;;chr10:102491405..102491416,-!p1@Alx1!1.03!9.72!Alx1;;chr10:42303452..42303470,-!p2@Nr2e1!1.02!9.54!Nr2e1;;chr2:105515793..105515808,+!p3@Pax6!1.02!9.36!Pax6;;chr7:116154364..116154444,+!p1@Tub!1.01!16.21!Tub;;chr13:72766279..72766296,+!p2@Irx2!1.01!14.04!Irx2;;chr5:114724042..114724090,-!p2@Foxn4!1.01!9.18!Foxn4;;chr6:70906450..70906454,+!p1@Foxi3!1.01!9.18!Foxi3;;chr18:64499706..64499721,+!p2@Onecut2!1.00!12.78!Onecut2;;chr14:49282415..49282426,-!p4@Otx2!1.00!9.00!Otx2;;chr12:56700411..56700416,+!p@chr12:56700411..56700416,+!1.00!9.00!Insm2;;chr15:103164702..103164778,-!p3@Zfp385a!0.99!10.44!Zfp385a;;chr12:3891810..3891829,+!p2@Dnmt3a!0.98!13.50!Dnmt3a;;chr13:99124189..99124205,+!p1@Foxd1!0.98!13.32!Foxd1;;chr15:76352677..76352737,-!p3@Scrt1!0.98!8.64!Scrt1;;chr5:106887474..106887489,-!p1@Barhl2!0.98!8.64!Barhl2;;chr17:86020468..86020504,+!p6@Six3!0.98!8.46!Six3;;chr12:3891753..3891801,+!p4@Dnmt3a!0.97!13.68!Dnmt3a;;chrX:58146612..58146615,-!p1@Sox3!0.97!8.28!Sox3;;chr7:144506077..144506128,-!p1@Ebf3!0.95!18.73!Ebf3;;chr19:7342725..7342784,+!p1@Rcor2!0.94!32.41!Rcor2;;chr4:124334894..124334899,+!p1@Pou3f1!0.94!10.08!Pou3f1;;chr1:9690398..9690410,-!p2@Mybl1!0.94!9.36!Mybl1;;chr10:129717308..129717319,-!p2@Neurod4!0.94!7.74!Neurod4;;chr9:106356211..106356242,+!p1@Pcbp4!0.93!151.79!Pcbp4;;chr10:126778916..126778974,-!p1@Gli1!0.93!17.47!Gli1;;chr4:150503457..150503498,-!p3@Camta1!0.93!8.46!Camta1;;chr3:34548946..34548972,+!p2@Sox2!0.93!8.46!Sox2;;chr17:86087592..86087615,-!p1@Six2!0.93!7.56!Six2;;chr12:74147689..74147711,-!p1@Six1!0.92!16.39!Six1;;chr15:76352740..76352781,-!p5@Scrt1!0.91!7.20!Scrt1;;chr7:53631837..53631850,+!p1@Myod1!0.91!7.20!Myod1;;chr8:94325321..94325366,-!p1@Irx3!0.90!17.65!Irx3;;chr14:49287107..49287125,-!p3@Otx2!0.90!7.02!Otx2;;chr1:165243379..165243402,-!p3@Prrx1!0.89!10.44!Prrx1;;chr9:118387300..118387317,+!p1@Eomes!0.89!6.84!Eomes;;chrX:55283799..55283813,+!p1@Zic3!0.89!6.84!Zic3;;chr9:31720843..31720888,-!p1@Barx2!0.88!7.38!Barx2;;chr13:83643159..83643226,+!p3@Mef2c!0.88!6.66!Mef2c;;chr12:12948633..12948651,-!p1@Mycn!0.87!65.54!Mycn;;chr14:98568761..98568814,-!p2@Dach1!0.87!46.10!Dach1;;chr2:93482464..93482491,+!p1@Alx4!0.87!6.48!Alx4;;chr18:64499674..64499696,+!p1@Onecut2!0.86!11.16!Onecut2;;chr2:65768174..65768247,+!p2@Csrnp3!0.86!6.30!Csrnp3;;chr1:19202352..19202354,+!p2@Tfap2b!0.86!6.30!Tfap2b;;chr17:25707623..25707639,-!p1@Sox8!0.85!27.37!Sox8;;chr4:97248607..97248649,+!p15@Nfia!0.85!6.12!Nfia;;chr3:128902837..128902861,+!p3@Pitx2!0.84!5.94!Pitx2;;chr16:25801993..25802014,+!p1@Trp63!0.84!5.94!Trp63;;chr1:19199221..19199234,+!p6@Tfap2b!0.84!5.94!Tfap2b;;chr13:72101178..72101203,-!p1@Irx1!0.83!9.36!Irx1;;chr8:107793737..107793757,+!p2@Hsf4!0.83!6.66!Hsf4;;chr15:76352832..76352900,-!p1@Scrt1!0.83!5.76!Scrt1;;chr4:97248473..97248496,+!p16@Nfia!0.83!5.76!Nfia;;chr10:42303410..42303422,-!p3@Nr2e1!0.83!5.76!Nr2e1;;chr13:40829137..40829205,-!p1@Tfap2a!0.82!6.30!Tfap2a;;chr14:13178147..13178185,-!p1@Fezf2!0.82!5.58!Fezf2;;chr4:109650609..109650653,+!p1@Dmrta2!0.82!5.58!Dmrta2;;chr14:98568971..98569025,-!p1@Dach1!0.81!45.38!Dach1;;chr9:106356243..106356264,+!p2@Pcbp4!0.81!25.39!Pcbp4;;chr8:94881733..94881790,+!p1@Irx5!0.81!11.16!Irx5;;chr10:44178521..44178557,-!p1@Prdm1!0.81!10.08!Prdm1;;chr9:98855868..98855895,+!p1@Foxl2!0.81!5.40!Foxl2;;chr12:74040716..74040745,+!p3@Six6!0.81!5.40!Six6;;chr1:19199119..19199134,+!p4@Tfap2b!0.81!5.40!Tfap2b;;chr4:150482563..150482655,-!p2@Camta1!0.80!20.17!Camta1;;chr2:120365588..120365602,-!p2@Zfp106!0.80!9.18!Zfp106;;chr1:179374784..179374800,+!p2@Zfp238!0.80!6.30!Zfp238;;chr1:9690424..9690467,-!p1@Mybl1!0.79!11.34!Mybl1;;chr9:96159147..96159204,+!p2@Tfdp2!0.79!10.26!Tfdp2;;chr7:38554763..38554780,-!p1@Zfp536!0.79!9.72!Zfp536;;chr1:165243591..165243625,-!p2@Prrx1!0.79!8.28!Prrx1;;chr10:44178493..44178520,-!p3@Prdm1!0.78!7.20!Prdm1;;chr2:17976799..17976829,+!p5@Mllt10!0.78!6.30!Mllt10;;chr7:144505957..144505972,-!p2@Ebf3!0.78!6.30!Ebf3;;chr15:75447162..75447217,+!p2@Zfp41!0.77!15.67!Zfp41;;chr14:34791937..34791977,-!p1@Zfp488!0.77!4.86!Zfp488;;chr1:19199095..19199114,+!p5@Tfap2b!0.77!4.86!Tfap2b;;chr11:85646263..85646278,+!p2@Tbx2!0.76!13.14!Tbx2;;chr18:55149735..55149776,-!p4@Zfp608!0.76!12.42!Zfp608;;chr10:119913546..119913583,-!p3@Hmga2!0.76!10.62!Hmga2;;chr2:65683890..65683907,+!p1@Csrnp3!0.76!9.72!Csrnp3;;chr9:87626083..87626108,-!p1@Tbx18!0.75!10.80!Tbx18;;chr13:72101161..72101177,-!p2@Irx1!0.75!6.66!Irx1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!0.75!5.94!Pou3f3;;chr9:98855944..98855971,+!p4@Foxl2!0.75!4.68!Foxl2;;chr18:66098752..66098757,-!p3@Rax!0.75!4.68!Rax;;chr3:66785857..66785873,-!p1@Shox2!0.75!4.68!Shox2;;chr1:14746065..14746079,-!p1@Msc!0.74!5.58!Msc;;chr7:38557752..38557793,-!p3@Zfp536!0.74!5.40!Zfp536;;chr13:73398004..73398017,+!p2@Irx4!0.74!4.50!Irx4;;chr17:86020186..86020195,+!p9@Six3!0.74!4.50!Six3;;chr19:7342786..7342803,+!p2@Rcor2!0.73!6.12!Rcor2;;chr2:181501710..181501742,+!p2@Myt1!0.73!4.32!Myt1;;chr9:24578720..24578735,-!p1@Tbx20!0.73!4.32!Tbx20;;chr7:144505980..144506010,-!p3@Ebf3!0.72!5.22!Ebf3;;chr13:55932591..55932622,-!p1@Pitx1!0.72!5.22!Pitx1;;chr4:54957910..54957954,+!p2@Zfp462!0.71!13.68!Zfp462;;chr14:52634234..52634281,-!p3@Zfp219!0.71!12.60!Zfp219;;chr12:37835120..37835133,+!p2@Meox2!0.71!6.12!Meox2;;chr11:21901587..21901604,-!p2@Otx1!0.71!4.14!Otx1;;chr2:181501988..181502026,+!p3@Myt1!0.71!4.14!Myt1;;chr1:169528720..169528749,+!p6@Rxrg!0.71!4.14!Rxrg;;chr1:6720216..6720232,+!p1@St18!0.71!4.14!St18;;chr17:86020293..86020318,+!p7@Six3!0.71!4.14!Six3;;chr7:17647736..17647772,-!p1@Hif3a!0.70!15.67!Hif3a;;chr1:93698030..93698064,+!p1@Twist2!0.70!8.82!Twist2;;chr11:121380640..121380655,-!p1@Zfp750!0.70!7.02!Zfp750;;chr3:5218516..5218544,+!p2@Zfhx4!0.70!6.30!Zfhx4;;chr1:173987720..173987729,-!p1@Nhlh1!0.70!3.96!Nhlh1;;chr15:76353005..76353021,-!p2@Scrt1!0.70!3.96!Scrt1;;chr14:13178361..13178386,-!p2@Fezf2!0.70!3.96!Fezf2;;chr14:122874593..122874610,+!p2@Zic2!0.70!3.96!Zic2;;chr4:135129538..135129558,-!p1@Grhl3!0.69!6.30!Grhl3;;chr11:85646303..85646329,+!p1@Tbx2!0.68!28.45!Tbx2;;chr14:17407970..17408015,-!p2@Rarb!0.68!11.34!Rarb;;chr2:152223586..152223604,-!p5@Sox12!0.68!5.76!Sox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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0003056,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011344
 |is_obsolete=
+|library_id=CNhs10593
+|library_id_phase_based=2:CNhs10593
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;426
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;426
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E15.CNhs10593.426-16C9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E15.CNhs10593.426-16C9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E15.CNhs10593.426-16C9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E15.CNhs10593.426-16C9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520embryo%2520E15.CNhs10593.426-16C9.mm9.nobarcode.rdna.fa.gz
 |name=eyeball, embryo E15
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10593,LSID654,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0,0,0,0,0,0,-0.0839514728246974,0,0,0,0,0.439512235937596,0,0,0,0,0,0,-0.00432006965869353,0,0,0,0,0,0,0,0,0,0,0,0,0.0261548706843232,-0.279598190250039,0,0,0,0,0.00383132066022168,-0.0487467914347812,0.0454598294438435,-0.159254470133251,0,0.932760155601906,0,0,0,0,0,0,0,0,0,0,0,0,0.0675730393347682,0,0,0,0,-0.00812611369700689,0,-0.0316336597748709,0,0,0,-0.0688638337989711,-0.031826055265394,0.0775001499096768,-0.0109486059847897,0,-0.0780086007519514,0.0781176910602561,0,0,0,0.0700070398711675,-0.00229116492649815,-0.12159902776557,-0.0788315948399074,0,0,0,0,0,0,-0.116844694267823,-0.149027103355857,-0.197898128890274,0,0,0,0,0
 |rna_box=16
 |rna_catalog_number=
@@ Line 60: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 80: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:426-16C9;search_select_hide=table117:426-16C9
 }}

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FF:426-16C9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:16, 4 June 2020

CNhs10593

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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