FF:398-44A5: Difference between revisions

Latest revision as of 19:15, 4 June 2020

Name:	pituitary gland, embryo E14
Species:	Mouse (Mus musculus)
Library ID:	CNhs11037
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	pituitary gland
dev stage	14 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		SAMD00005442

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11037		CAGE		DRX009069		DRR009943

Accession ID Mm9

Library id		BAM		CTSS
CNhs11037		DRZ001368		DRZ002751

Accession ID Mm10

Library id		BAM		CTSS
CNhs11037		DRZ012718		DRZ014101

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

CNhs11037

0	0
1	0.0843
10	0
100	0.0843
1000	0.0489
1001	0
1002	0.249
1003	-0.0633
1004	0.314
1005	-0.0389
1006	0.0123
1007	0.025
1008	0
1009	-0.0572
101	-0.0221
1010	0
1011	0.0381
1012	0
1013	-0.0891
1014	0.311
1015	0.211
1016	0.2
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	-0.0704
1023	0
1024	0.0416
1025	0.0232
1026	0
1027	0.155
1028	0
1029	-0.0916
103	0.176
1030	0
1031	0.337
1032	-0.0922
1033	0.052
1034	0
1035	0
1036	-0.0279
1037	0
1038	0.0519
1039	-0.104
104	0
1040	0
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: CNhs11037

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	1.50294e-4
MA0003.1	MA0003.1	0.257
MA0004.1	MA0004.1	0.779
MA0006.1	MA0006.1	0.409
MA0007.1	MA0007.1	0.666
MA0009.1	MA0009.1	0.485
MA0014.1	MA0014.1	0.541
MA0017.1	MA0017.1	4.98527e-7
MA0018.2	MA0018.2	0.121
MA0019.1	MA0019.1	0.587
MA0024.1	MA0024.1	0.0426
MA0025.1	MA0025.1	0.227
MA0027.1	MA0027.1	0.328
MA0028.1	MA0028.1	0.36
MA0029.1	MA0029.1	0.255
MA0030.1	MA0030.1	0.204
MA0031.1	MA0031.1	0.103
MA0035.2	MA0035.2	0.00277
MA0038.1	MA0038.1	0.0623
MA0039.2	MA0039.2	0.25
MA0040.1	MA0040.1	0.28
MA0041.1	MA0041.1	0.261
MA0042.1	MA0042.1	0.566
MA0043.1	MA0043.1	0.0316
MA0046.1	MA0046.1	3.02551e-24
MA0047.2	MA0047.2	9.08795e-4
MA0048.1	MA0048.1	0.72
MA0050.1	MA0050.1	0.00115
MA0051.1	MA0051.1	0.00508
MA0052.1	MA0052.1	1.95773e-6
MA0055.1	MA0055.1	0.197
MA0057.1	MA0057.1	0.0915
MA0058.1	MA0058.1	0.794
MA0059.1	MA0059.1	0.718
MA0060.1	MA0060.1	3.90768e-11
MA0061.1	MA0061.1	0.0224
MA0062.2	MA0062.2	0.741
MA0065.2	MA0065.2	6.97524e-5
MA0066.1	MA0066.1	0.0148
MA0067.1	MA0067.1	0.369
MA0068.1	MA0068.1	0.0668
MA0069.1	MA0069.1	0.282
MA0070.1	MA0070.1	0.803
MA0071.1	MA0071.1	0.113
MA0072.1	MA0072.1	0.0555
MA0073.1	MA0073.1	0.806
MA0074.1	MA0074.1	0.724
MA0076.1	MA0076.1	0.145
MA0077.1	MA0077.1	0.0324
MA0078.1	MA0078.1	0.967
MA0079.2	MA0079.2	0.303
MA0080.2	MA0080.2	8.73642e-10
MA0081.1	MA0081.1	0.286
MA0083.1	MA0083.1	0.0345
MA0084.1	MA0084.1	0.377
MA0087.1	MA0087.1	0.16
MA0088.1	MA0088.1	0.296
MA0090.1	MA0090.1	0.236
MA0091.1	MA0091.1	0.472
MA0092.1	MA0092.1	0.523
MA0093.1	MA0093.1	0.86
MA0099.2	MA0099.2	3.73742e-5
MA0100.1	MA0100.1	0.927
MA0101.1	MA0101.1	0.138
MA0102.2	MA0102.2	0.27
MA0103.1	MA0103.1	0.325
MA0104.2	MA0104.2	0.81
MA0105.1	MA0105.1	0.00174
MA0106.1	MA0106.1	0.0741
MA0107.1	MA0107.1	0.0508
MA0108.2	MA0108.2	0.475
MA0111.1	MA0111.1	0.834
MA0112.2	MA0112.2	4.35109e-7
MA0113.1	MA0113.1	0.58
MA0114.1	MA0114.1	5.30766e-6
MA0115.1	MA0115.1	4.79412e-5
MA0116.1	MA0116.1	0.0184
MA0117.1	MA0117.1	0.511
MA0119.1	MA0119.1	0.0239
MA0122.1	MA0122.1	0.597
MA0124.1	MA0124.1	0.532
MA0125.1	MA0125.1	0.0161
MA0131.1	MA0131.1	0.391
MA0135.1	MA0135.1	0.769
MA0136.1	MA0136.1	2.28705e-5
MA0137.2	MA0137.2	0.0589
MA0138.2	MA0138.2	0.0334
MA0139.1	MA0139.1	0.144
MA0140.1	MA0140.1	0.00695
MA0141.1	MA0141.1	0.00184
MA0142.1	MA0142.1	0.523
MA0143.1	MA0143.1	0.061
MA0144.1	MA0144.1	0.108
MA0145.1	MA0145.1	0.0552
MA0146.1	MA0146.1	0.517
MA0147.1	MA0147.1	0.908
MA0148.1	MA0148.1	1.53852e-4
MA0149.1	MA0149.1	0.0144
MA0150.1	MA0150.1	5.51819e-4
MA0152.1	MA0152.1	0.92
MA0153.1	MA0153.1	2.52776e-16
MA0154.1	MA0154.1	0.0031
MA0155.1	MA0155.1	0.904
MA0156.1	MA0156.1	0.0421
MA0157.1	MA0157.1	0.334
MA0159.1	MA0159.1	0.00275
MA0160.1	MA0160.1	0.00679
MA0162.1	MA0162.1	0.53
MA0163.1	MA0163.1	0.00784
MA0164.1	MA0164.1	0.984
MA0258.1	MA0258.1	1.4885e-4
MA0259.1	MA0259.1	0.858

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: CNhs11037

Novel motif	Logo	P-value
1	1	0.061
10	10	0.128
100	100	0.893
101	101	0.54
102	102	0.89
103	103	0.134
104	104	0.883
105	105	0.232
106	106	0.0066
107	107	0.0265
108	108	0.652
109	109	0.244
11	11	0.175
110	110	0.148
111	111	0.0277
112	112	0.0233
113	113	0.547
114	114	0.0289
115	115	0.897
116	116	0.566
117	117	0.142
118	118	0.756
119	119	0.126
12	12	0.806
120	120	0.718
121	121	0.626
122	122	0.787
123	123	0.196
124	124	0.889
125	125	0.3
126	126	0.658
127	127	0.0326
128	128	0.0448
129	129	0.205
13	13	0.114
130	130	0.266
131	131	0.335
132	132	0.477
133	133	0.575
134	134	0.445
135	135	0.0688
136	136	0.532
137	137	0.772
138	138	0.421
139	139	0.0452
14	14	0.406
140	140	0.0836
141	141	0.145
142	142	0.194
143	143	0.632
144	144	0.912
145	145	0.271
146	146	0.421
147	147	0.506
148	148	0.385
149	149	0.253
15	15	0.0551
150	150	0.383
151	151	0.112
152	152	0.164
153	153	0.737
154	154	0.571
155	155	0.466
156	156	1.52968e-6
157	157	0.41
158	158	0.145
159	159	0.0666
160	160	0.469
161	161	0.86
162	162	0.636
163	163	0.27
164	164	0.0458
165	165	0.108
166	166	0.841
167	167	0.355
168	168	0.44
169	169	0.00167
17	17	0.142
18	18	0.23
19	19	0.214
2	2	0.671
20	20	0.685
21	21	0.728
22	22	0.253
23	23	0.0968
24	24	0.684
25	25	0.241
26	26	0.152
27	27	0.565
28	28	0.388
29	29	0.217
3	3	0.22
30	30	0.747
31	31	0.553
32	32	0.178
33	33	0.425
34	34	0.818
35	35	0.309
36	36	0.287
37	37	0.0481
38	38	0.377
39	39	0.761
4	4	0.537
40	40	0.441
41	41	0.252
42	42	0.604
43	43	0.14
44	44	0.133
45	45	0.488
46	46	0.14
47	47	0.225
48	48	0.133
49	49	0.123
5	5	0.0698
50	50	0.875
51	51	0.524
52	52	0.267
53	53	0.595
54	54	0.412
55	55	0.472
56	56	0.512
57	57	0.388
58	58	0.249
59	59	0.0923
6	6	0.777
60	60	0.0503
61	61	0.591
62	62	0.0518
63	63	0.113
64	64	0.626
65	65	0.164
66	66	0.252
67	67	0.71
68	68	0.273
69	69	0.859
7	7	0.114
70	70	0.00301
71	71	0.083
72	72	0.562
73	73	0.0988
74	74	0.658
75	75	0.105
76	76	0.62
77	77	0.208
78	78	0.0715
79	79	0.369
8	8	0.164
80	80	0.183
81	81	0.318
82	82	0.0945
83	83	0.334
84	84	0.168
85	85	0.0121
86	86	0.413
87	87	0.791
88	88	0.478
89	89	0.147
9	9	0.395
90	90	0.268
91	91	0.34
92	92	0.142
93	93	0.12
94	94	0.271
95	95	0.234
96	96	0.224
97	97	0.785
98	98	0.453
99	99	0.657

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: CNhs11037

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011334 mouse pituitary gland- embryo E14 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)
0000296 (mouse embryonic day 14 sample)
0011334 (mouse pituitary gland- embryo E14 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@SAMD00005442
+|accession_numbers=CAGE;DRX009069;DRR009943;DRZ001368;DRZ002751;DRZ012718;DRZ014101
 |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!2.13!158.82!Pitx1;;chr16:65520838..65520853,+!p1@ENSMUST00000004964!2.09!123.24!Pou1f1;;chr12:74040861..74040875,+!p1@Six6!2.04!108.03!Six6;;chr12:74147689..74147711,-!p1@Six1!2.03!226.13!Six1;;chr2:26062055..26062100,-!p1@Lhx3!1.95!87.24!Lhx3;;chr13:99124189..99124205,+!p1@Foxd1!1.90!117.24!Foxd1;;chr12:74040895..74040916,+!p2@Six6!1.83!66.44!Six6;;chr17:86087592..86087615,-!p1@Six2!1.81!64.30!Six2;;chr11:50767247..50767270,-!p1@Prop1!1.80!62.37!Prop1;;chr17:86020510..86020589,+!p3@Six3!1.61!40.08!Six3;;chr3:128916868..128916890,+!p1@Pitx2!1.58!50.80!Pitx2;;chr2:79296783..79296801,-!p1@Neurod1!1.57!36.01!Neurod1;;chr18:66098702..66098742,-!p1@Rax!1.54!33.65!Rax;;chr5:38215819..38215823,-!p1@Msx1!1.49!76.73!Msx1;;chr2:146047829..146047847,+!p1@Insm1!1.49!52.73!Insm1;;chr4:109650609..109650653,+!p1@Dmrta2!1.48!29.15!Dmrta2;;chr10:86956396..86956411,-!p1@Ascl1!1.45!41.58!Ascl1;;chr13:31898767..31898785,+!p4@Foxc1!1.45!33.01!Foxc1;;chrX:58146612..58146615,-!p1@Sox3!1.45!27.22!Sox3;;chr12:3891810..3891829,+!p2@Dnmt3a!1.44!40.51!Dnmt3a;;chr16:65521021..65521032,+!p@chr16:65521021..65521032,+!1.42!25.29!Pou1f1;;chr3:34548909..34548927,+!p1@Sox2!1.41!41.15!Sox2;;chr12:34642510..34642530,+!p1@Twist1!1.37!69.87!Twist1;;chrX:108009761..108009788,+!p1@Pou3f4!1.36!21.86!Pou3f4;;chr8:24780125..24780143,+!p1@Zmat4!1.35!30.44!Zmat4;;chr3:128917187..128917223,+!p2@Pitx2!1.32!23.36!Pitx2;;chr14:122874619..122874634,+!p1@Zic2!1.31!19.50!Zic2;;chr17:86020156..86020183,+!p1@Six3!1.30!18.86!Six3;;chr13:55932624..55932641,-!p2@Pitx1!1.29!18.65!Pitx1;;chr19:19185671..19185693,-!p1@Rorb!1.25!40.08!Rorb;;chr2:26063801..26063813,-!p2@Lhx3!1.24!16.50!Lhx3;;chr8:123640063..123640077,+!p1@Foxc2!1.23!28.51!Foxc2;;chr10:119913310..119913366,-!p1@Hmga2!1.18!108.24!Hmga2;;chr9:91260594..91260612,-!p1@Zic1!1.18!14.15!Zic1;;chr12:74147860..74147888,-!p2@Six1!1.17!13.93!Six1;;chr9:91260616..91260653,-!p2@Zic1!1.17!13.72!Zic1;;chr13:55937467..55937516,-!p3@Pitx1!1.16!13.50!Pitx1;;chr17:86020115..86020128,+!p2@Six3!1.15!13.29!Six3;;chr13:31898729..31898761,+!p1@Foxc1!1.13!30.44!Foxc1;;chr7:6649134..6649167,-!p1@Zim1!1.11!64.94!Zim1;;chr14:49287186..49287225,-!p1@Otx2!1.11!11.79!Otx2;;chr17:86020468..86020504,+!p6@Six3!1.08!10.93!Six3;;chr13:55937432..55937460,-!p4@Pitx1!1.07!10.72!Pitx1;;chr12:28027561..28027591,-!p1@Sox11!1.06!69.66!Sox11;;chr2:38206580..38206600,+!p2@Lhx2!1.06!12.86!Lhx2;;chr14:17407970..17408015,-!p2@Rarb!1.04!27.01!Rarb;;chr7:108966820..108966835,+!p1@Phox2a!1.04!9.86!Phox2a;;chr1:173987720..173987729,-!p1@Nhlh1!1.04!9.86!Nhlh1;;chr3:128902837..128902861,+!p3@Pitx2!1.04!9.86!Pitx2;;chr10:119913278..119913298,-!p2@Hmga2!1.03!22.29!Hmga2;;chr12:3891753..3891801,+!p4@Dnmt3a!1.03!15.86!Dnmt3a;;chr2:38206744..38206766,+!p1@Lhx2!1.03!11.79!Lhx2;;chr13:31717548..31717596,+!p1@Foxf2!1.02!18.86!Foxf2;;chr10:119914001..119914078,-!p4@Hmga2!1.00!12.43!Hmga2;;chr2:146911200..146911219,-!p1@Nkx2-4!1.00!9.00!Nkx2-4;;chr2:147190749..147190769,+!p1@Pax1!0.99!8.79!Pax1;;chr13:117099847..117099907,-!p1@Isl1!0.98!16.08!Isl1;;chr3:34548946..34548972,+!p2@Sox2!0.97!9.22!Sox2;;chr17:86012772..86012825,+!p4@Six3!0.97!8.36!Six3;;chr12:74147842..74147856,-!p3@Six1!0.97!8.36!Six1;;chr8:12395603..12395621,+!p1@Sox1!0.96!8.14!Sox1;;chr19:19185697..19185711,-!p2@Rorb!0.94!10.07!Rorb;;chr3:99057269..99057306,+!p1@Tbx15!0.94!9.43!Tbx15;;chrX:48559194..48559210,-!p4@Mbnl3!0.93!9.65!Mbnl3;;chr1:167090803..167090816,-!p1@Tbx19!0.92!7.29!Tbx19;;chr3:107398056..107398082,+!p1@Alx3!0.91!7.07!Alx3;;chr14:52948124..52948148,-!p7@Sall2!0.91!7.07!Sall2;;chr7:17647736..17647772,-!p1@Hif3a!0.90!25.93!Hif3a;;chr14:17407878..17407926,-!p1@Rarb!0.89!15.65!Rarb;;chr9:87626083..87626108,-!p1@Tbx18!0.89!15.22!Tbx18;;chr3:8666963..8666978,-!p1@Hey1!0.88!45.01!Hey1;;chr12:57796615..57796687,+!p1@Pax9!0.88!6.64!Pax9;;chr7:52472041..52472065,+!p2@Tead2!0.87!7.50!Tead2;;chr3:128916838..128916856,+!p4@Pitx2!0.87!6.43!Pitx2;;chr12:74040716..74040745,+!p3@Six6!0.86!6.22!Six6;;chr7:52471143..52471186,+!p1@Tead2!0.85!68.16!Tead2;;chr13:99124236..99124243,+!p2@Foxd1!0.85!6.00!Foxd1;;chr15:103164702..103164778,-!p3@Zfp385a!0.84!7.07!Zfp385a;;chr2:150514750..150514756,-!p1@Vsx1!0.83!5.79!Vsx1;;chr10:84218800..84218829,+!p2@Rfx4!0.83!5.79!Rfx4;;chr10:22539932..22539956,-!p1@Tcf21!0.82!15.65!Tcf21;;chr12:74147444..74147463,-!p4@Six1!0.82!5.57!Six1;;chr7:6683123..6683142,-!p1@Peg3!0.81!305.00!Peg3;;chr6:88148650..88148669,+!p1@Gata2!0.81!48.65!Gata2;;chr4:150503457..150503498,-!p3@Camta1!0.81!6.22!Camta1;;chr10:119913546..119913583,-!p3@Hmga2!0.80!11.79!Hmga2;;chr17:86020293..86020318,+!p7@Six3!0.80!5.36!Six3;;chr10:129717274..129717298,-!p1@Neurod4!0.79!5.14!Neurod4;;chr12:57636220..57636236,-!p3@Nkx2-1!0.79!5.14!Nkx2-1;;chr11:90252223..90252240,-!p1@Hlf!0.78!45.87!Hlf;;chr11:3189683..3189744,+!p2@Patz1!0.77!10.50!Patz1;;chr14:17407549..17407575,-!p3@Rarb!0.77!7.72!Rarb;;chr3:101814061..101814094,+!p1@Nhlh2!0.77!4.93!Nhlh2;;chr9:99776566..99776612,-!p1@Sox14!0.77!4.93!Sox14;;chr14:52634234..52634281,-!p3@Zfp219!0.76!14.15!Zfp219;;chr3:8666997..8667012,-!p2@Hey1!0.76!11.57!Hey1;;chr1:170361991..170362015,-!p6@Pbx1!0.76!11.36!Pbx1;;chr9:55388997..55389016,+!p1@Isl2!0.76!4.72!Isl2;;chrX:55284180..55284195,+!p2@Zic3!0.76!4.72!Zic3;;chr10:12810631..12810649,+!p1@Plagl1!0.74!132.03!Plagl1;;chr10:126778916..126778974,-!p1@Gli1!0.74!10.93!Gli1;;chr13:31898496..31898519,+!p3@Foxc1!0.74!7.72!Foxc1;;chr14:122874593..122874610,+!p2@Zic2!0.74!4.50!Zic2;;chr12:57636240..57636256,-!p4@Nkx2-1!0.74!4.50!Nkx2-1;;chr17:86087581..86087588,-!p2@Six2!0.74!4.50!Six2;;chr17:35031460..35031518,+!p1@Zbtb12!0.73!24.22!Zbtb12;;chr14:67853425..67853454,+!p1@Ebf2!0.73!6.43!Ebf2;;chr2:71384802..71384815,-!p1@Dlx2!0.72!5.36!Dlx2;;chr18:52775562..52775650,+!p1@Zfp474!0.72!4.29!Zfp474;;chrX:108009798..108009815,+!p3@Pou3f4!0.72!4.29!Pou3f4;;chr2:147190725..147190747,+!p2@Pax1!0.72!4.29!Pax1;;chr14:69808725..69808748,+!p1@Nkx3-1!0.72!4.29!Nkx3-1;;chr17:86020137..86020149,+!p5@Six3!0.71!4.07!Six3;;chr4:82351639..82351658,-!p14@Nfib!0.71!4.07!Nfib;;chr15:76287876..76287894,+!p1@Scx!0.70!24.86!Scx;;chr13:31898637..31898653,+!p2@Foxc1!0.70!7.72!Foxc1;;chr11:121380594..121380609,-!p2@Zfp750!0.70!7.50!Zfp750;;chr12:105711446..105711464,-!p1@Gsc!0.69!3.86!Gsc;;chr3:5218629..5218684,+!p1@Zfhx4!0.68!13.72!Zfhx4;;chr8:90483433..90483457,-!p2@Zfp423!0.68!5.36!Zfp423;;chr5:24107676..24107722,-!p4@Smarcd3!0.68!5.36!Smarcd3;;chr7:130644017..130644092,-!p1@Zkscan2!0.67!7.72!Zkscan2;;chr8:72676653..72676668,+!p4@2310045N01Rik,p4@Mef2b!0.67!3.64!Mef2b;;chr19:59245978..59245982,-!p1@Vax1!0.67!3.64!Vax1;;chr19:26822880..26822964,+!p2@Smarca2!0.66!34.94!Smarca2;;chr6:14851440..14851497,+!p2@Foxp2!0.66!9.65!Foxp2;;chr2:130120884..130120972,+!p1@Ebf4!0.65!23.36!Ebf4;;chr18:65741358..65741415,+!p1@Zfp532!0.65!17.36!Zfp532;;chr2:152223783..152223812,-!p4@Sox12!0.65!8.79!Sox12;;chr6:23198371..23198390,-!p1@Fezf1!0.65!3.43!Fezf1;;chr9:24578720..24578735,-!p1@Tbx20!0.65!3.43!Tbx20;;chr19:7342725..7342784,+!p1@Rcor2!0.64!15.86!Rcor2;;chr16:18587076..18587106,-!p1@Tbx1!0.64!5.14!Tbx1;;chr9:36954842..36954908,-!p1@Pknox2!0.63!45.23!Pknox2;;chr12:109242266..109242295,-!p1@Bcl11b!0.62!31.29!Bcl11b;;chr11:50700965..50701027,-!p1@Zfp454!0.62!13.07!Zfp454;;chr11:90251852..90251855,-!p4@Hlf!0.62!4.07!Hlf;;chr7:56892217..56892221,-!p1@Dbx1!0.62!3.22!Dbx1;;chr16:91225808..91225824,+!p1@Olig2!0.62!3.22!Olig2;;chr4:82351566..82351607,-!p10@Nfib!0.62!3.22!Nfib;;chr3:128902878..128902893,+!p6@Pitx2!0.62!3.22!Pitx2;;chr4:114581497..114581519,-!p2@Foxd2!0.62!3.22!Foxd2;;chr5:148000254..148000260,+!p1@Gsx1!0.62!3.22!Gsx1;;chr17:48061584..48061601,-!p2@Foxp4!0.61!23.58!Foxp4;;chrX:45245679..45245702,-!p1@Smarca1!0.61!16.29!Smarca1;;chr7:77511403..77511450,-!p3@Nr2f2!0.61!7.29!Nr2f2;;chr9:106356211..106356242,+!p1@Pcbp4!0.60!70.09!Pcbp4;;chr8:123640090..123640101,+!p2@Foxc2!0.60!3.43!Foxc2;;chr13:31717597..31717613,+!p2@Foxf2!0.60!3.00!Foxf2;;chr14:27813852..27813865,+!p1@Hesx1!0.60!3.00!Hesx1;;chr13:48356475..48356492,+!p1@Id4!0.59!76.73!Id4;;chr7:91558392..91558434,-!p1@Arnt2!0.59!9.22!Arnt2;;chr11:85646303..85646329,+!p1@Tbx2!0.58!22.72!Tbx2;;chr7:77511234..77511302,-!p2@Nr2f2!0.58!22.51!Nr2f2;;chrX:45245644..45245666,-!p2@Smarca1!0.58!10.50!Smarca1;;chr4:6917921..6917970,-!p2@Tox!0.58!9.00!Tox;;chr7:135019147..135019187,-!p3@Zfp668!0.58!7.07!Zfp668;;chr11:90250944..90250982,-!p2@Hlf!0.58!5.14!Hlf;;chr11:98789140..98789168,+!p5@Rara!0.58!4.93!Rara;;chr14:67853457..67853482,+!p2@Ebf2!0.58!4.29!Ebf2;;chr14:122874718..122874729,+!p3@Zic2!0.58!2.79!Zic2;;chr2:105515793..105515808,+!p3@Pax6!0.58!2.79!Pax6;;chr1:19199236..19199258,+!p1@Tfap2b!0.58!2.79!Tfap2b;;chr1:6720216..6720232,+!p1@St18!0.58!2.79!St18;;chr14:52935876..52935928,-!p1@Sall2!0.57!27.22!Sall2;;chr4:54960870..54960926,+!p1@Zfp462!0.57!11.79!Zfp462;;chr15:102034510..102034549,+!p4@Zfp740!0.57!7.72!Zfp740;;chr10:119913792..119913820,-!p5@Hmga2!0.57!5.14!Hmga2;;chr4:129118044..129118067,-!p1@Zbtb8b!0.57!3.64!Zbtb8b;;chr12:54349410..54349461,+!p1@Npas3!0.57!3.43!Npas3;;chr11:94981424..94981439,+!p1@Dlx3!0.57!3.22!Dlx3;;chr4:84321300..84321315,-!p2@Bnc2!0.56!3.43!Bnc2;;chr8:72356532..72356611,+!p1@Pbx4!0.55!12.86!Pbx4;;chr15:102087737..102087801,-!p3@Rarg!0.55!4.72!Rarg;;chr2:151969288..151969294,+!p1@Tcf15!0.55!4.29!Tcf15;;chr7:17642018..17642045,-!p4@Hif3a!0.55!3.00!Hif3a;;chr13:56353536..56353542,-!p1@Neurog1!0.55!2.57!Neurog1;;chr11:21901608..21901634,-!p1@Otx1!0.55!2.57!Otx1;;chr7:38557752..38557793,-!p3@Zfp536!0.54!3.00!Zfp536;;chr12:39506873..39506913,+!p1@Etv1!0.53!31.29!Etv1;;chr11:99092233..99092273,-!p2@Smarce1!0.53!14.36!Smarce1;;chr9:18278055..18278126,-!p1@Zfp558!0.53!8.14!Zfp558;;chr1:170361826..170361844,-!p9@Pbx1!0.53!6.22!Pbx1;;chr14:56443806..56443848,+!p1@Nfatc4!0.53!5.57!Nfatc4;;chr2:156666727..156666753,+!p2@Tgif2!0.53!3.86!Tgif2;;chr7:91558631..91558652,-!p3@Arnt2!0.53!3.86!Arnt2;;chr7:17642053..17642066,-!p2@Hif3a!0.53!3.6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504184,+!p3@Tcf4!0.20!8.36!Tcf4;;chr7:6238191..6238224,+!p1@Zfp667!0.20!7.93!Zfp667;;chr7:119822957..119822980,+!p2@Tead1!0.20!6.22!Tead1;;chr19:55816398..55816409,+!p5@Tcf7l2!0.20!6.00!Tcf7l2;;chr11:44431687..44431706,+!p2@Ebf1!0.20!6.00!Ebf1;;chr17:23004042..23004077,-!p2@Zfp945!0.20!4.72!Zfp945;;chr2:119698528..119698571,+!p3@Mga!0.20!4.29!Mga;;chr4:149862477..149862553,+!p3@Rere!0.20!4.29!Rere;;chr19:8876976..8877011,+!p1@Zbtb3!0.20!4.07!Zbtb3;;chr7:135020324..135020368,-!p4@Zfp668!0.20!3.43!Zfp668;;chr4:154010918..154010931,-!p1@Prdm16!0.20!3.43!Prdm16;;chr19:53384910..53384937,+!p3@Mxi1!0.20!3.22!Mxi1;;chr6:115803317..115803361,-!p2@Mbd4!0.20!2.79!Mbd4;;chr5:24107993..24108036,-!p2@Smarcd3!0.20!2.57!Smarcd3;;chr6:116578939..116578952,-!p2@Zfp422!0.20!2.57!Zfp422;;chr4:97444261..97444272,+!p9@Nfia!0.20!2.57!Nfia;;chr3:152058408..152058453,+!p5@Gm8261,p5@Zzz3!0.20!2.36!Zzz3;;chr14:76903992..76904056,+!p6@Tsc22d1!0.20!2.14!Tsc22d1;;chr17:25151251..25151279,-!p4@Cramp1l!0.20!1.71!Cramp1l;;chr18:39648811..39648818,-!p4@Nr3c1!0.20!1.71!Nr3c1;;chr18:79306603..79306620,-!p4@Setbp1!0.20!1.50!Setbp1;;chr11:44431710..44431725,+!p7@Ebf1!0.20!1.50!Ebf1;;chr17:44873258..44873281,-!p5@Runx2!0.20!1.07!Runx2;;chr4:135840623..135840632,+!p5@Zfp46!0.20!1.07!Zfp46;;chr12:85534937..85534948,-!p10@C130039O16Rik!0.20!1.07!C130039O16Rik;;chr14:22808697..22808715,-!p4@Zfp503!0.20!0.86!Zfp503;;chr2:152223734..152223756,-!p6@Sox12!0.20!0.86!Sox12;;chr1:9690398..9690410,-!p2@Mybl1!0.20!0.86!Mybl1;;chr7:25292118..25292129,+!p8@Zfp428!0.20!0.86!Zfp428;;chr4:13670441..13670463,+!p8@Runx1t1!0.20!0.86!Runx1t1;;chr7:134169357..134169366,-!p18@Maz!0.20!0.86!Maz;;chr19:5912771..5912822,-!p1@Dpf2!0.19!59.37!Dpf2;;chr1:170362273..170362317,-!p1@Pbx1!0.19!39.44!Pbx1;;chr10:67741461..67741483,-!p1@Arid5b!0.19!37.72!Arid5b;;chr8:108939219..108939296,+!p1@Zfp90!0.19!14.15!Zfp90;;chr7:17200307..17200370,-!p2@Grlf1!0.19!9.65!Grlf1;;chr7:134170660..134170711,-!p6@Maz!0.19!7.29!Maz;;chr2:181194069..181194144,-!p1@Zbtb46!0.19!7.29!Zbtb46;;chr19:5610038..5610066,-!p1@Kat5!0.19!6.00!Kat5;;chr11:62545367..62545412,-!p1@Zfp287!0.19!4.93!Zfp287;;chr11:59285934..59285962,-!p1@Zfp867!0.19!4.50!Zfp867;;chr7:46773114..46773155,+!p1@Zfp619!0.19!4.50!Zfp619;;chr3:14578786..14578807,+!p2@E2f5!0.19!4.50!E2f5;;chrX:92907025..92907051,+!p1@Zc3h12b!0.19!3.22!Zc3h12b;;chr9:63605691..63605705,-!p3@Smad3!0.19!2.79!Smad3;;chr18:55149735..55149776,-!p4@Zfp608!0.19!2.57!Zfp608;;chr7:148008023..148008092,-!p1@Zfp941!0.19!2.57!Zfp941;;chr4:62626682..62626705,+!p2@Zfp618!0.19!2.36!Zfp618;;chr17:32506357..32506377,-!p3@Wiz!0.19!2.14!Wiz;;chr15:75672367..75672384,-!p2@Zc3h3!0.19!2.14!Zc3h3;;chr3:30993616..30993634,+!p3@Skil!0.19!1.71!Skil;;chr11:85646469..85646488,+!p5@Tbx2!0.19!1.29!Tbx2;;chr13:29045321..29045337,-!p2@Sox4!0.19!1.07!Sox4;;chr18:65741911..65741929,+!p3@Zfp532!0.19!1.07!Zfp532;;chr3:95032515..95032553,-!p5@Mllt11!0.19!0.86!Mllt11;;chrX:110411840..110411860,+!p1@Dach2!0.19!0.86!Dach2;;chr7:91558537..91558558,-!p4@Arnt2!0.19!0.86!Arnt2;;chr9:63869705..63869713,-!p8@Smad6!0.19!0.86!Smad6;;chr1:14746065..14746079,-!p1@Msc!0.19!0.86!Msc;;chr5:34530319..34530398,-!p1@Mxd4!0.18!66.87!Mxd4;;chr5:125343044..125343141,+!p1@Zfp664!0.18!58.73!Zfp664;;chr7:119822841..119822887,+!p1@Tead1!0.18!43.30!Tead1;;chr7:30954720..30954785,-!p1@LOC677248,p1@Zfp146!0.18!34.72!Zfp146;;chr7:134388025..134388092,+!p1@Zfp771!0.18!27.86!Zfp771;;chr16:50432467..50432522,-!p1@Bbx!0.18!26.15!Bbx;;chr13:44826937..44826952,+!p2@Jarid2!0.18!18.86!Jarid2;;chr17:32967140..32967197,-!p1@Zfp799!0.18!18.22!Zfp799;;chr2:181327438..181327495,-!p1@Znf512b!0.18!17.58!Znf512b;;
+|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:0011334
 |is_obsolete=
+|library_id=CNhs11037
+|library_id_phase_based=2:CNhs11037
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;398
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;398
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E14.CNhs11037.398-44A5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E14.CNhs11037.398-44A5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E14.CNhs11037.398-44A5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E14.CNhs11037.398-44A5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520embryo%2520E14.CNhs11037.398-44A5.mm9.nobarcode.rdna.fa.gz
 |name=pituitary gland, embryo E14
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11037,LSID732,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.081205609397341,0,0,0,0.0843392403965415,0,-0.0497638380912089,0,0,0,0,0,0,0,0,0,0,0,0.0769999643622936,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0879213795629655,0,0,0,0,0.0190827531612201,0.0263057348952844,0.0826833621377858,0.0867129716507187,0.653665782358535,0.12813377346509,0,0,0,0,0,0,0,0,0,0,0,0,0.149634951273376,0,0,0,0,0,0,0,0,0,0.0192271810555677,0.111441891203107,0.0484297881931515,0.0575494560657343,0.051066911497759,0,0,0.0477561378411036,0.0762250004995387,0,0,0.065901438535188,0.0258179312728891,0.177121635278138,-0.0788315948399074,0,0,0,0,0,0,0.178355181736912,0.475970986414434,0.240017578963201,0.00395829768560783,0,0,0,0
 |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=table111:398-44A5;search_select_hide=table117:398-44A5
 }}

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FF:398-44A5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:15, 4 June 2020

CNhs11037

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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