FF:1273-19G4: Difference between revisions

Latest revision as of 18:43, 4 June 2020

Name:	thymus, embryo E18
Species:	Mouse (Mus musculus)
Library ID:	CNhs10595
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	thymus
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		SAMD00004709

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10595		CAGE		DRX009117		DRR009991

Accession ID Mm9

Library id		BAM		CTSS
CNhs10595		DRZ001416		DRZ002799

Accession ID Mm10

Library id		BAM		CTSS
CNhs10595		DRZ012766		DRZ014149

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

CNhs10595

0	0
1	0
10	0
100	0
1000	0
1001	0
1002	0
1003	-0.063
1004	0
1005	0
1006	-0.064
1007	0.108
1008	0
1009	-0.111
101	0.128
1010	0
1011	0
1012	0.254
1013	-0.138
1014	0.109
1015	0.0493
1016	-0.262
1017	0
1018	0.0787
1019	0
102	0
1020	0
1021	0.145
1022	-0.17
1023	0
1024	-0.0112
1025	0
1026	0
1027	0
1028	0
1029	0.152
103	0
1030	0
1031	-0.331
1032	-0.328
1033	0.0787
1034	0
1035	0
1036	0.189
1037	0
1038	-0.22
1039	-0.196
104	0
1040	-0.0422
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: CNhs10595

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	9.71499e-5
MA0003.1	MA0003.1	0.837
MA0004.1	MA0004.1	0.464
MA0006.1	MA0006.1	0.709
MA0007.1	MA0007.1	0.295
MA0009.1	MA0009.1	0.324
MA0014.1	MA0014.1	0.195
MA0017.1	MA0017.1	0.111
MA0018.2	MA0018.2	0.0735
MA0019.1	MA0019.1	0.754
MA0024.1	MA0024.1	8.20631e-6
MA0025.1	MA0025.1	0.00352
MA0027.1	MA0027.1	0.888
MA0028.1	MA0028.1	2.08695e-6
MA0029.1	MA0029.1	0.0827
MA0030.1	MA0030.1	0.466
MA0031.1	MA0031.1	0.297
MA0035.2	MA0035.2	0.815
MA0038.1	MA0038.1	0.422
MA0039.2	MA0039.2	0.503
MA0040.1	MA0040.1	0.444
MA0041.1	MA0041.1	0.8
MA0042.1	MA0042.1	0.736
MA0043.1	MA0043.1	0.343
MA0046.1	MA0046.1	1.54099e-17
MA0047.2	MA0047.2	0.716
MA0048.1	MA0048.1	0.85
MA0050.1	MA0050.1	3.76841e-6
MA0051.1	MA0051.1	3.85684e-6
MA0052.1	MA0052.1	0.122
MA0055.1	MA0055.1	0.711
MA0057.1	MA0057.1	0.615
MA0058.1	MA0058.1	0.605
MA0059.1	MA0059.1	0.0766
MA0060.1	MA0060.1	1.32299e-6
MA0061.1	MA0061.1	1.32032e-6
MA0062.2	MA0062.2	4.81714e-19
MA0065.2	MA0065.2	0.694
MA0066.1	MA0066.1	0.041
MA0067.1	MA0067.1	0.81
MA0068.1	MA0068.1	0.521
MA0069.1	MA0069.1	0.881
MA0070.1	MA0070.1	0.535
MA0071.1	MA0071.1	0.583
MA0072.1	MA0072.1	3.30373e-7
MA0073.1	MA0073.1	0.756
MA0074.1	MA0074.1	0.859
MA0076.1	MA0076.1	1.00861e-8
MA0077.1	MA0077.1	0.323
MA0078.1	MA0078.1	0.756
MA0079.2	MA0079.2	0.0925
MA0080.2	MA0080.2	8.96815e-14
MA0081.1	MA0081.1	0.0145
MA0083.1	MA0083.1	0.606
MA0084.1	MA0084.1	0.526
MA0087.1	MA0087.1	0.549
MA0088.1	MA0088.1	0.137
MA0090.1	MA0090.1	0.0681
MA0091.1	MA0091.1	0.0619
MA0092.1	MA0092.1	0.95
MA0093.1	MA0093.1	0.511
MA0099.2	MA0099.2	0.179
MA0100.1	MA0100.1	0.00868
MA0101.1	MA0101.1	6.64733e-6
MA0102.2	MA0102.2	0.285
MA0103.1	MA0103.1	2.74279e-5
MA0104.2	MA0104.2	0.139
MA0105.1	MA0105.1	8.7407e-9
MA0106.1	MA0106.1	0.786
MA0107.1	MA0107.1	5.2512e-6
MA0108.2	MA0108.2	0.454
MA0111.1	MA0111.1	0.383
MA0112.2	MA0112.2	0.0593
MA0113.1	MA0113.1	0.776
MA0114.1	MA0114.1	0.0555
MA0115.1	MA0115.1	0.354
MA0116.1	MA0116.1	0.00142
MA0117.1	MA0117.1	0.703
MA0119.1	MA0119.1	0.996
MA0122.1	MA0122.1	0.699
MA0124.1	MA0124.1	0.397
MA0125.1	MA0125.1	0.939
MA0131.1	MA0131.1	0.0383
MA0135.1	MA0135.1	0.355
MA0136.1	MA0136.1	1.72414e-23
MA0137.2	MA0137.2	0.0294
MA0138.2	MA0138.2	2.1379e-4
MA0139.1	MA0139.1	0.259
MA0140.1	MA0140.1	0.817
MA0141.1	MA0141.1	0.128
MA0142.1	MA0142.1	0.775
MA0143.1	MA0143.1	0.3
MA0144.1	MA0144.1	0.333
MA0145.1	MA0145.1	0.611
MA0146.1	MA0146.1	0.408
MA0147.1	MA0147.1	0.0673
MA0148.1	MA0148.1	0.758
MA0149.1	MA0149.1	0.242
MA0150.1	MA0150.1	0.264
MA0152.1	MA0152.1	0.953
MA0153.1	MA0153.1	2.46036e-9
MA0154.1	MA0154.1	0.0529
MA0155.1	MA0155.1	0.549
MA0156.1	MA0156.1	7.5479e-29
MA0157.1	MA0157.1	0.518
MA0159.1	MA0159.1	0.0751
MA0160.1	MA0160.1	0.16
MA0162.1	MA0162.1	0.223
MA0163.1	MA0163.1	5.5199e-4
MA0164.1	MA0164.1	0.624
MA0258.1	MA0258.1	0.169
MA0259.1	MA0259.1	0.707

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: CNhs10595

Novel motif	Logo	P-value
1	1	0.493
10	10	0.0278
100	100	0.905
101	101	0.925
102	102	0.423
103	103	0.319
104	104	0.553
105	105	0.914
106	106	0.742
107	107	0.726
108	108	0.467
109	109	0.177
11	11	0.103
110	110	0.0887
111	111	0.945
112	112	0.302
113	113	0.202
114	114	0.758
115	115	0.466
116	116	0.727
117	117	0.00174
118	118	0.231
119	119	0.534
12	12	0.296
120	120	0.242
121	121	0.183
122	122	0.667
123	123	0.433
124	124	0.652
125	125	0.064
126	126	0.947
127	127	0.745
128	128	0.613
129	129	0.372
13	13	0.016
130	130	0.304
131	131	0.961
132	132	0.599
133	133	0.899
134	134	0.39
135	135	0.268
136	136	0.7
137	137	0.247
138	138	0.218
139	139	0.987
14	14	0.781
140	140	0.774
141	141	0.918
142	142	0.88
143	143	0.114
144	144	0.113
145	145	0.144
146	146	0.618
147	147	0.268
148	148	0.582
149	149	0.804
15	15	0.108
150	150	0.279
151	151	0.188
152	152	0.264
153	153	0.31
154	154	0.42
155	155	0.0811
156	156	0.523
157	157	0.628
158	158	0.141
159	159	0.0107
160	160	0.755
161	161	0.401
162	162	0.352
163	163	0.737
164	164	0.271
165	165	0.16
166	166	0.359
167	167	0.532
168	168	0.456
169	169	0.236
17	17	0.747
18	18	0.878
19	19	0.59
2	2	0.175
20	20	0.592
21	21	0.289
22	22	0.926
23	23	0.893
24	24	0.0666
25	25	0.258
26	26	0.036
27	27	0.258
28	28	0.248
29	29	0.0771
3	3	0.344
30	30	0.208
31	31	0.436
32	32	0.0793
33	33	0.532
34	34	0.511
35	35	0.158
36	36	0.283
37	37	0.261
38	38	0.276
39	39	0.614
4	4	0.727
40	40	0.417
41	41	0.834
42	42	0.0226
43	43	0.67
44	44	0.777
45	45	0.793
46	46	0.104
47	47	0.356
48	48	0.213
49	49	0.348
5	5	0.321
50	50	0.698
51	51	0.974
52	52	0.262
53	53	0.678
54	54	0.219
55	55	0.362
56	56	0.878
57	57	0.484
58	58	0.224
59	59	0.778
6	6	0.208
60	60	0.997
61	61	0.0888
62	62	0.0704
63	63	0.618
64	64	0.543
65	65	0.459
66	66	0.948
67	67	0.793
68	68	0.359
69	69	0.738
7	7	0.0872
70	70	0.695
71	71	0.0206
72	72	0.445
73	73	0.397
74	74	0.768
75	75	0.0483
76	76	0.279
77	77	0.543
78	78	0.0797
79	79	0.965
8	8	0.619
80	80	0.0417
81	81	0.897
82	82	0.655
83	83	0.964
84	84	0.322
85	85	0.418
86	86	0.144
87	87	0.303
88	88	0.243
89	89	0.406
9	9	0.246
90	90	0.154
91	91	0.575
92	92	0.311
93	93	0.862
94	94	0.361
95	95	0.326
96	96	0.141
97	97	0.466
98	98	0.423
99	99	0.44

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: CNhs10595

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011516 mouse thymus- 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)
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)
0000302 (mouse embryonic day 18 sample)
0011516 (mouse thymus- 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: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
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+|DRA_sample_Accession=CAGE@SAMD00004709
+|accession_numbers=CAGE;DRX009117;DRR009991;DRZ001416;DRZ002799;DRZ012766;DRZ014149
+|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:0000302,FF:0011516
 |comment=fantom:1273-19G4
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:52096066..52096081,-!p2@Tcf7!2.64!521.34!Tcf7;;chr17:51971960..51971979,-!p1@Satb1!2.14!181.40!Satb1;;chr17:51971932..51971958,-!p2@Satb1!2.00!132.32!Satb1;;chr11:52096804..52096896,-!p1@Tcf7!1.91!606.57!Tcf7;;chr3:130815703..130815721,+!p2@Lef1!1.90!94.37!Lef1;;chr11:52095821..52095836,-!p3@Tcf7!1.89!76.29!Tcf7;;chr1:38721792..38721845,-!p1@Aff3!1.88!93.38!Aff3;;chr12:109242266..109242295,-!p1@Bcl11b!1.84!542.00!Bcl11b;;chr3:94181376..94181403,+!p2@Rorc!1.84!68.15!Rorc;;chr16:92826249..92826325,-!p1@Runx1!1.74!128.94!Runx1;;chr2:147190749..147190769,+!p1@Pax1!1.74!53.45!Pax1;;chr11:52095797..52095809,-!p5@Tcf7!1.59!38.35!Tcf7;;chr3:130813200..130813252,+!p1@Lef1!1.51!136.69!Lef1;;chr11:11584970..11585030,+!p2@Ikzf1!1.49!41.92!Ikzf1;;chr3:94181427..94181449,+!p3@Rorc!1.46!27.62!Rorc;;chr10:20880731..20880775,-!p2@Myb!1.45!55.43!Myb;;chr11:11590117..11590138,+!p4@Ikzf1!1.45!27.42!Ikzf1;;chr10:20880629..20880683,-!p1@Myb!1.44!75.10!Myb;;chr16:25801993..25802014,+!p1@Trp63!1.43!26.23!Trp63;;chr17:51971991..51972003,-!p4@Satb1!1.43!26.03!Satb1;;chr11:98407264..98407295,-!p1@Ikzf3!1.43!26.03!Ikzf3;;chr12:109241728..109241781,-!p2@Bcl11b!1.41!26.23!Bcl11b;;chr11:11590140..11590187,+!p3@Ikzf1!1.36!26.42!Ikzf1;;chr2:147190725..147190747,+!p2@Pax1!1.36!22.05!Pax1;;chr4:135728311..135728342,+!p3@E2f2!1.33!20.46!E2f2;;chr2:9800207..9800234,-!p1@Gata3!1.32!59.80!Gata3;;chr11:98407234..98407259,-!p2@Ikzf3!1.32!20.07!Ikzf3;;chr12:57796615..57796687,+!p1@Pax9!1.31!19.27!Pax9;;chr3:94181331..94181345,+!p4@Rorc!1.30!18.87!Rorc;;chr14:79915425..79915501,+!p1@Elf1!1.25!144.44!Elf1;;chr4:102787521..102787588,+!p4@Mier1!1.25!30.00!Mier1;;chr17:51972530..51972571,-!p7@Satb1!1.24!16.29!Satb1;;chr1:52065454..52065495,+!p1@Stat4!1.23!26.03!Stat4;;chr19:25746898..25746910,+!p1@Dmrt2!1.23!23.44!Dmrt2;;chr11:98826178..98826197,+!p7@Rara!1.22!15.70!Rara;;chr11:98338697..98338709,-!p9@Ikzf3!1.21!15.10!Ikzf3;;chr4:6917606..6917681,-!p1@Tox!1.19!60.00!Tox;;chr11:11586218..11586285,+!p1@Ikzf1!1.19!45.50!Ikzf1;;chr7:51787434..51787448,-!p1@Spib!1.18!20.07!Spib;;chr3:94181355..94181373,+!p5@Rorc!1.16!13.31!Rorc;;chr10:20880698..20880717,-!p3@Myb!1.15!20.46!Myb;;chr11:11585912..11585950,+!p6@Ikzf1!1.15!16.69!Ikzf1;;chr8:108583550..108583595,+!p2@Nfatc3!1.14!57.02!Nfatc3;;chr11:52096750..52096772,-!p4@Tcf7!1.14!20.07!Tcf7;;chr12:74147689..74147711,-!p1@Six1!1.11!26.03!Six1;;chr5:108494765..108494786,+!p2@Mtf2!1.10!15.50!Mtf2;;chr17:48025139..48025166,-!p8@Foxp4!1.10!13.51!Foxp4;;chr17:51952856..51952876,-!p12@Satb1!1.10!11.72!Satb1;;chr4:63064364..63064384,-!p1@Akna!1.06!30.99!Akna;;chr11:11585678..11585745,+!p5@Ikzf1!1.06!15.30!Ikzf1;;chr5:108155007..108155034,-!p1@Gfi1!1.06!10.53!Gfi1;;chr8:124984566..124984595,-!p1@Snai3!1.05!15.89!Snai3;;chr4:135728282..135728310,+!p4@E2f2!1.05!11.52!E2f2;;chr4:135728181..135728203,+!p2@E2f2!1.04!13.11!E2f2;;chr17:51972400..51972428,-!p11@Satb1!1.04!9.93!Satb1;;chr9:32503590..32503680,+!p1@Ets1!1.03!359.81!Ets1;;chr8:125921689..125921725,+!p3@Tcf25!1.03!9.74!Tcf25;;chr17:51972603..51972624,-!p9@Satb1!1.03!9.74!Satb1;;chr11:98407142..98407159,-!p5@Ikzf3!1.03!9.74!Ikzf3;;chr17:51972438..51972463,-!p8@Satb1!1.01!9.34!Satb1;;chr3:130813254..130813263,+!p4@Lef1!1.01!9.14!Lef1;;chr11:52096732..52096741,-!p6@Tcf7!1.00!8.94!Tcf7;;chr11:52070502..52070527,-!p7@Tcf7!0.99!8.74!Tcf7;;chr5:138186979..138187025,+!p4@Tsc22d4!0.96!30.40!Tsc22d4;;chr2:173044380..173044432,-!p1@Zbp1!0.95!19.47!Zbp1;;chr5:104182963..104182982,+!p5@Aff1!0.95!17.29!Aff1;;chr4:134708451..134708469,+!p1@Runx3!0.94!13.91!Runx3;;chr12:3891810..3891829,+!p2@Dnmt3a!0.94!12.32!Dnmt3a;;chr3:130813736..130813752,+!p3@Lef1!0.94!10.93!Lef1;;chr3:94181408..94181419,+!p7@Rorc!0.94!7.75!Rorc;;chr3:94181461..94181472,+!p6@Rorc!0.93!7.55!Rorc;;chr10:77506405..77506441,-!p1@Aire!0.93!7.55!Aire;;chr11:98407340..98407359,-!p4@Ikzf3!0.92!7.35!Ikzf3;;chr17:45692676..45692695,+!p2@Nfkbie!0.90!14.50!Nfkbie;;chr17:51972575..51972595,-!p13@Satb1!0.90!6.95!Satb1;;chr11:52074095..52074127,-!p8@Tcf7!0.90!6.95!Tcf7;;chr17:51965903..51965926,-!p5@Satb1!0.88!6.56!Satb1;;chr16:92697560..92697592,-!p2@Runx1!0.87!42.12!Runx1;;chr1:69732354..69732402,-!p1@Ikzf2!0.87!7.35!Ikzf2;;chr11:52070563..52070589,-!p9@Tcf7!0.87!6.36!Tcf7;;chr11:98407370..98407395,-!p3@Ikzf3!0.87!6.36!Ikzf3;;chr10:88145766..88145770,-!p1@Spic!0.86!8.34!Spic;;chr11:100800901..100800921,-!p4@Stat3!0.86!7.55!Stat3;;chr17:45692642..45692663,+!p1@Nfkbie!0.85!20.27!Nfkbie;;chr16:23988711..23988727,-!p1@Bcl6!0.84!74.90!Bcl6;;chr9:71959562..71959624,-!p3@Tcf12!0.83!21.06!Tcf12;;chr1:38721779..38721790,-!p6@Aff3!0.83!5.76!Aff3;;chr11:106134241..106134320,-!p2@Smarcd2!0.82!68.74!Smarcd2;;chr1:133904862..133904893,+!p6@Elk4!0.82!12.12!Elk4;;chr1:52065508..52065522,+!p2@Stat4!0.82!6.76!Stat4;;chr11:98407121..98407133,-!p10@Ikzf3!0.82!5.56!Ikzf3;;chr11:98407210..98407221,-!p7@Ikzf3!0.82!5.56!Ikzf3;;chr15:61816932..61816952,+!p2@Myc!0.80!47.68!Myc;;chr11:100721761..100721851,+!p1@Stat5a!0.80!42.52!Stat5a;;chr11:52096305..52096328,-!p11@Tcf7!0.80!5.36!Tcf7;;chr10:77506352..77506356,-!p2@Aire!0.80!5.36!Aire;;chr17:86087592..86087615,-!p1@Six2!0.80!5.36!Six2;;chr11:100683839..100683890,-!p2@Stat5b!0.79!12.91!Stat5b;;chr12:109242296..109242307,-!p3@Bcl11b!0.79!7.75!Bcl11b;;chr11:98826216..98826227,+!p10@Rara!0.79!5.17!Rara;;chr2:147190772..147190783,+!p3@Pax1!0.79!5.17!Pax1;;chr6:51382677..51382783,+!p1@Nfe2l3!0.78!13.71!Nfe2l3;;chr2:173044357..173044377,-!p2@Zbp1!0.78!7.55!Zbp1;;chr11:3191741..3191769,+!p5@Patz1!0.78!6.56!Patz1;;chr11:78200071..78200100,-!p1@Foxn1!0.78!4.97!Foxn1;;chr8:72676653..72676668,+!p4@2310045N01Rik,p4@Mef2b!0.78!4.97!Mef2b;;chr1:133904901..133904934,+!p3@Elk4!0.77!15.50!Elk4;;chr12:109241852..109241873,-!p4@Bcl11b!0.77!5.96!Bcl11b;;chr5:138187341..138187406,+!p3@Tsc22d4!0.76!56.03!Tsc22d4;;chr12:100802113..100802127,-!p5@Foxn3!0.76!6.36!Foxn3;;chr3:130815472..130815497,+!p6@Lef1!0.75!4.57!Lef1;;chr7:147129777..147129814,+!p2@Utf1!0.75!4.57!Utf1;;chr1:52065530..52065548,+!p3@Stat4!0.75!4.57!Stat4;;chr14:65568469..65568511,-!p2@Hmbox1!0.73!15.50!Hmbox1;;chrX:48559079..48559108,-!p2@Mbnl3!0.73!10.93!Mbnl3;;chr12:77470718..77470752,-!p4@Zbtb25!0.73!6.36!Zbtb25;;chr11:98407305..98407321,-!p6@Ikzf3!0.73!4.37!Ikzf3;;chr11:98407164..98407177,-!p8@Ikzf3!0.73!4.37!Ikzf3;;chr1:52176315..52176343,+!p1@Stat1!0.72!68.15!Stat1;;chr7:134169762..134169795,-!p3@Maz!0.72!42.72!Maz;;chr5:104183477..104183548,+!p6@Aff1!0.71!8.74!Aff1;;chr11:11590085..11590106,+!p7@Ikzf1!0.71!4.17!Ikzf1;;chr9:32348943..32349001,-!p1@Fli1!0.70!36.76!Fli1;;chr1:87495371..87495397,-!p1@Sp110!0.70!3.97!Sp110;;chr9:71958979..71959032,-!p4@Tcf12!0.69!5.17!Tcf12;;chr9:57684520..57684612,-!p1@Arid3b!0.68!38.15!Arid3b;;chr2:91077082..91077122,-!p1@Ddb2!0.68!26.82!Ddb2;;chr11:3190303..3190351,+!p3@Patz1!0.68!8.15!Patz1;;chr10:20881160..20881175,-!p4@Myb!0.68!3.77!Myb;;chr12:109241804..109241823,-!p5@Bcl11b!0.68!3.77!Bcl11b;;chr11:52070478..52070500,-!p10@Tcf7!0.68!3.77!Tcf7;;chr9:24578720..24578735,-!p1@Tbx20!0.68!3.77!Tbx20;;chr5:108155037..108155060,-!p2@Gfi1!0.68!3.77!Gfi1;;chr16:95924005..95924042,+!p2@Ets2!0.67!75.70!Ets2;;chr18:80904854..80904919,-!p2@Nfatc1!0.67!50.47!Nfatc1;;chr9:71959634..71959702,-!p2@Tcf12!0.67!32.39!Tcf12;;chrX:45807489..45807502,-!p2@Elf4!0.67!12.72!Elf4;;chr11:60036258..60036276,-!p3@Srebf1!0.67!6.95!Srebf1;;chrX:48559055..48559077,-!p6@Mbnl3!0.67!4.97!Mbnl3;;chr8:108160490..108160512,+!p2@Ctcf!0.66!34.57!Ctcf;;chr5:138187583..138187602,+!p6@Tsc22d4!0.66!7.15!Tsc22d4;;chr3:130813268..130813275,+!p12@Lef1!0.66!3.58!Lef1;;chr18:74375772..74375799,+!p2@Cxxc1!0.65!11.32!Cxxc1;;chr4:135736690..135736705,+!p6@E2f2!0.65!4.17!E2f2;;chr19:46380235..46380277,+!p3@Nfkb2!0.64!8.15!Nfkb2;;chr17:27693622..27693635,+!p11@Hmga1-rs1,p12@Hmga1!0.64!4.37!Hmga1;;chr17:51972017..51972022,-!p17@Satb1!0.64!3.38!Satb1;;chr17:51951383..51951409,-!p19@Satb1!0.64!3.38!Satb1;;chr9:32349051..32349061,-!p5@Fli1!0.64!3.38!Fli1;;chr4:135728343..135728357,+!p9@E2f2!0.64!3.38!E2f2;;chrX:98449898..98449913,+!p2@Foxo4!0.63!12.12!Foxo4;;chr13:30841099..30841116,+!p1@Irf4!0.63!5.56!Irf4;;chr5:108494686..108494701,+!p3@Mtf2!0.63!4.97!Mtf2;;chr8:72520015..72520053,-!p2@Gatad2a!0.62!24.84!Gatad2a;;chrX:48558950..48559016,-!p1@Mbnl3!0.62!11.52!Mbnl3;;chr17:51951634..51951651,-!p6@Satb1!0.62!6.76!Satb1;;chr1:14746065..14746079,-!p1@Msc!0.62!3.97!Msc;;chr4:102787381..102787397,+!p9@Mier1!0.62!3.77!Mier1;;chr3:130815382..130815401,+!p14@Lef1!0.62!3.18!Lef1;;chr10:13686012..13686028,+!p8@Hivep2!0.62!3.18!Hivep2;;chr10:20862857..20862868,-!p7@Myb!0.62!3.18!Myb;;chr11:11590188..11590200,+!p8@Ikzf1!0.62!3.18!Ikzf1;;chr7:147129712..147129774,+!p1@Utf1!0.62!3.18!Utf1;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.61!173.85!Hmga1;;chr7:134170081..134170122,-!p2@Maz!0.61!67.35!Maz;;chr11:62272010..62272050,-!p2@Ncor1!0.61!11.32!Ncor1;;chr3:135271185..135271254,-!p4@Nfkb1!0.61!6.16!Nfkb1;;chr7:71083729..71083742,-!p4@Klf13!0.61!5.96!Klf13;;chr12:100802129..100802145,-!p4@Foxn3!0.61!5.36!Foxn3;;chr10:86956396..86956411,-!p1@Ascl1!0.61!5.17!Ascl1;;chr10:13685980..13686007,+!p6@Hivep2!0.61!3.97!Hivep2;;chr1:64579555..64579570,+!p3@Creb1!0.60!16.89!Creb1;;chr7:134169810..134169824,-!p7@Maz!0.60!13.31!Maz;;chr12:3891753..3891801,+!p4@Dnmt3a!0.60!5.36!Dnmt3a;;chr3:130813586..130813604,+!p7@Lef1!0.60!2.98!Lef1;;chr4:135728473..135728494,+!p5@E2f2!0.60!2.98!E2f2;;chr4:134676555..134676575,+!p2@Runx3!0.60!2.98!Runx3;;chr11:98407087..98407102,-!p11@Ikzf3!0.60!2.98!Ikzf3;;chr11:120624106..120624107,+!p13@Hmga1-rs1,p14@Hmga1!0.60!2.98!Hmga1;;chr16:95924055..95924077,+!p1@Ets2!0.59!192.92!Ets2;;chr3:95021663..95021687,-!p3@Gabpb2!0.59!11.52!Gabpb2;;chr9:21420744..21420755,+!p3@Smarca4!0.59!9.74!Smarca4;;chr4:102792009..102792021,+!p6@Mier1!0.59!5.36!Mier1;;chr17:51952537..51952552,-!p15@Satb1!0.59!3.18!Satb1;;chr10:67000609..67000625,+!p1@Egr2!0.58!7.35!Egr2;;chr2:91077034..91077078,-!p2@Ddb2!0.58!7.15!Ddb2;;chr11:52096260..52096274,-!p12@Tcf7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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 36: / Line 42: @@
 |has_quality=
 |id=FF:1273-19G4
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011516
+|is_a=EFO:0002091;;FF:0011516
+|is_obsolete=
+|library_id=CNhs10595
+|library_id_phase_based=2:CNhs10595
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1273
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1273
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E18.CNhs10595.1273-19G4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E18.CNhs10595.1273-19G4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E18.CNhs10595.1273-19G4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E18.CNhs10595.1273-19G4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E18.CNhs10595.1273-19G4.mm9.nobarcode.rdna.fa.gz
 |name=thymus, embryo E18
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10595,LSID654,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0451410216598463,0,0,0.0787037500278776,0.641234392262142,0,0.031961519578585,0,0,0,0,0.169658773475735,0,0,0,0,0,0,0.107702578845067,0,0.101522438694443,0,0,0.0787037500278776,0,0,0,0,0,0,0,0,0.171631535706864,0,0,0,0,0,0.062628718267499,-0.0559200499617537,-0.0513528256254545,-0.208452863524135,-0.191164887982474,0,0,0,0,0,0,0,0,0,0,0.0787037500278776,0,-0.0660055475634404,0,0,0,0,0.00360444876585128,0,0.0191013994130339,0,0.0787037500278776,0,-0.00538335321385398,0.0678870463867263,0.095906971101194,-0.0253912242425617,0,0,-0.0505638029256881,0,0,0,0,-0.0315625600720058,-0.217377177014457,0.175166419032369,0,0,0,0,0,0,-0.188168664874566,-0.359799900004152,-0.157796552536927,0,0,0,0,0
 |rna_box=19
 |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=thymus
 |top_motifs=RORA:2.45678212257;ALX4:2.22445099907;SPZ1:2.16750391206;ELF1,2,4:1.76196493817;E2F1..5:1.75514081711;TLX2:1.71048682884;RUNX1..3:1.69336111533;PPARG:1.65438443217;ETS1,2:1.62828629673;NFY{A,B,C}:1.59231030398;DMAP1_NCOR{1,2}_SMARC:1.46206422826;SPI1:1.35721804493;SPIB:1.25436824808;GFI1:1.10062267024;TEF:1.07892362978;IRF1,2:1.06719837284;NFATC1..3:1.03717975218;NFKB1_REL_RELA:1.02354521727;MYB:0.844916324912;ELK1,4_GABP{A,B1}:0.768807949204;PITX1..3:0.762959277431;AIRE:0.736628604728;POU1F1:0.735291848029;STAT1,3:0.680708671118;LMO2:0.668722474133;IRF7:0.655851423184;ZEB1:0.623792669403;STAT5{A,B}:0.589828660824;TOPORS:0.584622184572;ZNF143:0.523539456166;SNAI1..3:0.519205758999;ZNF238:0.513744401619;RXRA_VDR{dimer}:0.509783316827;TBX4,5:0.498127109618;NRF1:0.479583140391;SOX{8,9,10}:0.409722357571;RBPJ:0.377939216098;POU5F1:0.367361353143;EN1,2:0.277097258539;BPTF:0.267474082824;TBP:0.251923842716;NR1H4:0.226141417679;FOXD3:0.216757058866;ZBTB16:0.212909860716;HOX{A4,D4}:0.193533972438;NHLH1,2:0.174598778107;T:0.162121664195;TAL1_TCF{3,4,12}:0.15427857834;LEF1_TCF7_TCF7L1,2:0.151706948606;POU2F1..3:0.142364880178;HES1:0.140617154719;YY1:0.137677235801;NANOG{mouse}:0.0731466937744;CDX1,2,4:0.0689410084868;NR6A1:0.0680911276909;SOX2:0.0548749207866;PAX6:0.0294787039555;NANOG:0.0290573063275;SRF:0.0177352052333;IKZF2:0.000295608264099;HLF:-0.0182490729847;TFDP1:-0.0350539511304;ATF5_CREB3:-0.0453136858276;SOX17:-0.0505273368615;FOXP1:-0.053345882464;RREB1:-0.0890084033576;ESR1:-0.0895535395311;MYOD1:-0.0901788961296;FOXL1:-0.108607349052;GATA6:-0.152472926377;PAX4:-0.156072134194;PDX1:-0.158223194563;CRX:-0.161459154454;SREBF1,2:-0.16365227454;PRDM1:-0.16575892537;ARID5B:-0.171966372022;KLF4:-0.182677760975;PBX1:-0.188710884678;BREu{core}:-0.196503020493;NFIX:-0.20426785092;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.205760880119;TGIF1:-0.209015577738;RXR{A,B,G}:-0.219165850164;OCT4_SOX2{dimer}:-0.222174516828;NFE2L1:-0.223179613083;FOXP3:-0.240263305926;FOX{D1,D2}:-0.241466943451;bHLH_family:-0.24211147825;FOXQ1:-0.250730117158;EBF1:-0.256519591975;FOXO1,3,4:-0.257629603667;ZNF384:-0.284554223335;RFX2..5_RFXANK_RFXAP:-0.30202716184;CUX2:-0.304162785982;HMX1:-0.30493815782;MZF1:-0.305121151985;FOX{I1,J2}:-0.309505845558;HBP1_HMGB_SSRP1_UBTF:-0.316128344032;AR:-0.325405533658;PATZ1:-0.348772692304;FOS_FOS{B,L1}_JUN{B,D}:-0.355014316534;TP53:-0.356841283123;MYBL2:-0.3771710014;SOX5:-0.390641169468;MEF2{A,B,C,D}:-0.409058391836;CEBPA,B_DDIT3:-0.418196268998;NKX2-1,4:-0.433070398244;HMGA1,2:-0.435047090142;EP300:-0.435975758805;ZNF148:-0.443717401526;BACH2:-0.445245920524;SMAD1..7,9:-0.447503009176;MTF1:-0.465651720143;ZFP161:-0.486270577227;PAX1,9:-0.520883439819;JUN:-0.535855597705;NR5A1,2:-0.537290430488;AHR_ARNT_ARNT2:-0.538206688513;STAT2,4,6:-0.540524364768;XCPE1{core}:-0.542005418544;VSX1,2:-0.550812295187;MYFfamily:-0.562366414512;TFAP4:-0.566162790275;POU6F1:-0.566603351391;FOSL2:-0.578175362651;RFX1:-0.603975073391;HNF4A_NR2F1,2:-0.612773587171;MAFB:-0.613009474975;HOX{A5,B5}:-0.615437334065;NKX2-3_NKX2-5:-0.622839052736;PAX8:-0.637164778767;CREB1:-0.638213546297;ZNF423:-0.657332682414;TEAD1:-0.658001365383;EVI1:-0.678602706913;PRRX1,2:-0.68367365335;TFCP2:-0.722896784358;HNF1A:-0.72728894819;GATA4:-0.72839110997;HIC1:-0.729598426721;FOXM1:-0.742134413022;ATF4:-0.749784110315;ATF2:-0.762042283039;MED-1{core}:-0.762113963791;GTF2I:-0.771319614708;MAZ:-0.776595306758;NKX3-1:-0.777321238507;MTE{core}:-0.781281492956;POU3F1..4:-0.785463473506;NKX2-2,8:-0.814100214229;NKX3-2:-0.824316116175;PAX2:-0.824381182238;FOXA2:-0.835061391416;UFEwm:-0.836434486693;DBP:-0.856629518293;NFE2:-0.880051869236;REST:-0.880747597198;TLX1..3_NFIC{dimer}:-0.883324398564;NKX6-1,2:-0.88473688344;CDC5L:-0.963701589629;FOX{F1,F2,J1}:-0.965533192026;ALX1:-0.997342644571;GZF1:-1.01663361442;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.02126842736;GCM1,2:-1.02329848958;TFAP2B:-1.05003886838;EGR1..3:-1.05461375512;ZIC1..3:-1.06280757356;IKZF1:-1.08386613008;LHX3,4:-1.16096899298;ZBTB6:-1.1942180524;TFAP2{A,C}:-1.19768984124;GFI1B:-1.22294987902;ONECUT1,2:-1.24328117718;SP1:-1.25882981493;HSF1,2:-1.28802180641;NFIL3:-1.29884422471;FOXN1:-1.32060201301;NR3C1:-1.3238901351;ESRRA:-1.33194020068;NFE2L2:-1.36350331767;ATF6:-1.38500962423;HAND1,2:-1.41312468122;ADNP_IRX_SIX_ZHX:-1.46495067659;HOXA9_MEIS1:-1.48018649664;GTF2A1,2:-1.67461202128;PAX5:-1.68786006525;GLI1..3:-1.70023910812;HIF1A:-1.70031485342
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1273-19G4;search_select_hide=table117:1273-19G4
 }}

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FF:1273-19G4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:43, 4 June 2020

CNhs10595

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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