FF:449-43F6: Difference between revisions

Latest revision as of 19:16, 4 June 2020

Name:	pituitary gland, embryo E16
Species:	Mouse (Mus musculus)
Library ID:	CNhs11036
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	pituitary gland
dev stage	16 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		SAMD00004899

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11036		CAGE		DRX009071		DRR009945

Accession ID Mm9

Library id		BAM		CTSS
CNhs11036		DRZ001370		DRZ002753

Accession ID Mm10

Library id		BAM		CTSS
CNhs11036		DRZ012720		DRZ014103

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

CNhs11036

0	0
1	0.132
10	0
100	0.0713
1000	0
1001	0.111
1002	0.217
1003	0.109
1004	0.374
1005	0
1006	0.11
1007	1.901339e-4
1008	0
1009	0.116
101	-0.064
1010	0
1011	0.0713
1012	0.132
1013	0.0555
1014	0.329
1015	0.172
1016	0.227
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	-0.0383
1023	0
1024	0.132
1025	0.0714
1026	0
1027	0.0431
1028	0
1029	0.133
103	0.514
1030	0
1031	0.552
1032	-0.0126
1033	0.0713
1034	0
1035	0
1036	0.048
1037	0
1038	0.0426
1039	-0.00758
104	0
1040	0.147
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: CNhs11036

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	7.35335e-7
MA0003.1	MA0003.1	0.15
MA0004.1	MA0004.1	0.514
MA0006.1	MA0006.1	0.517
MA0007.1	MA0007.1	0.497
MA0009.1	MA0009.1	0.712
MA0014.1	MA0014.1	0.353
MA0017.1	MA0017.1	1.19637e-9
MA0018.2	MA0018.2	0.0609
MA0019.1	MA0019.1	0.545
MA0024.1	MA0024.1	0.3
MA0025.1	MA0025.1	0.0817
MA0027.1	MA0027.1	0.991
MA0028.1	MA0028.1	0.69
MA0029.1	MA0029.1	0.897
MA0030.1	MA0030.1	0.498
MA0031.1	MA0031.1	0.686
MA0035.2	MA0035.2	0.00112
MA0038.1	MA0038.1	0.231
MA0039.2	MA0039.2	0.258
MA0040.1	MA0040.1	0.124
MA0041.1	MA0041.1	0.446
MA0042.1	MA0042.1	0.753
MA0043.1	MA0043.1	0.0716
MA0046.1	MA0046.1	3.62383e-25
MA0047.2	MA0047.2	8.77191e-4
MA0048.1	MA0048.1	0.373
MA0050.1	MA0050.1	0.00518
MA0051.1	MA0051.1	0.0068
MA0052.1	MA0052.1	2.77157e-7
MA0055.1	MA0055.1	0.956
MA0057.1	MA0057.1	0.113
MA0058.1	MA0058.1	0.448
MA0059.1	MA0059.1	0.177
MA0060.1	MA0060.1	1.59034e-4
MA0061.1	MA0061.1	0.0301
MA0062.2	MA0062.2	0.105
MA0065.2	MA0065.2	2.2187e-6
MA0066.1	MA0066.1	0.0133
MA0067.1	MA0067.1	0.592
MA0068.1	MA0068.1	0.118
MA0069.1	MA0069.1	0.14
MA0070.1	MA0070.1	0.916
MA0071.1	MA0071.1	0.022
MA0072.1	MA0072.1	0.0203
MA0073.1	MA0073.1	0.686
MA0074.1	MA0074.1	0.358
MA0076.1	MA0076.1	0.707
MA0077.1	MA0077.1	0.412
MA0078.1	MA0078.1	0.307
MA0079.2	MA0079.2	0.17
MA0080.2	MA0080.2	1.88611e-9
MA0081.1	MA0081.1	0.184
MA0083.1	MA0083.1	0.104
MA0084.1	MA0084.1	0.0696
MA0087.1	MA0087.1	0.682
MA0088.1	MA0088.1	0.312
MA0090.1	MA0090.1	0.372
MA0091.1	MA0091.1	0.847
MA0092.1	MA0092.1	0.527
MA0093.1	MA0093.1	0.581
MA0099.2	MA0099.2	2.92432e-5
MA0100.1	MA0100.1	0.455
MA0101.1	MA0101.1	0.0689
MA0102.2	MA0102.2	0.981
MA0103.1	MA0103.1	0.393
MA0104.2	MA0104.2	0.501
MA0105.1	MA0105.1	9.55398e-4
MA0106.1	MA0106.1	0.16
MA0107.1	MA0107.1	0.0431
MA0108.2	MA0108.2	0.306
MA0111.1	MA0111.1	0.787
MA0112.2	MA0112.2	2.59777e-7
MA0113.1	MA0113.1	0.876
MA0114.1	MA0114.1	1.36454e-7
MA0115.1	MA0115.1	5.16575e-7
MA0116.1	MA0116.1	0.0123
MA0117.1	MA0117.1	0.54
MA0119.1	MA0119.1	0.106
MA0122.1	MA0122.1	0.669
MA0124.1	MA0124.1	0.374
MA0125.1	MA0125.1	0.0284
MA0131.1	MA0131.1	0.642
MA0135.1	MA0135.1	0.42
MA0136.1	MA0136.1	8.22581e-8
MA0137.2	MA0137.2	0.0349
MA0138.2	MA0138.2	0.528
MA0139.1	MA0139.1	0.221
MA0140.1	MA0140.1	0.00276
MA0141.1	MA0141.1	0.00107
MA0142.1	MA0142.1	0.863
MA0143.1	MA0143.1	0.522
MA0144.1	MA0144.1	0.059
MA0145.1	MA0145.1	0.24
MA0146.1	MA0146.1	0.104
MA0147.1	MA0147.1	0.422
MA0148.1	MA0148.1	2.23136e-4
MA0149.1	MA0149.1	0.00817
MA0150.1	MA0150.1	4.10936e-4
MA0152.1	MA0152.1	0.529
MA0153.1	MA0153.1	5.72728e-20
MA0154.1	MA0154.1	0.00975
MA0155.1	MA0155.1	0.823
MA0156.1	MA0156.1	0.00255
MA0157.1	MA0157.1	0.737
MA0159.1	MA0159.1	5.66226e-4
MA0160.1	MA0160.1	9.52512e-4
MA0162.1	MA0162.1	0.377
MA0163.1	MA0163.1	8.6483e-4
MA0164.1	MA0164.1	0.668
MA0258.1	MA0258.1	4.48369e-5
MA0259.1	MA0259.1	0.78

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: CNhs11036

Novel motif	Logo	P-value
1	1	0.0759
10	10	0.0668
100	100	0.992
101	101	0.524
102	102	0.835
103	103	0.134
104	104	0.586
105	105	0.608
106	106	0.013
107	107	0.0601
108	108	0.711
109	109	0.148
11	11	0.135
110	110	0.0856
111	111	0.0329
112	112	0.0454
113	113	0.669
114	114	0.0908
115	115	0.627
116	116	0.49
117	117	0.0275
118	118	0.703
119	119	0.0606
12	12	0.812
120	120	0.635
121	121	0.564
122	122	0.72
123	123	0.598
124	124	0.809
125	125	0.346
126	126	0.261
127	127	0.0144
128	128	0.0743
129	129	0.33
13	13	0.00733
130	130	0.913
131	131	0.644
132	132	0.736
133	133	0.4
134	134	0.765
135	135	0.251
136	136	0.693
137	137	0.615
138	138	0.474
139	139	0.0361
14	14	0.573
140	140	0.0528
141	141	0.618
142	142	0.181
143	143	0.97
144	144	0.671
145	145	0.157
146	146	0.463
147	147	0.655
148	148	0.41
149	149	0.366
15	15	0.0508
150	150	0.228
151	151	0.276
152	152	0.291
153	153	0.946
154	154	0.655
155	155	0.633
156	156	4.37932e-4
157	157	0.712
158	158	0.202
159	159	0.311
160	160	0.481
161	161	0.559
162	162	0.972
163	163	0.0696
164	164	0.0339
165	165	0.0194
166	166	0.503
167	167	0.238
168	168	0.772
169	169	2.75037e-4
17	17	0.126
18	18	0.461
19	19	0.203
2	2	0.976
20	20	0.774
21	21	0.901
22	22	0.28
23	23	0.321
24	24	0.353
25	25	0.276
26	26	0.0294
27	27	0.593
28	28	0.412
29	29	0.0813
3	3	0.162
30	30	0.956
31	31	0.603
32	32	0.496
33	33	0.293
34	34	0.829
35	35	0.425
36	36	0.157
37	37	0.0489
38	38	0.295
39	39	0.662
4	4	0.412
40	40	0.249
41	41	0.0532
42	42	0.493
43	43	0.0942
44	44	0.103
45	45	0.588
46	46	0.103
47	47	0.181
48	48	0.0821
49	49	0.0904
5	5	0.0413
50	50	0.839
51	51	0.45
52	52	0.301
53	53	0.935
54	54	0.487
55	55	0.184
56	56	0.613
57	57	0.441
58	58	0.268
59	59	0.147
6	6	0.729
60	60	0.0384
61	61	0.15
62	62	0.0611
63	63	0.113
64	64	0.546
65	65	0.175
66	66	0.879
67	67	0.788
68	68	0.0868
69	69	0.83
7	7	0.0695
70	70	0.0118
71	71	0.0311
72	72	0.468
73	73	0.0996
74	74	0.39
75	75	0.0272
76	76	0.975
77	77	0.266
78	78	0.00834
79	79	0.726
8	8	0.0432
80	80	0.253
81	81	0.443
82	82	0.121
83	83	0.292
84	84	0.236
85	85	0.0161
86	86	0.199
87	87	0.357
88	88	0.36
89	89	0.0941
9	9	0.523
90	90	0.209
91	91	0.265
92	92	0.183
93	93	0.0675
94	94	0.37
95	95	0.174
96	96	0.274
97	97	0.756
98	98	0.259
99	99	0.84

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: CNhs11036

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011353 mouse pituitary gland- embryo E16 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)
0000955 (brain)
0000007 (pituitary gland)
0001894 (diencephalon)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0003296 (gland of diencephalon)
0010133 (neuroendocrine gland)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001890 (forebrain)
0000949 (endocrine system)

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)
0000299 (mouse embryonic day 16 sample)
0011353 (mouse pituitary gland- embryo E16 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:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008934
+|DRA_sample_Accession=CAGE@SAMD00004899
+|accession_numbers=CAGE;DRX009071;DRR009945;DRZ001370;DRZ002753;DRZ012720;DRZ014103
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000007,UBERON:0001894,UBERON:0000479,UBERON:0004121,UBERON:0003296,UBERON:0010133,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0002616,UBERON:0002780,UBERON:0002530,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001890,UBERON:0000949
 |ancestors_in_cell_lineage_facet=
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:65520838..65520853,+!p1@ENSMUST00000004964!2.47!292.88!Pou1f1;;chr13:99124189..99124205,+!p1@Foxd1!2.02!153.75!Foxd1;;chr12:74147689..74147711,-!p1@Six1!1.89!163.03!Six1;;chr12:74040861..74040875,+!p1@Six6!1.85!69.03!Six6;;chr13:55932591..55932622,-!p1@Pitx1!1.78!71.17!Pitx1;;chr2:26062055..26062100,-!p1@Lhx3!1.78!59.93!Lhx3;;chr12:74040895..74040916,+!p2@Six6!1.77!57.43!Six6;;chr10:86956396..86956411,-!p1@Ascl1!1.55!52.44!Ascl1;;chr17:86087592..86087615,-!p1@Six2!1.54!33.53!Six2;;chr2:146047829..146047847,+!p1@Insm1!1.47!50.30!Insm1;;chr12:34642510..34642530,+!p1@Twist1!1.46!85.62!Twist1;;chr13:31898767..31898785,+!p4@Foxc1!1.46!33.53!Foxc1;;chr14:122874619..122874634,+!p1@Zic2!1.44!26.76!Zic2;;chr17:86020510..86020589,+!p3@Six3!1.43!25.69!Six3;;chr3:128916868..128916890,+!p1@Pitx2!1.42!34.60!Pitx2;;chr8:123640063..123640077,+!p1@Foxc2!1.40!42.63!Foxc2;;chr11:50767247..50767270,-!p1@Prop1!1.40!24.26!Prop1;;chr10:129717274..129717298,-!p1@Neurod4!1.35!21.40!Neurod4;;chr5:38215819..38215823,-!p1@Msx1!1.34!53.51!Msx1;;chr2:79296783..79296801,-!p1@Neurod1!1.34!20.69!Neurod1;;chr1:167090803..167090816,-!p1@Tbx19!1.31!19.62!Tbx19;;chr9:91260616..91260653,-!p2@Zic1!1.31!19.62!Zic1;;chr17:86020156..86020183,+!p1@Six3!1.31!19.44!Six3;;chr16:65521021..65521032,+!p@chr16:65521021..65521032,+!1.27!17.48!Pou1f1;;chr9:91260594..91260612,-!p1@Zic1!1.27!17.48!Zic1;;chr3:34548909..34548927,+!p1@Sox2!1.25!28.18!Sox2;;chr18:66098702..66098742,-!p1@Rax!1.23!15.87!Rax;;chr17:86020115..86020128,+!p2@Six3!1.21!15.16!Six3;;chr13:55932624..55932641,-!p2@Pitx1!1.20!14.98!Pitx1;;chr3:99057269..99057306,+!p1@Tbx15!1.19!17.48!Tbx15;;chr4:109650609..109650653,+!p1@Dmrta2!1.18!14.27!Dmrta2;;chr19:19185671..19185693,-!p1@Rorb!1.15!31.39!Rorb;;chr10:84218800..84218829,+!p2@Rfx4!1.15!13.20!Rfx4;;chr7:17647736..17647772,-!p1@Hif3a!1.14!44.77!Hif3a;;chr3:128917187..128917223,+!p2@Pitx2!1.14!14.98!Pitx2;;chr12:74147860..74147888,-!p2@Six1!1.13!12.49!Six1;;chr1:169528491..169528505,+!p4@Rxrg!1.12!12.31!Rxrg;;chr7:6649134..6649167,-!p1@Zim1!1.11!64.39!Zim1;;chr2:147190749..147190769,+!p1@Pax1!1.09!11.42!Pax1;;chr1:169528520..169528542,+!p2@Rxrg!1.09!11.24!Rxrg;;chr8:24780125..24780143,+!p1@Zmat4!1.08!16.23!Zmat4;;chr13:31898729..31898761,+!p1@Foxc1!1.06!25.69!Foxc1;;chr2:26063801..26063813,-!p2@Lhx3!1.05!10.35!Lhx3;;chr1:169528581..169528607,+!p7@Rxrg!1.04!9.99!Rxrg;;chr13:31717548..31717596,+!p1@Foxf2!1.03!19.44!Foxf2;;chr18:52775562..52775650,+!p1@Zfp474!1.03!9.63!Zfp474;;chr12:3891810..3891829,+!p2@Dnmt3a!1.02!14.80!Dnmt3a;;chr17:86012772..86012825,+!p4@Six3!1.01!9.28!Six3;;chr3:128916838..128916856,+!p4@Pitx2!1.00!9.10!Pitx2;;chr10:12810631..12810649,+!p1@Plagl1!0.97!225.10!Plagl1;;chr1:169528457..169528482,+!p3@Rxrg!0.97!8.38!Rxrg;;chrX:58146612..58146615,-!p1@Sox3!0.97!8.38!Sox3;;chr14:17407549..17407575,-!p3@Rarb!0.96!12.66!Rarb;;chr12:28027561..28027591,-!p1@Sox11!0.95!54.05!Sox11;;chr10:22539932..22539956,-!p1@Tcf21!0.95!21.76!Tcf21;;chr2:181501745..181501778,+!p1@Myt1!0.95!7.85!Myt1;;chr13:31898496..31898519,+!p3@Foxc1!0.93!12.49!Foxc1;;chr10:129717308..129717319,-!p2@Neurod4!0.93!7.49!Neurod4;;chr3:128902837..128902861,+!p3@Pitx2!0.93!7.49!Pitx2;;chr13:55937467..55937516,-!p3@Pitx1!0.92!7.31!Pitx1;;chr13:117099847..117099907,-!p1@Isl1!0.91!13.38!Isl1;;chr12:30219426..30219506,+!p2@Myt1l!0.91!7.13!Myt1l;;chr13:99124236..99124243,+!p2@Foxd1!0.91!7.13!Foxd1;;chr2:31495237..31495243,+!p1@Prdm12!0.91!7.13!Prdm12;;chr11:90252223..90252240,-!p1@Hlf!0.90!60.82!Hlf;;chr14:17407970..17408015,-!p2@Rarb!0.89!19.09!Rarb;;chr14:49287186..49287225,-!p1@Otx2!0.88!6.60!Otx2;;chr9:55388997..55389016,+!p1@Isl2!0.88!6.60!Isl2;;chr2:147190725..147190747,+!p2@Pax1!0.87!6.42!Pax1;;chr1:169528433..169528456,+!p10@Rxrg!0.87!6.42!Rxrg;;chr13:31898637..31898653,+!p2@Foxc1!0.86!11.42!Foxc1;;chr8:123640090..123640101,+!p2@Foxc2!0.86!7.13!Foxc2;;chr19:59245978..59245982,-!p1@Vax1!0.86!6.24!Vax1;;chrX:108009761..108009788,+!p1@Pou3f4!0.83!5.71!Pou3f4;;chr6:14851440..14851497,+!p2@Foxp2!0.82!14.27!Foxp2;;chr1:120879128..120879183,-!p3@Gli2!0.82!11.24!Gli2;;chr7:38557752..38557793,-!p3@Zfp536!0.82!6.60!Zfp536;;chr1:167090905..167090912,-!p2@Tbx19!0.81!5.53!Tbx19;;chr2:181501988..181502026,+!p3@Myt1!0.81!5.53!Myt1;;chr12:57796615..57796687,+!p1@Pax9!0.81!5.53!Pax9;;chr14:104867201..104867258,-!p1@Pou4f1!0.80!7.67!Pou4f1;;chr2:146911200..146911219,-!p1@Nkx2-4!0.79!5.17!Nkx2-4;;chr4:84321300..84321315,-!p2@Bnc2!0.78!6.24!Bnc2;;chr19:26822880..26822964,+!p2@Smarca2!0.77!45.13!Smarca2;;chr7:52963269..52963305,+!p4@Dbp!0.77!7.13!Dbp;;chr3:34548946..34548972,+!p2@Sox2!0.77!5.53!Sox2;;chr1:169528551..169528569,+!p8@Rxrg!0.76!4.82!Rxrg;;chr2:181501710..181501742,+!p2@Myt1!0.75!4.64!Myt1;;chr4:114581497..114581519,-!p2@Foxd2!0.75!4.64!Foxd2;;chr3:107398056..107398082,+!p1@Alx3!0.75!4.64!Alx3;;chr17:86020468..86020504,+!p6@Six3!0.75!4.64!Six3;;chr12:74040716..74040745,+!p3@Six6!0.75!4.64!Six6;;chr10:126778916..126778974,-!p1@Gli1!0.74!10.70!Gli1;;chr12:72149325..72149343,+!p2@Arid4a!0.74!6.60!Arid4a;;chr1:169528720..169528749,+!p6@Rxrg!0.74!4.46!Rxrg;;chr1:167090920..167090924,-!p3@Tbx19!0.74!4.46!Tbx19;;chr1:6720216..6720232,+!p1@St18!0.74!4.46!St18;;chr9:87626083..87626108,-!p1@Tbx18!0.73!10.35!Tbx18;;chr19:19185697..19185711,-!p2@Rorb!0.72!5.53!Rorb;;chr3:99057677..99057730,+!p2@Tbx15!0.72!4.28!Tbx15;;chr14:17407878..17407926,-!p1@Rarb!0.71!9.99!Rarb;;chr7:38558574..38558611,-!p2@Zfp536!0.71!5.35!Zfp536;;chr4:139388835..139388867,-!p1@Pax7!0.71!4.10!Pax7;;chr10:84218895..84218909,+!p1@Rfx4!0.71!4.10!Rfx4;;chr12:30213247..30213333,+!p1@Myt1l!0.71!4.10!Myt1l;;chr14:122874718..122874729,+!p3@Zic2!0.71!4.10!Zic2;;chr7:91558392..91558434,-!p1@Arnt2!0.70!12.31!Arnt2;;chr11:121380594..121380609,-!p2@Zfp750!0.70!7.49!Zfp750;;chr16:18587076..18587106,-!p1@Tbx1!0.70!6.06!Tbx1;;chr10:80870405..80870428,-!p4@Nfic!0.69!11.59!Nfic;;chr11:90250944..90250982,-!p2@Hlf!0.69!6.96!Hlf;;chr15:102087737..102087801,-!p3@Rarg!0.69!6.78!Rarg;;chr9:98855847..98855866,+!p3@Foxl2!0.69!3.92!Foxl2;;chr3:5218629..5218684,+!p1@Zfhx4!0.68!13.91!Zfhx4;;chr4:114581524..114581551,-!p1@Foxd2!0.68!5.89!Foxd2;;chr14:52948124..52948148,-!p7@Sall2!0.68!3.75!Sall2;;chr13:31717597..31717613,+!p2@Foxf2!0.68!3.75!Foxf2;;chr14:18814381..18814390,+!p7@Thrb!0.68!3.75!Thrb;;chr14:100683672..100683717,-!p1@Klf12!0.67!19.44!Klf12;;chr10:5636374..5636421,-!p1@Esr1!0.67!4.82!Esr1;;chr7:6683123..6683142,-!p1@Peg3!0.66!217.07!Peg3;;chr2:167363692..167363710,+!p1@Snai1!0.65!48.87!Snai1;;chr6:88148650..88148669,+!p1@Gata2!0.65!33.53!Gata2;;chr3:5218516..5218544,+!p2@Zfhx4!0.65!5.53!Zfhx4;;chr7:17642018..17642045,-!p4@Hif3a!0.65!4.10!Hif3a;;chr5:24107676..24107722,-!p4@Smarcd3!0.64!4.82!Smarcd3;;chr2:130120884..130120972,+!p1@Ebf4!0.63!22.47!Ebf4;;chr4:84320893..84320910,-!p1@Bnc2!0.63!8.03!Bnc2;;chr6:14851250..14851277,+!p4@Foxp2!0.63!4.46!Foxp2;;chr2:38206744..38206766,+!p1@Lhx2!0.63!4.10!Lhx2;;chr9:31720843..31720888,-!p1@Barx2!0.63!3.75!Barx2;;chr4:150503457..150503498,-!p3@Camta1!0.63!3.75!Camta1;;chr7:130644017..130644092,-!p1@Zkscan2!0.62!6.78!Zkscan2;;chr2:38206580..38206600,+!p2@Lhx2!0.62!4.10!Lhx2;;chr7:52472041..52472065,+!p2@Tead2!0.62!3.75!Tead2;;chr13:55937432..55937460,-!p4@Pitx1!0.62!3.21!Pitx1;;chr17:86020137..86020149,+!p5@Six3!0.62!3.21!Six3;;chr3:95032091..95032183,-!p1@Mllt11!0.61!31.21!Mllt11;;chr12:34642682..34642753,+!p2@Twist1!0.61!9.28!Twist1;;chr11:5761979..5761992,+!p2@Aebp1!0.61!6.96!Aebp1;;chr12:74147842..74147856,-!p3@Six1!0.61!3.03!Six1;;chr9:99776566..99776612,-!p1@Sox14!0.61!3.03!Sox14;;chr8:12395603..12395621,+!p1@Sox1!0.61!3.03!Sox1;;chr6:30908793..30908815,-!p1@Klf14!0.61!3.03!Klf14;;chr3:99057256..99057268,+!p3@Tbx15!0.61!3.03!Tbx15;;chr11:5761889..5761969,+!p1@Aebp1!0.60!150.36!Aebp1;;chr14:56443806..56443848,+!p1@Nfatc4!0.60!6.78!Nfatc4;;chr18:53623836..53623839,+!p1@Prdm6!0.60!3.57!Prdm6;;chr12:9581262..9581282,+!p1@Osr1!0.59!41.92!Osr1;;chr12:39506873..39506913,+!p1@Etv1!0.59!35.85!Etv1;;chr8:79426176..79426275,+!p1@Nr3c2!0.59!17.12!Nr3c2;;chrX:45245679..45245702,-!p1@Smarca1!0.59!15.52!Smarca1;;chr12:39507680..39507715,+!p2@Etv1!0.59!6.42!Etv1;;chr2:127347067..127347093,-!p1@Kcnip3!0.59!5.35!Kcnip3;;chr16:50429979..50429997,-!p4@Bbx!0.59!4.99!Bbx;;chr11:116196664..116196679,-!p1@Foxj1!0.59!4.82!Foxj1;;chrX:70656436..70656464,+!p1@Zfp92!0.59!2.85!Zfp92;;chr12:57636240..57636256,-!p4@Nkx2-1!0.59!2.85!Nkx2-1;;chr14:122874593..122874610,+!p2@Zic2!0.59!2.85!Zic2;;chr14:69808725..69808748,+!p1@Nkx3-1!0.59!2.85!Nkx3-1;;chr10:119913310..119913366,-!p1@Hmga2!0.58!26.93!Hmga2;;chr19:28754692..28754757,-!p1@Glis3!0.58!13.91!Glis3;;chr8:72356532..72356611,+!p1@Pbx4!0.58!13.91!Pbx4;;chr7:77511403..77511450,-!p3@Nr2f2!0.58!6.78!Nr2f2;;chr2:30700857..30700873,+!p3@Prrx2!0.58!4.10!Prrx2;;chr11:90251852..90251855,-!p4@Hlf!0.58!3.57!Hlf;;chrX:110411840..110411860,+!p1@Dach2!0.58!3.57!Dach2;;chr14:55711198..55711258,-!p1@Zfhx2!0.57!18.91!Zfhx2;;chr6:14851287..14851342,+!p1@Foxp2!0.57!10.70!Foxp2;;chr17:56970339..56970428,-!p1@Rfx2!0.57!10.17!Rfx2;;chr19:7342786..7342803,+!p2@Rcor2!0.57!3.92!Rcor2;;chr3:128902878..128902893,+!p6@Pitx2!0.57!2.68!Pitx2;;chr9:48644306..48644364,-!p1@Zbtb16!0.56!12.66!Zbtb16;;chr18:55150011..55150059,-!p3@Zfp608!0.56!10.17!Zfp608;;chr8:90483459..90483475,-!p1@Zfp423!0.56!8.56!Zfp423;;chr11:3189683..3189744,+!p2@Patz1!0.55!6.06!Patz1;;chr12:9581284..9581303,+!p2@Osr1!0.55!5.53!Osr1;;chr2:127347094..127347111,-!p2@Kcnip3!0.55!4.64!Kcnip3;;chr15:103164702..103164778,-!p3@Zfp385a!0.55!3.21!Zfp385a;;chr6:98978245..98978289,-!p1@Foxp1!0.54!46.38!Foxp1;;chr7:52471143..52471186,+!p1@Tead2!0.54!33.53!Tead2;;chr14:98568971..98569025,-!p1@Dach1!0.54!23.90!Dach1;;chr7:25292160..25292213,+!p3@Zfp428!0.54!7.31!Zfp428;;chr1:170361991..170362015,-!p6@Pbx1!0.54!6.42!Pbx1;;chr2:30700881..30700916,+!p1@Prrx2!0.54!5.35!Prrx2;;chr18:3281725..3281740,-!p3@Crem!0.54!3.39!Crem;;chr1:169528823..169528860,+!p5@Rxrg!0.54!2.50!Rxrg;;chr4:139389439..139389450,-!p3@Pax7!0.54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3!0.30!1.61!Gli3;;chr17:44873258..44873281,-!p5@Runx2!0.30!1.61!Runx2;;chr2:152561980..152561997,+!p1@Id1!0.29!50.84!Id1;;chr13:48356475..48356492,+!p1@Id4!0.29!38.35!Id4;;chr13:96095213..96095255,+!p1@Zbed3!0.29!26.22!Zbed3;;chr10:80893549..80893590,-!p2@Nfic!0.29!19.44!Nfic;;chr9:122795920..122795977,+!p1@Zfp167!0.29!14.09!Zfp167;;chr18:69504157..69504184,+!p3@Tcf4!0.29!10.35!Tcf4;;chr8:97856080..97856150,-!p2@Zfp319!0.29!9.45!Zfp319;;chr6:38204109..38204155,-!p1@D630045J12Rik!0.29!8.74!D630045J12Rik;;chr7:148513409..148513455,-!p2@Deaf1!0.29!7.67!Deaf1;;chr11:98636575..98636607,-!p2@Nr1d1!0.29!5.71!Nr1d1;;chr11:59285966..59285990,-!p2@Zfp867!0.29!3.75!Zfp867;;chr4:45024965..45025031,-!p3@Zbtb5!0.29!3.57!Zbtb5;;chr16:42907656..42907675,+!p10@Zbtb20!0.29!3.03!Zbtb20;;chr1:170361777..170361797,-!p10@Pbx1!0.29!2.32!Pbx1;;chr2:152223586..152223604,-!p5@Sox12!0.29!1.78!Sox12;;chr5:144951153..144951203,+!p1@Bhlha15!0.29!1.78!Bhlha15;;chr7:91558631..91558652,-!p3@Arnt2!0.29!1.78!Arnt2;;chr8:118231350..118231385,-!p7@Maf!0.29!1.78!Maf;;chr18:55149778..55149798,-!p11@Zfp608!0.29!1.61!Zfp608;;chr19:23215554..23215567,+!p5@Klf9!0.29!1.61!Klf9;;chr13:78339428..78339466,-!p2@Nr2f1!0.29!1.61!Nr2f1;;chr2:17986337..17986349,+!p8@Mllt10!0.29!1.61!Mllt10;;chr5:125538905..125538910,-!p4@Ncor2!0.29!1.43!Ncor2;;chr4:129118044..129118067,-!p1@Zbtb8b!0.29!1.43!Zbtb8b;;chr13:78339382..78339420,-!p3@Nr2f1!0.29!1.25!Nr2f1;;chr6:6832076..6832092,-!p1@Dlx5!0.29!1.25!Dlx5;;chr5:125659525..125659599,-!p1@Ncor2!0.28!105.42!Ncor2;;chr12:114336410..114336478,+!p1@Mta1!0.28!54.40!Mta1;;chr11:96691218..96691265,-!p2@Nfe2l1!0.28!47.98!Nfe2l1;;chr15:76701830..76701883,-!p1@Zfp251!0.28!22.65!Zfp251;;chr4:122911086..122911112,+!p1@Heyl!0.28!19.44!Heyl;;chr15:81575569..81575599,+!p2@Zc3h7b!0.28!18.55!Zc3h7b;;chr10:79862089..79862129,-!p2@Mbd3!0.28!18.02!Mbd3;;chr5:138187341..138187406,+!p3@Tsc22d4!0.28!17.84!Tsc22d4;;chr4:133276801..133276891,-!p3@Arid1a!0.28!17.30!Arid1a;;chr19:55816770..55816793,+!p2@Tcf7l2!0.28!14.45!Tcf7l2;;chr4:97444012..97444045,+!p4@Nfia!0.28!12.49!Nfia;;chr6:120314411..120314466,+!p2@Kdm5a!0.28!11.77!Kdm5a;;chr18:3281034..3281104,-!p1@Crem!0.28!11.59!Crem;;chr4:128483534..128483613,-!p1@Zfp362!0.28!11.42!Zfp362;;chr6:53018556..53018650,-!p1@Jazf1!0.28!10.88!Jazf1;;chr11:50872733..50872809,+!p1@Zfp354a!0.28!7.13!Zfp354a;;chr9:32443818..32443854,+!p2@Ets1!0.28!6.96!Ets1;;chrX:132420488..132420517,+!p4@Bhlhb9!0.28!6.78!Bhlhb9;;chrX:132420525..132420558,+!p3@Bhlhb9!0.28!6.60!Bhlhb9;;chr15:103170533..103170556,-!p1@Zfp385a!0.28!5.71!Zfp385a;;chr3:152059326..152059358,+!p3@Gm8261,p3@Zzz3!0.28!4.99!Zzz3;;chr10:127984472..127984504,-!p2@Zc3h10!0.28!4.82!Zc3h10;;chr8:87225670..87225697,+!p2@Lyl1!0.28!4.28!Lyl1;;chr17:48061631..48061648,-!p7@Foxp4!0.28!3.92!Foxp4;;chr10:75495410..75495444,+!p2@Zfp280b!0.28!3.57!Zfp280b;;chr7:135020412..135020433,+!p2@Zfp646!0.28!3.57!Zfp646;;chr8:112229540..112229566,+!p2@Zfp821!0.28!3.03!Zfp821;;chr4:6917971..6918000,-!p3@Tox!0.28!2.68!Tox;;chr14:56443698..56443726,+!p2@Nfatc4!0.28!2.50!Nfatc4;;chr10:119913792..119913820,-!p5@Hmga2!0.28!2.14!Hmga2;;chr14:98568822..98568837,-!p5@Dach1!0.28!1.78!Dach1;;chr12:3806513..3806527,+!p9@Dnmt3a!0.28!1.78!Dnmt3a;;chr7:25292310..25292329,+!p5@Zfp428!0.28!1.61!Zfp428;;chr2:165213716..165213732,-!p2@Zfp334!0.28!1.43!Zfp334;;chr10:62328027..62328038,-!p6@Tet1!0.28!1.25!Tet1;;chr11:96685444..96685473,-!p5@Nfe2l1!0.28!0.89!Nfe2l1;;chr11:90252071..90252093,-!p7@Hlf!0.28!0.89!Hlf;;chr9:91263173..91263220,+!p2@Zic4!0.28!0.89!Zic4;;chr9:91263879..91263911,+!p1@Zic4!0.28!0.89!Zic4;;chr8:86590801..86590818,+!p2@Rfx1!0.28!0.89!Rfx1;;chr12:39510206..39510249,+!p3@Etv1!0.28!0.89!Etv1;;chr4:13678723..13678739,+!p10@Runx1t1!0.28!0.89!Runx1t1;;chr3:130813586..130813604,+!p7@Lef1!0.28!0.89!Lef1;;chr4:150503544..150503561,-!p8@Camta1!0.28!0.89!Camta1;;chr3:101814061..101814094,+!p1@Nhlh2!0.28!0.89!Nhlh2;;chr4:84321317..84321332,-!p4@Bnc2!0.28!0.89!Bnc2;;chr6:23198371..23198390,-!p1@Fezf1!0.28!0.89!Fezf1;;chr5:98609885..98609900,+!p1@Prdm8!0.28!0.89!Prdm8;;chr7:150155143..150155156,-!p1@Ascl2!0.28!0.89!Ascl2;;chr6:14853484..14853504,+!p14@Foxp2!0.28!0.89!Foxp2;;chr6:144157991..144158007,-!p9@Sox5!0.28!0.89!Sox5;;chr2:38567715..38567730,-!p2@Nr5a1!0.28!0.89!Nr5a1;;chr1:19199095..19199114,+!p5@Tfap2b!0.28!0.89!Tfap2b;;chr2:150514750..150514756,-!p1@Vsx1!0.28!0.89!Vsx1;;chr1:191993385..191993405,-!p3@Prox1!0.28!0.89!Prox1;;chr1:19202352..19202354,+!p2@Tfap2b!0.28!0.89!Tfap2b;;chrX:55283799..55283813,+!p1@Zic3!0.28!0.89!Zic3;;chr17:44951431..44951445,-!p3@Runx2!0.28!0.89!Runx2;;chr16:91225808..91225824,+!p1@Olig2!0.28!0.89!Olig2;;chr17:51952856..51952876,-!p12@Satb1!0.28!0.89!Satb1;;chr4:55545337..55545357,-!p1@Klf4!0.27!24.44!Klf4;;chr4:97439116..97439202,+!p5@Nfia!0.27!14.27!Nfia;;chr2:128793119..128793179,+!p1@Zc3h6!0.27!13.20!Zc3h6;;chr7:88005795..88005858,+!p1@Zscan2!0.27!11.42!Zscan2;;chr8:125897750..125897758,+!p2@Tcf25!0.27!10.70!Tcf25;;chr16:17530781..17530882,-!p2@Thap7!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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011353
 |is_obsolete=
-|library_ids=CNhs11036
+|library_id=CNhs11036
+|library_id_phase_based=2:CNhs11036
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;449
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;449
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E16.CNhs11036.449-43F6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E16.CNhs11036.449-43F6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E16.CNhs11036.449-43F6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E16.CNhs11036.449-43F6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E16.CNhs11036.449-43F6.mm9.nobarcode.rdna.fa.gz
 |name=pituitary gland, embryo E16
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11036,LSID732,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.184979200574972,0,0,0,0,0,0.229314767972976,0,0,0,0,0.436641138156444,0,0,0,0,0,0,0.223967615562185,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.0147068619812181,0,0,0,0,0.0630779256815929,0.0656237007648384,0.132495872273197,0.0760090903629289,1.0180834530254,0.11519228786039,0,0,0,0,0,0,0,0,0,0,0.132495872273197,0,0.250009464066367,0,0,0,0,0,0,-0.0137576450050263,0,0.0712812415377886,0.0575973258424905,0.143232117986806,0.0744102685313551,0.257769923673677,0.130572259459229,0,0.05619002939954,0.0537921222453194,0.0910009099833808,0,0,0.092036150701614,0.0837264257983393,-0.0989263425630443,0.0536642774332896,0,0,0,0,0,0,0.0712812415377886,0.370995696651876,0.0641588417516565,0,0,0,0,0
@@ Line 85: / Line 97: @@
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 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:449-43F6;search_select_hide=table117:449-43F6
-|DRA_sample_Accession=CAGE@DRS008934
-|accession_numbers=DRX009071;DRR009945;DRZ001370;DRZ002753;CAGE
-|library_id=CNhs11036
 }}

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From FANTOM5_SSTAR

Latest revision as of 19:16, 4 June 2020

CNhs11036

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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