FF:370-44C7: Difference between revisions

Latest revision as of 19:13, 4 June 2020

Name:	pituitary gland, embryo E13
Species:	Mouse (Mus musculus)
Library ID:	CNhs11009
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	pituitary gland
dev stage	13 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		SAMD00005549

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11009		CAGE		DRX009068		DRR009942

Accession ID Mm9

Library id		BAM		CTSS
CNhs11009		DRZ001367		DRZ002750

Accession ID Mm10

Library id		BAM		CTSS
CNhs11009		DRZ012717		DRZ014100

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

CNhs11009

0	0
1	0.0356
10	0
100	0.0999
1000	0
1001	-0.0395
1002	0.251
1003	-0.0731
1004	0.377
1005	0
1006	-2.404932e-4
1007	0.141
1008	0
1009	-0.0786
101	-0.0813
1010	0
1011	-0.0178
1012	0
1013	-0.138
1014	0.383
1015	0.358
1016	0.247
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.0528
1022	-0.0704
1023	0
1024	0.0101
1025	0
1026	0
1027	0
1028	0
1029	-0.148
103	0.0683
1030	0
1031	0.374
1032	-0.177
1033	0.0859
1034	0
1035	0
1036	0.152
1037	0
1038	-0.0488
1039	-0.0702
104	0
1040	0.0134
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: CNhs11009

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0106
MA0003.1	MA0003.1	0.973
MA0004.1	MA0004.1	0.661
MA0006.1	MA0006.1	0.339
MA0007.1	MA0007.1	0.636
MA0009.1	MA0009.1	0.464
MA0014.1	MA0014.1	0.36
MA0017.1	MA0017.1	8.28548e-6
MA0018.2	MA0018.2	0.305
MA0019.1	MA0019.1	0.723
MA0024.1	MA0024.1	0.017
MA0025.1	MA0025.1	0.164
MA0027.1	MA0027.1	0.284
MA0028.1	MA0028.1	0.115
MA0029.1	MA0029.1	0.0915
MA0030.1	MA0030.1	0.243
MA0031.1	MA0031.1	0.124
MA0035.2	MA0035.2	0.0637
MA0038.1	MA0038.1	0.254
MA0039.2	MA0039.2	0.338
MA0040.1	MA0040.1	0.414
MA0041.1	MA0041.1	0.36
MA0042.1	MA0042.1	0.949
MA0043.1	MA0043.1	0.0242
MA0046.1	MA0046.1	2.73061e-16
MA0047.2	MA0047.2	0.00327
MA0048.1	MA0048.1	0.498
MA0050.1	MA0050.1	8.36892e-7
MA0051.1	MA0051.1	1.12121e-4
MA0052.1	MA0052.1	6.99843e-6
MA0055.1	MA0055.1	0.0287
MA0057.1	MA0057.1	0.129
MA0058.1	MA0058.1	0.654
MA0059.1	MA0059.1	0.832
MA0060.1	MA0060.1	4.49789e-15
MA0061.1	MA0061.1	0.0426
MA0062.2	MA0062.2	0.631
MA0065.2	MA0065.2	0.00315
MA0066.1	MA0066.1	0.11
MA0067.1	MA0067.1	0.0257
MA0068.1	MA0068.1	0.48
MA0069.1	MA0069.1	0.622
MA0070.1	MA0070.1	0.716
MA0071.1	MA0071.1	0.348
MA0072.1	MA0072.1	0.0873
MA0073.1	MA0073.1	0.964
MA0074.1	MA0074.1	0.391
MA0076.1	MA0076.1	0.0573
MA0077.1	MA0077.1	0.0114
MA0078.1	MA0078.1	0.402
MA0079.2	MA0079.2	0.333
MA0080.2	MA0080.2	4.46986e-9
MA0081.1	MA0081.1	0.415
MA0083.1	MA0083.1	0.054
MA0084.1	MA0084.1	0.174
MA0087.1	MA0087.1	0.23
MA0088.1	MA0088.1	0.271
MA0090.1	MA0090.1	0.2
MA0091.1	MA0091.1	0.654
MA0092.1	MA0092.1	0.558
MA0093.1	MA0093.1	0.68
MA0099.2	MA0099.2	8.4466e-4
MA0100.1	MA0100.1	0.899
MA0101.1	MA0101.1	0.207
MA0102.2	MA0102.2	0.381
MA0103.1	MA0103.1	0.528
MA0104.2	MA0104.2	0.337
MA0105.1	MA0105.1	0.522
MA0106.1	MA0106.1	0.139
MA0107.1	MA0107.1	0.0349
MA0108.2	MA0108.2	0.857
MA0111.1	MA0111.1	0.954
MA0112.2	MA0112.2	3.2139e-5
MA0113.1	MA0113.1	0.947
MA0114.1	MA0114.1	1.03346e-4
MA0115.1	MA0115.1	0.0162
MA0116.1	MA0116.1	0.747
MA0117.1	MA0117.1	0.101
MA0119.1	MA0119.1	0.0108
MA0122.1	MA0122.1	0.455
MA0124.1	MA0124.1	0.632
MA0125.1	MA0125.1	0.00947
MA0131.1	MA0131.1	0.643
MA0135.1	MA0135.1	0.00366
MA0136.1	MA0136.1	1.28535e-4
MA0137.2	MA0137.2	0.0831
MA0138.2	MA0138.2	0.0195
MA0139.1	MA0139.1	0.815
MA0140.1	MA0140.1	0.124
MA0141.1	MA0141.1	0.0151
MA0142.1	MA0142.1	0.798
MA0143.1	MA0143.1	0.00446
MA0144.1	MA0144.1	0.116
MA0145.1	MA0145.1	0.352
MA0146.1	MA0146.1	0.406
MA0147.1	MA0147.1	0.267
MA0148.1	MA0148.1	7.30044e-6
MA0149.1	MA0149.1	0.0137
MA0150.1	MA0150.1	4.84486e-5
MA0152.1	MA0152.1	0.618
MA0153.1	MA0153.1	4.24745e-12
MA0154.1	MA0154.1	0.0145
MA0155.1	MA0155.1	0.328
MA0156.1	MA0156.1	0.0214
MA0157.1	MA0157.1	0.23
MA0159.1	MA0159.1	0.0385
MA0160.1	MA0160.1	0.0345
MA0162.1	MA0162.1	0.506
MA0163.1	MA0163.1	0.956
MA0164.1	MA0164.1	0.579
MA0258.1	MA0258.1	7.59046e-4
MA0259.1	MA0259.1	0.687

FANTOM5 phase1 novel unique motifsSummary:Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above Analyst: Michiel de Hoon link to dataset. data

library id: CNhs11009

Novel motif	Logo	P-value
1	1	0.0316
10	10	0.204
100	100	0.66
101	101	0.675
102	102	0.744
103	103	0.126
104	104	0.902
105	105	0.18
106	106	0.0118
107	107	0.0252
108	108	0.995
109	109	0.66
11	11	0.299
110	110	0.295
111	111	0.0445
112	112	0.0849
113	113	0.401
114	114	0.168
115	115	0.838
116	116	0.894
117	117	0.536
118	118	0.979
119	119	0.28
12	12	0.98
120	120	0.931
121	121	0.887
122	122	0.491
123	123	0.151
124	124	0.867
125	125	0.343
126	126	0.877
127	127	0.133
128	128	0.0774
129	129	0.211
13	13	0.0925
130	130	0.399
131	131	0.338
132	132	0.576
133	133	0.651
134	134	0.435
135	135	0.168
136	136	0.327
137	137	0.51
138	138	0.706
139	139	0.013
14	14	0.362
140	140	0.0145
141	141	0.0542
142	142	0.00375
143	143	0.846
144	144	0.9
145	145	0.335
146	146	0.357
147	147	0.465
148	148	0.361
149	149	0.512
15	15	0.0909
150	150	0.525
151	151	0.0918
152	152	0.685
153	153	0.419
154	154	0.168
155	155	0.887
156	156	7.45976e-4
157	157	0.743
158	158	0.217
159	159	0.24
160	160	0.438
161	161	0.741
162	162	0.492
163	163	0.0981
164	164	0.0658
165	165	0.198
166	166	0.852
167	167	0.239
168	168	0.419
169	169	0.373
17	17	0.163
18	18	0.679
19	19	0.214
2	2	0.977
20	20	0.631
21	21	0.564
22	22	0.53
23	23	0.0989
24	24	0.923
25	25	0.142
26	26	0.378
27	27	0.781
28	28	0.362
29	29	0.398
3	3	0.423
30	30	0.907
31	31	0.615
32	32	0.258
33	33	0.637
34	34	0.678
35	35	0.484
36	36	0.561
37	37	0.0682
38	38	0.329
39	39	0.874
4	4	0.741
40	40	0.956
41	41	0.645
42	42	0.967
43	43	0.142
44	44	0.537
45	45	0.621
46	46	0.2
47	47	0.209
48	48	0.192
49	49	0.101
5	5	0.0446
50	50	0.665
51	51	0.463
52	52	0.325
53	53	0.701
54	54	0.352
55	55	0.936
56	56	0.776
57	57	0.272
58	58	0.233
59	59	0.379
6	6	0.784
60	60	0.0675
61	61	0.869
62	62	0.087
63	63	0.269
64	64	0.963
65	65	0.305
66	66	0.16
67	67	0.607
68	68	0.399
69	69	0.879
7	7	0.118
70	70	0.0089
71	71	0.239
72	72	0.735
73	73	0.584
74	74	0.274
75	75	0.69
76	76	0.746
77	77	0.449
78	78	0.0548
79	79	0.365
8	8	0.445
80	80	0.148
81	81	0.376
82	82	0.467
83	83	0.295
84	84	0.759
85	85	0.0721
86	86	0.557
87	87	0.226
88	88	0.484
89	89	0.301
9	9	0.376
90	90	0.178
91	91	0.457
92	92	0.0672
93	93	0.215
94	94	0.302
95	95	0.983
96	96	0.272
97	97	0.686
98	98	0.792
99	99	0.669

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: CNhs11009

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011325 mouse pituitary gland- embryo E13 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)
0000293 (mouse embryonic day 13 sample)
0011325 (mouse pituitary gland- embryo E13 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@SAMD00005549
+|accession_numbers=CAGE;DRX009068;DRR009942;DRZ001367;DRZ002750;DRZ012717;DRZ014100
 |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=chr13:55932591..55932622,-!p1@Pitx1!2.24!206.72!Pitx1;;chr12:74040861..74040875,+!p1@Six6!2.13!132.72!Six6;;chr2:26062055..26062100,-!p1@Lhx3!2.06!112.80!Lhx3;;chr12:74147689..74147711,-!p1@Six1!2.04!228.32!Six1;;chr13:99124189..99124205,+!p1@Foxd1!1.99!145.40!Foxd1;;chr11:50767247..50767270,-!p1@Prop1!1.92!82.53!Prop1;;chr12:74040895..74040916,+!p2@Six6!1.89!75.93!Six6;;chrX:58146612..58146615,-!p1@Sox3!1.84!67.53!Sox3;;chr18:66098702..66098742,-!p1@Rax!1.82!64.94!Rax;;chr17:86020510..86020589,+!p3@Six3!1.74!54.33!Six3;;chr3:128916868..128916890,+!p1@Pitx2!1.62!54.72!Pitx2;;chr17:86087592..86087615,-!p1@Six2!1.61!39.71!Six2;;chrX:108009761..108009788,+!p1@Pou3f4!1.60!39.20!Pou3f4;;chr4:109650609..109650653,+!p1@Dmrta2!1.58!37.13!Dmrta2;;chr13:55932624..55932641,-!p2@Pitx1!1.50!30.79!Pitx1;;chr3:34548909..34548927,+!p1@Sox2!1.48!49.16!Sox2;;chr5:38215819..38215823,-!p1@Msx1!1.47!73.48!Msx1;;chr10:86956396..86956411,-!p1@Ascl1!1.46!42.30!Ascl1;;chr14:122874619..122874634,+!p1@Zic2!1.46!27.68!Zic2;;chr13:31898767..31898785,+!p4@Foxc1!1.44!32.21!Foxc1;;chr13:55937467..55937516,-!p3@Pitx1!1.44!26.26!Pitx1;;chr12:3891810..3891829,+!p2@Dnmt3a!1.41!37.77!Dnmt3a;;chr17:86020156..86020183,+!p1@Six3!1.41!24.84!Six3;;chr2:146047829..146047847,+!p1@Insm1!1.39!41.65!Insm1;;chr12:34642510..34642530,+!p1@Twist1!1.38!71.79!Twist1;;chr8:12395603..12395621,+!p1@Sox1!1.35!21.21!Sox1;;chr9:91260616..91260653,-!p2@Zic1!1.33!20.44!Zic1;;chr10:119913310..119913366,-!p1@Hmga2!1.32!151.87!Hmga2;;chr9:91260594..91260612,-!p1@Zic1!1.31!19.53!Zic1;;chr10:119913278..119913298,-!p2@Hmga2!1.27!39.07!Hmga2;;chr2:38206744..38206766,+!p1@Lhx2!1.26!20.70!Lhx2;;chr17:86020115..86020128,+!p2@Six3!1.26!17.08!Six3;;chr3:128917187..128917223,+!p2@Pitx2!1.24!19.27!Pitx2;;chr13:55937432..55937460,-!p4@Pitx1!1.21!15.39!Pitx1;;chr7:56892217..56892221,-!p1@Dbx1!1.20!15.01!Dbx1;;chr2:146911200..146911219,-!p1@Nkx2-4!1.20!14.75!Nkx2-4;;chr12:57636240..57636256,-!p4@Nkx2-1!1.19!14.36!Nkx2-1;;chr8:123640063..123640077,+!p1@Foxc2!1.18!25.74!Foxc2;;chr12:74147860..74147888,-!p2@Six1!1.18!14.23!Six1;;chr13:31717548..31717596,+!p1@Foxf2!1.17!27.42!Foxf2;;chr3:34548946..34548972,+!p2@Sox2!1.17!15.26!Sox2;;chr12:28027561..28027591,-!p1@Sox11!1.13!82.66!Sox11;;chr2:38206580..38206600,+!p2@Lhx2!1.13!15.39!Lhx2;;chr17:86020468..86020504,+!p6@Six3!1.10!11.51!Six3;;chr10:126778916..126778974,-!p1@Gli1!1.09!25.35!Gli1;;chr13:117099847..117099907,-!p1@Isl1!1.07!20.05!Isl1;;chr14:27813852..27813865,+!p1@Hesx1!1.04!9.96!Hesx1;;chr3:127336052..127336058,+!p1@Neurog2!1.03!9.83!Neurog2;;chr17:86012772..86012825,+!p4@Six3!1.03!9.83!Six3;;chr10:119913546..119913583,-!p3@Hmga2!1.02!20.31!Hmga2;;chr10:119914001..119914078,-!p4@Hmga2!1.02!12.94!Hmga2;;chr14:49287186..49287225,-!p1@Otx2!1.02!9.57!Otx2;;chr12:57636220..57636236,-!p3@Nkx2-1!1.02!9.57!Nkx2-1;;chr2:147190749..147190769,+!p1@Pax1!1.02!9.44!Pax1;;chr3:128902837..128902861,+!p3@Pitx2!1.01!9.31!Pitx2;;chr5:148000254..148000260,+!p1@Gsx1!1.01!9.18!Gsx1;;chr19:19185671..19185693,-!p1@Rorb!1.00!21.86!Rorb;;chr9:99776566..99776612,-!p1@Sox14!1.00!8.93!Sox14;;chr12:3891753..3891801,+!p4@Dnmt3a!0.99!14.36!Dnmt3a;;chr14:52948124..52948148,-!p7@Sall2!0.99!8.80!Sall2;;chr12:74040716..74040745,+!p3@Six6!0.99!8.67!Six6;;chr13:31898729..31898761,+!p1@Foxc1!0.98!21.47!Foxc1;;chr4:154335024..154335039,+!p1@Hes5!0.98!10.35!Hes5;;chr12:74147842..74147856,-!p3@Six1!0.98!8.54!Six1;;chr2:71384802..71384815,-!p1@Dlx2!0.97!10.48!Dlx2;;chr13:99124236..99124243,+!p2@Foxd1!0.97!8.28!Foxd1;;chr3:8666963..8666978,-!p1@Hey1!0.96!54.33!Hey1;;chr2:26063801..26063813,-!p2@Lhx3!0.96!8.02!Lhx3;;chr15:103164702..103164778,-!p3@Zfp385a!0.94!9.18!Zfp385a;;chr8:24780125..24780143,+!p1@Zmat4!0.93!11.00!Zmat4;;chr7:52471143..52471186,+!p1@Tead2!0.91!78.78!Tead2;;chr14:52634234..52634281,-!p3@Zfp219!0.91!20.44!Zfp219;;chr7:52472041..52472065,+!p2@Tead2!0.91!8.41!Tead2;;chrX:108009734..108009752,+!p2@Pou3f4!0.91!7.11!Pou3f4;;chr2:79296783..79296801,-!p1@Neurod1!0.89!6.73!Neurod1;;chr13:31898637..31898653,+!p2@Foxc1!0.88!12.16!Foxc1;;chr3:128916838..128916856,+!p4@Pitx2!0.87!6.47!Pitx2;;chr6:88148650..88148669,+!p1@Gata2!0.86!54.98!Gata2;;chr3:99057269..99057306,+!p1@Tbx15!0.86!7.76!Tbx15;;chrX:55284180..55284195,+!p2@Zic3!0.86!6.21!Zic3;;chr7:17647736..17647772,-!p1@Hif3a!0.85!22.64!Hif3a;;chr11:90251852..90251855,-!p4@Hlf!0.85!7.63!Hlf;;chr9:106356211..106356242,+!p1@Pcbp4!0.84!123.54!Pcbp4;;chr14:17407970..17408015,-!p2@Rarb!0.84!16.82!Rarb;;chr3:34549096..34549111,+!p3@Sox2!0.84!5.95!Sox2;;chr10:119913792..119913820,-!p5@Hmga2!0.82!10.09!Hmga2;;chr17:35031460..35031518,+!p1@Zbtb12!0.81!29.24!Zbtb12;;chr13:31898496..31898519,+!p3@Foxc1!0.81!9.06!Foxc1;;chr3:107398056..107398082,+!p1@Alx3!0.81!5.43!Alx3;;chr9:87626083..87626108,-!p1@Tbx18!0.80!12.29!Tbx18;;chr5:24107676..24107722,-!p4@Smarcd3!0.79!7.11!Smarcd3;;chr4:114581497..114581519,-!p2@Foxd2!0.79!5.17!Foxd2;;chr3:8666997..8667012,-!p2@Hey1!0.77!12.03!Hey1;;chrX:108009798..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Zfp608!0.26!3.88!Zfp608;;chr2:166888481..166888548,-!p3@Znfx1!0.26!3.62!Znfx1;;chr10:127896315..127896333,+!p2@Smarcc2!0.26!3.62!Smarcc2;;chr9:63605691..63605705,-!p3@Smad3!0.26!3.49!Smad3;;chr8:81923398..81923409,-!p4@Smad1!0.26!3.36!Smad1;;chr11:87881818..87881834,+!p4@Vezf1!0.26!3.36!Vezf1;;chr14:76903992..76904056,+!p6@Tsc22d1!0.26!2.59!Tsc22d1;;chr7:87171256..87171280,+!p4@Zfp710!0.26!2.46!Zfp710;;chr7:25862363..25862382,+!p2@Zfp574!0.26!2.20!Zfp574;;chr4:54957886..54957907,+!p3@Zfp462!0.26!2.07!Zfp462;;chr8:72498017..72498059,-!p13@Gatad2a!0.26!1.94!Gatad2a;;chr11:85646469..85646488,+!p5@Tbx2!0.26!1.68!Tbx2;;chr6:99471223..99471254,-!p7@Foxp1!0.26!1.68!Foxp1;;chr15:103085660..103085681,-!p1@Nfe2!0.26!1.68!Nfe2;;chr10:119913839..119913869,-!p7@Hmga2!0.26!1.29!Hmga2;;chr16:98073382..98073395,-!p4@Prdm15!0.26!1.29!Prdm15;;chr6:14851344..14851364,+!p6@Foxp2!0.26!1.16!Foxp2;;chr7:26067803..26067814,+!p11@Cic!0.26!1.03!Cic;;chr17:57170891..57170961,-!p1@Khsrp!0.25!143.98!Khsrp;;chr9:21420674..21420725,+!p1@Smarca4!0.25!127.03!Smarca4;;chr19:53384985..53385042,+!p1@Mxi1!0.25!49.54!Mxi1;;chr8:108378986..108379049,+!p1@Thap11!0.25!37.26!Thap11;;chr9:113840108..113840184,+!p2@Ubp1!0.25!14.36!Ubp1;;chr14:55482892..55482988,-!p1@Homez!0.25!10.22!Homez;;chr14:52640373..52640412,-!p1@Zfp219!0.25!8.80!Zfp219;;chr14:100683672..100683717,-!p1@Klf12!0.25!6.86!Klf12;;chr9:32443818..32443854,+!p2@Ets1!0.25!6.47!Ets1;;chr4:151401741..151401793,-!p1@Zbtb48!0.25!6.21!Zbtb48;;chr15:57526469..57526534,+!p1@Zhx2!0.25!5.04!Zhx2;;chr17:56970339..56970428,-!p1@Rfx2!0.25!4.27!Rfx2;;chr6:117791276..117791304,+!p2@Zfp637!0.25!3.88!Zfp637;;chrX:98449805..98449834,+!p3@Foxo4!0.25!3.75!Foxo4;;chr13:22036953..22037009,+!p1@Zfp184!0.25!3.49!Zfp184;;chr11:5761979..5761992,+!p2@Aebp1!0.25!2.46!Aebp1;;chr2:181327403..181327432,-!p3@Znf512b!0.25!2.33!Znf512b;;chr7:4947625..4947634,-!p6@Zfp579!0.25!1.81!Zfp579;;chr8:124984566..124984595,-!p1@Snai3!0.25!1.68!Snai3;;chr8:72356384..72356434,+!p2@Pbx4!0.25!1.68!Pbx4;;chr7:52960663..52960677,+!p6@Dbp!0.25!0.78!Dbp;;chr8:87238155..87238187,-!p13@Nfix!0.25!0.78!Nfix;;chr9:91263649..91263666,+!p3@Zic4!0.25!0.78!Zic4;;chr19:55969923..55969944,+!p6@Tcf7l2!0.25!0.78!Tcf7l2;;chr2:181501988..181502026,+!p3@Myt1!0.25!0.78!Myt1;;chr19:59244875..59244895,-!p2@Vax1!0.25!0.78!Vax1;;chr19:59533139..59533152,+!p2@Emx2!0.25!0.78!Emx2;;chr1:169528823..169528860,+!p5@Rxrg!0.25!0.78!Rxrg;;chr19:59533163..59533185,+!p3@Emx2!0.25!0.78!Emx2;;chr15:102196790..102196799,-!p3@Sp7!0.25!0.78!Sp7;;chr12:57637595..57637608,-!p7@Nkx2-1!0.25!0.78!Nkx2-1;;chr15:37163124..37163153,+!p3@Grhl2!0.25!0.78!Grhl2;;chr12:30213247..30213333,+!p1@Myt1l!0.25!0.78!Myt1l;;chr3:99044284..99044308,+!p4@Tbx15!0.25!0.78!Tbx15;;chr4:22415290..22415307,-!p2@Pou3f2!0.25!0.78!Pou3f2;;chr6:144157991..144158007,-!p9@Sox5!0.25!0.78!Sox5;;chr6:85137520..85137563,+!p1@Emx1!0.25!0.78!Emx1;;chr1:136456767..136456790,+!p2@Kdm5b!0.24!32.34!Kdm5b;;chr5:143996822..143996930,+!p1@Zfp12!0.24!31.95!Zfp12;;chr12:16817746..16817784,+!p1@E2f6!0.24!27.04!E2f6;;chr4:118846783..118846826,-!p1@Zfp691!0.24!20.83!Zfp691;;chr5:134790384..134790418,-!p2@Gtf2i!0.24!19.66!Gtf2i;;chr16:4594683..4594735,+!p2@Glis2!0.24!19.66!Glis2;;chr2:181100122..181100143,+!p2@Zgpat!0.24!14.75!Zgpat;;chr17:4994904..4994953,+!p3@Arid1b!0.24!11.64!Arid1b;;chr3:94176733..94176794,+!p1@Rorc!0.24!11.51!Rorc;;chr16:22439654..22439676,-!p2@Etv5!0.24!8.67!Etv5;;chr16:17530781..17530882,-!p2@Thap7!0.24!8.54!Thap7;;chr3:94641455..94641486,+!p4@Pogz!0.24!3.36!Pogz;;chr9:32349240..32349276,-!p2@Fli1!0.24!2.98!Fli1;;chr12:87027598..87027652,+!p1@Batf!0.24!2.85!Batf;;chr10:80812991..80813004,-!p3@Hmg20b!0.24!2.46!Hmg20b;;chr18:60720468..60720472,+!p2@Rbm22!0.24!2.33!Rbm22;;chr2:30700881..30700916,+!p1@Prrx2!0.24!2.20!Prrx2;;chr11:85646427..85646451,+!p4@Tbx2!0.24!1.94!Tbx2;;chr11:121380594..121380609,-!p2@Zfp750!0.24!1.94!Zfp750;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.24!1.94!Zfhx3;;chr18:14131045..14131062,-!p3@Zfp521!0.24!1.68!Zfp521;;chr19:28754600..28754612,-!p2@Glis3!0.24!1.68!Glis3;;chr7:5003102..5003113,+!p4@Zfp580!0.24!1.42!Zfp580;;chr6:98978189..98978198,-!p10@Foxp1!0.24!1.16!Foxp1;;chr6:144157924..144157955,-!p2@Sox5!0.24!1.16!Sox5;;chr17:48025139..48025166,-!p8@Foxp4!0.24!1.03!Foxp4;;chr17:37139519..37139531,+!p5@Zfp57!0.24!1.03!Zfp57;;chr15:37162834..37162849,+!p2@Grhl2!0.24!1.03!Grhl2;;chr11:69393894..69393921,+!p1@Trp53!0.23!142.29!Trp53;;chr8:72663586..72663633,+!p1@2310045N01Rik,p1@Mef2b!0.23!76.19!Mef2b;;chr9:110034519..110034606,+!p1@Smarcc1!0.23!66.62!Smarcc1;;chr12:114336410..114336478,+!p1@Mta1!0.23!48.90!Mta1;;chr17:57074836..57074927,-!p1@Mllt1!0.23!41.78!Mllt1;;chr5:138558139..138558214,+!p1@Zscan21!0.23!41.65!Zscan21;;chr11:23978022..23978076,+!p1@Bcl11a!0.23!32.73!Bcl11a;;chr7:134388025..134388092,+!p1@Zfp771!0.23!31.43!Zfp771;;chr17:3557742..3557775,-!p1@Tfb1m!0.23!20.96!Tfb1m;;chr10:79862175..79862221,-!p1@Mbd3!0.23!20.83!Mbd3;;chr10:80813050..80813114,-!p2@Hmg20b!0.23!16.17!Hmg20b;;chr15:102076870..102076941,-!p1@Rarg!0.23!16.04!Rarg;;chr5:138596922..138596968,-!p1@Zfp113!0.23!14.62!Zfp113;;chr1:170362242..170362256,-!p3@Pbx1!0.23!10.35!Pbx1;;chr18:80909801..80909819,-!p1@Nfatc1!0.23!8.41!Nfatc1;;chr14:55711198..55711258,-!p1@Zfhx2!0.23!8.15!Zfhx2;;chr7:26067619..26067702,+!p2@Cic!0.23!8.02!Cic;;chr17:48061409..48061431,-!p4@Foxp4!0.23!7.37!Foxp4;;chr5:147760305..147760324,+!p2@Gtf3a!0.23!6.73!Gtf3a;;chr8:87225670..87225697,+!p2@Lyl1!0.23!3.75!Lyl1;;chr4:126703093..126703158,+!p3@Sfpq!0.23!3.62!Sfpq;;chr4:128483731..128483757,-!p4@Zfp362!0.23!2.72!Zfp362;;chr7:144506077..144506128,-!p1@Ebf3!0.23!2.72!Ebf3;;chr10:75384291..75384298,-!p2@Smarcb1!0.23!2.59!Smarcb1;;chr17:3557785..3557797,-!p3@Tfb1m!0.23!2.20!Tfb1m;;chr2:35960919..35960954,-!p1@Lhx6!0.23!2.07!Lhx6;;chr2:91864449..91864492,-!p3@Creb3l1!0.23!1.68!Creb3l1;;chr16:4594853..4594884,+!p3@Glis2!0.23!1.68!Glis2;;chr17:37139455..37139469,+!p3@Zfp57!0.23!1.55!Zfp57;;chr12:109242296..109242307,-!p3@Bcl11b!0.23!1.42!Bcl11b;;chr11:98605517..98605539,+!p5@Thra!0.23!1.42!Thra;;chr7:4947786..4947797,-!p9@Zfp579!0.23!0.91!Zfp579;;chr2:181406327..181406350,-!p1@Sox18!0.22!46.70!Sox18;;chr9:20757246..20757278,-!p1@Dnmt1!0.22!43.46!Dnmt1;;chr15:81575487..81575561,+!p1@Zc3h7b!0.22!31.69!Zc3h7b;;chr3:96001503..96001557,-!p1@Bola1!0.22!31.30!Bola1;;chr7:13595144..13595205,-!p1@Zbtb45!0.22!28.59!Zbtb45;;chr7:13551180..13551243,+!p1@Zfp324!0.22!11.51!Zfp324;;chr5:24107779..24107825,-!p1@Smarcd3!0.22!9.31!Smarcd3;;chr8:72498266..72498306,-!p3@Gatad2a!0.22!9.31!Gatad2a;;chr14:65977498..65977528,+!p1@Zfp395!0.22!9.31!Zfp395;;chr18:83084030..83084056,+!p1@Zfp516!0.22!6.99!Zfp516;;chr7:148513409..148513455,-!p2@Deaf1!0.22!6.34!Deaf1;;chr4:135842030..135842065,+!p3@Zfp46!0.22!3.23!Zfp46;;chr10:30562571..30562597,-!p1@Hey2!0.22!2.72!Hey2;;chr15:98126545..98126588,-!p1@Zfp641!0.22!2.46!Zfp641;;chr11:101645830..101645881,-!p2@Etv4!0.22!1.94!Etv4;;chr11:70043257..70043263,-!p1@Bcl6b!0.22!1.81!Bcl6b;;chr18:76219118..76219155,+!p1@Zbtb7c!0.22!1.81!Zbtb7c;;chr2:127347067..127347093,-!p1@Kcnip3!0.22!1.68!Kcnip3;;chr18:76219161..76219176,+!p4@Zbtb7c!0.22!1.16!Zbtb7c;;chr18:14131020..14131033,-!p4@Zfp521!0.22!1.16!Zfp521;;chr10:127095407..127095440,+!p3@Stat6!0.22!1.03!Stat6;;chr7:25292246..25292259,+!p6@Zfp428!0.22!1.03!Zfp428;;chr4:133309775..133309784,-!p15@Arid1a!0.22!1.03!Arid1a;;chr13:78339134..78339185,-!p5@Nr2f1!0.22!1.03!Nr2f1;;chr12:12947199..12947213,-!p2@Mycn!0.22!0.65!Mycn;;chr15:76353005..76353021,-!p2@Scrt1!0.22!0.65!Scrt1;;chr15:76352740..76352781,-!p5@Scrt1!0.22!0.65!Scrt1;;chr12:39510042..39510069,+!p8@Etv1!0.22!0.65!Etv1;;chr12:57637700..57637717,-!p9@Nkx2-1!0.22!0.65!Nkx2-1;;chr12:56700411..56700416,+!p@chr12:56700411..56700416,+!0.22!0.65!Insm2;;chr12:57637649..57637665,-!p8@Nkx2-1!0.22!0.65!Nkx2-1;;chr14:122864676..122864708,-!p1@Zic5!0.22!0.65!Zic5;;chr9:74709695..74709722,+!p1@Onecut1!0.22!0.65!Onecut1;;chr9:63869510..63869530,-!p10@Smad6!0.22!0.65!Smad6;;chr9:62996985..62996990,-!p1@Skor1!0.22!0.65!Skor1;;chr8:12395287..12395295,+!p9@Sox1!0.22!0.65!Sox1;;chr9:118387969..118387984,+!p2@Eomes!0.22!0.65!Eomes;;chr7:30089006..30089022,+!p3@Dpf1!0.22!0.65!Dpf1;;chr9:87626109..87626120,-!p3@Tbx18!0.22!0.65!Tbx18;;chr16:65521021..65521032,+!p@chr16:65521021..65521032,+!0.22!0.65!Pou1f1;;chr1:167090920..167090924,-!p3@Tbx19!0.22!0.65!Tbx19;;chr2:105515826..105515837,+!p7@Pax6!0.22!0.65!Pax6;;chr1:169528720..169528749,+!p6@Rxrg!0.22!0.65!Rxrg;;chr1:169528457..169528482,+!p3@Rxrg!0.22!0.65!Rxrg;;chr19:59533429..59533470,+!p4@Emx2!0.22!0.65!Emx2;;chr11:59319796..59319801,-!p6@Zkscan17!0.22!0.65!Zkscan17;;chr10:42303385..42303401,-!p1@Nr2e1!0.22!0.65!Nr2e1;;chr11:23978291..23978323,+!p7@Bcl11a!0.22!0.65!Bcl11a;;chr11:98190918..98190951,-!p1@Neurod2!0.22!0.65!Neurod2;;chr10:62562530..62562540,+!p1@Atoh7!0.22!0.65!Atoh7;;chr4:21612929..21612952,-!p1@Prdm13!0.22!0.65!Prdm13;;chr2:71367979..71367993,+!p7@Dlx1!0.22!0.65!Dlx1;;chr4:97248607..97248649,+!p15@Nfia!0.22!0.65!Nfia;;chr3:130813756..130813767,+!p8@Lef1!0.22!0.65!Lef1;;chr4:22415443..22415506,-!p1@Pou3f2!0.22!0.65!Pou3f2;;chr7:147234982..147234988,-!p1@Msx3!0.22!0.65!Msx3;;chr6:15135215..15135244,+!p11@Foxp2!0.22!0.65!Foxp2;;chr7:135019127..135019137,-!p6@Zfp668!0.22!0.65!Zfp668;;chr5:98609885..98609900,+!p1@Prdm8!0.22!0.65!Prdm8;;chr10:116661536..116661555,-!p1@Yeats4!0.21!83.57!Yeats4;;chr5:147760216..147760292,+!p1@Gtf3a!0.21!65.33!Gtf3a;;chr18:14131126..14131211,-!p1@Zfp521!0.21!30.79!Zfp521;;chr7:4966247..4966286,-!p1@Fiz1!0.21!27.81!Fiz1;;chr6:117791192..117791269,+!p1@Zfp637!0.21!23.16!Zfp637;;chr10:22451142..22451191,-!p2@Tbpl1!0.21!13.97!Tbpl1;;chr7:13483149..13483234,+!p1@Zscan22!0.21!13.58!Zscan22;;chr5:134790355..134790369,-!p4@Gtf2i!0.21!6.34!Gtf2i;;chr10:92773818..92773906,-!p2@Elk3!0.21!6.21!Elk3;;chr7:134170038..134170055,-!p8@Maz!0.21!5.56!Maz;;chr7:134592623..134592680,-!p1@Zfp689!0.21!5.04!Zfp689;;chr7:4947697..4947718,-!p2@Zfp579!0.21!3.62!Zfp579;;chr1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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011325
 |is_obsolete=
+|library_id=CNhs11009
+|library_id_phase_based=2:CNhs11009
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;370
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;370
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E13.CNhs11009.370-44C7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E13.CNhs11009.370-44C7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E13.CNhs11009.370-44C7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E13.CNhs11009.370-44C7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E13.CNhs11009.370-44C7.mm9.nobarcode.rdna.fa.gz
 |name=pituitary gland, embryo E13
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11009,LSID730,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0964064946357865,0,0,0,0,0,-0.220717052035795,0,0,0,0,-0.0315073448417742,0,0,0,0,0,0,0.215039085173593,0,0,0,0,0,0,0,0,0,0,0,0,0.0093296895145921,-0.308942638013624,0,0,0,0,0,-0.0346185360612493,0.0838510141337896,-0.0503622102276218,0.69781235139661,0.252374222427063,0,0,0,0,0,0,0,0,0,0,0.0528318955547673,0,0.033922676995306,0,0,0,0,0.0570812694758716,0,0,0,0,0,-0.102514196138434,0.138213521238851,-0.158091042771083,-0.00595217411171993,0,0,0,0.0654812342161275,0.0528318955547673,0,0.0170584691429434,-0.0266216789805231,0.166483911743562,-0.0788315948399074,0,0,0,0,0,0,0.0999282245587464,0.519362697212777,0.124656682577935,0,0,0,0,0
 |rna_box=44
 |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=table111:370-44C7;search_select_hide=table117:370-44C7
 }}

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FF:370-44C7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:13, 4 June 2020

CNhs11009

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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