FF:1308-22E9: Difference between revisions

Latest revision as of 18:50, 4 June 2020

Name:	pituitary gland, neonate N00
Species:	Mouse (Mus musculus)
Library ID:	CNhs11190
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	pituitary gland
dev stage	0 day neonate
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		SAMD00004923

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11190		CAGE		DRX009073		DRR009947

Accession ID Mm9

Library id		BAM		CTSS
CNhs11190		DRZ001372		DRZ002755

Accession ID Mm10

Library id		BAM		CTSS
CNhs11190		DRZ012722		DRZ014105

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

CNhs11190

0	0
1	0.128
10	0
100	0
1000	0
1001	-0.0749
1002	0
1003	0.203
1004	0.244
1005	-0.0389
1006	0.17
1007	-0.258
1008	0
1009	0.0165
101	-0.15
1010	0
1011	0.115
1012	0
1013	0.157
1014	0.441
1015	0.106
1016	0.24
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.115
1022	0.0573
1023	0
1024	0.192
1025	0
1026	0.086
1027	0
1028	0
1029	-0.0674
103	0.394
1030	0
1031	0.441
1032	0.0282
1033	0.14
1034	0
1035	0
1036	-0.0932
1037	0
1038	0.0276
1039	0.0487
104	0
1040	0.174
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: CNhs11190

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0222
MA0003.1	MA0003.1	0.646
MA0004.1	MA0004.1	0.517
MA0006.1	MA0006.1	0.704
MA0007.1	MA0007.1	0.0132
MA0009.1	MA0009.1	0.495
MA0014.1	MA0014.1	0.399
MA0017.1	MA0017.1	2.51495e-9
MA0018.2	MA0018.2	2.65857e-4
MA0019.1	MA0019.1	0.816
MA0024.1	MA0024.1	0.641
MA0025.1	MA0025.1	0.406
MA0027.1	MA0027.1	0.891
MA0028.1	MA0028.1	0.192
MA0029.1	MA0029.1	0.73
MA0030.1	MA0030.1	0.141
MA0031.1	MA0031.1	0.127
MA0035.2	MA0035.2	0.0622
MA0038.1	MA0038.1	0.345
MA0039.2	MA0039.2	0.841
MA0040.1	MA0040.1	0.313
MA0041.1	MA0041.1	0.103
MA0042.1	MA0042.1	0.364
MA0043.1	MA0043.1	6.99592e-4
MA0046.1	MA0046.1	1.86597e-12
MA0047.2	MA0047.2	0.0354
MA0048.1	MA0048.1	0.0315
MA0050.1	MA0050.1	0.201
MA0051.1	MA0051.1	0.67
MA0052.1	MA0052.1	0.134
MA0055.1	MA0055.1	0.661
MA0057.1	MA0057.1	0.519
MA0058.1	MA0058.1	0.521
MA0059.1	MA0059.1	0.0814
MA0060.1	MA0060.1	0.0025
MA0061.1	MA0061.1	0.0815
MA0062.2	MA0062.2	0.0306
MA0065.2	MA0065.2	0.00129
MA0066.1	MA0066.1	0.00447
MA0067.1	MA0067.1	0.859
MA0068.1	MA0068.1	0.346
MA0069.1	MA0069.1	0.166
MA0070.1	MA0070.1	0.338
MA0071.1	MA0071.1	0.136
MA0072.1	MA0072.1	0.0638
MA0073.1	MA0073.1	0.968
MA0074.1	MA0074.1	0.762
MA0076.1	MA0076.1	0.922
MA0077.1	MA0077.1	0.177
MA0078.1	MA0078.1	0.201
MA0079.2	MA0079.2	0.0316
MA0080.2	MA0080.2	2.58426e-6
MA0081.1	MA0081.1	0.313
MA0083.1	MA0083.1	0.747
MA0084.1	MA0084.1	0.443
MA0087.1	MA0087.1	0.967
MA0088.1	MA0088.1	0.0449
MA0090.1	MA0090.1	0.534
MA0091.1	MA0091.1	0.624
MA0092.1	MA0092.1	0.692
MA0093.1	MA0093.1	0.592
MA0099.2	MA0099.2	0.171
MA0100.1	MA0100.1	0.192
MA0101.1	MA0101.1	0.0824
MA0102.2	MA0102.2	0.872
MA0103.1	MA0103.1	0.639
MA0104.2	MA0104.2	0.361
MA0105.1	MA0105.1	0.0209
MA0106.1	MA0106.1	0.0213
MA0107.1	MA0107.1	0.0684
MA0108.2	MA0108.2	0.00229
MA0111.1	MA0111.1	0.816
MA0112.2	MA0112.2	8.09445e-5
MA0113.1	MA0113.1	0.504
MA0114.1	MA0114.1	5.85671e-9
MA0115.1	MA0115.1	1.93184e-6
MA0116.1	MA0116.1	0.0776
MA0117.1	MA0117.1	0.892
MA0119.1	MA0119.1	0.127
MA0122.1	MA0122.1	0.582
MA0124.1	MA0124.1	0.875
MA0125.1	MA0125.1	0.096
MA0131.1	MA0131.1	0.525
MA0135.1	MA0135.1	3.05436e-4
MA0136.1	MA0136.1	1.01554e-5
MA0137.2	MA0137.2	0.246
MA0138.2	MA0138.2	0.157
MA0139.1	MA0139.1	0.445
MA0140.1	MA0140.1	4.99261e-4
MA0141.1	MA0141.1	0.0101
MA0142.1	MA0142.1	0.735
MA0143.1	MA0143.1	0.656
MA0144.1	MA0144.1	0.671
MA0145.1	MA0145.1	0.75
MA0146.1	MA0146.1	0.916
MA0147.1	MA0147.1	0.354
MA0148.1	MA0148.1	0.00607
MA0149.1	MA0149.1	0.0437
MA0150.1	MA0150.1	0.00231
MA0152.1	MA0152.1	0.482
MA0153.1	MA0153.1	1.38151e-10
MA0154.1	MA0154.1	0.126
MA0155.1	MA0155.1	0.22
MA0156.1	MA0156.1	0.00333
MA0157.1	MA0157.1	0.265
MA0159.1	MA0159.1	0.00475
MA0160.1	MA0160.1	0.0187
MA0162.1	MA0162.1	0.298
MA0163.1	MA0163.1	0.11
MA0164.1	MA0164.1	0.87
MA0258.1	MA0258.1	0.00445
MA0259.1	MA0259.1	0.486

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: CNhs11190

Novel motif	Logo	P-value
1	1	0.027
10	10	0.0143
100	100	0.925
101	101	0.572
102	102	0.69
103	103	0.0551
104	104	0.691
105	105	0.873
106	106	0.186
107	107	0.18
108	108	0.537
109	109	0.645
11	11	0.282
110	110	0.0324
111	111	0.0367
112	112	0.0737
113	113	0.837
114	114	0.38
115	115	0.589
116	116	0.807
117	117	0.00596
118	118	0.245
119	119	0.171
12	12	0.847
120	120	0.864
121	121	0.732
122	122	0.182
123	123	0.803
124	124	0.744
125	125	0.333
126	126	0.171
127	127	0.14
128	128	0.314
129	129	0.315
13	13	0.00542
130	130	0.716
131	131	0.274
132	132	0.803
133	133	0.427
134	134	0.822
135	135	0.22
136	136	0.0729
137	137	0.688
138	138	0.333
139	139	0.0394
14	14	0.928
140	140	0.0112
141	141	0.857
142	142	0.0824
143	143	0.719
144	144	0.627
145	145	0.0916
146	146	0.965
147	147	0.748
148	148	0.406
149	149	0.805
15	15	0.0609
150	150	0.418
151	151	0.734
152	152	0.263
153	153	0.481
154	154	0.198
155	155	0.873
156	156	0.00472
157	157	0.383
158	158	0.151
159	159	0.158
160	160	0.194
161	161	0.68
162	162	0.681
163	163	0.172
164	164	0.0356
165	165	0.262
166	166	0.89
167	167	0.038
168	168	0.535
169	169	0.146
17	17	0.456
18	18	0.744
19	19	0.156
2	2	0.419
20	20	0.464
21	21	0.73
22	22	0.628
23	23	0.571
24	24	0.576
25	25	0.307
26	26	0.00411
27	27	0.924
28	28	0.319
29	29	0.0427
3	3	0.157
30	30	0.427
31	31	0.884
32	32	0.941
33	33	0.788
34	34	0.562
35	35	0.281
36	36	0.545
37	37	0.123
38	38	0.617
39	39	0.602
4	4	0.606
40	40	0.823
41	41	0.418
42	42	0.422
43	43	0.0636
44	44	0.444
45	45	0.966
46	46	0.0279
47	47	0.29
48	48	0.229
49	49	0.0562
5	5	0.0325
50	50	0.77
51	51	0.46
52	52	0.727
53	53	0.828
54	54	0.506
55	55	0.329
56	56	0.868
57	57	0.223
58	58	0.169
59	59	0.853
6	6	0.622
60	60	0.142
61	61	0.0882
62	62	0.0692
63	63	0.277
64	64	0.815
65	65	0.633
66	66	0.298
67	67	0.747
68	68	0.28
69	69	0.904
7	7	0.0401
70	70	0.163
71	71	0.0142
72	72	0.605
73	73	0.737
74	74	0.109
75	75	0.0738
76	76	0.292
77	77	0.645
78	78	0.0022
79	79	0.767
8	8	0.0533
80	80	0.307
81	81	0.525
82	82	0.454
83	83	0.342
84	84	0.559
85	85	0.0895
86	86	0.325
87	87	0.0433
88	88	0.179
89	89	0.231
9	9	0.754
90	90	0.066
91	91	0.294
92	92	0.217
93	93	0.0135
94	94	0.0398
95	95	0.798
96	96	0.135
97	97	0.7
98	98	0.828
99	99	0.784

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: CNhs11190

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011507 mouse pituitary gland- neonate N00 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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011507 (mouse pituitary gland- neonate N00 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@SAMD00004923
+|accession_numbers=CAGE;DRX009073;DRR009947;DRZ001372;DRZ002755;DRZ012722;DRZ014105
 |ancestors_in_anatomy_facet=UBERON:0000468,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!2.05!112.04!Pou1f1;;chr2:26062055..26062100,-!p1@Lhx3!1.86!70.64!Lhx3;;chr13:55932591..55932622,-!p1@Pitx1!1.78!71.24!Pitx1;;chr13:99124189..99124205,+!p1@Foxd1!1.76!84.64!Foxd1;;chr12:74147689..74147711,-!p1@Six1!1.67!98.34!Six1;;chr12:74040895..74040916,+!p2@Six6!1.60!38.67!Six6;;chr10:86956396..86956411,-!p1@Ascl1!1.51!47.80!Ascl1;;chr12:74040861..74040875,+!p1@Six6!1.51!31.66!Six6;;chr5:38215819..38215823,-!p1@Msx1!1.49!77.03!Msx1;;chr17:86020510..86020589,+!p3@Six3!1.47!28.62!Six3;;chr2:146047829..146047847,+!p1@Insm1!1.44!46.89!Insm1;;chr17:86087592..86087615,-!p1@Six2!1.40!24.36!Six2;;chr3:128916868..128916890,+!p1@Pitx2!1.36!29.84!Pitx2;;chr1:167090803..167090816,-!p1@Tbx19!1.30!19.18!Tbx19;;chr3:34548909..34548927,+!p1@Sox2!1.26!29.23!Sox2;;chr12:34642510..34642530,+!p1@Twist1!1.24!51.45!Twist1;;chr17:86020156..86020183,+!p1@Six3!1.24!16.44!Six3;;chr4:109650609..109650653,+!p1@Dmrta2!1.23!15.83!Dmrta2;;chr13:31898637..31898653,+!p2@Foxc1!1.22!27.71!Foxc1;;chr18:66098702..66098742,-!p1@Rax!1.22!15.53!Rax;;chr13:55932624..55932641,-!p2@Pitx1!1.21!15.22!Pitx1;;chr3:128917187..128917223,+!p2@Pitx2!1.19!17.05!Pitx2;;chr17:86020115..86020128,+!p2@Six3!1.16!13.40!Six3;;chr14:122874619..122874634,+!p1@Zic2!1.15!13.09!Zic2;;chr19:19185671..19185693,-!p1@Rorb!1.08!26.49!Rorb;;chr5:138199361..138199441,+!p2@Tsc22d4!1.08!21.01!Tsc22d4;;chr7:17647736..17647772,-!p1@Hif3a!1.07!38.06!Hif3a;;chr10:22539932..22539956,-!p1@Tcf21!1.07!28.62!Tcf21;;chr8:123640063..123640077,+!p1@Foxc2!1.07!19.49!Foxc2;;chr10:129717274..129717298,-!p1@Neurod4!1.07!10.66!Neurod4;;chr13:31717548..31717596,+!p1@Foxf2!1.06!21.01!Foxf2;;chr17:86012772..86012825,+!p4@Six3!1.04!10.05!Six3;;chr2:79296783..79296801,-!p1@Neurod1!1.04!10.05!Neurod1;;chr2:147190749..147190769,+!p1@Pax1!1.03!9.74!Pax1;;chr13:31898767..31898785,+!p4@Foxc1!1.02!11.57!Foxc1;;chrX:58146612..58146615,-!p1@Sox3!1.02!9.44!Sox3;;chr9:55388997..55389016,+!p1@Isl2!1.01!9.13!Isl2;;chr13:31898729..31898761,+!p1@Foxc1!1.00!22.53!Foxc1;;chr18:35020854..35020869,+!p1@Egr1!0.99!343.74!Egr1;;chr18:52775562..52775650,+!p1@Zfp474!0.98!8.53!Zfp474;;chr11:50767247..50767270,-!p1@Prop1!0.98!8.53!Prop1;;chr10:12810631..12810649,+!p1@Plagl1!0.97!225.00!Plagl1;;chr16:15887371..15887385,+!p1@Cebpd!0.96!286.81!Cebpd;;chr8:12395603..12395621,+!p1@Sox1!0.96!8.22!Sox1;;chr2:26063801..26063813,-!p2@Lhx3!0.96!8.22!Lhx3;;chr3:128916838..128916856,+!p4@Pitx2!0.96!8.22!Pitx2;;chr4:139388835..139388867,-!p1@Pax7!0.95!7.92!Pax7;;chr17:86020336..86020352,+!p8@Six3!0.95!7.92!Six3;;chr1:169528457..169528482,+!p3@Rxrg!0.95!7.92!Rxrg;;chr1:169528581..169528607,+!p7@Rxrg!0.94!7.61!Rxrg;;chr9:91260594..91260612,-!p1@Zic1!0.94!7.61!Zic1;;chr10:84218800..84218829,+!p2@Rfx4!0.94!7.61!Rfx4;;chr3:128902837..128902861,+!p3@Pitx2!0.92!7.31!Pitx2;;chr16:65521021..65521032,+!p@chr16:65521021..65521032,+!0.92!7.31!Pou1f1;;chr3:107398056..107398082,+!p1@Alx3!0.90!7.00!Alx3;;chr14:104867201..104867258,-!p1@Pou4f1!0.89!9.74!Pou4f1;;chr6:90412582..90412601,+!p1@Klf15!0.87!32.27!Klf15;;chr2:31495237..31495243,+!p1@Prdm12!0.87!6.39!Prdm12;;chr10:84218895..84218909,+!p1@Rfx4!0.87!6.39!Rfx4;;chr6:90412608..90412630,+!p2@Klf15!0.86!13.40!Klf15;;chr9:48644306..48644364,-!p1@Zbtb16!0.85!25.58!Zbtb16;;chr1:169528491..169528505,+!p4@Rxrg!0.85!6.09!Rxrg;;chr17:86020468..86020504,+!p6@Six3!0.85!6.09!Six3;;chr2:38206744..38206766,+!p1@Lhx2!0.84!7.31!Lhx2;;chr3:34548946..34548972,+!p2@Sox2!0.84!6.70!Sox2;;chr13:117099847..117099907,-!p1@Isl1!0.83!10.96!Isl1;;chr19:59245978..59245982,-!p1@Vax1!0.83!5.78!Vax1;;chr9:48644037..48644067,-!p2@Zbtb16!0.82!14.61!Zbtb16;;chr1:120879128..120879183,-!p3@Gli2!0.82!11.27!Gli2;;chr2:127347067..127347093,-!p1@Kcnip3!0.82!9.74!Kcnip3;;chr19:19185697..19185711,-!p2@Rorb!0.82!7.31!Rorb;;chr11:98636508..98636524,-!p3@Nr1d1!0.82!7.00!Nr1d1;;chr8:87502608..87502623,-!p1@Junb!0.81!96.52!Junb;;chr15:101097270..101097290,+!p1@Nr4a1!0.81!60.28!Nr4a1;;chr1:137155026..137155042,-!p1@Elf3!0.81!33.80!Elf3;;chr11:121380594..121380609,-!p2@Zfp750!0.81!9.74!Zfp750;;chr2:146911200..146911219,-!p1@Nkx2-4!0.81!5.48!Nkx2-4;;chr6:30908793..30908815,-!p1@Klf14!0.81!5.48!Klf14;;chr14:49287186..49287225,-!p1@Otx2!0.81!5.48!Otx2;;chr9:98855692..98855710,+!p2@Foxl2!0.81!5.48!Foxl2;;chr13:31898496..31898519,+!p3@Foxc1!0.80!8.83!Foxc1;;chr13:55937467..55937516,-!p3@Pitx1!0.79!5.18!Pitx1;;chr1:169528433..169528456,+!p10@Rxrg!0.79!5.18!Rxrg;;chr1:169528720..169528749,+!p6@Rxrg!0.79!5.18!Rxrg;;chr10:129717308..129717319,-!p2@Neurod4!0.79!5.18!Neurod4;;chr7:6649134..6649167,-!p1@Zim1!0.78!29.84!Zim1;;chr7:52963269..52963305,+!p4@Dbp!0.78!7.31!Dbp;;chr8:123640090..123640101,+!p2@Foxc2!0.78!5.78!Foxc2;;chr11:98636531..98636559,-!p1@Nr1d1!0.77!30.45!Nr1d1;;chrX:137135036..137135064,-!p4@Tsc22d3!0.77!10.05!Tsc22d3;;chr2:127347094..127347111,-!p2@Kcnip3!0.77!8.53!Kcnip3;;chr17:86020293..86020318,+!p7@Six3!0.77!4.87!Six3;;chr13:55937432..55937460,-!p4@Pitx1!0.77!4.87!Pitx1;;chr3:94176733..94176794,+!p1@Rorc!0.75!39.28!Rorc;;chr4:114581497..114581519,-!p2@Foxd2!0.75!4.57!Foxd2;;chr17:86020137..86020149,+!p5@Six3!0.75!4.57!Six3;;chr1:169528520..169528542,+!p2@Rxrg!0.75!4.57!Rxrg;;chr2:147190725..147190747,+!p2@Pax1!0.75!4.57!Pax1;;chr11:90252223..90252240,-!p1@Hlf!0.74!41.71!Hlf;;chr15:78994907..78994926,-!p1@Sox10!0.74!12.48!Sox10;;chr7:116154364..116154444,+!p1@Tub!0.74!8.22!Tub;;chr16:91270004..91270023,+!p1@Olig1!0.74!5.18!Olig1;;chr3:95032091..95032183,-!p1@Mllt11!0.72!40.80!Mllt11;;chr5:144951153..144951203,+!p1@Bhlha15!0.72!6.39!Bhlha15;;chr14:122874593..122874610,+!p2@Zic2!0.72!4.26!Zic2;;chr2:163028808..163028869,+!p1@Tox2!0.70!16.14!Tox2;;chr17:86020186..86020195,+!p9@Six3!0.70!3.96!Six3;;chr13:31717597..31717613,+!p2@Foxf2!0.70!3.96!Foxf2;;chr4:139389439..139389450,-!p3@Pax7!0.70!3.96!Pax7;;chr14:56443806..56443848,+!p1@Nfatc4!0.69!8.53!Nfatc4;;chr16:18587076..18587106,-!p1@Tbx1!0.69!5.78!Tbx1;;chr2:25562263..25562314,+!p2@Bmyc!0.68!16.44!Bmyc;;chr10:80870405..80870428,-!p4@Nfic!0.68!11.27!Nfic;;chr7:148008023..148008092,-!p1@Zfp941!0.67!9.74!Zfp941;;chr7:17642053..17642066,-!p2@Hif3a!0.67!5.48!Hif3a;;chr9:91260616..91260653,-!p2@Zic1!0.67!3.65!Zic1;;chr15:79178559..79178584,+!p8@Maff!0.67!3.65!Maff;;chr7:52960555..52960662,+!p1@Dbp!0.66!35.32!Dbp;;chr11:98636575..98636607,-!p2@Nr1d1!0.66!14.92!Nr1d1;;chr2:25562315..25562344,+!p3@Bmyc!0.66!13.40!Bmyc;;chr2:152223881..152223933,-!p3@Sox12!0.66!13.40!Sox12;;chr11:90250944..90250982,-!p2@Hlf!0.66!6.39!Hlf;;chr11:85646303..85646329,+!p1@Tbx2!0.65!26.79!Tbx2;;chr4:119960301..119960359,-!p1@Foxo6!0.64!12.48!Foxo6;;chr7:17642018..17642045,-!p4@Hif3a!0.64!3.96!Hif3a;;chr3:34549096..34549111,+!p3@Sox2!0.64!3.35!Sox2;;chr9:99776566..99776612,-!p1@Sox14!0.64!3.35!Sox14;;chr1:167090905..167090912,-!p2@Tbx19!0.64!3.35!Tbx19;;chr1:167090920..167090924,-!p3@Tbx19!0.64!3.35!Tbx19;;chr12:74040716..74040745,+!p3@Six6!0.64!3.35!Six6;;chr8:87297280..87297326,-!p2@Nfix!0.63!8.53!Nfix;;chr14:55711114..55711159,-!p2@Zfhx2!0.63!8.22!Zfhx2;;chr6:88148650..88148669,+!p1@Gata2!0.62!31.66!Gata2;;chr12:34642682..34642753,+!p2@Twist1!0.62!9.44!Twist1;;chr2:38206580..38206600,+!p2@Lhx2!0.61!3.96!Lhx2;;chr2:181501745..181501778,+!p1@Myt1!0.61!3.04!Myt1;;chr2:127347042..127347058,-!p3@Kcnip3!0.61!3.04!Kcnip3;;chr1:6720216..6720232,+!p1@St18!0.61!3.04!St18;;chr6:83020355..83020371,-!p1@Tlx2!0.61!3.04!Tlx2;;chr13:99124236..99124243,+!p2@Foxd1!0.61!3.04!Foxd1;;chr13:55932739..55932756,-!p5@Pitx1!0.61!3.04!Pitx1;;chr2:25562346..25562433,+!p1@Bmyc!0.60!65.76!Bmyc;;chr8:72356532..72356611,+!p1@Pbx4!0.60!14.61!Pbx4;;chr4:99322820..99322845,+!p1@Foxd3!0.60!3.96!Foxd3;;chr19:23215673..23215753,+!p1@Klf9!0.59!50.85!Klf9;;chr2:130120884..130120972,+!p1@Ebf4!0.59!20.40!Ebf4;;chr19:9016975..9017004,+!p2@Mta2!0.59!10.05!Mta2;;chr3:99057269..99057306,+!p1@Tbx15!0.59!3.65!Tbx15;;chr19:28754692..28754757,-!p1@Glis3!0.58!14.01!Glis3;;chr14:17407970..17408015,-!p2@Rarb!0.58!8.83!Rarb;;chr4:128483731..128483757,-!p4@Zfp362!0.58!7.31!Zfp362;;chr14:55711198..55711258,-!p1@Zfhx2!0.57!18.88!Zfhx2;;chr10:126778916..126778974,-!p1@Gli1!0.57!7.00!Gli1;;chr11:116196664..116196679,-!p1@Foxj1!0.57!4.57!Foxj1;;chr14:17407549..17407575,-!p3@Rarb!0.57!4.57!Rarb;;chr8:24780125..24780143,+!p1@Zmat4!0.57!4.26!Zmat4;;chr6:108610428..108610440,+!p4@Bhlhe40!0.57!3.96!Bhlhe40;;chr15:103164702..103164778,-!p3@Zfp385a!0.57!3.35!Zfp385a;;chr17:48015839..48015915,-!p3@Foxp4!0.57!3.35!Foxp4;;chr14:52948124..52948148,-!p7@Sall2!0.57!2.74!Sall2;;chr12:30219426..30219506,+!p2@Myt1l!0.57!2.74!Myt1l;;chr1:169528551..169528569,+!p8@Rxrg!0.57!2.74!Rxrg;;chr2:181501988..181502026,+!p3@Myt1!0.57!2.74!Myt1;;chr9:98855847..98855866,+!p3@Foxl2!0.57!2.74!Foxl2;;chr4:128483347..128483411,-!p2@Zfp362!0.56!24.36!Zfp362;;chr17:28314341..28314394,+!p2@Zfp523!0.56!18.88!Zfp523;;chr17:56970339..56970428,-!p1@Rfx2!0.56!9.74!Rfx2;;chr18:3281750..3281776,-!p2@Crem!0.56!6.09!Crem;;chr11:121380640..121380655,-!p1@Zfp750!0.56!4.87!Zfp750;;chr7:19895354..19895369,-!p1@Fosb!0.56!3.96!Fosb;;chr14:56443781..56443800,+!p3@Nfatc4!0.56!3.65!Nfatc4;;chr4:150503457..150503498,-!p3@Camta1!0.56!3.04!Camta1;;chr7:6683123..6683142,-!p1@Peg3!0.55!169.89!Peg3;;chr12:86814833..86814846,+!p1@Fos!0.55!75.51!Fos;;chr7:5003117..5003159,+!p1@Zfp580!0.55!23.75!Zfp580;;chr4:149862477..149862553,+!p3@Rere!0.55!10.96!Rere;;chr9:63869729..63869749,-!p4@Smad6!0.55!5.78!Smad6;;chr3:52072329..52072346,+!p1@Foxo1!0.54!48.11!Foxo1;;chr7:4866804..4866832,+!p1@Zfp628!0.54!34.71!Zfp628;;chr3:52072296..52072310,+!p3@Foxo1!0.54!15.53!Foxo1;;chr7:130644017..130644092,-!p1@Zkscan2!0.54!5.48!Zkscan2;;chr5:120120667..120120685,+!p3@Tbx3!0.54!5.48!Tbx3;;chr12:74214394..74214422,-!p1@Six4!0.54!3.65!Six4;;chr2:30700857..30700873,+!p3@Prrx2!0.54!3.65!Prrx2;;chr10:5636374..5636421,-!p1@Esr1!0.54!3.35!Esr1;;chr11:90250894..90250916,-!p5@Hlf!0.54!2.44!Hlf;;chr11:90252071..90252093,-!p7@Hlf!0.54!2.44!Hlf;;chr1:173987720..173987729,-!p1@Nhlh1!0.54!2.44!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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011507
 |is_obsolete=
+|library_id=CNhs11190
+|library_id_phase_based=2:CNhs11190
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1308
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1308
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520neonate%2520N00.CNhs11190.1308-22E9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520neonate%2520N00.CNhs11190.1308-22E9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520neonate%2520N00.CNhs11190.1308-22E9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520neonate%2520N00.CNhs11190.1308-22E9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/pituitary%2520gland%252c%2520neonate%2520N00.CNhs11190.1308-22E9.mm9.nobarcode.rdna.fa.gz
 |name=pituitary gland, neonate N00
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11190,LSID746,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0808229107741237,0,0,0,0,0,-0.225944453781503,0,0,0,0,0.0310931737329704,0,0,0,0,0,0,-0.0764609367530626,0,0,0,0,0,0.115432414129512,0,0,0,0,0,0,0,-0.442990378194519,0,0,0,0,0.0156142478736827,0.119592585253961,0.20207149809696,-0.0239750936165377,0.135657842821677,0.498875928971012,0,0,0,0,0,0,0,0,0,0,0.281804600099495,0,0.33579545304434,0.115432414129512,0,0,0,0,0,0,0,0,0,-0.0870100065676679,-0.0288460572398916,-0.0426586286415706,0.0211234980679025,0,0,0.0657313460545639,0.14031474140774,0,0,0,0.0882824610253434,0.354259498463255,-0.0788315948399074,0,0,0,0,0,0,0.510413439923369,0.914685647924334,0.520369151988338,0,0,0,0,0
 |rna_box=22
 |rna_catalog_number=
@@ Line 58: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=22E9
+|rna_tube_id=2.20E+10
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1308-22E9;search_select_hide=table117:1308-22E9
 }}

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FF:1308-22E9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:50, 4 June 2020

CNhs11190

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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