FF:1254-43D6: Difference between revisions

Latest revision as of 18:40, 4 June 2020

Name:	adrenal gland, embryo E16
Species:	Mouse (Mus musculus)
Library ID:	CNhs11004
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	adrenal gland
dev stage	16 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		SAMD00005675

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11004		CAGE		DRX008929		DRR009803

Accession ID Mm9

Library id		BAM		CTSS
CNhs11004		DRZ001228		DRZ002611

Accession ID Mm10

Library id		BAM		CTSS
CNhs11004		DRZ012578		DRZ013961

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

CNhs11004

0	0
1	0
10	0
100	0
1000	0.115
1001	0.0405
1002	0.438
1003	-0.102
1004	0
1005	-0.0465
1006	0.0227
1007	-0.125
1008	0
1009	0.0773
101	0.0161
1010	0
1011	-0.0912
1012	0
1013	-0.0365
1014	0.451
1015	-0.021
1016	-0.0406
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.0487
1022	0
1023	0
1024	0.161
1025	0.115
1026	0
1027	0
1028	0
1029	0.105
103	0.303
1030	0
1031	0.292
1032	-0.0238
1033	0
1034	0
1035	0
1036	0.0542
1037	0
1038	-0.182
1039	0.0621
104	0
1040	0.0803
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: CNhs11004

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.278
MA0003.1	MA0003.1	0.239
MA0004.1	MA0004.1	0.00293
MA0006.1	MA0006.1	0.973
MA0007.1	MA0007.1	0.529
MA0009.1	MA0009.1	0.0704
MA0014.1	MA0014.1	0.906
MA0017.1	MA0017.1	0.137
MA0018.2	MA0018.2	0.219
MA0019.1	MA0019.1	0.489
MA0024.1	MA0024.1	0.282
MA0025.1	MA0025.1	0.0367
MA0027.1	MA0027.1	0.0015
MA0028.1	MA0028.1	0.0304
MA0029.1	MA0029.1	6.63752e-6
MA0030.1	MA0030.1	0.0345
MA0031.1	MA0031.1	0.00575
MA0035.2	MA0035.2	0.00956
MA0038.1	MA0038.1	0.584
MA0039.2	MA0039.2	0.993
MA0040.1	MA0040.1	0.00446
MA0041.1	MA0041.1	0.417
MA0042.1	MA0042.1	0.245
MA0043.1	MA0043.1	0.00544
MA0046.1	MA0046.1	0.479
MA0047.2	MA0047.2	0.0368
MA0048.1	MA0048.1	0.737
MA0050.1	MA0050.1	1.95275e-6
MA0051.1	MA0051.1	1.58863e-8
MA0052.1	MA0052.1	0.215
MA0055.1	MA0055.1	0.172
MA0057.1	MA0057.1	0.907
MA0058.1	MA0058.1	0.0135
MA0059.1	MA0059.1	0.636
MA0060.1	MA0060.1	0.561
MA0061.1	MA0061.1	0.392
MA0062.2	MA0062.2	8.45735e-7
MA0065.2	MA0065.2	0.223
MA0066.1	MA0066.1	0.648
MA0067.1	MA0067.1	0.0369
MA0068.1	MA0068.1	0.00943
MA0069.1	MA0069.1	0.037
MA0070.1	MA0070.1	0.0855
MA0071.1	MA0071.1	0.0431
MA0072.1	MA0072.1	0.578
MA0073.1	MA0073.1	0.581
MA0074.1	MA0074.1	0.702
MA0076.1	MA0076.1	0.00252
MA0077.1	MA0077.1	0.288
MA0078.1	MA0078.1	0.536
MA0079.2	MA0079.2	0.831
MA0080.2	MA0080.2	1.44226e-6
MA0081.1	MA0081.1	0.0297
MA0083.1	MA0083.1	0.512
MA0084.1	MA0084.1	0.0877
MA0087.1	MA0087.1	0.0701
MA0088.1	MA0088.1	0.357
MA0090.1	MA0090.1	0.645
MA0091.1	MA0091.1	0.0426
MA0092.1	MA0092.1	0.774
MA0093.1	MA0093.1	0.00681
MA0099.2	MA0099.2	0.735
MA0100.1	MA0100.1	0.0419
MA0101.1	MA0101.1	0.181
MA0102.2	MA0102.2	0.0248
MA0103.1	MA0103.1	6.20356e-7
MA0104.2	MA0104.2	0.451
MA0105.1	MA0105.1	0.0175
MA0106.1	MA0106.1	0.576
MA0107.1	MA0107.1	0.0478
MA0108.2	MA0108.2	0.216
MA0111.1	MA0111.1	0.849
MA0112.2	MA0112.2	0.0539
MA0113.1	MA0113.1	0.537
MA0114.1	MA0114.1	0.821
MA0115.1	MA0115.1	0.426
MA0116.1	MA0116.1	0.0295
MA0117.1	MA0117.1	0.847
MA0119.1	MA0119.1	0.00995
MA0122.1	MA0122.1	0.762
MA0124.1	MA0124.1	0.47
MA0125.1	MA0125.1	0.269
MA0131.1	MA0131.1	0.0585
MA0135.1	MA0135.1	0.603
MA0136.1	MA0136.1	3.12613e-6
MA0137.2	MA0137.2	0.0228
MA0138.2	MA0138.2	0.129
MA0139.1	MA0139.1	0.547
MA0140.1	MA0140.1	4.84934e-7
MA0141.1	MA0141.1	2.35033e-4
MA0142.1	MA0142.1	0.833
MA0143.1	MA0143.1	0.246
MA0144.1	MA0144.1	0.367
MA0145.1	MA0145.1	0.233
MA0146.1	MA0146.1	0.832
MA0147.1	MA0147.1	0.609
MA0148.1	MA0148.1	0.149
MA0149.1	MA0149.1	0.983
MA0150.1	MA0150.1	0.76
MA0152.1	MA0152.1	0.802
MA0153.1	MA0153.1	0.0624
MA0154.1	MA0154.1	0.0146
MA0155.1	MA0155.1	0.245
MA0156.1	MA0156.1	1.54569e-7
MA0157.1	MA0157.1	0.00625
MA0159.1	MA0159.1	0.92
MA0160.1	MA0160.1	0.335
MA0162.1	MA0162.1	0.182
MA0163.1	MA0163.1	0.0133
MA0164.1	MA0164.1	0.966
MA0258.1	MA0258.1	0.198
MA0259.1	MA0259.1	0.47

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: CNhs11004

Novel motif	Logo	P-value
1	1	0.295
10	10	0.915
100	100	0.934
101	101	0.529
102	102	0.431
103	103	0.335
104	104	0.794
105	105	0.141
106	106	0.822
107	107	0.154
108	108	0.837
109	109	0.466
11	11	0.408
110	110	0.105
111	111	0.487
112	112	0.782
113	113	0.658
114	114	0.953
115	115	0.762
116	116	0.12
117	117	0.496
118	118	0.563
119	119	0.58
12	12	0.782
120	120	0.173
121	121	0.384
122	122	0.699
123	123	0.113
124	124	0.127
125	125	0.0702
126	126	0.181
127	127	0.349
128	128	0.615
129	129	0.28
13	13	0.718
130	130	0.168
131	131	0.396
132	132	0.336
133	133	0.269
134	134	0.17
135	135	0.0574
136	136	0.388
137	137	0.711
138	138	0.175
139	139	0.395
14	14	0.898
140	140	0.501
141	141	0.44
142	142	0.804
143	143	0.0869
144	144	0.053
145	145	0.796
146	146	0.508
147	147	0.396
148	148	0.205
149	149	0.0602
15	15	0.56
150	150	0.621
151	151	0.913
152	152	0.585
153	153	0.819
154	154	0.23
155	155	0.733
156	156	1.61369e-5
157	157	0.368
158	158	0.147
159	159	0.621
160	160	0.0754
161	161	0.742
162	162	0.733
163	163	0.795
164	164	0.612
165	165	0.183
166	166	0.403
167	167	0.402
168	168	0.38
169	169	0.0889
17	17	0.517
18	18	0.0366
19	19	0.0527
2	2	0.139
20	20	0.0482
21	21	0.196
22	22	0.105
23	23	0.793
24	24	0.679
25	25	0.725
26	26	0.816
27	27	0.581
28	28	0.166
29	29	0.98
3	3	0.341
30	30	0.451
31	31	0.675
32	32	0.331
33	33	0.604
34	34	0.404
35	35	0.74
36	36	0.897
37	37	0.462
38	38	0.885
39	39	0.378
4	4	0.614
40	40	0.364
41	41	0.00393
42	42	0.483
43	43	0.371
44	44	0.329
45	45	0.764
46	46	0.864
47	47	0.582
48	48	0.719
49	49	0.783
5	5	0.677
50	50	0.283
51	51	0.67
52	52	0.763
53	53	0.0575
54	54	0.794
55	55	0.119
56	56	0.298
57	57	0.523
58	58	0.379
59	59	0.0588
6	6	0.906
60	60	0.592
61	61	0.138
62	62	0.975
63	63	0.423
64	64	0.299
65	65	0.678
66	66	0.472
67	67	0.524
68	68	0.461
69	69	0.152
7	7	0.766
70	70	0.067
71	71	0.0841
72	72	0.445
73	73	0.577
74	74	0.583
75	75	0.384
76	76	0.259
77	77	0.288
78	78	0.424
79	79	0.9
8	8	0.191
80	80	0.351
81	81	0.525
82	82	0.0548
83	83	0.0754
84	84	0.556
85	85	0.772
86	86	0.745
87	87	0.0428
88	88	0.471
89	89	0.74
9	9	0.844
90	90	0.52
91	91	0.632
92	92	0.267
93	93	0.473
94	94	0.86
95	95	0.746
96	96	0.26
97	97	0.713
98	98	0.681
99	99	0.12

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: CNhs11004

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011522 mouse adrenal gland - embryo E16 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)
0002369 (adrenal gland)
0002100 (trunk)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0005172 (abdomen element)
0002530 (gland)
0006858 (adrenal/interrenal gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0000916 (abdomen)

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)
0000299 (mouse embryonic day 16 sample)
0011522 (mouse adrenal gland - embryo E16 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:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008792
+|DRA_sample_Accession=CAGE@SAMD00005675
-|accession_numbers=CAGE;DRX008929;DRR009803;DRZ001228;DRZ002611
+|accession_numbers=CAGE;DRX008929;DRR009803;DRZ001228;DRZ002611;DRZ012578;DRZ013961
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002369,UBERON:0002100,UBERON:0000479,UBERON:0010314,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0005172,UBERON:0002530,UBERON:0006858,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0000916
 |ancestors_in_cell_lineage_facet=
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:38570011..38570034,-!p1@Nr5a1!2.22!165.93!Nr5a1;;chr8:59799772..59799789,+!p1@Hand2!1.85!194.55!Hand2;;chr7:108966820..108966835,+!p1@Phox2a!1.80!62.11!Phox2a;;chr11:57645506..57645523,-!p1@Hand1!1.67!45.67!Hand1;;chr6:83020355..83020371,-!p1@Tlx2!1.52!31.97!Tlx2;;chr11:96143666..96143725,+!p1@Hoxb8!1.30!21.62!Hoxb8;;chr9:24578720..24578735,-!p1@Tbx20!1.26!17.35!Tbx20;;chr10:22539932..22539956,-!p1@Tcf21!1.24!43.23!Tcf21;;chr5:67490284..67490302,-!p1@Phox2b!1.23!16.14!Phox2b;;chr15:102828658..102828678,+!p1@Hoxc6!1.23!16.14!Hoxc6;;chr11:96153767..96153822,+!p1@Hoxb6!1.17!21.31!Hoxb6;;chr4:133109285..133109308,+!p1@Nr0b2!1.17!13.70!Nr0b2;;chr18:3281750..3281776,-!p2@Crem!1.16!27.40!Crem;;chrX:83437105..83437121,+!p1@Nr0b1!1.15!13.09!Nr0b1;;chr15:101097270..101097290,+!p1@Nr4a1!1.13!127.27!Nr4a1;;chr15:103085660..103085681,-!p1@Nfe2!1.13!18.88!Nfe2;;chr2:38567715..38567730,-!p2@Nr5a1!1.12!12.18!Nr5a1;;chr2:9800207..9800234,-!p1@Gata3!1.11!35.93!Gata3;;chr8:87425854..87425891,+!p1@Klf1!1.10!11.57!Klf1;;chr18:3281725..3281740,-!p3@Crem!1.09!14.31!Crem;;chr13:117099847..117099907,-!p1@Isl1!1.07!19.79!Isl1;;chr13:99124189..99124205,+!p1@Foxd1!1.07!16.44!Foxd1;;chr11:96143962..96144035,+!p2@Hoxb8!1.07!10.66!Hoxb8;;chr1:19202352..19202354,+!p2@Tfap2b!1.07!10.66!Tfap2b;;chr5:120120667..120120685,+!p3@Tbx3!1.06!20.40!Tbx3;;chr12:56700411..56700416,+!p@chr12:56700411..56700416,+!1.06!10.35!Insm2;;chr10:88996295..88996335,-!p3@Nr1h4!1.02!11.27!Nr1h4;;chr11:96132637..96132652,+!p1@Hoxb9!1.02!9.44!Hoxb9;;chr7:6649134..6649167,-!p1@Zim1!1.01!50.54!Zim1;;chr7:17647736..17647772,-!p1@Hif3a!0.98!31.36!Hif3a;;chr11:96147952..96147967,+!p1@Hoxb7!0.96!10.35!Hoxb7;;chr2:146047829..146047847,+!p1@Insm1!0.94!14.31!Insm1;;chr11:5761979..5761992,+!p2@Aebp1!0.93!15.53!Aebp1;;chr11:96145450..96145517,+!p2@Hoxb7!0.93!11.57!Hoxb7;;chr11:5761889..5761969,+!p1@Aebp1!0.90!306.60!Aebp1;;chr4:43575544..43575565,+!p2@Creb3!0.90!42.63!Creb3;;chr7:116154364..116154444,+!p1@Tub!0.90!12.18!Tub;;chr5:67490474..67490494,-!p2@Phox2b!0.90!7.00!Phox2b;;chr10:12810631..12810649,+!p1@Plagl1!0.89!185.72!Plagl1;;chr10:88996336..88996380,-!p2@Nr1h4!0.89!8.53!Nr1h4;;chr5:125538737..125538781,-!p2@Ncor2!0.85!22.83!Ncor2;;chr11:96132767..96132796,+!p2@Hoxb9!0.85!6.09!Hoxb9;;chr6:88148650..88148669,+!p1@Gata2!0.84!52.67!Gata2;;chr6:88143711..88143717,+!p2@Gata2!0.84!9.74!Gata2;;chr15:102839948..102839975,+!p3@Hoxc6!0.83!5.78!Hoxc6;;chr15:102865088..102865107,+!p1@Hoxc4!0.82!7.61!Hoxc4;;chr1:19199236..19199258,+!p1@Tfap2b!0.81!5.48!Tfap2b;;chr5:67490391..67490404,-!p3@Phox2b!0.81!5.48!Phox2b;;chr18:11052456..11052477,+!p3@Gata6!0.80!17.66!Gata6;;chr5:35731493..35731531,+!p1@Hmx1!0.79!5.18!Hmx1;;chr2:44965856..44965896,-!p5@Zeb2!0.77!20.40!Zeb2;;chr8:123640063..123640077,+!p1@Foxc2!0.77!9.44!Foxc2;;chr10:80809447..80809515,-!p5@Hmg20b!0.77!6.09!Hmg20b;;chr12:30213247..30213333,+!p1@Myt1l!0.77!4.87!Myt1l;;chr18:11052485..11052508,+!p2@Gata6!0.76!14.31!Gata6;;chr10:86956396..86956411,-!p1@Ascl1!0.76!7.61!Ascl1;;chr5:120121446..120121461,+!p2@Tbx3!0.75!16.75!Tbx3;;chr5:92391466..92391471,+!p2@Thap6!0.75!7.00!Thap6;;chr5:120120834..120120845,+!p8@Tbx3!0.75!4.57!Tbx3;;chr15:102820964..102821006,+!p1@Hoxc8!0.75!4.57!Hoxc8;;chr18:3281034..3281104,-!p1@Crem!0.74!35.01!Crem;;chr2:28477452..28477483,-!p1@Gfi1b!0.74!5.78!Gfi1b;;chr4:48058129..48058179,+!p2@Nr4a3!0.72!8.53!Nr4a3;;chr15:102865048..102865073,+!p3@Hoxc4!0.72!5.48!Hoxc4;;chr2:181501745..181501778,+!p1@Myt1!0.72!4.26!Myt1;;chr12:34642510..34642530,+!p1@Twist1!0.71!14.31!Twist1;;chr3:95032091..95032183,-!p1@Mllt11!0.69!37.75!Mllt11;;chr9:68501522..68501538,+!p4@Rora!0.68!7.61!Rora;;chrX:45245679..45245702,-!p1@Smarca1!0.67!18.88!Smarca1;;chr1:19199221..19199234,+!p6@Tfap2b!0.67!3.65!Tfap2b;;chr10:126778916..126778974,-!p1@Gli1!0.65!8.53!Gli1;;chr9:96159147..96159204,+!p2@Tfdp2!0.65!7.00!Tfdp2;;chr5:120121169..120121171,+!p4@Tbx3!0.65!6.70!Tbx3;;chr14:65977324..65977372,+!p2@Zfp395!0.64!22.23!Zfp395;;chr4:114732112..114732158,+!p1@Tal1!0.64!8.22!Tal1;;chr7:77511403..77511450,-!p3@Nr2f2!0.64!7.92!Nr2f2;;chr6:52163319..52163342,-!p1@Hoxa3!0.64!5.18!Hoxa3;;chr11:33103563..33103583,-!p1@Tlx3!0.64!3.35!Tlx3;;chr11:57645586..57645597,-!p2@Hand1!0.64!3.35!Hand1;;chr11:96160360..96160397,+!p3@Hoxb6!0.64!3.35!Hoxb6;;chr2:181501710..181501742,+!p2@Myt1!0.64!3.35!Myt1;;chr15:102839912..102839938,+!p5@Hoxc6!0.64!3.35!Hoxc6;;chr14:63864056..63864102,-!p1@Gata4!0.62!6.09!Gata4;;chr2:74542918..74542971,+!p1@Hoxd8!0.62!5.18!Hoxd8;;chr6:52167459..52167492,-!p1@Hoxa7!0.62!3.96!Hoxa7;;chr15:102865131..102865151,+!p2@Hoxc4!0.62!3.65!Hoxc4;;chr3:54559496..54559511,+!p1@Smad9!0.61!7.61!Smad9;;chr4:87452200..87452229,-!p2@Mllt3!0.61!7.31!Mllt3;;chr7:122989594..122989626,-!p1@Sox6!0.61!3.04!Sox6;;chr7:122989632..122989668,-!p2@Sox6!0.61!3.04!Sox6;;chr1:136186574..136186592,+!p1@Myog!0.61!3.04!Myog;;chr2:74549968..74549996,+!p1@Hoxd3!0.60!3.96!Hoxd3;;chr19:37509324..37509337,+!p1@Hhex!0.58!24.05!Hhex;;chr11:85646303..85646329,+!p1@Tbx2!0.57!22.23!Tbx2;;chr9:69137716..69137744,+!p1@Rora!0.57!21.01!Rora;;chr9:48644037..48644067,-!p2@Zbtb16!0.57!7.92!Zbtb16;;chr4:87452180..87452196,-!p3@Mllt3!0.57!6.09!Mllt3;;chr1:165243591..165243625,-!p2@Prrx1!0.57!4.57!Prrx1;;chr2:104966933..104966966,+!p3@Wt1!0.57!2.74!Wt1;;chr7:53631837..53631850,+!p1@Myod1!0.57!2.74!Myod1;;chrX:7544943..7545001,-!p1@Gata1!0.57!2.74!Gata1;;chr10:88996274..88996286,-!p4@Nr1h4!0.57!2.74!Nr1h4;;chr5:120130377..120130432,+!p10@Tbx3!0.57!2.74!Tbx3;;chr6:52161666..52161711,-!p1@Hoxa6!0.57!2.74!Hoxa6;;chr5:67490333..67490342,-!p5@Phox2b!0.57!2.74!Phox2b;;chr3:54559463..54559493,+!p3@Smad9!0.56!5.48!Smad9;;chr2:104966766..104966786,+!p1@Wt1!0.56!4.57!Wt1;;chr11:18918434..18918489,-!p3@Meis1!0.56!4.57!Meis1;;chr9:96159225..96159249,+!p5@Tfdp2!0.56!3.04!Tfdp2;;chr8:87225670..87225697,+!p2@Lyl1!0.55!8.83!Lyl1;;chr11:101755669..101755686,-!p1@Meox1!0.55!5.18!Meox1;;chr10:76424613..76424689,-!p1@Pcbp3!0.54!66.37!Pcbp3;;chr15:102828642..102828653,+!p2@Hoxc6!0.54!2.44!Hoxc6;;chr2:104966874..104966907,+!p2@Wt1!0.54!2.44!Wt1;;chr6:52190467..52190500,-!p1@Hoxa10!0.54!2.44!Hoxa10;;chr5:135582751..135582788,+!p1@Mlxipl!0.53!11.87!Mlxipl;;chr1:165243379..165243402,-!p3@Prrx1!0.53!3.96!Prrx1;;chr11:52096804..52096896,-!p1@Tcf7!0.52!24.05!Tcf7;;chr7:77511234..77511302,-!p2@Nr2f2!0.52!19.49!Nr2f2;;chr13:31898729..31898761,+!p1@Foxc1!0.52!6.70!Foxc1;;chr2:91864449..91864492,-!p3@Creb3l1!0.52!4.26!Creb3l1;;chr7:77505617..77505632,-!p1@Nr2f2!0.51!135.18!Nr2f2;;chr11:96690797..96690813,-!p1@Nfe2l1!0.51!56.63!Nfe2l1;;chr10:119913310..119913366,-!p1@Hmga2!0.51!22.53!Hmga2;;chr16:43363190..43363242,+!p2@Zbtb20!0.51!8.53!Zbtb20;;chr2:115891409..115891425,-!p2@Meis2!0.51!7.92!Meis2;;chr6:108610766..108610781,+!p2@Bhlhe40!0.51!4.57!Bhlhe40;;chr13:44936126..44936164,+!p6@Jarid2!0.51!2.74!Jarid2;;chr15:78994907..78994926,-!p1@Sox10!0.50!6.70!Sox10;;chr18:11052606..11052633,+!p4@Gata6!0.50!6.70!Gata6;;chr2:115891427..115891441,-!p4@Meis2!0.50!5.48!Meis2;;chr1:6720216..6720232,+!p1@St18!0.50!2.13!St18;;chr12:30219426..30219506,+!p2@Myt1l!0.50!2.13!Myt1l;;chr15:102820946..102820961,+!p3@Hoxc8!0.50!2.13!Hoxc8;;chr15:103082088..103082136,-!p2@Nfe2!0.50!2.13!Nfe2;;chr13:83643159..83643226,+!p3@Mef2c!0.50!2.13!Mef2c;;chr6:83301243..83301258,+!p2@Bola3!0.50!2.13!Bola3;;chr11:96160426..96160443,+!p2@Hoxb6!0.50!2.13!Hoxb6;;chr2:74536026..74536039,+!p1@Hoxd9!0.50!2.13!Hoxd9;;chr2:74550015..74550057,+!p2@Hoxd3!0.50!2.13!Hoxd3;;chr2:181406327..181406350,-!p1@Sox18!0.49!88.29!Sox18;;chr4:48058047..48058062,+!p1@Nr4a3!0.49!3.65!Nr4a3;;chr11:52096750..52096772,-!p4@Tcf7!0.49!3.65!Tcf7;;chr3:54559550..54559570,+!p4@Smad9!0.49!3.35!Smad9;;chr4:150503457..150503498,-!p3@Camta1!0.49!2.44!Camta1;;chr2:167514456..167514473,+!p1@Cebpb!0.48!122.09!Cebpb;;chr2:25562346..25562433,+!p1@Bmyc!0.48!49.63!Bmyc;;chr2:115891534..115891589,-!p1@Meis2!0.48!38.67!Meis2;;chr2:163028808..163028869,+!p1@Tox2!0.48!9.13!Tox2;;chr7:77511311..77511352,-!p4@Nr2f2!0.48!4.87!Nr2f2;;chr13:31898637..31898653,+!p2@Foxc1!0.48!4.26!Foxc1;;chr2:92886587..92886622,-!p3@Prdm11!0.48!3.35!Prdm11;;chr19:25746898..25746910,+!p1@Dmrt2!0.48!3.35!Dmrt2;;chr7:17642018..17642045,-!p4@Hif3a!0.48!2.44!Hif3a;;chr12:37835141..37835194,+!p1@Meox2!0.47!7.61!Meox2;;chr11:85646427..85646451,+!p4@Tbx2!0.47!3.96!Tbx2;;chr2:115890953..115890974,-!p6@Meis2!0.47!3.35!Meis2;;chr2:152758938..152758954,-!p2@Foxs1!0.47!3.04!Foxs1;;chr12:39507404..39507441,+!p4@Etv1!0.47!3.04!Etv1;;chr5:120121091..120121100,+!p7@Tbx3!0.47!2.44!Tbx3;;chr1:4483679..4483695,-!p1@Sox17!0.46!11.87!Sox17;;chr11:85646263..85646278,+!p2@Tbx2!0.46!6.09!Tbx2;;chr17:47278081..47278103,+!p1@Trerf1!0.46!5.48!Trerf1;;chrX:7339915..7339935,+!p4@Tfe3!0.46!5.18!Tfe3;;chr14:55711114..55711159,-!p2@Zfhx2!0.46!5.18!Zfhx2;;chr15:103085690..103085710,-!p3@Nfe2!0.46!2.13!Nfe2;;chr2:152561980..152561997,+!p1@Id1!0.45!74.29!Id1;;chr18:11052642..11052659,+!p1@Gata6!0.45!12.48!Gata6;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.45!3.65!Hoxb2;;chr10:119913792..119913820,-!p5@Hmga2!0.45!3.65!Hmga2;;chr2:115890469..115890485,-!p7@Meis2!0.45!3.35!Meis2;;chr11:96143843..96143868,+!p3@Hoxb8!0.45!1.83!Hoxb8;;chr6:30908793..30908815,-!p1@Klf14!0.45!1.83!Klf14;;chr6:83301229..83301242,+!p3@Bola3!0.45!1.83!Bola3;;chr2:9809357..9809371,-!p2@Gata3!0.45!1.83!Gata3;;chr2:74536050..74536065,+!p2@Hoxd9!0.45!1.83!Hoxd9;;chr4:135728473..135728494,+!p5@E2f2!0.45!1.83!E2f2;;chr2:167363692..167363710,+!p1@Snai1!0.44!30.14!Snai1;;chr4:3865501..3865548,-!p1@Plag1!0.44!12.18!Plag1;;chrX:45245644..45245666,-!p2@Smarca1!0.44!7.31!Smarca1;;chr6:52154414..52154462,-!p1@Hoxa5!0.44!2.74!Hoxa5;;chr16:3847206..3847307,+!p1@Zfp174!0.43!11.27!Zfp174;;chr11:11584970..11585030,+!p2@Ikzf1!0.43!2.74!Ikzf1;;chr10:88145766..88145770,-!p1@Spic!0.43!2.44!Spic;;chr7:19608891..19608895,-!p1@Foxa3!0.43!2.44!Foxa3;;chr1:170362273..170362317,-!p1@Pbx1!0.42!68.50!Pbx1;;chr12:9581262..9581282,+!p1@Osr1!0.42!28.32!Osr1;;chr5:120121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Csrnp3;;chr1:19199021..19199048,+!p8@Tfap2b!0.35!1.22!Tfap2b;;chr13:44936077..44936096,+!p9@Jarid2!0.35!1.22!Jarid2;;chr14:63890459..63890484,-!p4@Gata4!0.35!1.22!Gata4;;chr15:76352832..76352900,-!p1@Scrt1!0.35!1.22!Scrt1;;chr14:99697871..99697934,+!p1@Klf5!0.34!38.67!Klf5;;chr1:191994550..191994623,-!p1@Prox1!0.34!13.09!Prox1;;chr10:119913278..119913298,-!p2@Hmga2!0.34!3.65!Hmga2;;chr17:3557785..3557797,-!p3@Tfb1m!0.34!3.04!Tfb1m;;chr7:130644017..130644092,-!p1@Zkscan2!0.34!3.04!Zkscan2;;chr18:76219118..76219155,+!p1@Zbtb7c!0.34!2.74!Zbtb7c;;chr18:76219161..76219176,+!p4@Zbtb7c!0.34!1.83!Zbtb7c;;chr9:106356211..106356242,+!p1@Pcbp4!0.33!37.14!Pcbp4;;chr1:165243792..165243808,-!p1@Prrx1!0.33!6.09!Prrx1;;chr13:55206625..55206636,+!p2@Zfp346!0.33!3.04!Zfp346;;chr4:114581524..114581551,-!p1@Foxd2!0.33!2.13!Foxd2;;chr17:51971960..51971979,-!p1@Satb1!0.33!1.83!Satb1;;chr12:56593574..56593592,-!p1@Nfkbia!0.32!98.65!Nfkbia;;chr8:72662966..72662991,-!p3@LOC100048268,p3@Rfxank!0.32!6.09!Rfxank;;chr2:38206744..38206766,+!p1@Lhx2!0.32!1.52!Lhx2;;chr1:165243272..165243283,-!p6@Prrx1!0.32!1.52!Prrx1;;chr10:92773591..92773623,-!p1@Elk3!0.31!41.10!Elk3;;chr2:152223881..152223933,-!p3@Sox12!0.31!5.48!Sox12;;chr15:35225845..35225867,+!p1@Osr2!0.31!3.96!Osr2;;chr14:52639709..52639753,-!p5@Zfp219!0.31!3.35!Zfp219;;chr2:65683890..65683907,+!p1@Csrnp3!0.31!2.74!Csrnp3;;chr13:37917716..37917742,+!p9@Rreb1!0.31!2.44!Rreb1;;chr6:52167513..52167549,-!p2@Hoxa7!0.31!1.83!Hoxa7;;chr7:144505957..144505972,-!p2@Ebf3!0.31!1.52!Ebf3;;chr11:96213264..96213282,+!p@chr11:96213264..96213282,+!0.31!1.52!Hoxb2;;chr7:56136349..56136360,-!p5@E2f8!0.31!1.52!E2f8;;chr9:96159116..96159130,+!p6@Tfdp2!0.31!1.52!Tfdp2;;chr18:76401314..76401395,+!p2@Smad2!0.30!12.18!Smad2;;chr4:120498356..120498401,-!p2@Nfyc!0.30!9.44!Nfyc;;chr2:152758901..152758925,-!p1@Foxs1!0.30!7.31!Foxs1;;chr3:5218629..5218684,+!p1@Zfhx4!0.30!5.18!Zfhx4;;chr11:5761871..5761882,+!p3@Aebp1!0.30!3.96!Aebp1;;chr2:152223783..152223812,-!p4@Sox12!0.30!3.35!Sox12;;chr1:170361777..170361797,-!p10@Pbx1!0.30!2.44!Pbx1;;chr8:24780125..24780143,+!p1@Zmat4!0.30!1.83!Zmat4;;chr12:37835120..37835133,+!p2@Meox2!0.30!1.83!Meox2;;chr1:4486453..4486470,-!p3@Sox17!0.30!1.52!Sox17;;chr6:52154386..52154407,-!p2@Hoxa5!0.30!1.52!Hoxa5;;chr6:6831950..6831985,-!p2@Dlx5!0.30!1.22!Dlx5;;chr2:74550178..74550214,+!p5@Hoxd3!0.30!1.22!Hoxd3;;chr4:48058102..48058110,+!p5@Nr4a3!0.30!1.22!Nr4a3;;chr14:76904356..76904367,+!p3@Tsc22d1!0.29!12.18!Tsc22d1;;chr8:123260252..123260264,+!p1@Irf8!0.29!11.87!Irf8;;chr2:130120884..130120972,+!p1@Ebf4!0.29!9.74!Ebf4;;chr4:120488308..120488366,-!p1@Nfyc!0.29!9.44!Nfyc;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.29!3.96!Zfhx3;;chr11:85646341..85646352,+!p3@Tbx2!0.29!2.74!Tbx2;;chr2:169458838..169458859,+!p4@Tshz2!0.29!2.74!Tshz2;;chr11:102178005..102178022,-!p8@Ubtf!0.29!2.13!Ubtf;;chr11:85646469..85646488,+!p5@Tbx2!0.29!1.83!Tbx2;;chr8:123608252..123608268,+!p1@Foxf1a!0.29!1.83!Foxf1a;;chr4:135728181..135728203,+!p2@E2f2!0.29!1.52!E2f2;;chr1:120950269..120950287,-!p6@Gli2!0.29!1.52!Gli2;;chr4:135699731..135699747,+!p1@Id3!0.28!193.03!Id3;;chr14:22807083..22807104,-!p1@Zfp503!0.28!29.84!Zfp503;;chr2:162880327..162880385,+!p2@Mybl2!0.28!10.96!Mybl2;;chr8:72663347..72663398,+!p2@2310045N01Rik,p2@Mef2b!0.28!8.22!Mef2b;;chr9:32443818..32443854,+!p2@Ets1!0.28!7.00!Ets1;;chr15:79177964..79177986,+!p1@Maff!0.28!5.18!Maff;;chr19:19185671..19185693,-!p1@Rorb!0.28!3.35!Rorb;;chr1:170361826..170361844,-!p9@Pbx1!0.28!3.04!Pbx1;;chr4:84320893..84320910,-!p1@Bnc2!0.28!3.04!Bnc2;;chr7:135019147..135019187,-!p3@Zfp668!0.28!3.04!Zfp668;;chr1:189821714..189821761,+!p1@Esrrg!0.28!2.44!Esrrg;;chrX:103070839..103070856,-!p4@Atrx!0.28!1.83!Atrx;;chr14:17407549..17407575,-!p3@Rarb!0.28!1.83!Rarb;;chr13:83663600..83663625,+!p6@Mef2c!0.28!1.83!Mef2c;;chr12:58646974..58647003,-!p1@Foxa1!0.28!1.52!Foxa1;;chr8:111227354..111227401,+!p@chr8:111227354..111227401,+!0.28!1.52!Zfhx3;;chr1:64168228..64168250,-!p7@Klf7!0.28!1.52!Klf7;;chr2:180069370..180069409,-!p1@Gata5!0.28!1.22!Gata5;;chr17:48015839..48015915,-!p3@Foxp4!0.28!1.22!Foxp4;;chr10:80555320..80555378,-!p1@Creb3l3!0.28!1.22!Creb3l3;;chr11:96160451..96160462,+!p5@Hoxb6!0.28!0.91!Hoxb6;;chr10:79884592..79884621,-!p5@Tcf3!0.28!0.91!Tcf3;;chr11:90249521..90249551,-!p3@Hlf!0.28!0.91!Hlf;;chr11:96145362..96145389,+!p4@Hoxb7!0.28!0.91!Hoxb7;;chr11:96144050..96144065,+!p5@Hoxb8!0.28!0.91!Hoxb8;;chr11:50641158..50641165,-!p3@Zfp354c!0.28!0.91!Zfp354c;;chr10:12844757..12844771,+!p2@Plagl1!0.28!0.91!Plagl1;;chr10:126778639..126778670,-!p3@Gli1!0.28!0.91!Gli1;;chr19:46380399..46380417,+!p4@Nfkb2!0.28!0.91!Nfkb2;;chr19:5447886..5447905,+!p1@Fosl1!0.28!0.91!Fosl1;;chr18:11052516..11052525,+!p5@Gata6!0.28!0.91!Gata6;;chr18:3281015..3281028,-!p18@Crem!0.28!0.91!Crem;;chr15:76701495..76701535,-!p3@Zfp251!0.28!0.91!Zfp251;;chr2:154395524..154395535,-!p5@E2f1!0.28!0.91!E2f1;;chr2:181501988..181502026,+!p3@Myt1!0.28!0.91!Myt1;;chr2:156665551..156665562,+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@@ Line 44: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11004
+|library_id_phase_based=2:CNhs11004
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1254
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1254
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E16.CNhs11004.1254-43D6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E16.CNhs11004.1254-43D6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E16.CNhs11004.1254-43D6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E16.CNhs11004.1254-43D6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E16.CNhs11004.1254-43D6.mm9.nobarcode.rdna.fa.gz
 |name=adrenal gland, embryo E16
 |namespace=FANTOM5
@@ Line 49: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11004,LSID730,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0231068838819107,0,0,0,0,0,0.128862091360986,0,0,0,0,0.958919297016703,0,0,0,0,0,0,0.209908105311768,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.212488289366187,0,0,0,0,0,0.141805428943962,0.000180718683569225,-0.0725120528170229,0.769503282326624,0.131932818183991,0,0,0,0,0,0,0,0,0,0,0,0.115432590314795,0.140531860239475,0.206537407802916,0,0,0,0.0725856352319198,0,0.0577162951573975,0,0.115432590314795,0,-0.016964789264172,0.0352838456184585,0.24371041342326,0.028297125211384,0,0,0,-0.0161131906174743,0.115432590314795,0,0,0.0713701028482217,0.215685499090635,0.202973365604673,0,0,0,0,0.115432590314795,0,0.196696045577842,0.715874865003031,0.131998453962943,0,0,0,0,0
@@ Line 86: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1254-43D6;search_select_hide=table117:1254-43D6
 }}

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FF:1254-43D6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:40, 4 June 2020

CNhs11004

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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