FF:346-16E6: Difference between revisions

Latest revision as of 19:10, 4 June 2020

Name:	pituitary gland, embryo E12
Species:	Mouse (Mus musculus)
Library ID:	CNhs11018
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	pituitary gland
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		SAMD00005702

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11018		CAGE		DRX009067		DRR009941

Accession ID Mm9

Library id		BAM		CTSS
CNhs11018		DRZ001366		DRZ002749

Accession ID Mm10

Library id		BAM		CTSS
CNhs11018		DRZ012716		DRZ014099

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

CNhs11018

0	0
1	0.0537
10	0
100	0.116
1000	-0.0355
1001	0
1002	0.353
1003	-0.102
1004	0.418
1005	-0.0967
1006	-0.0538
1007	0.17
1008	0
1009	-0.0241
101	0.0875
1010	0
1011	0.0204
1012	0
1013	-0.203
1014	0.318
1015	0.318
1016	0.167
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.0232
1022	0
1023	0
1024	-0.0607
1025	0.134
1026	0
1027	0.229
1028	0
1029	-0.014
103	0
1030	0
1031	0.238
1032	-0.0878
1033	0.024
1034	0
1035	0
1036	0.109
1037	0
1038	-0.0194
1039	-0.123
104	0
1040	0.0199
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: CNhs11018

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	2.48882e-5
MA0003.1	MA0003.1	0.12
MA0004.1	MA0004.1	0.768
MA0006.1	MA0006.1	0.372
MA0007.1	MA0007.1	0.364
MA0009.1	MA0009.1	0.368
MA0014.1	MA0014.1	0.402
MA0017.1	MA0017.1	1.3671e-5
MA0018.2	MA0018.2	0.187
MA0019.1	MA0019.1	0.823
MA0024.1	MA0024.1	9.89778e-4
MA0025.1	MA0025.1	0.00292
MA0027.1	MA0027.1	0.202
MA0028.1	MA0028.1	0.239
MA0029.1	MA0029.1	0.384
MA0030.1	MA0030.1	0.174
MA0031.1	MA0031.1	0.00677
MA0035.2	MA0035.2	0.00937
MA0038.1	MA0038.1	0.00386
MA0039.2	MA0039.2	0.0358
MA0040.1	MA0040.1	0.0706
MA0041.1	MA0041.1	0.24
MA0042.1	MA0042.1	0.444
MA0043.1	MA0043.1	0.0362
MA0046.1	MA0046.1	1.89899e-26
MA0047.2	MA0047.2	4.2476e-5
MA0048.1	MA0048.1	0.293
MA0050.1	MA0050.1	1.64522e-5
MA0051.1	MA0051.1	4.90417e-4
MA0052.1	MA0052.1	3.67965e-8
MA0055.1	MA0055.1	0.145
MA0057.1	MA0057.1	0.0276
MA0058.1	MA0058.1	0.793
MA0059.1	MA0059.1	0.809
MA0060.1	MA0060.1	7.18174e-16
MA0061.1	MA0061.1	0.0402
MA0062.2	MA0062.2	0.546
MA0065.2	MA0065.2	2.25613e-5
MA0066.1	MA0066.1	0.0518
MA0067.1	MA0067.1	0.366
MA0068.1	MA0068.1	0.237
MA0069.1	MA0069.1	0.327
MA0070.1	MA0070.1	0.653
MA0071.1	MA0071.1	0.16
MA0072.1	MA0072.1	0.0979
MA0073.1	MA0073.1	0.667
MA0074.1	MA0074.1	0.534
MA0076.1	MA0076.1	0.128
MA0077.1	MA0077.1	0.0419
MA0078.1	MA0078.1	0.41
MA0079.2	MA0079.2	0.943
MA0080.2	MA0080.2	1.16685e-10
MA0081.1	MA0081.1	0.244
MA0083.1	MA0083.1	0.0349
MA0084.1	MA0084.1	0.704
MA0087.1	MA0087.1	0.139
MA0088.1	MA0088.1	0.478
MA0090.1	MA0090.1	0.233
MA0091.1	MA0091.1	0.58
MA0092.1	MA0092.1	0.272
MA0093.1	MA0093.1	0.819
MA0099.2	MA0099.2	1.43858e-6
MA0100.1	MA0100.1	0.668
MA0101.1	MA0101.1	0.244
MA0102.2	MA0102.2	0.609
MA0103.1	MA0103.1	0.0351
MA0104.2	MA0104.2	0.76
MA0105.1	MA0105.1	0.00817
MA0106.1	MA0106.1	0.214
MA0107.1	MA0107.1	0.114
MA0108.2	MA0108.2	0.944
MA0111.1	MA0111.1	0.51
MA0112.2	MA0112.2	6.38339e-7
MA0113.1	MA0113.1	0.43
MA0114.1	MA0114.1	1.87445e-4
MA0115.1	MA0115.1	0.0199
MA0116.1	MA0116.1	0.0119
MA0117.1	MA0117.1	0.553
MA0119.1	MA0119.1	0.00473
MA0122.1	MA0122.1	0.755
MA0124.1	MA0124.1	0.4
MA0125.1	MA0125.1	0.00315
MA0131.1	MA0131.1	0.389
MA0135.1	MA0135.1	0.942
MA0136.1	MA0136.1	1.95343e-6
MA0137.2	MA0137.2	0.294
MA0138.2	MA0138.2	0.00196
MA0139.1	MA0139.1	0.0526
MA0140.1	MA0140.1	0.0507
MA0141.1	MA0141.1	0.00389
MA0142.1	MA0142.1	0.186
MA0143.1	MA0143.1	0.00538
MA0144.1	MA0144.1	0.193
MA0145.1	MA0145.1	0.0127
MA0146.1	MA0146.1	0.233
MA0147.1	MA0147.1	0.855
MA0148.1	MA0148.1	1.42278e-5
MA0149.1	MA0149.1	0.011
MA0150.1	MA0150.1	0.00529
MA0152.1	MA0152.1	0.1
MA0153.1	MA0153.1	9.98276e-18
MA0154.1	MA0154.1	9.94653e-4
MA0155.1	MA0155.1	0.602
MA0156.1	MA0156.1	0.0242
MA0157.1	MA0157.1	0.0556
MA0159.1	MA0159.1	0.0125
MA0160.1	MA0160.1	0.0142
MA0162.1	MA0162.1	0.53
MA0163.1	MA0163.1	0.0143
MA0164.1	MA0164.1	0.669
MA0258.1	MA0258.1	1.39695e-4
MA0259.1	MA0259.1	0.733

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: CNhs11018

Novel motif	Logo	P-value
1	1	0.0845
10	10	0.266
100	100	0.76
101	101	0.653
102	102	0.859
103	103	0.0917
104	104	0.631
105	105	0.12
106	106	0.00973
107	107	0.0922
108	108	0.717
109	109	0.134
11	11	0.0995
110	110	0.167
111	111	0.00907
112	112	0.0234
113	113	0.45
114	114	0.0448
115	115	0.856
116	116	0.476
117	117	0.393
118	118	0.945
119	119	0.0962
12	12	0.898
120	120	0.608
121	121	0.7
122	122	0.922
123	123	0.279
124	124	0.196
125	125	0.395
126	126	0.448
127	127	0.032
128	128	0.0412
129	129	0.188
13	13	0.0997
130	130	0.474
131	131	0.163
132	132	0.442
133	133	0.494
134	134	0.706
135	135	0.0978
136	136	0.983
137	137	0.722
138	138	0.549
139	139	0.0162
14	14	0.337
140	140	0.00611
141	141	0.0744
142	142	0.461
143	143	0.425
144	144	0.971
145	145	0.196
146	146	0.327
147	147	0.702
148	148	0.244
149	149	0.147
15	15	0.0983
150	150	0.535
151	151	0.135
152	152	0.0444
153	153	0.655
154	154	0.599
155	155	0.613
156	156	0.9
157	157	0.982
158	158	0.392
159	159	0.495
160	160	0.571
161	161	0.832
162	162	0.565
163	163	0.0917
164	164	0.138
165	165	0.123
166	166	0.773
167	167	0.934
168	168	0.15
169	169	0.0011
17	17	0.0697
18	18	0.502
19	19	0.135
2	2	0.404
20	20	0.551
21	21	0.977
22	22	0.206
23	23	0.0597
24	24	0.431
25	25	0.447
26	26	0.154
27	27	0.395
28	28	0.471
29	29	0.463
3	3	0.177
30	30	0.657
31	31	0.576
32	32	0.0868
33	33	0.611
34	34	0.661
35	35	0.503
36	36	0.357
37	37	0.0461
38	38	0.2
39	39	0.61
4	4	0.386
40	40	0.319
41	41	0.345
42	42	0.511
43	43	0.129
44	44	0.108
45	45	0.405
46	46	0.196
47	47	0.135
48	48	0.114
49	49	0.133
5	5	0.138
50	50	0.907
51	51	0.523
52	52	0.26
53	53	0.563
54	54	0.473
55	55	0.603
56	56	0.386
57	57	0.456
58	58	0.277
59	59	0.0374
6	6	0.647
60	60	0.0663
61	61	0.865
62	62	0.0944
63	63	0.102
64	64	0.48
65	65	0.0896
66	66	0.439
67	67	0.654
68	68	0.147
69	69	0.363
7	7	0.165
70	70	9.87886e-4
71	71	0.128
72	72	0.329
73	73	0.0673
74	74	0.51
75	75	0.234
76	76	0.663
77	77	0.138
78	78	0.0859
79	79	0.185
8	8	0.24
80	80	0.182
81	81	0.325
82	82	0.0566
83	83	0.505
84	84	0.5
85	85	0.0163
86	86	0.366
87	87	0.603
88	88	0.765
89	89	0.126
9	9	0.339
90	90	0.25
91	91	0.362
92	92	0.0892
93	93	0.191
94	94	0.423
95	95	0.174
96	96	0.208
97	97	0.699
98	98	0.238
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: CNhs11018

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011317 mouse pituitary gland- 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)
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)
0000295 (mouse embryonic day 12 sample)
0011317 (mouse pituitary gland- 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:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005702
+|accession_numbers=CAGE;DRX009067;DRR009941;DRZ001366;DRZ002749;DRZ012716;DRZ014099
 |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 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr12:74040861..74040875,+!p1@Six6!1.98!93.45!Six6;;chr13:55932591..55932622,-!p1@Pitx1!1.90!94.35!Pitx1;;chr13:99124189..99124205,+!p1@Foxd1!1.86!106.60!Foxd1;;chr18:66098702..66098742,-!p1@Rax!1.84!68.06!Rax;;chr10:62562530..62562540,+!p1@Atoh7!1.80!62.66!Atoh7;;chr11:50767247..50767270,-!p1@Prop1!1.79!60.32!Prop1;;chr12:74147689..74147711,-!p1@Six1!1.70!104.80!Six1;;chrX:58146612..58146615,-!p1@Sox3!1.68!46.46!Sox3;;chr2:26062055..26062100,-!p1@Lhx3!1.67!45.74!Lhx3;;chr12:74040895..74040916,+!p2@Six6!1.66!44.84!Six6;;chr19:19185671..19185693,-!p1@Rorb!1.60!89.49!Rorb;;chr12:34642510..34642530,+!p1@Twist1!1.56!107.32!Twist1;;chr17:86087592..86087615,-!p1@Six2!1.54!33.67!Six2;;chr17:86020510..86020589,+!p3@Six3!1.51!31.15!Six3;;chr3:34548909..34548927,+!p1@Sox2!1.49!49.34!Sox2;;chr3:128916868..128916890,+!p1@Pitx2!1.44!36.19!Pitx2;;chr13:31898767..31898785,+!p4@Foxc1!1.43!31.69!Foxc1;;chr4:109650609..109650653,+!p1@Dmrta2!1.38!23.23!Dmrta2;;chr17:86020156..86020183,+!p1@Six3!1.38!22.87!Six3;;chr12:3891810..3891829,+!p2@Dnmt3a!1.36!33.85!Dnmt3a;;chr12:28027561..28027591,-!p1@Sox11!1.34!132.52!Sox11;;chr14:122874619..122874634,+!p1@Zic2!1.34!20.71!Zic2;;chr10:119913310..119913366,-!p1@Hmga2!1.33!154.67!Hmga2;;chr4:154335024..154335039,+!p1@Hes5!1.33!24.49!Hes5;;chr14:27813852..27813865,+!p1@Hesx1!1.33!20.35!Hesx1;;chr2:147190749..147190769,+!p1@Pax1!1.31!19.45!Pax1;;chr17:86020115..86020128,+!p2@Six3!1.31!19.45!Six3;;chrX:108009761..108009788,+!p1@Pou3f4!1.31!19.27!Pou3f4;;chr8:12395603..12395621,+!p1@Sox1!1.27!17.65!Sox1;;chr2:38206744..38206766,+!p1@Lhx2!1.26!20.71!Lhx2;;chr10:119913546..119913583,-!p3@Hmga2!1.24!34.21!Hmga2;;chr13:55932624..55932641,-!p2@Pitx1!1.24!16.39!Pitx1;;chr10:119913278..119913298,-!p2@Hmga2!1.23!35.83!Hmga2;;chr2:146047829..146047847,+!p1@Insm1!1.23!28.45!Insm1;;chr9:91260594..91260612,-!p1@Zic1!1.23!16.03!Zic1;;chr9:91260616..91260653,-!p2@Zic1!1.22!15.67!Zic1;;chr13:31717548..31717596,+!p1@Foxf2!1.21!29.89!Foxf2;;chr10:119914001..119914078,-!p4@Hmga2!1.21!20.89!Hmga2;;chr13:117099847..117099907,-!p1@Isl1!1.20!27.19!Isl1;;chr2:71384802..71384815,-!p1@Dlx2!1.18!17.65!Dlx2;;chr3:99057269..99057306,+!p1@Tbx15!1.18!17.11!Tbx15;;chr10:86956396..86956411,-!p1@Ascl1!1.16!20.89!Ascl1;;chr2:105509045..105509071,+!p1@Pax6!1.16!13.50!Pax6;;chr2:38206580..38206600,+!p2@Lhx2!1.14!15.85!Lhx2;;chr12:57636240..57636256,-!p4@Nkx2-1!1.13!12.42!Nkx2-1;;chr8:123640063..123640077,+!p1@Foxc2!1.12!21.97!Foxc2;;chr14:49287186..49287225,-!p1@Otx2!1.12!12.24!Otx2;;chr5:38215819..38215823,-!p1@Msx1!1.10!30.61!Msx1;;chr13:55937467..55937516,-!p3@Pitx1!1.09!11.16!Pitx1;;chr2:79296783..79296801,-!p1@Neurod1!1.07!10.80!Neurod1;;chr4:114598669..114598674,-!p1@Foxe3!1.05!10.26!Foxe3;;chr9:99776566..99776612,-!p1@Sox14!1.05!10.26!Sox14;;chr8:24780125..24780143,+!p1@Zmat4!1.03!14.22!Zmat4;;chr6:14851440..14851497,+!p2@Foxp2!1.01!22.87!Foxp2;;chr5:35731493..35731531,+!p1@Hmx1!1.01!9.18!Hmx1;;chr2:147190725..147190747,+!p2@Pax1!1.00!9.00!Pax1;;chr10:126778916..126778974,-!p1@Gli1!0.99!20.17!Gli1;;chr12:3891753..3891801,+!p4@Dnmt3a!0.99!14.58!Dnmt3a;;chr3:34548946..34548972,+!p2@Sox2!0.98!9.54!Sox2;;chr12:57796615..57796687,+!p1@Pax9!0.98!8.64!Pax9;;chr2:105522662..105522687,+!p2@Pax6!0.98!8.46!Pax6;;chr17:86012772..86012825,+!p4@Six3!0.98!8.46!Six3;;chr12:74040716..74040745,+!p3@Six6!0.97!8.28!Six6;;chr2:146911200..146911219,-!p1@Nkx2-4!0.97!8.28!Nkx2-4;;chr2:31495237..31495243,+!p1@Prdm12!0.97!8.28!Prdm12;;chr7:6649134..6649167,-!p1@Zim1!0.96!45.38!Zim1;;chr17:86020468..86020504,+!p6@Six3!0.95!7.92!Six3;;chr3:128902837..128902861,+!p3@Pitx2!0.94!7.74!Pitx2;;chr12:74147860..74147888,-!p2@Six1!0.94!7.74!Six1;;chr13:31898729..31898761,+!p1@Foxc1!0.92!18.37!Foxc1;;chr12:85910771..85910785,+!p1@Vsx2!0.92!7.38!Vsx2;;chr17:48061584..48061601,-!p2@Foxp4!0.91!48.08!Foxp4;;chrX:55283799..55283813,+!p1@Zic3!0.90!7.02!Zic3;;chr7:56892217..56892221,-!p1@Dbx1!0.90!7.02!Dbx1;;chr3:127336052..127336058,+!p1@Neurog2!0.90!7.02!Neurog2;;chr14:17407970..17408015,-!p2@Rarb!0.89!18.73!Rarb;;chr12:57636220..57636236,-!p3@Nkx2-1!0.89!6.84!Nkx2-1;;chr13:55937432..55937460,-!p4@Pitx1!0.88!6.66!Pitx1;;chr2:105515635..105515661,+!p5@Pax6!0.88!6.66!Pax6;;chr6:83661226..83661282,+!p1@Vax2!0.88!6.66!Vax2;;chr14:17407878..17407926,-!p1@Rarb!0.87!14.95!Rarb;;chr3:128917187..128917223,+!p2@Pitx2!0.87!7.56!Pitx2;;chr6:70906450..70906454,+!p1@Foxi3!0.87!6.48!Foxi3;;chr9:71743854..71743909,-!p1@Tcf12!0.86!52.76!Tcf12;;chr8:90483433..90483457,-!p2@Zfp423!0.86!8.64!Zfp423;;chr5:148000254..148000260,+!p1@Gsx1!0.86!6.30!Gsx1;;chr2:71367871..71367898,+!p1@Dlx1!0.86!6.30!Dlx1;;chr14:52948124..52948148,-!p7@Sall2!0.85!6.12!Sall2;;chr11:21901608..21901634,-!p1@Otx1!0.85!6.12!Otx1;;chr11:3189683..3189744,+!p2@Patz1!0.84!12.60!Patz1;;chr7:116154364..116154444,+!p1@Tub!0.84!10.44!Tub;;chr9:87626083..87626108,-!p1@Tbx18!0.83!13.14!Tbx18;;chr13:31898496..31898519,+!p3@Foxc1!0.83!9.54!Foxc1;;chr5:24107676..24107722,-!p4@Smarcd3!0.83!7.92!Smarcd3;;chr13:99124236..99124243,+!p2@Foxd1!0.83!5.76!Foxd1;;chr2:163028808..163028869,+!p1@Tox2!0.82!21.43!Tox2;;chr10:12810631..12810649,+!p1@Plagl1!0.81!153.59!Plagl1;;chr7:52471143..52471186,+!p1@Tead2!0.80!61.40!Tead2;;chr10:119913792..119913820,-!p5@Hmga2!0.80!9.54!Hmga2;;chr1:93698095..93698113,+!p3@Twist2!0.80!6.48!Twist2;;chr17:35031460..35031518,+!p1@Zbtb12!0.79!28.27!Zbtb12;;chr10:50614546..50614568,+!p@chr10:50614546..50614568,+!0.79!5.22!Sim1;;chr3:8666963..8666978,-!p1@Hey1!0.78!35.65!Hey1;;chr15:102087737..102087801,-!p3@Rarg!0.78!8.64!Rarg;;chr14:27813891..27813902,+!p3@Hesx1!0.78!5.04!Hesx1;;chr1:19199236..19199258,+!p1@Tfap2b!0.78!5.04!Tfap2b;;chrX:55284180..55284195,+!p2@Zic3!0.78!5.04!Zic3;;chrX:108009798..108009815,+!p3@Pou3f4!0.78!5.04!Pou3f4;;chr1:170361695..170361722,-!p12@Pbx1!0.77!6.48!Pbx1;;chr13:31717597..31717613,+!p2@Foxf2!0.77!4.86!Foxf2;;chr17:86020137..86020149,+!p5@Six3!0.77!4.86!Six3;;chr19:7342725..7342784,+!p1@Rcor2!0.76!21.43!Rcor2;;chr1:170361991..170362015,-!p6@Pbx1!0.76!11.34!Pbx1;;chr9:106356211..106356242,+!p1@Pcbp4!0.75!100.29!Pcbp4;;chr15:75447162..75447217,+!p2@Zfp41!0.75!14.58!Zfp41;;chr15:103164702..103164778,-!p3@Zfp385a!0.75!5.58!Zfp385a;;chr14:52948033..52948045,-!p12@Sall2!0.75!4.68!Sall2;;chr2:147012125..147012149,-!p1@Nkx2-2!0.75!4.68!Nkx2-2;;chr2:105515793..105515808,+!p3@Pax6!0.75!4.68!Pax6;;chr3:101814061..101814094,+!p1@Nhlh2!0.75!4.68!Nhlh2;;chr6:14851287..14851342,+!p1@Foxp2!0.74!16.03!Foxp2;;chr6:14851250..14851277,+!p4@Foxp2!0.74!5.94!Foxp2;;chr9:98855868..98855895,+!p1@Foxl2!0.74!4.50!Foxl2;;chr7:91558392..91558434,-!p1@Arnt2!0.73!13.14!Arnt2;;chr3:30408603..30408668,-!p1@Mecom!0.73!10.80!Mecom;;chr6:15135456..15135520,+!p3@Foxp2!0.73!10.08!Foxp2;;chr6:88148650..88148669,+!p1@Gata2!0.72!39.79!Gata2;;chr14:52634234..52634281,-!p3@Zfp219!0.72!12.78!Zfp219;;chr19:7342786..7342803,+!p2@Rcor2!0.72!5.94!Rcor2;;chr19:19185697..19185711,-!p2@Rorb!0.72!5.58!Rorb;;chr1:170361826..170361844,-!p9@Pbx1!0.71!9.90!Pbx1;;chr13:31898637..31898653,+!p2@Foxc1!0.71!7.92!Foxc1;;chr17:35031524..35031539,+!p4@Zbtb12!0.71!5.58!Zbtb12;;chr2:17976799..17976829,+!p5@Mllt10!0.71!5.22!Mllt10;;chr1:170361678..170361689,-!p13@Pbx1!0.71!5.22!Pbx1;;chr4:150503457..150503498,-!p3@Camta1!0.71!4.68!Camta1;;chr6:14851212..14851226,+!p12@Foxp2!0.71!4.14!Foxp2;;chr7:135019147..135019187,-!p3@Zfp668!0.70!9.54!Zfp668;;chr10:61595830..61595846,+!p1@Neurog3!0.70!3.96!Neurog3;;chr9:99776617..99776631,-!p2@Sox14!0.70!3.96!Sox14;;chr18:66098673..66098684,-!p2@Rax!0.70!3.96!Rax;;chr8:123640090..123640101,+!p2@Foxc2!0.69!4.50!Foxc2;;chr3:5218629..5218684,+!p1@Zfhx4!0.68!13.86!Zfhx4;;chr2:65683890..65683907,+!p1@Csrnp3!0.68!7.92!Csrnp3;;chr4:114581524..114581551,-!p1@Foxd2!0.68!5.94!Foxd2;;chr16:18587076..18587106,-!p1@Tbx1!0.68!5.76!Tbx1;;chr17:86020293..86020318,+!p7@Six3!0.68!3.78!Six3;;chrX:108009734..108009752,+!p2@Pou3f4!0.68!3.78!Pou3f4;;chr5:42155788..42155800,-!p1@Nkx3-2!0.68!3.78!Nkx3-2;;chr13:95645580..95645598,+!p1@Otp!0.68!3.78!Otp;;chr2:93482464..93482491,+!p1@Alx4!0.68!3.78!Alx4;;chr2:71367142..71367167,+!p2@Dlx1!0.68!3.78!Dlx1;;chr13:48356475..48356492,+!p1@Id4!0.67!93.45!Id4;;chr7:25292331..25292421,+!p1@Zfp428!0.66!29.35!Zfp428;;chr4:54957910..54957954,+!p2@Zfp462!0.65!11.88!Zfp462;;chr13:72101178..72101203,-!p1@Irx1!0.65!5.76!Irx1;;chr7:52472041..52472065,+!p2@Tead2!0.65!4.14!Tead2;;chr9:74709695..74709722,+!p1@Onecut1!0.65!3.42!Onecut1;;chr19:26822880..26822964,+!p2@Smarca2!0.63!32.77!Smarca2;;chr7:17647736..17647772,-!p1@Hif3a!0.63!13.14!Hif3a;;chr1:170361730..170361769,-!p7@Pbx1!0.63!8.28!Pbx1;;chr17:86020186..86020195,+!p9@Six3!0.63!3.24!Six3;;chr8:12395670..12395682,+!p3@Sox1!0.63!3.24!Sox1;;chr4:114581497..114581519,-!p2@Foxd2!0.63!3.24!Foxd2;;chr6:144157968..144157989,-!p7@Sox5!0.63!3.24!Sox5;;chr14:118636238..118636257,-!p2@Sox21!0.63!3.24!Sox21;;chr10:102491405..102491416,-!p1@Alx1!0.63!3.24!Alx1;;chr11:99092233..99092273,-!p2@Smarce1!0.62!17.65!Smarce1;;chr4:54960870..54960926,+!p1@Zfp462!0.62!13.14!Zfp462;;chr7:130644017..130644092,-!p1@Zkscan2!0.62!6.84!Zkscan2;;chr2:156666727..156666753,+!p2@Tgif2!0.62!5.04!Tgif2;;chr7:6683123..6683142,-!p1@Peg3!0.61!194.65!Peg3;;chr17:37139472..37139514,+!p1@Zfp57!0.61!24.67!Zfp57;;chrX:110411840..110411860,+!p1@Dach2!0.61!3.96!Dach2;;chr9:98855847..98855866,+!p3@Foxl2!0.61!3.06!Foxl2;;chr17:86087581..86087588,-!p2@Six2!0.61!3.06!Six2;;chr1:19199151..19199170,+!p3@Tfap2b!0.61!3.06!Tfap2b;;chr2:105515586..105515606,+!p4@Pax6!0.61!3.06!Pax6;;chr6:14851403..14851422,+!p8@Foxp2!0.61!3.06!Foxp2;;chr6:14851377..14851396,+!p10@Foxp2!0.61!3.06!Foxp2;;chr3:128916838..128916856,+!p4@Pitx2!0.61!3.06!Pitx2;;chr3:128902878..128902893,+!p6@Pitx2!0.61!3.06!Pitx2;;chr10:119913266..119913277,-!p6@Hmga2!0.61!3.06!Hmga2;;chr11:21901587..21901604,-!p2@Otx1!0.61!3.06!Otx1;;chr19:55816414..55816425,+!p4@Tcf7l2!0.60!18.55!Tcf7l2;;chr9:106356243..106356264,+!p2@Pcbp4!0.60!15.13!Pcbp4;;chr12:34642682..34642753,+!p2@Twist1!0.60!9.18!Twist1;;chr12:12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f1!0.23!14.95!E2f1;;chr8:118231678..118231692,-!p2@Maf!0.23!13.32!Maf;;chr7:134170496..134170539,-!p4@Maz!0.23!12.96!Maz;;chr8:112229478..112229536,+!p1@Zfp821!0.23!12.78!Zfp821;;chr17:34169016..34169068,+!p2@Rxrb!0.23!10.44!Rxrb;;chr2:91077082..91077122,-!p1@Ddb2!0.23!8.82!Ddb2;;chr17:28314341..28314394,+!p2@Zfp523!0.23!8.28!Zfp523;;chr7:30644985..30645072,+!p1@Zfp420!0.23!8.28!Zfp420;;chr4:120488308..120488366,-!p1@Nfyc!0.23!8.10!Nfyc;;chr4:102787317..102787364,+!p3@Mier1!0.23!8.10!Mier1;;chr10:20032330..20032345,+!p3@Bclaf1!0.23!6.66!Bclaf1;;chr17:48061692..48061723,-!p5@Foxp4!0.23!6.66!Foxp4;;chr16:4559777..4559825,-!p2@Tfap4!0.23!6.30!Tfap4;;chr2:127410404..127410439,-!p1@Zfp661!0.23!5.76!Zfp661;;chr7:30638630..30638702,-!p1@Zfp940!0.23!4.50!Zfp940;;chr14:22319053..22319105,+!p2@Myst4!0.23!4.32!Myst4;;chr12:37835141..37835194,+!p1@Meox2!0.23!3.96!Meox2;;chr19:28086084..28086124,-!p6@Rfx3!0.23!3.60!Rfx3;;chr8:111227738..111227793,+!p@chr8:111227738..111227793,+!0.23!3.06!Zfhx3;;chr11:44430788..44430804,+!p3@Ebf1!0.23!3.06!Ebf1;;chr1:33871319..33871333,-!p3@Zfp451!0.23!2.88!Zfp451;;chr5:122500142..122500167,-!p2@Cux2!0.23!2.52!Cux2;;chr1:120879128..120879183,-!p3@Gli2!0.23!2.16!Gli2;;chr4:126700683..126700704,+!p6@Sfpq!0.23!2.16!Sfpq;;chr3:30993616..30993634,+!p3@Skil!0.23!1.98!Skil;;chr7:134758722..134758733,-!p2@Zfp629!0.23!1.62!Zfp629;;chr15:103170561..103170572,-!p4@Zfp385a!0.23!1.44!Zfp385a;;chr18:65741911..65741929,+!p3@Zfp532!0.23!1.26!Zfp532;;chrX:66613569..66613586,+!p2@Aff2!0.23!1.08!Aff2;;chr13:78338076..78338104,-!p4@Nr2f1!0.23!1.08!Nr2f1;;chr7:25292246..25292259,+!p6@Zfp428!0.23!1.08!Zfp428;;chr9:21420674..21420725,+!p1@Smarca4!0.22!119.92!Smarca4;;chr5:106305551..106305604,+!p1@Zfp326!0.22!55.64!Zfp326;;chr9:20757246..20757278,-!p1@Dnmt1!0.22!43.57!Dnmt1;;chr9:20757282..20757325,-!p2@Dnmt1!0.22!34.93!Dnmt1;;chr10:92773591..92773623,-!p1@Elk3!0.22!32.95!Elk3;;chr12:16817746..16817784,+!p1@E2f6!0.22!25.39!E2f6;;chr18:24179250..24179314,-!p1@Zfp191!0.22!23.95!Zfp191;;chr6:118429255..118429336,-!p1@Zfp9!0.22!23.59!Zfp9;;chr10:82226781..82226825,-!p1@Nfyb!0.22!18.01!Nfyb;;chr10:110182489..110182589,+!p1@E2f7!0.22!17.47!E2f7;;chr7:17199897..17199955,-!p1@Grlf1!0.22!16.39!Grlf1;;chr3:100773567..100773599,-!p1@Ttf2!0.22!16.03!Ttf2;;chr10:22451142..22451191,-!p2@Tbpl1!0.22!14.40!Tbpl1;;chr10:20032304..20032324,+!p2@Bclaf1!0.22!13.50!Bclaf1;;chr17:51952617..51952680,-!p3@Satb1!0.22!6.84!Satb1;;chr13:67552527..67552574,-!p1@Zfp874a!0.22!5.94!Zfp874a;;chr6:47827619..47827639,+!p2@Zfp282!0.22!5.76!Zfp282;;chr7:46773114..46773155,+!p1@Zfp619!0.22!4.86!Zfp619;;chr8:72498217..72498232,-!p8@Gatad2a!0.22!4.86!Gatad2a;;chr16:55966525..55966543,+!p5@Rpl24,p5@Zbtb11!0.22!4.50!Zbtb11;;chr17:69732364..69732405,+!p2@Zfp161!0.22!4.50!Zfp161;;chr11:23978078..23978096,+!p4@Bcl11a!0.22!3.78!Bcl11a;;chr6:38204087..38204108,-!p2@D630045J12Rik!0.22!3.60!D630045J12Rik;;chr9:63605691..63605705,-!p3@Smad3!0.22!3.06!Smad3;;chr4:154010940..154010962,-!p3@Prdm16!0.22!2.52!Prdm16;;chr4:6917971..6918000,-!p3@Tox!0.22!2.16!Tox;;chr12:39507680..39507715,+!p2@Etv1!0.22!2.16!Etv1;;chr13:96095124..96095144,+!p3@Zbed3!0.22!2.16!Zbed3;;chr2:169458838..169458859,+!p4@Tshz2!0.22!2.16!Tshz2;;chr9:68501522..68501538,+!p4@Rora!0.22!1.98!Rora;;chr18:69839537..69839544,+!p13@Tcf4!0.22!1.80!Tcf4;;chr16:4594853..4594884,+!p3@Glis2!0.22!1.62!Glis2;;chr15:100382267..100382287,-!p3@Tfcp2!0.22!1.62!Tfcp2;;chr3:5218563..5218587,+!p5@Zfhx4!0.22!1.62!Zfhx4;;chr4:54960713..54960727,+!p7@Zfp462!0.22!1.62!Zfp462;;chr11:44431710..44431725,+!p7@Ebf1!0.22!1.62!Ebf1;;chr12:119540395..119540415,-!p5@Sp4!0.22!1.44!Sp4;;
@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011317
 |is_obsolete=
+|library_id=CNhs11018
+|library_id_phase_based=2:CNhs11018
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;346
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;346
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E12.CNhs11018.346-16E6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E12.CNhs11018.346-16E6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E12.CNhs11018.346-16E6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E12.CNhs11018.346-16E6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E12.CNhs11018.346-16E6.mm9.nobarcode.rdna.fa.gz
 |name=pituitary gland, embryo E12
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11018,LSID731,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0772265823060104,0,0,0,0,0,0.152639451958224,0,0,0,0,0.389974952506189,0,0,0,0,0,0,0.22649907408305,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.140030367358406,0,0,0,0,0.0188477933013298,0.0782018822298187,0.0602797351082386,0.0579579320931125,0.437205218296024,0.298440638146166,0,0,0,0,0,0,0,0,0,0,0,0,0.0675723778785976,0.0719044921483595,0,0,0,0,0,0,0.0321851702490836,0.133577925442038,0.000950148678506256,0.054764361909009,0.0435399552744753,0.0294813622639038,0.207438504293783,0,0,0.0290934358591193,0,0.0719044921483595,0,0.0405104153373188,-0.0136763875705937,0.0669582956253316,0.108740810195079,0,0,0,0,0,0,0.0144995637937371,0.235307921977463,0.00706200369688207,0,0,0,0,0
@@ Line 59: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=16E6
+|rna_tube_id=1.60E+07
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 82: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:346-16E6;search_select_hide=table117:346-16E6
 }}

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FF:346-16E6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:10, 4 June 2020

CNhs11018

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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