FF:406-44C5: Difference between revisions

Latest revision as of 19:15, 4 June 2020

Name:	adrenal gland, embryo E14
Species:	Mouse (Mus musculus)
Library ID:	CNhs11038
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	adrenal 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		SAMD00005504

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11038		CAGE		DRX008928		DRR009802

Accession ID Mm9

Library id		BAM		CTSS
CNhs11038		DRZ001227		DRZ002610

Accession ID Mm10

Library id		BAM		CTSS
CNhs11038		DRZ012577		DRZ013960

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

CNhs11038

0	0
1	0
10	0
100	0
1000	0
1001	-0.0365
1002	0.499
1003	-0.0446
1004	0
1005	-0.138
1006	0.0695
1007	-0.00314
1008	0
1009	0.0289
101	0.0858
1010	0
1011	0.0475
1012	0
1013	-0.117
1014	0.315
1015	0.161
1016	0.287
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.0487
1022	-0.0545
1023	0
1024	0.00214
1025	0.0717
1026	0.0108
1027	0.0695
1028	0
1029	-0.0535
103	0.37
1030	0
1031	0.365
1032	-0.017
1033	0.0653
1034	0
1035	0
1036	0.128
1037	0
1038	-0.0567
1039	0.00745
104	0
1040	-0.0023
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: CNhs11038

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00393
MA0003.1	MA0003.1	0.83
MA0004.1	MA0004.1	0.434
MA0006.1	MA0006.1	0.371
MA0007.1	MA0007.1	0.925
MA0009.1	MA0009.1	0.0835
MA0014.1	MA0014.1	0.518
MA0017.1	MA0017.1	5.92242e-4
MA0018.2	MA0018.2	0.921
MA0019.1	MA0019.1	0.82
MA0024.1	MA0024.1	2.86489e-9
MA0025.1	MA0025.1	0.0869
MA0027.1	MA0027.1	3.1015e-4
MA0028.1	MA0028.1	0.553
MA0029.1	MA0029.1	0.00353
MA0030.1	MA0030.1	0.00292
MA0031.1	MA0031.1	0.0024
MA0035.2	MA0035.2	0.0355
MA0038.1	MA0038.1	0.0549
MA0039.2	MA0039.2	0.215
MA0040.1	MA0040.1	0.0292
MA0041.1	MA0041.1	0.145
MA0042.1	MA0042.1	0.258
MA0043.1	MA0043.1	0.788
MA0046.1	MA0046.1	9.68521e-5
MA0047.2	MA0047.2	1.40509e-4
MA0048.1	MA0048.1	0.0032
MA0050.1	MA0050.1	1.34247e-5
MA0051.1	MA0051.1	1.09077e-7
MA0052.1	MA0052.1	5.18523e-5
MA0055.1	MA0055.1	0.0126
MA0057.1	MA0057.1	0.115
MA0058.1	MA0058.1	0.71
MA0059.1	MA0059.1	0.464
MA0060.1	MA0060.1	8.56563e-10
MA0061.1	MA0061.1	0.275
MA0062.2	MA0062.2	0.375
MA0065.2	MA0065.2	0.00197
MA0066.1	MA0066.1	0.0629
MA0067.1	MA0067.1	0.284
MA0068.1	MA0068.1	0.427
MA0069.1	MA0069.1	0.363
MA0070.1	MA0070.1	0.254
MA0071.1	MA0071.1	0.246
MA0072.1	MA0072.1	0.322
MA0073.1	MA0073.1	0.966
MA0074.1	MA0074.1	0.743
MA0076.1	MA0076.1	0.635
MA0077.1	MA0077.1	0.125
MA0078.1	MA0078.1	0.77
MA0079.2	MA0079.2	0.807
MA0080.2	MA0080.2	1.52226e-7
MA0081.1	MA0081.1	0.454
MA0083.1	MA0083.1	0.843
MA0084.1	MA0084.1	0.331
MA0087.1	MA0087.1	0.238
MA0088.1	MA0088.1	0.838
MA0090.1	MA0090.1	0.353
MA0091.1	MA0091.1	0.643
MA0092.1	MA0092.1	0.785
MA0093.1	MA0093.1	0.451
MA0099.2	MA0099.2	0.0406
MA0100.1	MA0100.1	0.824
MA0101.1	MA0101.1	0.45
MA0102.2	MA0102.2	0.0122
MA0103.1	MA0103.1	3.57053e-6
MA0104.2	MA0104.2	0.666
MA0105.1	MA0105.1	0.678
MA0106.1	MA0106.1	0.241
MA0107.1	MA0107.1	0.127
MA0108.2	MA0108.2	0.827
MA0111.1	MA0111.1	0.571
MA0112.2	MA0112.2	0.0038
MA0113.1	MA0113.1	0.626
MA0114.1	MA0114.1	0.00246
MA0115.1	MA0115.1	0.195
MA0116.1	MA0116.1	0.786
MA0117.1	MA0117.1	0.456
MA0119.1	MA0119.1	0.777
MA0122.1	MA0122.1	0.71
MA0124.1	MA0124.1	0.412
MA0125.1	MA0125.1	0.0458
MA0131.1	MA0131.1	0.914
MA0135.1	MA0135.1	0.762
MA0136.1	MA0136.1	6.81303e-5
MA0137.2	MA0137.2	0.0224
MA0138.2	MA0138.2	0.0463
MA0139.1	MA0139.1	0.128
MA0140.1	MA0140.1	1.22867e-4
MA0141.1	MA0141.1	0.776
MA0142.1	MA0142.1	0.707
MA0143.1	MA0143.1	0.0729
MA0144.1	MA0144.1	0.155
MA0145.1	MA0145.1	0.0357
MA0146.1	MA0146.1	0.706
MA0147.1	MA0147.1	0.615
MA0148.1	MA0148.1	0.00479
MA0149.1	MA0149.1	0.12
MA0150.1	MA0150.1	0.0453
MA0152.1	MA0152.1	0.797
MA0153.1	MA0153.1	2.92312e-5
MA0154.1	MA0154.1	0.109
MA0155.1	MA0155.1	0.899
MA0156.1	MA0156.1	0.00226
MA0157.1	MA0157.1	0.00539
MA0159.1	MA0159.1	0.0105
MA0160.1	MA0160.1	0.178
MA0162.1	MA0162.1	0.746
MA0163.1	MA0163.1	0.367
MA0164.1	MA0164.1	0.844
MA0258.1	MA0258.1	0.00479
MA0259.1	MA0259.1	0.728

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: CNhs11038

Novel motif	Logo	P-value
1	1	0.0997
10	10	0.212
100	100	0.867
101	101	0.832
102	102	0.848
103	103	0.195
104	104	0.821
105	105	0.42
106	106	0.0303
107	107	0.318
108	108	0.723
109	109	0.369
11	11	0.47
110	110	0.857
111	111	0.0317
112	112	0.258
113	113	0.319
114	114	0.045
115	115	0.733
116	116	0.795
117	117	0.393
118	118	0.467
119	119	0.0761
12	12	0.616
120	120	0.338
121	121	0.84
122	122	0.763
123	123	0.973
124	124	0.63
125	125	0.0655
126	126	0.244
127	127	0.366
128	128	0.0271
129	129	0.107
13	13	0.183
130	130	0.438
131	131	0.814
132	132	0.336
133	133	0.285
134	134	0.319
135	135	0.533
136	136	0.755
137	137	0.858
138	138	0.368
139	139	0.0138
14	14	0.132
140	140	0.13
141	141	0.33
142	142	0.745
143	143	0.283
144	144	0.407
145	145	0.748
146	146	0.776
147	147	0.601
148	148	0.218
149	149	0.689
15	15	0.115
150	150	0.821
151	151	0.0445
152	152	0.518
153	153	0.567
154	154	0.538
155	155	0.912
156	156	2.8089e-7
157	157	0.158
158	158	0.087
159	159	0.0869
160	160	0.98
161	161	0.721
162	162	0.91
163	163	0.0379
164	164	0.344
165	165	0.0814
166	166	0.589
167	167	0.476
168	168	0.535
169	169	0.166
17	17	0.204
18	18	0.778
19	19	0.816
2	2	0.938
20	20	0.865
21	21	0.641
22	22	0.604
23	23	0.234
24	24	0.739
25	25	0.298
26	26	0.481
27	27	0.528
28	28	0.0995
29	29	0.64
3	3	0.576
30	30	0.871
31	31	0.531
32	32	0.975
33	33	0.667
34	34	0.912
35	35	0.106
36	36	0.582
37	37	0.203
38	38	0.693
39	39	0.575
4	4	0.706
40	40	0.915
41	41	0.0218
42	42	0.84
43	43	0.283
44	44	0.47
45	45	0.254
46	46	0.237
47	47	0.353
48	48	0.345
49	49	0.0961
5	5	0.142
50	50	0.533
51	51	0.64
52	52	0.334
53	53	0.898
54	54	0.409
55	55	0.225
56	56	0.689
57	57	0.854
58	58	0.0728
59	59	0.813
6	6	0.578
60	60	0.0673
61	61	0.405
62	62	0.087
63	63	0.347
64	64	0.982
65	65	0.401
66	66	0.621
67	67	0.889
68	68	0.141
69	69	0.623
7	7	0.125
70	70	3.90236e-4
71	71	0.416
72	72	0.486
73	73	0.212
74	74	0.512
75	75	0.425
76	76	0.922
77	77	0.426
78	78	0.313
79	79	0.28
8	8	0.852
80	80	0.15
81	81	0.544
82	82	0.272
83	83	0.57
84	84	0.114
85	85	0.0137
86	86	0.605
87	87	0.978
88	88	0.913
89	89	0.0838
9	9	0.581
90	90	0.328
91	91	0.37
92	92	0.285
93	93	0.213
94	94	0.98
95	95	0.597
96	96	0.887
97	97	0.836
98	98	0.364
99	99	0.82

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: CNhs11038

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011339 mouse adrenal 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)
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)
0000296 (mouse embryonic day 14 sample)
0011339 (mouse adrenal 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: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@SAMD00005504
+|accession_numbers=CAGE;DRX008928;DRR009802;DRZ001227;DRZ002610;DRZ012577;DRZ013960
 |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 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:38570011..38570034,-!p1@Nr5a1!1.99!97.33!Nr5a1;;chr8:59799772..59799789,+!p1@Hand2!1.88!206.97!Hand2;;chr7:108966820..108966835,+!p1@Phox2a!1.86!70.78!Phox2a;;chr11:57645506..57645523,-!p1@Hand1!1.69!48.40!Hand1;;chr6:83020355..83020371,-!p1@Tlx2!1.67!45.63!Tlx2;;chr13:99124189..99124205,+!p1@Foxd1!1.52!48.06!Foxd1;;chr8:87425854..87425891,+!p1@Klf1!1.34!20.64!Klf1;;chr10:22539932..22539956,-!p1@Tcf21!1.24!43.20!Tcf21;;chr10:86956396..86956411,-!p1@Ascl1!1.23!24.81!Ascl1;;chr15:102828658..102828678,+!p1@Hoxc6!1.23!16.13!Hoxc6;;chr12:56700411..56700416,+!p@chr12:56700411..56700416,+!1.20!14.75!Insm2;;chr5:67490284..67490302,-!p1@Phox2b!1.20!14.75!Phox2b;;chr12:34642510..34642530,+!p1@Twist1!1.14!41.12!Twist1;;chr2:146047829..146047847,+!p1@Insm1!1.13!22.55!Insm1;;chr10:119913278..119913298,-!p2@Hmga2!1.12!27.58!Hmga2;;chrX:83437105..83437121,+!p1@Nr0b1!1.08!10.93!Nr0b1;;chr15:101097270..101097290,+!p1@Nr4a1!1.07!111.20!Nr4a1;;chr2:9800207..9800234,-!p1@Gata3!1.06!31.92!Gata3;;chr2:147190749..147190769,+!p1@Pax1!1.06!10.41!Pax1;;chr4:133109285..133109308,+!p1@Nr0b2!1.05!10.24!Nr0b2;;chr10:119913310..119913366,-!p1@Hmga2!1.02!74.43!Hmga2;;chr9:24578720..24578735,-!p1@Tbx20!1.02!9.37!Tbx20;;chr2:38567715..38567730,-!p2@Nr5a1!1.02!9.37!Nr5a1;;chr13:117099847..117099907,-!p1@Isl1!1.00!17.00!Isl1;;chr10:12810631..12810649,+!p1@Plagl1!0.99!235.07!Plagl1;;chr10:119913546..119913583,-!p3@Hmga2!0.98!18.22!Hmga2;;chr11:96153767..96153822,+!p1@Hoxb6!0.98!13.53!Hoxb6;;chr10:119914001..119914078,-!p4@Hmga2!0.98!11.80!Hmga2;;chr11:96147952..96147967,+!p1@Hoxb7!0.95!9.89!Hoxb7;;chr5:67490474..67490494,-!p2@Phox2b!0.95!7.98!Phox2b;;chr7:17647736..17647772,-!p1@Hif3a!0.90!25.50!Hif3a;;chr5:67490391..67490404,-!p3@Phox2b!0.90!6.94!Phox2b;;chr13:31898767..31898785,+!p4@Foxc1!0.89!8.33!Foxc1;;chr14:63864056..63864102,-!p1@Gata4!0.88!11.80!Gata4;;chr15:103085660..103085681,-!p1@Nfe2!0.88!10.24!Nfe2;;chr6:52163319..52163342,-!p1@Hoxa3!0.88!9.72!Hoxa3;;chr11:96132767..96132796,+!p2@Hoxb9!0.88!6.59!Hoxb9;;chr11:96143666..96143725,+!p1@Hoxb8!0.87!7.46!Hoxb8;;chr1:19199236..19199258,+!p1@Tfap2b!0.87!6.42!Tfap2b;;chr11:18918434..18918489,-!p3@Meis1!0.86!10.24!Meis1;;chr2:74549968..74549996,+!p1@Hoxd3!0.85!7.63!Hoxd3;;chr5:120120667..120120685,+!p3@Tbx3!0.84!11.80!Tbx3;;chrX:7544943..7545001,-!p1@Gata1!0.84!5.90!Gata1;;chr18:11052485..11052508,+!p2@Gata6!0.83!17.35!Gata6;;chr15:102865088..102865107,+!p1@Hoxc4!0.83!7.81!Hoxc4;;chr7:116154364..116154444,+!p1@Tub!0.82!10.06!Tub;;chr11:96143962..96144035,+!p2@Hoxb8!0.82!5.55!Hoxb8;;chr2:28477452..28477483,-!p1@Gfi1b!0.80!6.77!Gfi1b;;chr1:19202352..19202354,+!p2@Tfap2b!0.80!5.38!Tfap2b;;chr1:136186574..136186592,+!p1@Myog!0.80!5.38!Myog;;chr11:33103563..33103583,-!p1@Tlx3!0.80!5.38!Tlx3;;chr7:6649134..6649167,-!p1@Zim1!0.79!30.19!Zim1;;chr18:3281750..3281776,-!p2@Crem!0.79!10.93!Crem;;chr8:123640063..123640077,+!p1@Foxc2!0.79!9.89!Foxc2;;chr11:101755669..101755686,-!p1@Meox1!0.79!9.72!Meox1;;chr11:85646303..85646329,+!p1@Tbx2!0.78!35.91!Tbx2;;chr10:126778916..126778974,-!p1@Gli1!0.77!11.62!Gli1;;chr11:96160360..96160397,+!p3@Hoxb6!0.77!4.86!Hoxb6;;chr11:96145450..96145517,+!p2@Hoxb7!0.75!7.29!Hoxb7;;chr6:52176164..52176195,-!p1@Hoxa9!0.74!5.73!Hoxa9;;chr15:102865131..102865151,+!p2@Hoxc4!0.74!5.20!Hoxc4;;chr15:102820964..102821006,+!p1@Hoxc8!0.74!4.51!Hoxc8;;chr11:96132637..96132652,+!p1@Hoxb9!0.74!4.51!Hoxb9;;chr6:88148650..88148669,+!p1@Gata2!0.73!40.77!Gata2;;chr18:3281725..3281740,-!p3@Crem!0.73!5.73!Crem;;chr2:181501745..181501778,+!p1@Myt1!0.73!4.34!Myt1;;chr18:11052642..11052659,+!p1@Gata6!0.72!23.94!Gata6;;chr7:77511403..77511450,-!p3@Nr2f2!0.72!9.72!Nr2f2;;chr11:11584970..11585030,+!p2@Ikzf1!0.72!6.42!Ikzf1;;chr15:102821007..102821021,+!p2@Hoxc8!0.71!4.16!Hoxc8;;chr2:104966874..104966907,+!p2@Wt1!0.70!3.99!Wt1;;chr2:104966766..104966786,+!p1@Wt1!0.69!6.59!Wt1;;chr2:71384802..71384815,-!p1@Dlx2!0.69!5.03!Dlx2;;chr11:18918406..18918431,-!p6@Meis1!0.68!5.38!Meis1;;chr18:11052456..11052477,+!p3@Gata6!0.67!12.84!Gata6;;chr11:85646427..85646451,+!p4@Tbx2!0.67!6.94!Tbx2;;chr15:102828642..102828653,+!p2@Hoxc6!0.67!3.64!Hoxc6;;chr5:35731493..35731531,+!p1@Hmx1!0.67!3.64!Hmx1;;chr6:52167513..52167549,-!p2@Hoxa7!0.65!5.20!Hoxa7;;chr15:102839948..102839975,+!p3@Hoxc6!0.65!3.47!Hoxc6;;chr11:96143843..96143868,+!p3@Hoxb8!0.65!3.47!Hoxb8;;chr11:96160426..96160443,+!p2@Hoxb6!0.65!3.47!Hoxb6;;chr11:85646263..85646278,+!p2@Tbx2!0.64!9.72!Tbx2;;chr12:3891810..3891829,+!p2@Dnmt3a!0.64!5.55!Dnmt3a;;chr15:78994907..78994926,-!p1@Sox10!0.63!9.37!Sox10;;chr17:86087592..86087615,-!p1@Six2!0.63!3.30!Six2;;chr2:147190725..147190747,+!p2@Pax1!0.63!3.30!Pax1;;chr12:28027561..28027591,-!p1@Sox11!0.62!24.46!Sox11;;chr5:120121446..120121461,+!p2@Tbx3!0.62!11.97!Tbx3;;chr13:31898729..31898761,+!p1@Foxc1!0.62!8.85!Foxc1;;chr4:114732112..114732158,+!p1@Tal1!0.62!7.81!Tal1;;chr4:84321300..84321315,-!p2@Bnc2!0.62!3.99!Bnc2;;chr15:102844431..102844445,+!p1@Hoxc5!0.62!3.12!Hoxc5;;chr15: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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011339
 |is_obsolete=
+|library_id=CNhs11038
+|library_id_phase_based=2:CNhs11038
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;406
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;406
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E14.CNhs11038.406-44C5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E14.CNhs11038.406-44C5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E14.CNhs11038.406-44C5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E14.CNhs11038.406-44C5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E14.CNhs11038.406-44C5.mm9.nobarcode.rdna.fa.gz
 |name=adrenal gland, embryo E14
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11038,LSID732,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.053116529417207,0,0,0,0,0,-0.127809669481619,0,0.0174177812894006,0,0,0.670322761513305,0,0,0,0,0,0,-0.122415687322347,0,0.0347388317801137,0,0,0,0,0,0,0,0,0,0,0,-0.0458305403405808,0,0,0,0.0694776635602275,0.00526053745037261,0.0812111842018738,0.0443775255695939,0.0427466112817849,0.463933732489178,0.00137491055024036,0,0,0,0,0,0,0,0,0,0,0,0,0.115968303559107,0.129358133846345,0,0,0,-0.0123465667488701,0,0.00158180957122103,0,0,0,0.0927804895732492,0.0673623161694392,0.305553923766408,0.0476845321043011,0,0.0694776635602275,0,-0.00205932941526066,0.0694776635602275,0,0.0302254098232649,0.0619271756064357,0.13139315847054,-0.00935393127967993,0,0,0,0,0,0,0.177602051593862,0.376934350122405,0.0254199080390297,0,0,0,0,0
@@ Line 62: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 82: / Line 97: @@
 |top_motifs=HOX{A5,B5}:1.55168249111;FOXD3:1.32691568294;SOX5:1.2891100219;PAX1,9:1.24967823365;CDC5L:1.11558910119;MYBL2:1.09922934433;RXR{A,B,G}:1.0666243681;NFY{A,B,C}:1.04969930185;HSF1,2:1.01582905377;GATA4:0.955658699274;PBX1:0.924234145475;GFI1:0.922689272855;E2F1..5:0.86871133767;NANOG:0.847815119438;ADNP_IRX_SIX_ZHX:0.822781160804;NKX3-1:0.795768765474;EVI1:0.793204772242;GLI1..3:0.790183582459;PATZ1:0.774100507541;RREB1:0.759054456189;ZIC1..3:0.754837316274;FOXP1:0.73192403001;IKZF2:0.722310206069;EP300:0.718668190425;GATA6:0.694804114487;UFEwm:0.642833866615;TFDP1:0.611253167674;TOPORS:0.570007345345;SOX{8,9,10}:0.554680496761;EN1,2:0.541452049399;TAL1_TCF{3,4,12}:0.540806895229;XCPE1{core}:0.539925104111;ZNF384:0.53680981277;VSX1,2:0.51841341273;GTF2I:0.512806009593;FOXL1:0.506805424443;ARID5B:0.501631410676;GZF1:0.463902854866;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.463307206506;MZF1:0.442164406202;ZNF143:0.402522814478;GFI1B:0.399292887144;MAZ:0.384831437737;ZNF423:0.38354428533;DBP:0.379157027045;MTE{core}:0.376621636554;HOXA9_MEIS1:0.363484473734;SOX17:0.357156428037;ZNF238:0.353818297141;IKZF1:0.338901024873;HES1:0.338787508871;NRF1:0.311641134162;AIRE:0.308752218273;TFAP2{A,C}:0.269838925026;BREu{core}:0.260131666402;NR1H4:0.256505640013;TFAP2B:0.25456577926;LEF1_TCF7_TCF7L1,2:0.241741335721;KLF4:0.240229003917;SOX2:0.23897683569;EGR1..3:0.228890190089;TFCP2:0.224656629405;MED-1{core}:0.222233480645;PDX1:0.197210018529;YY1:0.192923689207;ZBTB16:0.184726791243;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.18235140246;FOXM1:0.181342798929;PAX4:0.165895145322;TBX4,5:0.158645163214;PAX6:0.155480974332;PRRX1,2:0.15333821541;AHR_ARNT_ARNT2:0.150854153644;TLX1..3_NFIC{dimer}:0.14423871494;TFAP4:0.136534131464;SP1:0.130015208454;NR3C1:0.114085813254;ELK1,4_GABP{A,B1}:0.112743288295;ONECUT1,2:0.112480092006;ATF2:0.112430105484;HIC1:0.11041930988;PAX5:0.0901480075904;NANOG{mouse}:0.0844614708344;ELF1,2,4:0.0825299651135;NFE2L2:0.0819073780209;TEAD1:0.0762344247674;HMGA1,2:0.0756564359932;FOXP3:0.0658099516286;SRF:0.0594079045657;REST:0.0423802765564;SPZ1:0.0403698063592;NR5A1,2:0.025095801676;LHX3,4:0.019961293534;PRDM1:0.00627480431923;POU2F1..3:0.00525432713486;NKX3-2:-0.00028002197259;MYB:-0.00370877058925;ZNF148:-0.00482129063512;MTF1:-0.00625333459839;STAT5{A,B}:-0.0115213518688;ZFP161:-0.0138999097228;TBP:-0.020559428756;BACH2:-0.0249646632036;CUX2:-0.0307762710678;JUN:-0.0480502521899;OCT4_SOX2{dimer}:-0.0501863875046;PITX1..3:-0.0515550222733;RFX1:-0.059980130394;SPIB:-0.0641855288871;HIF1A:-0.0695387859674;HBP1_HMGB_SSRP1_UBTF:-0.0854629012393;TLX2:-0.0870787674746;GCM1,2:-0.0873882071502;CDX1,2,4:-0.0888839548425;TEF:-0.10146667072;POU3F1..4:-0.101478326755;ESR1:-0.107250524282;NKX2-3_NKX2-5:-0.117817649216;ATF4:-0.121547327108;ZBTB6:-0.148409631366;HAND1,2:-0.149732431552;NKX2-1,4:-0.159661981873;MYFfamily:-0.170330620243;HNF1A:-0.183410870009;TGIF1:-0.186342646255;PAX8:-0.192547561834;NR6A1:-0.199996323267;NFE2:-0.203343870101;ALX4:-0.212208475869;POU1F1:-0.214844112121;RUNX1..3:-0.223003475959;FOX{F1,F2,J1}:-0.223061654974;HOX{A4,D4}:-0.228584208177;GTF2A1,2:-0.229558594157;DMAP1_NCOR{1,2}_SMARC:-0.231162412308;SPI1:-0.246433032613;ALX1:-0.24823429765;CRX:-0.250099830899;ETS1,2:-0.255827332459;CEBPA,B_DDIT3:-0.259193204422;NFIX:-0.263778622661;FOSL2:-0.294987545981;MEF2{A,B,C,D}:-0.296189459881;HNF4A_NR2F1,2:-0.301477827032;FOX{I1,J2}:-0.303993722517;NFKB1_REL_RELA:-0.33235651637;RFX2..5_RFXANK_RFXAP:-0.338802538315;NHLH1,2:-0.345567287373;NKX6-1,2:-0.365749471863;HLF:-0.36952303691;CREB1:-0.382140039082;FOXA2:-0.401037568129;RORA:-0.405295476884;NFATC1..3:-0.414969665918;ATF5_CREB3:-0.415105432595;ESRRA:-0.421772008312;POU6F1:-0.428970593893;POU5F1:-0.447040511808;ATF6:-0.464065052535;TP53:-0.464721222472;RXRA_VDR{dimer}:-0.466558087996;LMO2:-0.470602193739;HMX1:-0.485133066638;FOXN1:-0.486601744355;EBF1:-0.49270520856;AR:-0.545520831903;STAT2,4,6:-0.557385675572;MAFB:-0.584626587595;RBPJ:-0.594501090551;STAT1,3:-0.630747719107;FOX{D1,D2}:-0.675396057911;SMAD1..7,9:-0.681163077798;NKX2-2,8:-0.690687121744;MYOD1:-0.693730670582;NFIL3:-0.741700509986;FOS_FOS{B,L1}_JUN{B,D}:-0.767732646402;PAX2:-0.783318646284;BPTF:-0.829287368981;IRF1,2:-0.876480099557;FOXO1,3,4:-0.893371954589;IRF7:-0.934593100858;SNAI1..3:-0.943067643386;T:-0.951180101682;bHLH_family:-0.966163792786;NFE2L1:-0.971305929193;PPARG:-1.08518803546;SREBF1,2:-1.20464591046;ZEB1:-1.26220891;FOXQ1:-1.51901289917
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:406-44C5;search_select_hide=table117:406-44C5
 }}

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FF:406-44C5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:15, 4 June 2020

CNhs11038

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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