FF:1262-18F5: Difference between revisions

Latest revision as of 18:41, 4 June 2020

Name:	adrenal gland, embryo E18
Species:	Mouse (Mus musculus)
Library ID:	CNhs11026
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	adrenal gland
dev stage	18 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		SAMD00005611

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11026		CAGE		DRX008931		DRR009805

Accession ID Mm9

Library id		BAM		CTSS
CNhs11026		DRZ001230		DRZ002613

Accession ID Mm10

Library id		BAM		CTSS
CNhs11026		DRZ012580		DRZ013963

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

CNhs11026

0	0
1	0.0595
10	0
100	0
1000	0.0522
1001	0.0246
1002	0.221
1003	-0.12
1004	0
1005	0
1006	0.132
1007	9.728956e-4
1008	0
1009	0.148
101	-0.00691
1010	0
1011	-0.0929
1012	0.0166
1013	0.0717
1014	0.313
1015	-0.0481
1016	-0.0358
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.00821
1022	0
1023	0
1024	0.061
1025	0
1026	0.0315
1027	0
1028	0
1029	0.0289
103	0.162
1030	0
1031	0.134
1032	-0.00893
1033	0
1034	0
1035	0
1036	-0.0143
1037	0
1038	-0.119
1039	0.196
104	0
1040	0.00921
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: CNhs11026

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.022
MA0003.1	MA0003.1	0.434
MA0004.1	MA0004.1	0.00832
MA0006.1	MA0006.1	0.833
MA0007.1	MA0007.1	0.816
MA0009.1	MA0009.1	0.0255
MA0014.1	MA0014.1	0.218
MA0017.1	MA0017.1	0.0285
MA0018.2	MA0018.2	0.864
MA0019.1	MA0019.1	0.562
MA0024.1	MA0024.1	0.864
MA0025.1	MA0025.1	0.446
MA0027.1	MA0027.1	0.00498
MA0028.1	MA0028.1	0.202
MA0029.1	MA0029.1	0.00103
MA0030.1	MA0030.1	0.481
MA0031.1	MA0031.1	0.54
MA0035.2	MA0035.2	0.807
MA0038.1	MA0038.1	0.327
MA0039.2	MA0039.2	0.657
MA0040.1	MA0040.1	0.0413
MA0041.1	MA0041.1	0.00973
MA0042.1	MA0042.1	0.258
MA0043.1	MA0043.1	0.277
MA0046.1	MA0046.1	0.0477
MA0047.2	MA0047.2	0.238
MA0048.1	MA0048.1	0.0178
MA0050.1	MA0050.1	0.887
MA0051.1	MA0051.1	0.22
MA0052.1	MA0052.1	0.0147
MA0055.1	MA0055.1	0.339
MA0057.1	MA0057.1	0.262
MA0058.1	MA0058.1	0.136
MA0059.1	MA0059.1	0.467
MA0060.1	MA0060.1	0.994
MA0061.1	MA0061.1	0.642
MA0062.2	MA0062.2	0.411
MA0065.2	MA0065.2	0.612
MA0066.1	MA0066.1	0.929
MA0067.1	MA0067.1	0.547
MA0068.1	MA0068.1	0.143
MA0069.1	MA0069.1	0.0837
MA0070.1	MA0070.1	0.0131
MA0071.1	MA0071.1	0.0259
MA0072.1	MA0072.1	0.0358
MA0073.1	MA0073.1	0.969
MA0074.1	MA0074.1	0.418
MA0076.1	MA0076.1	0.355
MA0077.1	MA0077.1	0.796
MA0078.1	MA0078.1	0.839
MA0079.2	MA0079.2	0.721
MA0080.2	MA0080.2	1.11528e-6
MA0081.1	MA0081.1	0.121
MA0083.1	MA0083.1	0.0972
MA0084.1	MA0084.1	0.119
MA0087.1	MA0087.1	0.0257
MA0088.1	MA0088.1	0.0912
MA0090.1	MA0090.1	0.244
MA0091.1	MA0091.1	0.461
MA0092.1	MA0092.1	0.947
MA0093.1	MA0093.1	0.0299
MA0099.2	MA0099.2	0.975
MA0100.1	MA0100.1	0.0646
MA0101.1	MA0101.1	0.172
MA0102.2	MA0102.2	0.201
MA0103.1	MA0103.1	1.25243e-9
MA0104.2	MA0104.2	0.138
MA0105.1	MA0105.1	0.364
MA0106.1	MA0106.1	0.497
MA0107.1	MA0107.1	0.0257
MA0108.2	MA0108.2	0.247
MA0111.1	MA0111.1	0.336
MA0112.2	MA0112.2	0.0525
MA0113.1	MA0113.1	0.56
MA0114.1	MA0114.1	0.586
MA0115.1	MA0115.1	0.171
MA0116.1	MA0116.1	0.198
MA0117.1	MA0117.1	0.592
MA0119.1	MA0119.1	0.0141
MA0122.1	MA0122.1	0.245
MA0124.1	MA0124.1	0.765
MA0125.1	MA0125.1	0.185
MA0131.1	MA0131.1	0.467
MA0135.1	MA0135.1	0.461
MA0136.1	MA0136.1	1.22874e-4
MA0137.2	MA0137.2	0.627
MA0138.2	MA0138.2	0.221
MA0139.1	MA0139.1	0.87
MA0140.1	MA0140.1	0.028
MA0141.1	MA0141.1	7.30535e-6
MA0142.1	MA0142.1	0.847
MA0143.1	MA0143.1	0.176
MA0144.1	MA0144.1	0.963
MA0145.1	MA0145.1	0.568
MA0146.1	MA0146.1	0.798
MA0147.1	MA0147.1	0.0786
MA0148.1	MA0148.1	0.498
MA0149.1	MA0149.1	0.216
MA0150.1	MA0150.1	0.306
MA0152.1	MA0152.1	0.78
MA0153.1	MA0153.1	0.00169
MA0154.1	MA0154.1	0.0446
MA0155.1	MA0155.1	0.768
MA0156.1	MA0156.1	0.00395
MA0157.1	MA0157.1	0.283
MA0159.1	MA0159.1	0.253
MA0160.1	MA0160.1	0.0423
MA0162.1	MA0162.1	0.254
MA0163.1	MA0163.1	0.026
MA0164.1	MA0164.1	0.997
MA0258.1	MA0258.1	0.532
MA0259.1	MA0259.1	0.371

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: CNhs11026

Novel motif	Logo	P-value
1	1	0.157
10	10	0.798
100	100	0.734
101	101	0.885
102	102	0.402
103	103	0.35
104	104	0.901
105	105	0.175
106	106	0.0905
107	107	0.962
108	108	0.12
109	109	0.921
11	11	0.717
110	110	0.0673
111	111	0.209
112	112	0.749
113	113	0.567
114	114	0.59
115	115	0.809
116	116	0.652
117	117	0.521
118	118	0.568
119	119	0.889
12	12	0.874
120	120	0.12
121	121	0.354
122	122	0.542
123	123	0.122
124	124	0.249
125	125	0.585
126	126	0.048
127	127	0.655
128	128	0.0261
129	129	0.81
13	13	0.685
130	130	0.427
131	131	0.398
132	132	0.571
133	133	0.208
134	134	0.163
135	135	0.0745
136	136	0.977
137	137	0.59
138	138	0.217
139	139	0.926
14	14	0.775
140	140	0.503
141	141	0.726
142	142	0.882
143	143	0.439
144	144	0.148
145	145	0.684
146	146	0.887
147	147	0.473
148	148	0.424
149	149	0.152
15	15	0.82
150	150	0.463
151	151	0.733
152	152	0.514
153	153	0.536
154	154	0.194
155	155	0.671
156	156	8.51262e-5
157	157	0.42
158	158	0.36
159	159	0.831
160	160	0.298
161	161	0.977
162	162	0.902
163	163	0.262
164	164	0.562
165	165	0.809
166	166	0.649
167	167	0.629
168	168	0.309
169	169	0.101
17	17	0.891
18	18	0.181
19	19	0.112
2	2	0.432
20	20	0.395
21	21	0.645
22	22	0.141
23	23	0.59
24	24	0.294
25	25	0.41
26	26	0.27
27	27	0.982
28	28	0.33
29	29	0.763
3	3	0.492
30	30	0.766
31	31	0.974
32	32	0.728
33	33	0.411
34	34	0.76
35	35	0.307
36	36	0.958
37	37	0.257
38	38	0.864
39	39	0.623
4	4	0.392
40	40	0.847
41	41	6.07432e-5
42	42	0.932
43	43	0.805
44	44	0.205
45	45	0.178
46	46	0.417
47	47	0.688
48	48	0.782
49	49	0.527
5	5	0.621
50	50	0.516
51	51	0.835
52	52	0.178
53	53	0.395
54	54	0.862
55	55	0.00934
56	56	0.825
57	57	0.44
58	58	0.268
59	59	0.83
6	6	0.375
60	60	0.068
61	61	0.304
62	62	0.377
63	63	0.813
64	64	0.606
65	65	0.556
66	66	0.356
67	67	0.913
68	68	0.586
69	69	0.323
7	7	0.218
70	70	0.0101
71	71	0.768
72	72	0.703
73	73	0.294
74	74	0.925
75	75	0.489
76	76	0.979
77	77	0.229
78	78	0.442
79	79	0.901
8	8	0.536
80	80	0.36
81	81	0.644
82	82	0.0908
83	83	0.138
84	84	0.374
85	85	0.198
86	86	0.856
87	87	0.0171
88	88	0.964
89	89	0.29
9	9	0.512
90	90	0.72
91	91	0.205
92	92	0.535
93	93	0.403
94	94	0.787
95	95	0.118
96	96	0.481
97	97	0.962
98	98	0.619
99	99	0.41

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: CNhs11026

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000302 mouse embryonic day 18 sample
FF:0011518 adrenal gland - embryo E18 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)
0000302 (mouse embryonic day 18 sample)
0011518 (adrenal gland - embryo E18 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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002369,UBERON:0002100,UBERON:0000483,UBERON:0002530,UBERON:0000926,UBERON:0000479,UBERON:0002346,UBERON:0002368,UBERON:0004121,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0009569,UBERON:0005291,UBERON:0005177,UBERON:0003104,UBERON:0005172,UBERON:0006858,UBERON:0005256,UBERON:0006598,UBERON:0005157,UBERON:0005173,UBERON:0002532,UBERON:0000924,UBERON:0002417,UBERON:0000949,UBERON:0000916,UBERON:0003075,UBERON:0002342,UBERON:0009142,UBERON:0003064,UBERON:0006601,UBERON:0006603,UBERON:0005062,UBERON:0007284
+|DRA_sample_Accession=CAGE@SAMD00005611
+|accession_numbers=CAGE;DRX008931;DRR009805;DRZ001230;DRZ002613;DRZ012580;DRZ013963
+|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=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000302,FF:0011518
 |comment=fantom:1262-18F5
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:38570011..38570034,-!p1@Nr5a1!2.22!163.68!Nr5a1;;chr8:59799772..59799789,+!p1@Hand2!1.75!154.34!Hand2;;chr7:108966820..108966835,+!p1@Phox2a!1.71!49.74!Phox2a;;chr11:57645506..57645523,-!p1@Hand1!1.43!26.23!Hand1;;chr6:83020355..83020371,-!p1@Tlx2!1.36!22.01!Tlx2;;chr4:133109285..133109308,+!p1@Nr0b2!1.32!19.74!Nr0b2;;chr11:96143666..96143725,+!p1@Hoxb8!1.29!21.10!Hoxb8;;chr11:96147952..96147967,+!p1@Hoxb7!1.26!21.25!Hoxb7;;chr2:38567715..38567730,-!p2@Nr5a1!1.25!16.88!Nr5a1;;chrX:83437105..83437121,+!p1@Nr0b1!1.25!16.73!Nr0b1;;chr15:102828658..102828678,+!p1@Hoxc6!1.24!16.28!Hoxc6;;chr11:96153767..96153822,+!p1@Hoxb6!1.22!24.27!Hoxb6;;chr11:96132637..96132652,+!p1@Hoxb9!1.22!15.68!Hoxb9;;chr10:88996295..88996335,-!p3@Nr1h4!1.19!17.48!Nr1h4;;chr5:120120667..120120685,+!p3@Tbx3!1.18!26.83!Tbx3;;chr9:24578720..24578735,-!p1@Tbx20!1.18!14.17!Tbx20;;chr10:22539932..22539956,-!p1@Tcf21!1.17!36.63!Tcf21;;chr15:101097270..101097290,+!p1@Nr4a1!1.08!114.10!Nr4a1;;chr5:67490284..67490302,-!p1@Phox2b!1.08!11.15!Phox2b;;chr10:88996336..88996380,-!p2@Nr1h4!1.06!13.11!Nr1h4;;chr18:3281750..3281776,-!p2@Crem!1.04!20.65!Crem;;chr4:43575544..43575565,+!p2@Creb3!1.03!57.12!Creb3;;chr11:5761979..5761992,+!p2@Aebp1!1.00!18.54!Aebp1;;chr2:9800207..9800234,-!p1@Gata3!0.98!26.83!Gata3;;chr15:102839948..102839975,+!p3@Hoxc6!0.98!8.59!Hoxc6;;chr13:117099847..117099907,-!p1@Isl1!0.97!15.68!Isl1;;chr11:5761889..5761969,+!p1@Aebp1!0.95!337.47!Aebp1;;chr7:116154364..116154444,+!p1@Tub!0.91!12.51!Tub;;chr5:67490474..67490494,-!p2@Phox2b!0.90!6.93!Phox2b;;chr7:6649134..6649167,-!p1@Zim1!0.89!38.58!Zim1;;chr12:56700411..56700416,+!p@chr12:56700411..56700416,+!0.89!6.78!Insm2;;chr11:96145450..96145517,+!p2@Hoxb7!0.86!9.65!Hoxb7;;chr18:11052485..11052508,+!p2@Gata6!0.85!17.94!Gata6;;chr13:99124189..99124205,+!p1@Foxd1!0.84!9.19!Foxd1;;chr15:102839912..102839938,+!p5@Hoxc6!0.84!5.88!Hoxc6;;chr7:17647736..17647772,-!p1@Hif3a!0.83!21.70!Hif3a;;chr2:44965856..44965896,-!p5@Zeb2!0.81!22.91!Zeb2;;chr15:102828642..102828653,+!p2@Hoxc6!0.81!5.43!Hoxc6;;chr6:88143711..88143717,+!p2@Gata2!0.80!8.89!Gata2;;chr18:3281725..3281740,-!p3@Crem!0.80!6.93!Crem;;chr5:120120834..120120845,+!p8@Tbx3!0.80!5.28!Tbx3;;chr5:35731493..35731531,+!p1@Hmx1!0.80!5.28!Hmx1;;chr2:115890953..115890974,-!p6@Meis2!0.79!8.14!Meis2;;chr11:96143962..96144035,+!p2@Hoxb8!0.79!5.12!Hoxb8;;chr1:52176315..52176343,+!p1@Stat1!0.77!76.87!Stat1;;chr18:3281034..3281104,-!p1@Crem!0.77!37.98!Crem;;chr16:3847206..3847307,+!p1@Zfp174!0.77!25.62!Zfp174;;chr10:80809447..80809515,-!p5@Hmg20b!0.77!6.18!Hmg20b;;chr5:67490391..67490404,-!p3@Phox2b!0.77!4.82!Phox2b;;chr6:88148650..88148669,+!p1@Gata2!0.76!43.41!Gata2;;chr9:68501522..68501538,+!p4@Rora!0.76!9.50!Rora;;chr10:12810631..12810649,+!p1@Plagl1!0.75!135.35!Plagl1;;chr9:69137716..69137744,+!p1@Rora!0.75!31.95!Rora;;chr10:88996274..88996286,-!p4@Nr1h4!0.75!4.67!Nr1h4;;chr1:19202352..19202354,+!p2@Tfap2b!0.75!4.67!Tfap2b;;chr5:120130377..120130432,+!p10@Tbx3!0.74!4.52!Tbx3;;chr11:96160360..96160397,+!p3@Hoxb6!0.73!4.37!Hoxb6;;chr1:19199236..19199258,+!p1@Tfap2b!0.72!4.22!Tfap2b;;chr5:125538737..125538781,-!p2@Ncor2!0.71!16.58!Ncor2;;chr11:96132767..96132796,+!p2@Hoxb9!0.70!4.07!Hoxb9;;chr2:74549968..74549996,+!p1@Hoxd3!0.69!4.97!Hoxd3;;chr6:52161666..52161711,-!p1@Hoxa6!0.68!3.77!Hoxa6;;chr5:120121446..120121461,+!p2@Tbx3!0.66!13.26!Tbx3;;chr15:103085660..103085681,-!p1@Nfe2!0.66!5.73!Nfe2;;chr16:43363190..43363242,+!p2@Zbtb20!0.65!12.06!Zbtb20;;chr18:11052456..11052477,+!p3@Gata6!0.65!12.06!Gata6;;chr15:102865088..102865107,+!p1@Hoxc4!0.65!4.82!Hoxc4;;chr11:96160403..96160416,+!p4@Hoxb6!0.65!3.47!Hoxb6;;chr7:148452314..148452329,-!p1@Irf7!0.64!27.28!Irf7;;chr15:102820964..102821006,+!p1@Hoxc8!0.64!3.32!Hoxc8;;chrX:45245679..45245702,-!p1@Smarca1!0.63!16.88!Smarca1;;chr4:48058129..48058179,+!p2@Nr4a3!0.63!6.78!Nr4a3;;chr11:96690797..96690813,-!p1@Nfe2l1!0.62!72.80!Nfe2l1;;chr11:96160426..96160443,+!p2@Hoxb6!0.62!3.17!Hoxb6;;chr15:102839976..102839989,+!p4@Hoxc6!0.62!3.17!Hoxc6;;chr19:37509324..37509337,+!p1@Hhex!0.61!25.92!Hhex;;chr9:96653072..96653154,-!p1@Zbtb38!0.61!9.34!Zbtb38;;chr2:74542918..74542971,+!p1@Hoxd8!0.61!4.97!Hoxd8;;chr5:92391466..92391471,+!p2@Thap6!0.61!4.82!Thap6;;chr8:123640063..123640077,+!p1@Foxc2!0.60!6.03!Foxc2;;chr6:52167513..52167549,-!p2@Hoxa7!0.60!4.52!Hoxa7;;chr8:87425854..87425891,+!p1@Klf1!0.60!3.01!Klf1;;chr15:102820946..102820961,+!p3@Hoxc8!0.60!3.01!Hoxc8;;chr3:95032091..95032183,-!p1@Mllt11!0.58!29.09!Mllt11;;chr3:54559496..54559511,+!p1@Smad9!0.58!7.08!Smad9;;chr10:86956396..86956411,-!p1@Ascl1!0.58!4.67!Ascl1;;chr11:96143843..96143868,+!p3@Hoxb8!0.57!2.71!Hoxb8;;chr15:102821007..102821021,+!p2@Hoxc8!0.57!2.71!Hoxc8;;chr15:78994907..78994926,-!p1@Sox10!0.56!7.99!Sox10;;chr5:120121169..120121171,+!p4@Tbx3!0.56!5.28!Tbx3;;chr2:146047829..146047847,+!p1@Insm1!0.56!5.28!Insm1;;chr4:99322820..99322845,+!p1@Foxd3!0.55!3.47!Foxd3;;chr2:74549945..74549965,+!p4@Hoxd3!0.55!2.56!Hoxd3;;chr12:30213247..30213333,+!p1@Myt1l!0.55!2.56!Myt1l;;chr11:85646303..85646329,+!p1@Tbx2!0.54!20.35!Tbx2;;chr15:35225845..35225867,+!p1@Osr2!0.53!7.23!Osr2;;chr17:47278081..47278103,+!p1@Trerf1!0.53!6.48!Trerf1;;chr3:54559463..54559493,+!p3@Smad9!0.53!4.97!Smad9;;chr11:96145393..96145407,+!p3@Hoxb7!0.53!2.41!Hoxb7;;chr15:102865131..102865151,+!p2@Hoxc4!0.52!2.71!Hoxc4;;chr2:167514456..167514473,+!p1@Cebpb!0.51!131.73!Cebpb;;chr7:77511234..77511302,-!p2@Nr2f2!0.51!18.84!Nr2f2;;chr3:51144740..51144743,-!p7@Elf2!0.51!4.22!Elf2;;chr2:115890864..115890869,-!p14@Meis2!0.51!2.26!Meis2;;chr10:77517570..77517581,+!p1@Dnmt3l!0.51!2.26!Dnmt3l;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.50!4.22!Hoxb2;;chr2:28477452..28477483,-!p1@Gfi1b!0.50!2.86!Gfi1b;;chr2:115891534..115891589,-!p1@Meis2!0.49!39.94!Meis2;;chr5:120121020..120121049,+!p1@Tbx3!0.49!16.58!Tbx3;;chr13:44936126..44936164,+!p6@Jarid2!0.49!2.56!Jarid2;;chr2:74543397..74543435,+!p2@Hoxd8!0.49!2.11!Hoxd8;;chr1:6720216..6720232,+!p1@St18!0.49!2.11!St18;;chr1:170362273..170362317,-!p1@Pbx1!0.48!79.13!Pbx1;;chr10:76424613..76424689,-!p1@Pcbp3!0.48!58.03!Pcbp3;;chr2:115891409..115891425,-!p2@Meis2!0.48!7.39!Meis2;;chr9:48644037..48644067,-!p2@Zbtb16!0.48!6.18!Zbtb16;;chr7:77511403..77511450,-!p3@Nr2f2!0.48!5.12!Nr2f2;;chr6:52163319..52163342,-!p1@Hoxa3!0.48!3.32!Hoxa3;;chr11:96180045..96180059,+!p1@Hoxb4!0.48!3.17!Hoxb4;;chrX:103070960..103070973,-!p7@Atrx!0.48!3.01!Atrx;;chr10:88145766..88145770,-!p1@Spic!0.48!2.86!Spic;;chr14:76904313..76904328,+!p1@Tsc22d1!0.47!517.13!Tsc22d1;;chr11:33103563..33103583,-!p1@Tlx3!0.47!1.96!Tlx3;;chr5:67490346..67490357,-!p4@Phox2b!0.47!1.96!Phox2b;;chr12:25780945..25780961,-!p1@Id2!0.46!441.47!Id2;;chr11:52096804..52096896,-!p1@Tcf7!0.46!20.50!Tcf7;;chr2:25562263..25562314,+!p2@Bmyc!0.46!9.50!Bmyc;;chr1:165243792..165243808,-!p1@Prrx1!0.46!8.59!Prrx1;;chr2:25562346..25562433,+!p1@Bmyc!0.45!46.57!Bmyc;;chr11:4604645..4604705,+!p1@Zmat5!0.45!33.31!Zmat5;;chrX:45245644..45245666,-!p2@Smarca1!0.45!7.54!Smarca1;;chr6:108610766..108610781,+!p2@Bhlhe40!0.45!3.92!Bhlhe40;;chr11:85646427..85646451,+!p4@Tbx2!0.45!3.77!Tbx2;;chr2:104966766..104966786,+!p1@Wt1!0.45!3.32!Wt1;;chr14:17407549..17407575,-!p3@Rarb!0.45!3.17!Rarb;;chr2:181501745..181501778,+!p1@Myt1!0.45!1.81!Myt1;;chr18:3281015..3281028,-!p18@Crem!0.45!1.81!Crem;;chr11:57645586..57645597,-!p2@Hand1!0.45!1.81!Hand1;;chr2:9809402..9809422,-!p5@Gata3!0.45!1.81!Gata3;;chr11:18918917..18918944,-!p1@Meis1!0.44!31.50!Meis1;;chr1:191994550..191994623,-!p1@Prox1!0.44!16.88!Prox1;;chr5:135582751..135582788,+!p1@Mlxipl!0.44!9.34!Mlxipl;;chr10:126778916..126778974,-!p1@Gli1!0.44!4.97!Gli1;;chr15:102865048..102865073,+!p3@Hoxc4!0.44!2.41!Hoxc4;;chr5:120121262..120121282,+!p6@Tbx3!0.44!2.11!Tbx3;;chr4:43575485..43575542,+!p1@Creb3!0.43!69.78!Creb3;;chr2:44965788..44965815,-!p11@Zeb2!0.43!3.92!Zeb2;;chr1:93309740..93309811,-!p1@Hes6!0.42!47.63!Hes6;;chr4:3865501..3865548,-!p1@Plag1!0.42!11.61!Plag1;;chr2:152758901..152758925,-!p1@Foxs1!0.42!10.10!Foxs1;;chr2:163028808..163028869,+!p1@Tox2!0.42!7.84!Tox2;;chr4:54957910..54957954,+!p2@Zfp462!0.42!6.48!Zfp462;;chr7:91558392..91558434,-!p1@Arnt2!0.42!5.88!Arnt2;;chr2:34227446..34227511,-!p1@Pbx3!0.42!4.82!Pbx3;;chr16:43363152..43363186,+!p3@Zbtb20!0.42!4.82!Zbtb20;;chr14:63864056..63864102,-!p1@Gata4!0.42!3.47!Gata4;;chr2:74543202..74543213,+!p3@Hoxd8!0.42!1.66!Hoxd8;;chrX:83437070..83437078,+!p2@Nr0b1!0.42!1.66!Nr0b1;;chr11:96180069..96180089,+!p3@Hoxb4!0.42!1.66!Hoxb4;;chr11:96143728..96143745,+!p4@Hoxb8!0.42!1.66!Hoxb8;;chr1:19202185..19202187,+!p9@Tfap2b!0.42!1.66!Tfap2b;;chr1:19199221..19199234,+!p6@Tfap2b!0.42!1.66!Tfap2b;;chr2:181501710..181501742,+!p2@Myt1!0.42!1.66!Myt1;;chr6:30908793..30908815,-!p1@Klf14!0.42!1.66!Klf14;;chr6:88148324..88148328,+!p3@Gata2!0.42!1.66!Gata2;;chr1:170362242..170362256,-!p3@Pbx1!0.41!16.28!Pbx1;;chr1:39250584..39250643,+!p1@Npas2!0.41!11.30!Npas2;;chr9:69137672..69137702,+!p2@Rora!0.41!9.34!Rora;;chr11:85646263..85646278,+!p2@Tbx2!0.41!5.28!Tbx2;;chr5:3647720..3647733,-!p3@Gatad1!0.41!3.62!Gatad1;;chr2:169458192..169458247,+!p1@Tshz2!0.40!19.90!Tshz2;;chr10:127707602..127707633,+!p1@Stat2!0.40!19.59!Stat2;;chr4:120488308..120488366,-!p1@Nfyc!0.40!12.66!Nfyc;;chr2:25562315..25562344,+!p3@Bmyc!0.40!6.93!Bmyc;;chr2:173044380..173044432,-!p1@Zbp1!0.40!4.67!Zbp1;;chrX:137135036..137135064,-!p4@Tsc22d3!0.40!3.77!Tsc22d3;;chr5:138199361..138199441,+!p2@Tsc22d4!0.40!3.62!Tsc22d4;;chr2:169458799..169458832,+!p5@Tshz2!0.40!3.01!Tshz2;;chr5:67490447..67490458,-!p7@Phox2b!0.40!1.51!Phox2b;;chr2:74550015..74550057,+!p2@Hoxd3!0.40!1.51!Hoxd3;;chr12:39506873..39506913,+!p1@Etv1!0.39!22.61!Etv1;;chr14:56223010..56223067,+!p1@Irf9!0.39!17.18!Irf9;;chr7:148008023..148008092,-!p1@Zfp941!0.39!4.67!Zfp941;;chr2:115891381..115891392,-!p5@Meis2!0.39!3.62!Meis2;;chr9:96159147..96159204,+!p2@Tfdp2!0.39!3.47!Tfdp2;;chr11:52096750..52096772,-!p4@Tcf7!0.39!2.71!Tcf7;;chr7:17642018..17642045,-!p4@Hif3a!0.39!1.81!Hif3a;;c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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:1262-18F5
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0000302;;FF:0011518
+|is_a=EFO:0002091;;FF:0000302;;FF:0011518
+|is_obsolete=
+|library_id=CNhs11026
+|library_id_phase_based=2:CNhs11026
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1262
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1262
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E18.CNhs11026.1262-18F5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E18.CNhs11026.1262-18F5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E18.CNhs11026.1262-18F5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E18.CNhs11026.1262-18F5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E18.CNhs11026.1262-18F5.mm9.nobarcode.rdna.fa.gz
 |name=adrenal gland, embryo E18
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11026,LSID731,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0386164965369281,0,0,0,0,0.0194540866222256,0.354483056668813,0,0,0,0,0.753134484858192,0,0,0,0,0,0,0.20730020215465,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.109921816033639,0,0,0,0.06097065795378,0,-0.0473058865196621,-0.00642423785310292,-0.173882657766085,0.59300833151961,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0.372268137966205,0.114425913041783,0.138898324228908,0.114425913041783,0,0,0,0,0,0.085922832509206,0,0,0,0.0539027174228833,0.113895993752317,0.411634787201429,0.0263951770572083,0,0,-0.0285448259420088,-0.0535013992750497,0,0,0.0028682622039967,0.101036392942574,-0.0825854431575437,0.165102211732605,0,0,0,0,0.0876982854977815,0,0.0479291029556382,0.35425202378969,0.101574982289396,0,0,0,0,0
 |rna_box=18
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=adrenal gland
 |top_motifs=EVI1:1.67485216051;PBX1:1.64054044423;FOXD3:1.42636241131;HOX{A5,B5}:1.41227024023;PAX1,9:1.10896922606;IKZF2:1.04698953964;HSF1,2:1.00614284367;NFIX:0.916021255566;ARID5B:0.915388704978;ZIC1..3:0.873679691721;GLI1..3:0.816870266869;IKZF1:0.800169556617;MYBL2:0.798732698238;TAL1_TCF{3,4,12}:0.788843058605;NFE2L2:0.783437352687;NR5A1,2:0.76061776772;UFEwm:0.756253055848;NFE2:0.745827705389;GATA4:0.732149314795;FOX{D1,D2}:0.706842654147;CDC5L:0.701693189429;SOX5:0.677433786428;RXR{A,B,G}:0.66923971324;CEBPA,B_DDIT3:0.64646684853;BACH2:0.641401129233;NKX3-1:0.579850997782;ONECUT1,2:0.554516702519;ZNF423:0.541807086939;GCM1,2:0.508224069732;XCPE1{core}:0.486225055471;PAX4:0.467210586576;NR1H4:0.421743677646;GFI1B:0.405086983562;ESRRA:0.400931052372;EN1,2:0.390816016141;POU1F1:0.371691320879;ZBTB16:0.368693958472;AR:0.364779227774;STAT2,4,6:0.33689089593;GZF1:0.334815985854;FOXP1:0.319909803773;EP300:0.283829542358;GFI1:0.281354425528;HOXA9_MEIS1:0.278489816991;LEF1_TCF7_TCF7L1,2:0.277382667996;GATA6:0.273221798693;PATZ1:0.271901637044;NR6A1:0.245703638148;TFAP4:0.243157704477;SP1:0.238211417478;TOPORS:0.217170710151;TLX1..3_NFIC{dimer}:0.216441015434;DBP:0.210618015809;MYFfamily:0.188898278644;KLF4:0.185998017478;RREB1:0.179208550826;GTF2I:0.178100809503;EBF1:0.177087653827;NANOG:0.17262179051;NFY{A,B,C}:0.144875853295;HMGA1,2:0.14051485412;NKX6-1,2:0.131425378487;CREB1:0.12401996128;PDX1:0.122174820048;REST:0.118826383235;NFIL3:0.115824409255;ELF1,2,4:0.114188271283;ZNF384:0.0990681971248;TEAD1:0.0958249249108;IRF1,2:0.0954738459151;CDX1,2,4:0.0829348913168;FOXP3:0.0791744809538;VSX1,2:0.0778194895299;RORA:0.0777221358479;NKX2-2,8:0.0768979113463;RXRA_VDR{dimer}:0.0729270985219;NR3C1:0.0708806943047;MTE{core}:0.0692766012245;ZNF238:0.0668372169937;PRRX1,2:0.0654850843122;FOXL1:0.0654417282394;TFCP2:0.0496536426499;FOXO1,3,4:0.0410586602626;MED-1{core}:0.0357660630636;NRF1:0.0338027885404;ELK1,4_GABP{A,B1}:0.0320679554926;NKX3-2:0.0302083302762;ADNP_IRX_SIX_ZHX:0.0259124728533;FOSL2:0.0247528362981;TFAP2{A,C}:0.0225339049942;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0173899814475;HNF1A:0.0139905521589;JUN:0.00791591892919;LHX3,4:0.00335631291473;MAZ:-0.00125005248702;HLF:-0.00270693279998;TBP:-0.00984675321772;TEF:-0.0165458722703;ATF2:-0.0366297192272;SPIB:-0.0390312481969;RFX1:-0.0410174893709;MZF1:-0.0453675783196;YY1:-0.0454033909228;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0508768349455;PITX1..3:-0.0517017854933;PAX5:-0.052883150229;ZBTB6:-0.0528981352467;BPTF:-0.0577500968373;ZNF143:-0.0625128100434;NFATC1..3:-0.0627153213312;NANOG{mouse}:-0.0796905111777;ALX4:-0.0806333911961;E2F1..5:-0.0956691182015;FOXA2:-0.0958192915126;TGIF1:-0.103468101115;SRF:-0.111720172501;AIRE:-0.11206235546;SOX{8,9,10}:-0.112099221443;PAX6:-0.119498015081;EGR1..3:-0.123728104013;ATF5_CREB3:-0.14501832731;ATF4:-0.146544094366;STAT1,3:-0.155903213515;HIF1A:-0.158167621024;MEF2{A,B,C,D}:-0.182903798983;AHR_ARNT_ARNT2:-0.203394086702;ZNF148:-0.210417473043;HOX{A4,D4}:-0.213315004734;PRDM1:-0.21819797829;ZFP161:-0.218440319927;TFDP1:-0.22114109874;MTF1:-0.222837707984;RFX2..5_RFXANK_RFXAP:-0.227021289171;TFAP2B:-0.23605927281;FOXN1:-0.238472874881;HNF4A_NR2F1,2:-0.247166619635;CUX2:-0.252832428814;POU5F1:-0.254042235412;ALX1:-0.258242167521;NHLH1,2:-0.269871923011;HIC1:-0.276246192735;NFE2L1:-0.27828517565;DMAP1_NCOR{1,2}_SMARC:-0.280018346747;GTF2A1,2:-0.290828809309;FOXM1:-0.295455845605;ETS1,2:-0.30157784413;MYB:-0.3218127688;SOX2:-0.328783016074;BREu{core}:-0.360291528552;IRF7:-0.372453054525;NKX2-3_NKX2-5:-0.382757553006;SPI1:-0.383109302232;FOX{F1,F2,J1}:-0.393890353849;LMO2:-0.401668966273;FOX{I1,J2}:-0.403398002717;NFKB1_REL_RELA:-0.432676657687;TP53:-0.441900079658;HBP1_HMGB_SSRP1_UBTF:-0.465536471459;SOX17:-0.510470120062;OCT4_SOX2{dimer}:-0.538260521142;TBX4,5:-0.542594335573;RUNX1..3:-0.546327380141;HES1:-0.546548555693;MAFB:-0.575701466945;CRX:-0.582007820732;RBPJ:-0.609251097759;POU6F1:-0.625829985609;ATF6:-0.642532691553;SREBF1,2:-0.659677457238;NKX2-1,4:-0.661679337048;POU3F1..4:-0.743947590188;TLX2:-0.756275598151;FOS_FOS{B,L1}_JUN{B,D}:-0.759548297189;HAND1,2:-0.761317618594;PAX8:-0.765149721807;ESR1:-0.771436226922;SMAD1..7,9:-0.775246579146;PAX2:-0.802396500686;SPZ1:-0.879261561467;MYOD1:-0.879372911385;POU2F1..3:-0.9120847277;STAT5{A,B}:-0.95496449539;bHLH_family:-1.05252292262;PPARG:-1.07449287571;SNAI1..3:-1.08744778842;T:-1.19420134617;HMX1:-1.25572506241;ZEB1:-1.27634516887;FOXQ1:-2.08005739365
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1262-18F5;search_select_hide=table117:1262-18F5
 }}

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FF:1262-18F5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:41, 4 June 2020

CNhs11026

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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