FF:478-18C1: Difference between revisions

Latest revision as of 19:17, 4 June 2020

Name:	thymus, embryo E17
Species:	Mouse (Mus musculus)
Library ID:	CNhs10581
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	thymus
dev stage	17 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		SAMD00004685

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10581		CAGE		DRX009116		DRR009990

Accession ID Mm9

Library id		BAM		CTSS
CNhs10581		DRZ001415		DRZ002798

Accession ID Mm10

Library id		BAM		CTSS
CNhs10581		DRZ012765		DRZ014148

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

CNhs10581

0	0
1	0
10	0
100	0
1000	0
1001	0.00829
1002	0.0389
1003	-0.0479
1004	0
1005	0
1006	-0.0762
1007	0.113
1008	0
1009	-0.0964
101	0.146
1010	0
1011	0.0288
1012	0.0715
1013	-0.128
1014	0.0478
1015	0.116
1016	-0.206
1017	0
1018	0.235
1019	0
102	0
1020	0
1021	0.0842
1022	-0.209
1023	0
1024	-0.00664
1025	0
1026	0
1027	-0.048
1028	0
1029	0.0719
103	0
1030	0
1031	-0.284
1032	-0.345
1033	0.0577
1034	0
1035	0.0715
1036	0.276
1037	0
1038	-0.15
1039	-0.134
104	0
1040	-0.0425
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: CNhs10581

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	9.40968e-5
MA0003.1	MA0003.1	0.695
MA0004.1	MA0004.1	0.307
MA0006.1	MA0006.1	0.935
MA0007.1	MA0007.1	0.215
MA0009.1	MA0009.1	0.721
MA0014.1	MA0014.1	0.202
MA0017.1	MA0017.1	0.0087
MA0018.2	MA0018.2	0.0509
MA0019.1	MA0019.1	0.43
MA0024.1	MA0024.1	1.76865e-10
MA0025.1	MA0025.1	0.00136
MA0027.1	MA0027.1	0.806
MA0028.1	MA0028.1	1.8151e-8
MA0029.1	MA0029.1	0.0442
MA0030.1	MA0030.1	0.519
MA0031.1	MA0031.1	0.472
MA0035.2	MA0035.2	0.401
MA0038.1	MA0038.1	0.162
MA0039.2	MA0039.2	0.576
MA0040.1	MA0040.1	0.666
MA0041.1	MA0041.1	0.979
MA0042.1	MA0042.1	0.864
MA0043.1	MA0043.1	0.377
MA0046.1	MA0046.1	2.64938e-18
MA0047.2	MA0047.2	0.906
MA0048.1	MA0048.1	0.43
MA0050.1	MA0050.1	1.08625e-7
MA0051.1	MA0051.1	5.6976e-7
MA0052.1	MA0052.1	0.00451
MA0055.1	MA0055.1	0.408
MA0057.1	MA0057.1	0.547
MA0058.1	MA0058.1	0.45
MA0059.1	MA0059.1	0.029
MA0060.1	MA0060.1	1.21326e-10
MA0061.1	MA0061.1	2.34278e-7
MA0062.2	MA0062.2	3.4721e-20
MA0065.2	MA0065.2	0.597
MA0066.1	MA0066.1	0.217
MA0067.1	MA0067.1	0.904
MA0068.1	MA0068.1	0.936
MA0069.1	MA0069.1	0.908
MA0070.1	MA0070.1	0.955
MA0071.1	MA0071.1	0.803
MA0072.1	MA0072.1	2.17557e-4
MA0073.1	MA0073.1	0.709
MA0074.1	MA0074.1	0.783
MA0076.1	MA0076.1	4.64894e-11
MA0077.1	MA0077.1	0.429
MA0078.1	MA0078.1	0.692
MA0079.2	MA0079.2	0.0666
MA0080.2	MA0080.2	1.51319e-13
MA0081.1	MA0081.1	0.00254
MA0083.1	MA0083.1	0.105
MA0084.1	MA0084.1	0.98
MA0087.1	MA0087.1	0.571
MA0088.1	MA0088.1	0.0572
MA0090.1	MA0090.1	0.124
MA0091.1	MA0091.1	0.166
MA0092.1	MA0092.1	0.843
MA0093.1	MA0093.1	0.332
MA0099.2	MA0099.2	0.111
MA0100.1	MA0100.1	0.00454
MA0101.1	MA0101.1	6.17705e-7
MA0102.2	MA0102.2	0.386
MA0103.1	MA0103.1	6.24812e-5
MA0104.2	MA0104.2	0.0317
MA0105.1	MA0105.1	5.61405e-8
MA0106.1	MA0106.1	0.55
MA0107.1	MA0107.1	3.06282e-7
MA0108.2	MA0108.2	0.0668
MA0111.1	MA0111.1	0.914
MA0112.2	MA0112.2	0.382
MA0113.1	MA0113.1	0.746
MA0114.1	MA0114.1	0.00306
MA0115.1	MA0115.1	0.149
MA0116.1	MA0116.1	0.00855
MA0117.1	MA0117.1	0.375
MA0119.1	MA0119.1	0.56
MA0122.1	MA0122.1	0.899
MA0124.1	MA0124.1	0.232
MA0125.1	MA0125.1	0.722
MA0131.1	MA0131.1	0.00537
MA0135.1	MA0135.1	0.833
MA0136.1	MA0136.1	3.26113e-26
MA0137.2	MA0137.2	0.00711
MA0138.2	MA0138.2	2.88543e-5
MA0139.1	MA0139.1	0.224
MA0140.1	MA0140.1	0.391
MA0141.1	MA0141.1	0.00925
MA0142.1	MA0142.1	0.658
MA0143.1	MA0143.1	0.147
MA0144.1	MA0144.1	0.246
MA0145.1	MA0145.1	0.275
MA0146.1	MA0146.1	0.289
MA0147.1	MA0147.1	0.0125
MA0148.1	MA0148.1	0.668
MA0149.1	MA0149.1	0.308
MA0150.1	MA0150.1	0.157
MA0152.1	MA0152.1	0.958
MA0153.1	MA0153.1	1.4306e-8
MA0154.1	MA0154.1	0.223
MA0155.1	MA0155.1	0.638
MA0156.1	MA0156.1	7.68435e-31
MA0157.1	MA0157.1	0.612
MA0159.1	MA0159.1	0.429
MA0160.1	MA0160.1	0.0687
MA0162.1	MA0162.1	0.232
MA0163.1	MA0163.1	4.86292e-4
MA0164.1	MA0164.1	0.849
MA0258.1	MA0258.1	0.782
MA0259.1	MA0259.1	0.348

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: CNhs10581

Novel motif	Logo	P-value
1	1	0.93
10	10	0.0341
100	100	0.9
101	101	0.897
102	102	0.499
103	103	0.363
104	104	0.693
105	105	0.741
106	106	0.815
107	107	0.46
108	108	0.37
109	109	0.315
11	11	0.187
110	110	0.0835
111	111	0.878
112	112	0.614
113	113	0.303
114	114	0.187
115	115	0.535
116	116	0.743
117	117	0.00403
118	118	0.197
119	119	0.485
12	12	0.329
120	120	0.336
121	121	0.246
122	122	0.795
123	123	0.608
124	124	0.556
125	125	0.174
126	126	0.958
127	127	0.78
128	128	0.907
129	129	0.368
13	13	0.0113
130	130	0.133
131	131	0.862
132	132	0.464
133	133	0.591
134	134	0.534
135	135	0.417
136	136	0.814
137	137	0.269
138	138	0.394
139	139	0.542
14	14	0.44
140	140	0.276
141	141	0.539
142	142	0.54
143	143	0.124
144	144	0.191
145	145	0.121
146	146	0.599
147	147	0.146
148	148	0.838
149	149	0.672
15	15	0.252
150	150	0.333
151	151	0.483
152	152	0.0893
153	153	0.417
154	154	0.434
155	155	0.318
156	156	0.605
157	157	0.399
158	158	0.38
159	159	0.213
160	160	0.949
161	161	0.63
162	162	0.159
163	163	0.867
164	164	0.226
165	165	0.384
166	166	0.211
167	167	0.859
168	168	0.42
169	169	0.673
17	17	0.839
18	18	0.876
19	19	0.305
2	2	0.0535
20	20	0.254
21	21	0.254
22	22	0.749
23	23	0.286
24	24	0.0365
25	25	0.251
26	26	0.0241
27	27	0.42
28	28	0.859
29	29	0.14
3	3	0.559
30	30	0.232
31	31	0.153
32	32	0.0217
33	33	0.571
34	34	0.459
35	35	0.531
36	36	0.343
37	37	0.715
38	38	0.322
39	39	0.528
4	4	0.992
40	40	0.261
41	41	0.875
42	42	0.0193
43	43	0.89
44	44	0.966
45	45	0.896
46	46	0.191
47	47	0.695
48	48	0.353
49	49	0.73
5	5	0.92
50	50	0.49
51	51	0.886
52	52	0.115
53	53	0.656
54	54	0.0846
55	55	0.695
56	56	0.844
57	57	0.898
58	58	0.299
59	59	0.913
6	6	0.251
60	60	0.519
61	61	0.0794
62	62	0.219
63	63	0.879
64	64	0.849
65	65	0.791
66	66	0.668
67	67	0.593
68	68	0.0854
69	69	0.991
7	7	0.144
70	70	0.969
71	71	0.0257
72	72	0.402
73	73	0.719
74	74	0.809
75	75	0.0989
76	76	0.109
77	77	0.163
78	78	0.231
79	79	0.702
8	8	0.923
80	80	0.0256
81	81	0.588
82	82	0.466
83	83	0.914
84	84	0.103
85	85	0.0725
86	86	0.487
87	87	0.72
88	88	0.15
89	89	0.356
9	9	0.301
90	90	0.472
91	91	0.328
92	92	0.0774
93	93	0.998
94	94	0.434
95	95	0.479
96	96	0.386
97	97	0.508
98	98	0.575
99	99	0.257

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: CNhs10581

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011366 mouse thymus- embryo E17 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)
0002370 (thymus)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

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)
0000300 (mouse embryonic day 17 sample)
0011366 (mouse thymus- embryo E17 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:0006595 (presumptive endoderm)
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:0002370,UBERON:0000483,UBERON:0002530,UBERON:0006562,UBERON:0000974,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0000077,UBERON:0002368,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005911,UBERON:0004921,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0005291,UBERON:0003929,UBERON:0000072,UBERON:0004807,UBERON:0003104,UBERON:0004177,UBERON:0005057,UBERON:0005058,UBERON:0001048,UBERON:0000925,UBERON:0003408,UBERON:0006598,UBERON:0003351,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0000065,UBERON:0001004,UBERON:0000153,UBERON:0007811,UBERON:0002390,UBERON:0007026,UBERON:0001041,UBERON:0000949,UBERON:0001557,UBERON:0001042,UBERON:0002193,UBERON:0002405,UBERON:0009113,UBERON:0008814,UBERON:0009142,UBERON:0003081,UBERON:0003295,UBERON:0009722,UBERON:0006595,UBERON:0006603,UBERON:0009145,UBERON:0005562,UBERON:0003061,UBERON:0007690
+|DRA_sample_Accession=CAGE@SAMD00004685
+|accession_numbers=CAGE;DRX009116;DRR009990;DRZ001415;DRZ002798;DRZ012765;DRZ014148
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002370,UBERON:0000479,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0004177,UBERON:0005057,UBERON:0002530,UBERON:0005058,UBERON:0010317,UBERON:0000153,UBERON:0002390,UBERON:0000949,UBERON:0002193,UBERON:0002405,UBERON:0009113
 |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:0000300,FF:0011366
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:52096066..52096081,-!p2@Tcf7!2.50!382.04!Tcf7;;chr17:51971960..51971979,-!p1@Satb1!2.01!133.20!Satb1;;chr2:147190749..147190769,+!p1@Pax1!1.96!91.12!Pax1;;chr17:51971932..51971958,-!p2@Satb1!1.81!85.75!Satb1;;chr3:130815703..130815721,+!p2@Lef1!1.80!73.94!Lef1;;chr11:52096804..52096896,-!p1@Tcf7!1.79!464.75!Tcf7;;chr11:52095821..52095836,-!p3@Tcf7!1.79!60.15!Tcf7;;chr12:109242266..109242295,-!p1@Bcl11b!1.78!472.99!Bcl11b;;chr1:38721792..38721845,-!p1@Aff3!1.75!67.67!Aff3;;chr3:94181376..94181403,+!p2@Rorc!1.74!53.71!Rorc;;chr16:92826249..92826325,-!p1@Runx1!1.72!121.56!Runx1;;chr11:11584970..11585030,+!p2@Ikzf1!1.57!51.56!Ikzf1;;chr3:130813200..130813252,+!p1@Lef1!1.45!116.55!Lef1;;chr4:135728311..135728342,+!p3@E2f2!1.44!26.32!E2f2;;chr2:147190725..147190747,+!p2@Pax1!1.43!25.78!Pax1;;chr11:52095797..52095809,-!p5@Tcf7!1.42!25.06!Tcf7;;chr10:20880629..20880683,-!p1@Myb!1.41!69.82!Myb;;chr16:25801993..25802014,+!p1@Trp63!1.40!23.99!Trp63;;chr10:20880731..20880775,-!p2@Myb!1.37!46.55!Myb;;chr10:20880698..20880717,-!p3@Myb!1.37!34.55!Myb;;chr12:57796615..57796687,+!p1@Pax9!1.34!20.95!Pax9;;chr11:11590117..11590138,+!p4@Ikzf1!1.30!18.98!Ikzf1;;chr19:25746898..25746910,+!p1@Dmrt2!1.27!26.32!Dmrt2;;chr3:94181427..94181449,+!p3@Rorc!1.27!17.54!Rorc;;chr11:98407264..98407295,-!p1@Ikzf3!1.26!17.01!Ikzf3;;chr11:11590140..11590187,+!p3@Ikzf1!1.24!19.87!Ikzf1;;chr5:108494765..108494786,+!p2@Mtf2!1.23!21.48!Mtf2;;chr12:109241728..109241781,-!p2@Bcl11b!1.23!17.19!Bcl11b;;chr2:9800207..9800234,-!p1@Gata3!1.22!46.90!Gata3;;chr7:51787434..51787448,-!p1@Spib!1.22!22.20!Spib;;chr11:11585912..11585950,+!p6@Ikzf1!1.21!19.16!Ikzf1;;chr17:51971991..51972003,-!p4@Satb1!1.21!15.22!Satb1;;chr17:51972530..51972571,-!p7@Satb1!1.21!15.04!Satb1;;chr3:94181331..94181345,+!p4@Rorc!1.20!14.68!Rorc;;chr11:98407234..98407259,-!p2@Ikzf3!1.18!13.96!Ikzf3;;chr14:79915425..79915501,+!p1@Elf1!1.16!118.69!Elf1;;chr12:74147689..74147711,-!p1@Six1!1.13!27.57!Six1;;chr11:98338697..98338709,-!p9@Ikzf3!1.13!12.53!Ikzf3;;chr8:125921689..125921725,+!p3@Tcf25!1.11!11.82!Tcf25;;chr3:94181355..94181373,+!p5@Rorc!1.10!11.64!Rorc;;chr1:52065454..52065495,+!p1@Stat4!1.08!18.26!Stat4;;chr17:51972603..51972624,-!p9@Satb1!1.06!10.38!Satb1;;chr11:52096750..52096772,-!p4@Tcf7!1.05!15.93!Tcf7;;chr8:124984566..124984595,-!p1@Snai3!1.05!15.93!Snai3;;chr4:135728181..135728203,+!p2@E2f2!1.05!13.61!E2f2;;chr4:135728282..135728310,+!p4@E2f2!1.05!11.64!E2f2;;chr11:11586218..11586285,+!p1@Ikzf1!1.04!32.40!Ikzf1;;chr17:51952856..51952876,-!p12@Satb1!1.04!10.03!Satb1;;chr8:108583550..108583595,+!p2@Nfatc3!1.03!44.58!Nfatc3;;chr15:61816932..61816952,+!p2@Myc!1.02!80.38!Myc;;chr11:98826178..98826197,+!p7@Rara!1.01!9.13!Rara;;chr17:51972438..51972463,-!p8@Satb1!0.99!8.77!Satb1;;chr17:51972575..51972595,-!p13@Satb1!0.99!8.77!Satb1;;chr4:6917606..6917681,-!p1@Tox!0.98!36.88!Tox;;chr10:77506405..77506441,-!p1@Aire!0.98!8.59!Aire;;chr17:86087592..86087615,-!p1@Six2!0.98!8.59!Six2;;chr3:130813736..130813752,+!p3@Lef1!0.97!11.82!Lef1;;chr2:147190772..147190783,+!p3@Pax1!0.97!8.41!Pax1;;chr12:3891810..3891829,+!p2@Dnmt3a!0.96!12.71!Dnmt3a;;chr3:130813254..130813263,+!p4@Lef1!0.96!8.06!Lef1;;chr1:69732354..69732402,-!p1@Ikzf2!0.94!8.77!Ikzf2;;chr5:108155007..108155034,-!p1@Gfi1!0.94!7.70!Gfi1;;chr4:63064364..63064384,-!p1@Akna!0.93!22.92!Akna;;chr11:78200071..78200100,-!p1@Foxn1!0.92!7.34!Foxn1;;chr5:138186979..138187025,+!p4@Tsc22d4!0.90!26.50!Tsc22d4;;chr9:32503590..32503680,+!p1@Ets1!0.89!256.72!Ets1;;chr4:134708451..134708469,+!p1@Runx3!0.89!12.17!Runx3;;chr17:45692642..45692663,+!p1@Nfkbie!0.88!22.02!Nfkbie;;chr4:102787521..102787588,+!p4@Mier1!0.88!12.35!Mier1;;chr5:104182963..104182982,+!p5@Aff1!0.87!13.96!Aff1;;chr11:11585678..11585745,+!p5@Ikzf1!0.87!9.67!Ikzf1;;chr17:48025139..48025166,-!p8@Foxp4!0.87!7.70!Foxp4;;chr10:77506352..77506356,-!p2@Aire!0.87!6.44!Aire;;chr3:94181461..94181472,+!p6@Rorc!0.87!6.44!Rorc;;chr17:51972400..51972428,-!p11@Satb1!0.86!6.27!Satb1;;chr8:72676653..72676668,+!p4@2310045N01Rik,p4@Mef2b!0.86!6.27!Mef2b;;chr7:134169762..134169795,-!p3@Maz!0.85!58.18!Maz;;chr16:92697560..92697592,-!p2@Runx1!0.85!40.10!Runx1;;chr17:45692676..45692695,+!p2@Nfkbie!0.85!12.71!Nfkbie;;chr11:98407370..98407395,-!p3@Ikzf3!0.85!6.09!Ikzf3;;chr7:147129712..147129774,+!p1@Utf1!0.85!6.09!Utf1;;chr11:98407142..98407159,-!p5@Ikzf3!0.84!5.91!Ikzf3;;chr3:130815472..130815497,+!p6@Lef1!0.83!5.73!Lef1;;chr7:147129777..147129814,+!p2@Utf1!0.83!5.73!Utf1;;chrX:48559079..48559108,-!p2@Mbnl3!0.82!13.61!Mbnl3;;chr5:108494686..108494701,+!p3@Mtf2!0.82!8.06!Mtf2;;chr11:52096732..52096741,-!p6@Tcf7!0.82!5.55!Tcf7;;chr12:100802113..100802127,-!p5@Foxn3!0.81!7.34!Foxn3;;chr2:153475178..153475196,+!p1@Dnmt3b!0.80!11.99!Dnmt3b;;chr4:135728343..135728357,+!p9@E2f2!0.80!5.37!E2f2;;chr10:86956396..86956411,-!p1@Ascl1!0.79!8.24!Ascl1;;chr9:71958979..71959032,-!p4@Tcf12!0.78!6.62!Tcf12;;chr11:98407121..98407133,-!p10@Ikzf3!0.78!5.01!Ikzf3;;chr11:98407340..98407359,-!p4@Ikzf3!0.77!4.83!Ikzf3;;chr6:52114821..52114828,-!p1@Hoxa2!0.76!7.52!Hoxa2;;chr5:138187341..138187406,+!p3@Tsc22d4!0.75!54.96!Tsc22d4;;chr9:71959562..71959624,-!p3@Tcf12!0.75!17.19!Tcf12;;chr11:98407210..98407221,-!p7@Ikzf3!0.75!4.65!Ikzf3;;chr3:94181408..94181419,+!p7@Rorc!0.75!4.65!Rorc;;chr2:173044380..173044432,-!p1@Zbp1!0.74!11.64!Zbp1;;chr1:52176315..52176343,+!p1@Stat1!0.73!70.72!Stat1;;chr1:52065508..52065522,+!p2@Stat4!0.73!5.19!Stat4;;chr11:106134241..106134320,-!p2@Smarcd2!0.72!54.07!Smarcd2;;chr11:3191741..3191769,+!p5@Patz1!0.72!5.55!Patz1;;chr10:13686012..13686028,+!p8@Hivep2!0.72!4.30!Hivep2;;chr11:52074095..52074127,-!p8@Tcf7!0.72!4.30!Tcf7;;chr11:11590085..11590106,+!p7@Ikzf1!0.72!4.30!Ikzf1;;chr5:108155037..108155060,-!p2@Gfi1!0.72!4.30!Gfi1;;chr1:133904901..133904934,+!p3@Elk4!0.71!13.25!Elk4;;chr2:91077034..91077078,-!p2@Ddb2!0.71!9.85!Ddb2;;chrX:48559055..48559077,-!p6@Mbnl3!0.70!5.37!Mbnl3;;chr7:134169810..134169824,-!p7@Maz!0.69!16.47!Maz;;chr16:92697354..92697362,-!p3@Runx1!0.69!6.44!Runx1;;chr3:130813756..130813767,+!p8@Lef1!0.69!3.94!Lef1;;chr3:130813268..130813275,+!p12@Lef1!0.69!3.94!Lef1;;chr11:52070502..52070527,-!p7@Tcf7!0.69!3.94!Tcf7;;chr7:134170081..134170122,-!p2@Maz!0.68!79.67!Maz;;chr2:91077082..91077122,-!p1@Ddb2!0.68!26.67!Ddb2;;chrX:45807489..45807502,-!p2@Elf4!0.68!13.07!Elf4;;chr1:133904946..133904974,+!p7@Elk4!0.68!6.09!Elk4;;chr9:71959634..71959702,-!p2@Tcf12!0.67!32.58!Tcf12;;chr14:65568469..65568511,-!p2@Hmbox1!0.67!13.43!Hmbox1;;chr7:148514080..148514108,-!p4@Deaf1!0.67!8.59!Deaf1;;chr11:3190303..3190351,+!p3@Patz1!0.67!7.88!Patz1;;chr11:100721761..100721851,+!p1@Stat5a!0.66!30.26!Stat5a;;chr1:133904862..133904893,+!p6@Elk4!0.66!8.06!Elk4;;chr2:173044357..173044377,-!p2@Zbp1!0.66!5.37!Zbp1;;chr17:27693622..27693635,+!p11@Hmga1-rs1,p12@Hmga1!0.66!4.65!Hmga1;;chr3:130815382..130815401,+!p14@Lef1!0.66!3.58!Lef1;;chrX:48558950..48559016,-!p1@Mbnl3!0.65!12.35!Mbnl3;;chr6:51382677..51382783,+!p1@Nfe2l3!0.65!9.85!Nfe2l3;;chr11:60036258..60036276,-!p3@Srebf1!0.65!6.62!Srebf1;;chr1:14746065..14746079,-!p1@Msc!0.65!4.30!Msc;;chr7:31206743..31206761,+!p1@Nfkbid!0.64!4.83!Nfkbid;;chr11:120624132..120624143,+!p10@Hmga1,p9@Hmga1-rs1!0.64!4.48!Hmga1;;chr12:109241852..109241873,-!p4@Bcl11b!0.64!4.12!Bcl11b;;chr8:125921676..125921687,+!p6@Tcf25!0.64!3.40!Tcf25;;chr2:162880327..162880385,+!p2@Mybl2!0.63!25.78!Mybl2;;chr12:77470718..77470752,-!p4@Zbtb25!0.63!4.83!Zbtb25;;chr1:52065530..52065548,+!p3@Stat4!0.63!3.22!Stat4;;chr11:98407164..98407177,-!p8@Ikzf3!0.63!3.22!Ikzf3;;chr11:120624106..120624107,+!p13@Hmga1-rs1,p14@Hmga1!0.63!3.22!Hmga1;;chr9:20757246..20757278,-!p1@Dnmt1!0.62!109.21!Dnmt1;;chr6:47544966..47545046,-!p1@Ezh2!0.62!78.77!Ezh2;;chr5:108494715..108494757,+!p1@Mtf2!0.62!56.57!Mtf2;;chr9:57684520..57684612,-!p1@Arid3b!0.62!33.66!Arid3b;;chr13:30077847..30077906,-!p1@E2f3!0.62!29.00!E2f3;;chr6:115803317..115803361,-!p2@Mbd4!0.62!8.77!Mbd4;;chr19:46380235..46380277,+!p3@Nfkb2!0.62!7.70!Nfkb2;;chr17:32506357..32506377,-!p3@Wiz!0.62!7.34!Wiz;;chr3:130813557..130813582,+!p5@Lef1!0.61!3.58!Lef1;;chr11:52096305..52096328,-!p11@Tcf7!0.61!3.04!Tcf7;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.60!168.11!Hmga1;;chr9:32348943..32349001,-!p1@Fli1!0.60!29.18!Fli1;;chr7:56136362..56136400,-!p1@E2f8!0.60!23.27!E2f8;;chr12:100802129..100802145,-!p4@Foxn3!0.59!5.01!Foxn3;;chr11:100800901..100800921,-!p4@Stat3!0.59!3.58!Stat3;;chr11:98407305..98407321,-!p6@Ikzf3!0.59!2.86!Ikzf3;;chr18:80904854..80904919,-!p2@Nfatc1!0.58!41.18!Nfatc1;;chr8:108160490..108160512,+!p2@Ctcf!0.58!28.29!Ctcf;;chr10:88145766..88145770,-!p1@Spic!0.58!3.94!Spic;;chr11:53583544..53583559,+!p1@Irf1!0.57!56.57!Irf1;;chr14:47896467..47896523,-!p1@Wdhd1!0.57!41.18!Wdhd1;;chr18:74375772..74375799,+!p2@Cxxc1!0.57!9.31!Cxxc1;;chr8:13339656..13339661,+!p3@Tfdp1!0.57!7.16!Tfdp1;;chr13:30841099..30841116,+!p1@Irf4!0.57!4.65!Irf4;;chr1:69732511..69732540,-!p2@Ikzf2!0.57!3.76!Ikzf2;;chr11:98407087..98407102,-!p11@Ikzf3!0.57!2.69!Ikzf3;;chr4:135728473..135728494,+!p5@E2f2!0.57!2.69!E2f2;;chr4:134676555..134676575,+!p2@Runx3!0.57!2.69!Runx3;;chr9:20757282..20757325,-!p2@Dnmt1!0.56!76.27!Dnmt1;;chr11:100711801..100711910,-!p1@Stat5b!0.56!45.47!Stat5b;;chr11:101413151..101413207,-!p1@Brca1!0.56!31.87!Brca1;;chr15:103170516..103170531,-!p2@Zfp385a!0.56!7.34!Zfp385a;;chr15:61817095..61817111,+!p1@Myc!0.55!194.06!Myc;;chr8:74405624..74405679,+!p3@Zfp709!0.55!5.01!Zfp709;;chrX:48559029..48559051,-!p7@Mbnl3!0.55!3.58!Mbnl3;;chr6:128312937..128313076,+!p1@Foxm1!0.54!43.15!Foxm1;;chr13:55431084..55431137,-!p1@Mxd3!0.54!24.17!Mxd3;;chr8:72520015..72520053,-!p2@Gatad2a!0.54!20.77!Gatad2a;;chr3:95021663..95021687,-!p3@Gabpb2!0.54!10.38!Gabpb2;;chr2:146047829..146047847,+!p1@Insm1!0.54!5.01!Insm1;;chr12:3891753..3891801,+!p4@Dnmt3a!0.54!4.48!Dnmt3a;;chr12:109242296..109242307,-!p3@Bcl11b!0.54!3.94!Bcl11b;;chr11:11590188..11590200,+!p8@Ikzf1!0.54!2.51!Ikzf1;;chr12:109241804..109241823,-!p5@Bcl11b!0.54!2.51!Bcl11b;;chr12:57792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b1;;chr1:87546619..87546627,+!p3@Sp100!0.19!0.54!Sp100;;chr2:115884524..115884535,-!p27@Meis2!0.19!0.54!Meis2;;chr2:168032254..168032259,-!p6@Adnp!0.19!0.54!Adnp;;chr2:156665889..156665900,+!p8@Tgif2!0.19!0.54!Tgif2;;chr12:37835248..37835260,+!p4@Meox2!0.19!0.54!Meox2;;chr12:77470660..77470671,-!p8@Zbtb25!0.19!0.54!Zbtb25;;chr15:100058744..100058772,+!p4@Gm1862,p6@Atf1!0.19!0.54!Atf1;;chr15:103085864..103085876,-!p5@Nfe2!0.19!0.54!Nfe2;;chr14:76887526..76887555,+!p10@Tsc22d1!0.19!0.54!Tsc22d1;;chr14:67853682..67853702,+!p4@Ebf2!0.19!0.54!Ebf2;;chr5:147760216..147760292,+!p1@Gtf3a!0.18!61.05!Gtf3a;;chr2:119722948..119723028,+!p1@Mga!0.18!39.03!Mga;;chr10:22451112..22451136,-!p1@Tbpl1!0.18!33.12!Tbpl1;;chr2:32218524..32218662,+!p1@Ciz1!0.18!30.43!Ciz1;;chr12:100801772..100801861,-!p1@Foxn3!0.18!27.93!Foxn3;;chr8:124806017..124806040,+!p2@Zfpm1!0.18!14.32!Zfpm1;;chr4:136604692..136604722,-!p1@Zbtb40!0.18!12.35!Zbtb40;;chr3:95032091..95032183,-!p1@Mllt11!0.18!11.10!Mllt11;;chr13:65380118..65380146,+!p2@Zfp369!0.18!8.59!Zfp369;;chr15:100382390..100382441,-!p1@Tfcp2!0.18!8.41!Tfcp2;;chr1:64168830..64168895,-!p2@Klf7!0.18!8.24!Klf7;;chr1:137155026..137155042,-!p1@Elf3!0.18!7.16!Elf3;;chr5:140267476..140267493,+!p1@Mafk!0.18!6.98!Mafk;;chr19:28086045..28086080,-!p4@Rfx3!0.18!5.73!Rfx3;;chr2:37278526..37278575,-!p2@Rc3h2!0.18!5.01!Rc3h2;;chr15:75799717..75799742,+!p1@Zfp707!0.18!4.65!Zfp707;;chr6:117813087..117813121,+!p1@Zfp239!0.18!4.48!Zfp239;;chr7:25101609..25101678,-!p1@Zfp94!0.18!4.30!Zfp94;;chr17:24592183..24592202,-!p2@E4f1!0.18!4.12!E4f1;;chr10:114821532..114821565,-!p4@Thap2!0.18!4.12!Thap2;;chr2:168781029..168781093,-!p2@LOC100502777,p2@Zfp64!0.18!3.94!Zfp64;;chr2:168032763..168032802,-!p3@Adnp!0.18!3.94!Adnp;;chr7:28764153..28764173,-!p2@Zfp780b!0.18!3.94!Zfp780b;;chr11:80196900..80196917,+!p3@Zfp207!0.18!3.76!Zfp207;;chr15:100058660..100058711,+!p1@Gm1862,p2@Atf1!0.18!3.76!Atf1;;chr7:30875418..30875454,-!p2@Zfp566,p2@Zfp82!0.18!3.04!Zfp566;;chr18:35721916..35721927,+!p3@Matr3!0.18!3.04!Matr3;;chr18:80348151..80348181,-!p2@Adnp2!0.18!2.69!Adnp2;;chr3:152059025..152059046,+!p4@Gm8261,p4@Zzz3!0.18!2.69!Zzz3;;chr3:9610074..9610086,-!p2@Zfp704!0.18!2.51!Zfp704;;chr13:37870307..37870337,+!p5@Rreb1!0.18!2.33!Rreb1;;chr4:87678673..87678706,-!p6@Mllt3!0.18!2.15!Mllt3;;chr17:46520518..46520571,+!p2@Zfp318!0.18!2.15!Zfp318;;chr2:27532479..27532509,+!p3@Rxra!0.18!1.97!Rxra;;chr11:106993257..106993268,-!p4@Bptf!0.18!1.61!Bptf;;chr11:98821858..98821907,+!p6@Rara!0.18!1.43!Rara;;chr15:37162796..37162828,+!p1@Grhl2!0.18!1.43!Grhl2;;chr3:51081392..51081407,-!p8@Elf2!0.18!1.43!Elf2;;chr10:80600725..80600737,+!p9@Zbtb7a!0.18!1.25!Zbtb7a;;chr17:32525943..32525992,-!p4@Wiz!0.18!1.25!Wiz;;chrX:103124672..103124721,-!p1@Atrx!0.17!59.26!Atrx;;chr9:56266612..56266654,+!p1@Hmg20a!0.17!36.88!Hmg20a;;chr5:25004592..25004630,-!p2@Mll3!0.17!26.32!Mll3;;chr7:117205217..117205246,+!p1@Zfp143!0.17!25.42!Zfp143;;chr18:74427905..74427991,+!p1@Mbd1!0.17!24.71!Mbd1;;chr17:27110106..27110164,+!p1@Ggnbp1,p1@Zbtb9!0.17!21.84!Zbtb9;;chr16:84835605..84835666,+!p1@Gabpa!0.17!20.95!Gabpa;;chr3:87329494..87329565,+!p1@Etv3!0.17!19.51!Etv3;;chr13:67654035..67654112,-!p1@Zfp748!0.17!19.16!Zfp748;;chr7:24866907..24866967,+!p1@LOC676710,p1@Zfp180!0.17!16.65!Zfp180;;chr3:94819338..94819384,-!p1@Zfp687!0.17!11.99!Zfp687;;chr2:72817320..72817399,-!p2@Sp3!0.17!10.92!Sp3;;chr7:30739068..30739108,-!p1@Zfp74!0.17!9.49!Zfp74;;chr5:31754831..31754876,+!p1@Zfp512!0.17!9.13!Zfp512;;chr2:120996843..120996894,-!p1@Zscan29!0.17!7.52!Zscan29;;chr3:135354289..135354334,-!p3@Nfkb1!0.17!6.09!Nfkb1;;chr11:83943060..83943082,-!p2@Tada2a!0.17!5.37!Tada2a;;chr5:134790428..134790441,-!p5@Gtf2i!0.17!4.12!Gtf2i;;chr4:87679193..87679219,-!p5@Mllt3!0.17!2.86!Mllt3;;chr17:3557785..3557797,-!p3@Tfb1m!0.17!1.79!Tfb1m;;chr1:167932722..167932740,-!p2@Pou2f1!0.17!1.43!Pou2f1;;chr2:168032516..168032525,-!p5@Adnp!0.17!1.25!Adnp;;chrX:7339674..7339688,+!p6@Tfe3!0.17!1.25!Tfe3;;chr5:134741947..134741948,-!p9@Gtf2i!0.17!1.25!Gtf2i;;chr4:87679181..87679192,-!p10@Mllt3!0.17!1.07!Mllt3;;chr12:37835120..37835133,+!p2@Meox2!0.17!1.07!Meox2;;chr3:87966965..87966975,+!p5@Mef2d!0.17!0.90!Mef2d;;chr2:90936886..90936898,+!p5@Sfpi1!0.17!0.72!Sfpi1;;chr14:57397138..57397189,-!p1@Pspc1!0.16!39.56!Pspc1;;chr19:5637736..5637766,+!p1@Rela!0.16!34.73!Rela;;chr11:102180255..102180318,-!p1@Ubtf!0.16!29.18!Ubtf;;chr2:84877326..84877362,+!p2@Ssrp1!0.16!27.57!Ssrp1;;chr3:51081233..51081365,-!p1@Elf2!0.16!27.03!Elf2;;chrX:45947560..45947670,-!p1@Zfp280c!0.16!24.17!Zfp280c;;chr12:85658052..85658097,+!p1@Zfp410!0.16!21.66!Zfp410;;chr8:74474953..74475029,+!p1@Zfp961!0.16!20.95!Zfp961;;chrX:20639107..20639188,-!p1@Zfp182!0.16!16.11!Zfp182;;chr11:115891618..115891699,+!p1@Unk!0.16!15.58!Unk;;chr4:133276801..133276891,-!p3@Arid1a!0.16!13.07!Arid1a;;chr17:25152711..25152736,-!p1@Cramp1l!0.16!12.35!Cramp1l;;chr1:64579364..64579389,+!p2@Creb1!0.16!11.10!Creb1;;chr11:65620712..65620729,+!p1@Zkscan6!0.16!10.20!Zkscan6;;ch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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0006603,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011366
 |is_obsolete=
+|library_id=CNhs10581
+|library_id_phase_based=2:CNhs10581
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;478
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;478
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E17.CNhs10581.478-18C1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E17.CNhs10581.478-18C1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E17.CNhs10581.478-18C1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E17.CNhs10581.478-18C1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E17.CNhs10581.478-18C1.mm9.nobarcode.rdna.fa.gz
 |name=thymus, embryo E17
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10581,LSID653,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.105027281687901,0,0,0,0.277639803678183,0.0357618192777494,-0.152188245929579,0,0,0,0,0.332507592831684,0,0,0,0,0,0,0.0426509569200094,0,0.093348248140603,0,0,0,0,0,0,0,0,0,0,0,-0.0857696424593962,0,0,0,0,0,-0.0495160551567869,0,-0.161520883397672,0.0214135759754598,-0.0353243302077673,0,0,0,0,0,0,0,0,0,0,0,0,0.066911296833432,0,0,0,0,-0.0428469550828748,0,0.0277245801033184,0,0.0715236385554987,0,-0.0260438148259286,0.0421465544031163,0.0764532650315014,0.0106048934431691,0,0,-0.0458400978272119,0,0,0,-0.0230335064246413,-0.153494069195301,-0.0738167804146672,0.054085249556965,0,0,0,0,0,0,-0.160342496178988,-0.325841975975144,-0.176454754090796,0,0,0,0,0
 |rna_box=18
 |rna_catalog_number=
@@ Line 59: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 79: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:478-18C1;search_select_hide=table117:478-18C1
 }}

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FF:478-18C1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:17, 4 June 2020

CNhs10581

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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