FF:427-16B9: Difference between revisions

Latest revision as of 19:16, 4 June 2020

Name:	pituitary gland, embryo E15
Species:	Mouse (Mus musculus)
Library ID:	CNhs10592
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	pituitary gland
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		SAMD00005651

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10592		CAGE		DRX009070		DRR009944

Accession ID Mm9

Library id		BAM		CTSS
CNhs10592		DRZ001369		DRZ002752

Accession ID Mm10

Library id		BAM		CTSS
CNhs10592		DRZ012719		DRZ014102

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

CNhs10592

0	0
1	0.105
10	0
100	0.0359
1000	0
1001	0.176
1002	0.0541
1003	-0.0308
1004	0.308
1005	0
1006	0.0674
1007	0.0911
1008	0
1009	-0.0709
101	-0.00159
1010	0
1011	0.0709
1012	0
1013	-0.013
1014	0.258
1015	0.177
1016	0.192
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.00785
1023	0
1024	0.0954
1025	0
1026	0
1027	0.0709
1028	0
1029	-0.0158
103	0.117
1030	0
1031	0.41
1032	-0.0935
1033	0.0516
1034	0
1035	0
1036	-0.028
1037	0
1038	0.0257
1039	-0.0457
104	0
1040	0.173
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: CNhs10592

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	3.00584e-5
MA0003.1	MA0003.1	0.234
MA0004.1	MA0004.1	0.65
MA0006.1	MA0006.1	0.477
MA0007.1	MA0007.1	0.66
MA0009.1	MA0009.1	0.761
MA0014.1	MA0014.1	0.432
MA0017.1	MA0017.1	3.1722e-7
MA0018.2	MA0018.2	0.0168
MA0019.1	MA0019.1	0.605
MA0024.1	MA0024.1	0.132
MA0025.1	MA0025.1	0.903
MA0027.1	MA0027.1	0.758
MA0028.1	MA0028.1	0.269
MA0029.1	MA0029.1	0.385
MA0030.1	MA0030.1	0.554
MA0031.1	MA0031.1	0.843
MA0035.2	MA0035.2	0.0205
MA0038.1	MA0038.1	0.032
MA0039.2	MA0039.2	0.526
MA0040.1	MA0040.1	0.815
MA0041.1	MA0041.1	0.139
MA0042.1	MA0042.1	0.734
MA0043.1	MA0043.1	0.00202
MA0046.1	MA0046.1	8.99287e-20
MA0047.2	MA0047.2	0.0316
MA0048.1	MA0048.1	0.255
MA0050.1	MA0050.1	0.0184
MA0051.1	MA0051.1	0.28
MA0052.1	MA0052.1	1.01935e-4
MA0055.1	MA0055.1	0.721
MA0057.1	MA0057.1	0.124
MA0058.1	MA0058.1	0.599
MA0059.1	MA0059.1	0.115
MA0060.1	MA0060.1	1.41195e-9
MA0061.1	MA0061.1	0.0408
MA0062.2	MA0062.2	0.358
MA0065.2	MA0065.2	5.73721e-5
MA0066.1	MA0066.1	0.00489
MA0067.1	MA0067.1	0.709
MA0068.1	MA0068.1	0.412
MA0069.1	MA0069.1	0.257
MA0070.1	MA0070.1	0.394
MA0071.1	MA0071.1	0.0796
MA0072.1	MA0072.1	0.141
MA0073.1	MA0073.1	0.769
MA0074.1	MA0074.1	0.293
MA0076.1	MA0076.1	0.0636
MA0077.1	MA0077.1	0.195
MA0078.1	MA0078.1	0.571
MA0079.2	MA0079.2	0.158
MA0080.2	MA0080.2	4.05386e-7
MA0081.1	MA0081.1	0.571
MA0083.1	MA0083.1	0.106
MA0084.1	MA0084.1	0.0698
MA0087.1	MA0087.1	0.128
MA0088.1	MA0088.1	0.665
MA0090.1	MA0090.1	0.341
MA0091.1	MA0091.1	0.716
MA0092.1	MA0092.1	0.415
MA0093.1	MA0093.1	0.722
MA0099.2	MA0099.2	6.95472e-4
MA0100.1	MA0100.1	0.989
MA0101.1	MA0101.1	0.233
MA0102.2	MA0102.2	0.98
MA0103.1	MA0103.1	0.507
MA0104.2	MA0104.2	0.676
MA0105.1	MA0105.1	1.80099e-4
MA0106.1	MA0106.1	0.0694
MA0107.1	MA0107.1	0.119
MA0108.2	MA0108.2	0.426
MA0111.1	MA0111.1	0.736
MA0112.2	MA0112.2	5.30851e-8
MA0113.1	MA0113.1	0.726
MA0114.1	MA0114.1	1.41116e-5
MA0115.1	MA0115.1	5.88474e-6
MA0116.1	MA0116.1	0.00324
MA0117.1	MA0117.1	0.659
MA0119.1	MA0119.1	0.0527
MA0122.1	MA0122.1	0.724
MA0124.1	MA0124.1	0.724
MA0125.1	MA0125.1	0.0123
MA0131.1	MA0131.1	0.438
MA0135.1	MA0135.1	0.0426
MA0136.1	MA0136.1	0.00455
MA0137.2	MA0137.2	0.579
MA0138.2	MA0138.2	0.244
MA0139.1	MA0139.1	0.192
MA0140.1	MA0140.1	0.013
MA0141.1	MA0141.1	0.00119
MA0142.1	MA0142.1	0.757
MA0143.1	MA0143.1	0.333
MA0144.1	MA0144.1	0.252
MA0145.1	MA0145.1	0.181
MA0146.1	MA0146.1	0.226
MA0147.1	MA0147.1	0.502
MA0148.1	MA0148.1	0.00532
MA0149.1	MA0149.1	0.00476
MA0150.1	MA0150.1	0.00263
MA0152.1	MA0152.1	0.503
MA0153.1	MA0153.1	1.2216e-14
MA0154.1	MA0154.1	0.00308
MA0155.1	MA0155.1	0.56
MA0156.1	MA0156.1	0.537
MA0157.1	MA0157.1	0.939
MA0159.1	MA0159.1	0.0064
MA0160.1	MA0160.1	0.0129
MA0162.1	MA0162.1	0.259
MA0163.1	MA0163.1	2.51373e-4
MA0164.1	MA0164.1	0.59
MA0258.1	MA0258.1	2.00199e-5
MA0259.1	MA0259.1	0.842

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: CNhs10592

Novel motif	Logo	P-value
1	1	0.0528
10	10	0.0665
100	100	0.99
101	101	0.606
102	102	0.853
103	103	0.0924
104	104	0.801
105	105	0.54
106	106	0.0066
107	107	0.0137
108	108	0.599
109	109	0.163
11	11	0.103
110	110	0.0941
111	111	0.00772
112	112	0.0387
113	113	0.839
114	114	0.0165
115	115	0.183
116	116	0.364
117	117	0.0629
118	118	0.653
119	119	0.0576
12	12	0.921
120	120	0.972
121	121	0.993
122	122	0.536
123	123	0.51
124	124	0.924
125	125	0.144
126	126	0.389
127	127	0.0508
128	128	0.0184
129	129	0.182
13	13	0.0437
130	130	0.543
131	131	0.385
132	132	0.563
133	133	0.431
134	134	0.826
135	135	0.28
136	136	0.639
137	137	0.964
138	138	0.499
139	139	0.0434
14	14	0.539
140	140	0.0192
141	141	0.591
142	142	0.0666
143	143	0.29
144	144	0.976
145	145	0.0892
146	146	0.664
147	147	0.781
148	148	0.179
149	149	0.312
15	15	0.0926
150	150	0.198
151	151	0.271
152	152	0.267
153	153	0.904
154	154	0.41
155	155	0.335
156	156	4.9211e-4
157	157	0.607
158	158	0.266
159	159	0.859
160	160	0.208
161	161	0.591
162	162	0.727
163	163	0.322
164	164	0.0736
165	165	0.143
166	166	0.676
167	167	0.154
168	168	0.786
169	169	1.56263e-4
17	17	0.0972
18	18	0.268
19	19	0.11
2	2	0.848
20	20	0.869
21	21	0.726
22	22	0.228
23	23	0.147
24	24	0.677
25	25	0.395
26	26	0.0325
27	27	0.733
28	28	0.562
29	29	0.152
3	3	0.116
30	30	0.959
31	31	0.542
32	32	0.0893
33	33	0.286
34	34	0.703
35	35	0.377
36	36	0.134
37	37	0.0681
38	38	0.349
39	39	0.597
4	4	0.402
40	40	0.319
41	41	0.347
42	42	0.428
43	43	0.0927
44	44	0.0854
45	45	0.679
46	46	0.0939
47	47	0.205
48	48	0.135
49	49	0.0957
5	5	0.0427
50	50	0.714
51	51	0.476
52	52	0.21
53	53	0.772
54	54	0.411
55	55	0.224
56	56	0.526
57	57	0.227
58	58	0.346
59	59	0.0682
6	6	0.684
60	60	0.0403
61	61	0.25
62	62	0.0865
63	63	0.103
64	64	0.451
65	65	0.165
66	66	0.455
67	67	0.69
68	68	0.0158
69	69	0.502
7	7	0.109
70	70	0.00364
71	71	0.0383
72	72	0.595
73	73	0.136
74	74	0.267
75	75	0.0925
76	76	0.977
77	77	0.186
78	78	0.0231
79	79	0.645
8	8	0.0516
80	80	0.445
81	81	0.346
82	82	0.125
83	83	0.139
84	84	0.82
85	85	0.0105
86	86	0.473
87	87	0.92
88	88	0.496
89	89	0.231
9	9	0.462
90	90	0.0931
91	91	0.131
92	92	0.143
93	93	0.117
94	94	0.302
95	95	0.156
96	96	0.102
97	97	0.776
98	98	0.289
99	99	0.626

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: CNhs10592

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011345 mouse pituitary gland- 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)
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)
0000298 (mouse embryonic day 15 sample)
0011345 (mouse pituitary gland- 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:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005651
+|accession_numbers=CAGE;DRX009070;DRR009944;DRZ001369;DRZ002752;DRZ012719;DRZ014102
 |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=chr16:65520838..65520853,+!p1@ENSMUST00000004964!2.69!485.91!Pou1f1;;chr12:74040861..74040875,+!p1@Six6!2.04!109.42!Six6;;chr2:26062055..26062100,-!p1@Lhx3!2.01!101.62!Lhx3;;chr12:74147689..74147711,-!p1@Six1!1.98!201.46!Six1;;chr13:55932591..55932622,-!p1@Pitx1!1.95!104.99!Pitx1;;chr12:74040895..74040916,+!p2@Six6!1.92!81.40!Six6;;chr13:99124189..99124205,+!p1@Foxd1!1.86!105.52!Foxd1;;chr16:65521021..65521032,+!p@chr16:65521021..65521032,+!1.82!65.62!Pou1f1;;chr2:79296783..79296801,-!p1@Neurod1!1.61!39.90!Neurod1;;chr3:128916868..128916890,+!p1@Pitx2!1.60!52.49!Pitx2;;chr10:86956396..86956411,-!p1@Ascl1!1.59!57.99!Ascl1;;chr2:146047829..146047847,+!p1@Insm1!1.58!65.79!Insm1;;chr17:86087592..86087615,-!p1@Six2!1.56!35.11!Six2;;chr11:50767247..50767270,-!p1@Prop1!1.55!34.58!Prop1;;chr10:129717274..129717298,-!p1@Neurod4!1.47!28.73!Neurod4;;chr17:86020510..86020589,+!p3@Six3!1.43!26.07!Six3;;chr5:38215819..38215823,-!p1@Msx1!1.40!62.42!Msx1;;chr8:24780125..24780143,+!p1@Zmat4!1.40!34.40!Zmat4;;chr12:34642510..34642530,+!p1@Twist1!1.38!71.65!Twist1;;chr3:128917187..128917223,+!p2@Pitx2!1.38!26.78!Pitx2;;chr12:3891810..3891829,+!p2@Dnmt3a!1.37!34.58!Dnmt3a;;chr4:109650609..109650653,+!p1@Dmrta2!1.37!22.52!Dmrta2;;chr17:86020156..86020183,+!p1@Six3!1.35!21.64!Six3;;chr7:6649134..6649167,-!p1@Zim1!1.32!105.52!Zim1;;chr14:122874619..122874634,+!p1@Zic2!1.32!20.04!Zic2;;chr18:66098702..66098742,-!p1@Rax!1.32!19.86!Rax;;chr13:55932624..55932641,-!p2@Pitx1!1.31!19.33!Pitx1;;chr17:86020115..86020128,+!p2@Six3!1.30!18.80!Six3;;chr13:31898767..31898785,+!p4@Foxc1!1.28!21.99!Foxc1;;chr2:26063801..26063813,-!p2@Lhx3!1.28!18.27!Lhx3;;chr1:167090803..167090816,-!p1@Tbx19!1.28!18.09!Tbx19;;chr1:169528581..169528607,+!p7@Rxrg!1.26!17.02!Rxrg;;chr19:19185671..19185693,-!p1@Rorb!1.25!39.55!Rorb;;chr3:34548909..34548927,+!p1@Sox2!1.23!26.78!Sox2;;chrX:108009761..108009788,+!p1@Pou3f4!1.21!15.25!Pou3f4;;chr1:169528520..169528542,+!p2@Rxrg!1.21!15.07!Rxrg;;chr13:55937467..55937516,-!p3@Pitx1!1.17!13.66!Pitx1;;chr10:84218800..84218829,+!p2@Rfx4!1.16!13.30!Rfx4;;chr1:169528457..169528482,+!p3@Rxrg!1.15!13.12!Rxrg;;chr8:123640063..123640077,+!p1@Foxc2!1.13!22.88!Foxc2;;chr13:31717548..31717596,+!p1@Foxf2!1.12!24.12!Foxf2;;chr12:74147860..74147888,-!p2@Six1!1.12!12.06!Six1;;chr1:169528491..169528505,+!p4@Rxrg!1.10!11.70!Rxrg;;chr12:74040716..74040745,+!p3@Six6!1.10!11.53!Six6;;chr3:99057269..99057306,+!p1@Tbx15!1.09!13.66!Tbx15;;chr9:91260616..91260653,-!p2@Zic1!1.09!11.17!Zic1;;chr1:6720216..6720232,+!p1@St18!1.09!11.17!St18;;chr18:52775562..52775650,+!p1@Zfp474!1.09!11.17!Zfp474;;chr10:22539932..22539956,-!p1@Tcf21!1.07!28.91!Tcf21;;chr17:86012772..86012825,+!p4@Six3!1.03!9.75!Six3;;chr3:128916838..128916856,+!p4@Pitx2!1.03!9.75!Pitx2;;chr10:129717308..129717319,-!p2@Neurod4!1.02!9.40!Neurod4;;chr9:91260594..91260612,-!p1@Zic1!1.02!9.40!Zic1;;chr12:28027561..28027591,-!p1@Sox11!1.01!62.25!Sox11;;chr7:17647736..17647772,-!p1@Hif3a!1.01!32.99!Hif3a;;chrX:58146612..58146615,-!p1@Sox3!0.99!8.87!Sox3;;chr17:86020468..86020504,+!p6@Six3!0.99!8.87!Six3;;chr1:169528720..169528749,+!p6@Rxrg!0.99!8.69!Rxrg;;chr11:90252223..90252240,-!p1@Hlf!0.98!73.24!Hlf;;chr14:17407970..17408015,-!p2@Rarb!0.98!23.23!Rarb;;chr14:17407549..17407575,-!p3@Rarb!0.95!12.24!Rarb;;chr3:34548946..34548972,+!p2@Sox2!0.95!8.87!Sox2;;chr10:119913310..119913366,-!p1@Hmga2!0.94!62.07!Hmga2;;chr12:30213247..30213333,+!p1@Myt1l!0.94!7.80!Myt1l;;chr1:173987720..173987729,-!p1@Nhlh1!0.94!7.80!Nhlh1;;chr2:147190749..147190769,+!p1@Pax1!0.94!7.63!Pax1;;chr10:12810631..12810649,+!p1@Plagl1!0.93!202.88!Plagl1;;chr7:52963269..52963305,+!p4@Dbp!0.93!10.64!Dbp;;chr14:18814381..18814390,+!p7@Thrb!0.93!7.45!Thrb;;chr3:107398056..107398082,+!p1@Alx3!0.92!7.27!Alx3;;chr11:121380594..121380609,-!p2@Zfp750!0.91!12.59!Zfp750;;chr13:55937432..55937460,-!p4@Pitx1!0.91!7.09!Pitx1;;chr13:117099847..117099907,-!p1@Isl1!0.90!13.12!Isl1;;chr6:88148650..88148669,+!p1@Gata2!0.89!58.70!Gata2;;chr12:57796615..57796687,+!p1@Pax9!0.89!6.74!Pax9;;chr1:169528433..169528456,+!p10@Rxrg!0.89!6.74!Rxrg;;chr10:119914001..119914078,-!p4@Hmga2!0.88!9.22!Hmga2;;chr3:128902837..128902861,+!p3@Pitx2!0.88!6.56!Pitx2;;chr4:150503457..150503498,-!p3@Camta1!0.86!7.09!Camta1;;chr1:169528551..169528569,+!p8@Rxrg!0.86!6.21!Rxrg;;chr14:98568971..98569025,-!p1@Dach1!0.85!49.66!Dach1;;chr19:59245978..59245982,-!p1@Vax1!0.85!6.03!Vax1;;chr19:26822880..26822964,+!p2@Smarca2!0.84!54.09!Smarca2;;chr10:119913278..119913298,-!p2@Hmga2!0.84!14.01!Hmga2;;chr10:126778916..126778974,-!p1@Gli1!0.84!13.83!Gli1;;chrX:48559194..48559210,-!p4@Mbnl3!0.83!7.45!Mbnl3;;chrX:110411840..110411860,+!p1@Dach2!0.83!7.27!Dach2;;chr9:31720843..31720888,-!p1@Barx2!0.83!6.38!Barx2;;chr13:31898729..31898761,+!p1@Foxc1!0.82!14.54!Foxc1;;chr1:170361991..170362015,-!p6@Pbx1!0.82!13.12!Pbx1;;chrX:95345005..95345053,+!p1@Ar!0.82!5.67!Ar;;chr11:90250944..90250982,-!p2@Hlf!0.81!9.58!Hlf;;chr15:103164702..103164778,-!p3@Zfp385a!0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3.90!Bcl11a;;chr19:5912834..5912852,-!p2@Dpf2!0.23!3.19!Dpf2;;chr3:152058408..152058453,+!p5@Gm8261,p5@Zzz3!0.23!2.66!Zzz3;;chr11:53583960..53584007,+!p2@Irf1!0.23!2.48!Irf1;;chr18:3281750..3281776,-!p2@Crem!0.23!2.31!Crem;;chr4:135840552..135840567,+!p4@Zfp46!0.23!1.60!Zfp46;;chr3:94668075..94668087,+!p6@Pogz!0.23!1.42!Pogz;;chr8:118231350..118231385,-!p7@Maf!0.23!1.42!Maf;;chr16:11176344..11176353,-!p2@Zc3h7a!0.23!1.24!Zc3h7a;;chr6:99471147..99471161,-!p9@Foxp1!0.23!1.24!Foxp1;;chr11:98636508..98636524,-!p3@Nr1d1!0.23!1.06!Nr1d1;;chr11:101646155..101646170,-!p3@Etv4!0.23!1.06!Etv4;;chrX:45245582..45245591,-!p4@Smarca1!0.23!1.06!Smarca1;;chr9:71743910..71743915,-!p7@Tcf12!0.23!0.89!Tcf12;;chr17:44951553..44951586,-!p2@Runx2!0.23!0.89!Runx2;;chr17:86020357..86020366,+!p11@Six3!0.23!0.71!Six3;;chr18:69681413..69681424,+!p24@Tcf4!0.23!0.71!Tcf4;;chr7:135019127..135019137,-!p6@Zfp668!0.23!0.71!Zfp668;;chr6:144157991..144158007,-!p9@Sox5!0.23!0.71!Sox5;;chr5:120120834..120120845,+!p8@Tbx3!0.23!0.71!Tbx3;;chr3:29911926..29911942,-!p13@Mecom!0.23!0.71!Mecom;;chr4:82351527..82351541,-!p16@Nfib!0.23!0.71!Nfib;;chr3:8667049..8667056,-!p5@Hey1!0.23!0.71!Hey1;;chr4:119487109..119487131,+!p4@Hivep3!0.23!0.71!Hivep3;;chr3:34548845..34548856,+!p4@Sox2!0.23!0.71!Sox2;;chr4:108132386..108132400,+!p14@Zcchc11!0.23!0.71!Zcchc11;;chr4:84321317..84321332,-!p4@Bnc2!0.23!0.71!Bnc2;;chr4:13678684..13678704,+!p17@Runx1t1!0.23!0.71!Runx1t1;;chr2:181498020..181498040,+!p5@Myt1!0.23!0.71!Myt1;;chr2:126501799..126501832,-!p4@Gabpb1!0.23!0.71!Gabpb1;;chr1:57028556..57028583,-!p5@Satb2!0.23!0.71!Satb2;;chr1:57028538..57028553,-!p6@Satb2!0.23!0.71!Satb2;;chr1:19199193..19199207,+!p11@Tfap2b!0.23!0.71!Tfap2b;;chr1:135557400..135557421,-!p4@Zbed6!0.23!0.71!Zbed6;;chrX:108009798..108009815,+!p3@Pou3f4!0.23!0.71!Pou3f4;;chr7:52960663..52960677,+!p6@Dbp!0.23!0.71!Dbp;;chr8:12395500..12395511,+!p5@Sox1!0.23!0.71!Sox1;;chr8:87238155..87238187,-!p13@Nfix!0.23!0.71!Nfix;;chr7:77511928..77511937,-!p12@Nr2f2!0.23!0.71!Nr2f2;;chr12:28027256..28027282,-!p2@Sox11!0.23!0.71!Sox11;;chr14:18493470..18493477,+!p4@Thrb!0.23!0.71!Thrb;;chr12:57636034..57636087,-!p1@Nkx2-1!0.23!0.71!Nkx2-1;;chr12:75002389..75002406,+!p4@Hif1a!0.23!0.71!Hif1a;;chr15:102197405..102197454,-!p1@Sp7!0.23!0.71!Sp7;;chr13:78338032..78338049,-!p8@Nr2f1!0.23!0.71!Nr2f1;;chr11:90251960..90251972,-!p9@Hlf!0.23!0.71!Hlf;;chr11:116196714..116196729,-!p2@Foxj1!0.23!0.71!Foxj1;;chr11:21901608..21901634,-!p1@Otx1!0.23!0.71!Otx1;;chr11:23978270..23978290,+!p9@Bcl11a!0.23!0.71!Bcl11a;;chr11:23978291..23978323,+!p7@Bcl11a!0.23!0.71!Bcl11a;;chr10:84218931..84218942,+!p4@Rfx4!0.23!0.71!Rfx4;;chr10:119913266..119913277,-!p6@Hmga2!0.23!0.71!Hmga2;;chr5:125343044..125343141,+!p1@Zfp664!0.22!64.02!Zfp664;;chr2:181406327..181406350,-!p1@Sox18!0.22!46.64!Sox18;;chr6:64992569..64992656,+!p1@Smarcad1!0.22!43.80!Smarcad1;;chr3:30993974..30994045,+!p1@Skil!0.22!41.85!Skil;;chr13:83663902..83663927,+!p1@Mef2c!0.22!35.82!Mef2c;;chr12:32635078..32635111,-!p1@Hbp1!0.22!31.57!Hbp1;;chr12:16817746..16817784,+!p1@E2f6!0.22!25.54!E2f6;;chr8:3493135..3493212,+!p1@Zfp358!0.22!24.65!Zfp358;;chr2:181327438..181327495,-!p1@Znf512b!0.22!19.33!Znf512b;;chr4:116480137..116480178,-!p1@Toe1!0.22!15.78!Toe1;;chr10:79862089..79862129,-!p2@Mbd3!0.22!15.61!Mbd3;;chr1:64168830..64168895,-!p2@Klf7!0.22!9.04!Klf7;;chr14:76814601..76814630,+!p5@Tsc22d1!0.22!8.51!Tsc22d1;;chr13:21454695..21454752,+!p1@Zscan12!0.22!7.80!Zscan12;;chr3:95032558..95032641,-!p2@Mllt11!0.22!7.63!Mllt11;;chr12:119539843..119539899,-!p1@Sp4!0.22!7.45!Sp4;;chr2:152223469..152223512,-!p1@Sox12!0.22!7.09!Sox12;;chrX:132420442..132420482,+!p2@Bhlhb9!0.22!7.09!Bhlhb9;;chr3:94819136..94819168,-!p2@Zfp687!0.22!6.74!Zfp687;;chr7:28623579..28623631,+!p1@Zfp59!0.22!6.38!Zfp59;;chr7:26067242..26067273,+!p3@Cic!0.22!5.67!Cic;;chr7:134170541..134170569,-!p9@Maz!0.22!4.97!Maz;;chr7:4990029..4990052,-!p1@Zfp784!0.22!4.26!Zfp784;;chrX:98449898..98449913,+!p2@Foxo4!0.22!4.08!Foxo4;;chr19:53384965..53384984,+!p4@Mxi1!0.22!3.55!Mxi1;;chr13:23460838..23460880,-!p2@Zfp322a!0.22!3.55!Zfp322a;;chr13:67182439..67182491,-!p2@Zfp708!0.22!3.01!Zfp708;;chr4:87678743..87678767,-!p7@Mllt3!0.22!2.84!Mllt3;;chr17:13897299..13897342,+!p3@Mllt4!0.22!2.66!Mllt4;;chr9:68501568..68501592,+!p3@Rora!0.22!2.66!Rora;;chr1:170361730..170361769,-!p7@Pbx1!0.22!2.66!Pbx1;;chr4:87678673..87678706,-!p6@Mllt3!0.22!2.48!Mllt3;;chr13:59924173..59924194,-!p4@Zcchc6!0.22!1.77!Zcchc6;;chr15:40486615..40486628,+!p3@Zfpm2!0.22!1.60!Zfpm2;;chr7:17200403..17200416,-!p5@Grlf1!0.22!1.60!Grlf1;;chr13:53568104..53568156,-!p1@Msx2!0.22!1.42!Msx2;;chr12:3806513..3806527,+!p9@Dnmt3a!0.22!1.42!Dnmt3a;;chr2:70313168..70313184,+!p1@Sp5!0.22!1.42!Sp5;;chr18:55149778..55149798,-!p11@Zfp608!0.22!1.24!Zfp608;;chr17:37139432..37139444,+!p4@Zfp57!0.22!1.24!Zfp57;;chr6:108610474..108610491,+!p5@Bhlhe40!0.22!1.06!Bhlhe40;;chr3:30993641..30993651,+!p7@Skil!0.22!0.89!Skil;;chr13:44936126..44936164,+!p6@Jarid2!0.22!0.89!Jarid2;;chr1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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011345
 |is_obsolete=
+|library_id=CNhs10592
+|library_id_phase_based=2:CNhs10592
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;427
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;427
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E15.CNhs10592.427-16B9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E15.CNhs10592.427-16B9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E15.CNhs10592.427-16B9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E15.CNhs10592.427-16B9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E15.CNhs10592.427-16B9.mm9.nobarcode.rdna.fa.gz
 |name=pituitary gland, embryo E15
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10592,LSID654,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.085298991461567,0,0,0,0,0.23037916400061,0,0,0,0,0,0,0.0409404235650797,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.207906983054083,0,0,0,0.131836868893058,0.0211640446524715,-0.143404291049297,0.089492609238416,-0.0377861544122156,0.843966591395272,0.29362472903866,0,0,0,0,0,0,0,0,0,0,0.0709019855629759,0,0.00489643799953557,0,0,0,0,-0.00986783170215752,0,0,0,0,0,-0.0199481415491655,0.0729352740058846,-0.0262541738780246,0.0894693110210932,0,0,0.0399538792855239,0,0,0,0.0902586885605737,0.0225830120438768,-0.125983558491362,-0.00792960927693151,0,0,0,0,0,0,-0.0135747894168494,0.051828331526222,0.0895549954882156,0,0,0,0,0
@@ Line 62: / Line 76: @@
 |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=table111:427-16B9;search_select_hide=table117:427-16B9
 }}

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FF:427-16B9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:16, 4 June 2020

CNhs10592

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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