FF:681-26C4: Difference between revisions

Latest revision as of 19:19, 4 June 2020

Name:	thymus, neonate N06
Species:	Mouse (Mus musculus)
Library ID:	CNhs11197
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	thymus
dev stage	6 days neonate
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		SAMD00005698

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11197		CAGE		DRX009120		DRR009994

Accession ID Mm9

Library id		BAM		CTSS
CNhs11197		DRZ001419		DRZ002802

Accession ID Mm10

Library id		BAM		CTSS
CNhs11197		DRZ012769		DRZ014152

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

CNhs11197

0	0
1	0
10	0
100	0
1000	-0.0317
1001	0.0737
1002	-0.0373
1003	-0.0968
1004	0
1005	0.0104
1006	-0.111
1007	0.0592
1008	0
1009	-0.112
101	0.165
1010	0
1011	-0.00767
1012	0.418
1013	-0.102
1014	-0.0851
1015	0.082
1016	-0.338
1017	0
1018	0.115
1019	0
102	0.0418
1020	0
1021	0.0986
1022	-0.124
1023	0
1024	-0.0899
1025	0
1026	0
1027	0
1028	0
1029	0.46
103	-0.0319
1030	0.0418
1031	-0.547
1032	-0.465
1033	0.0472
1034	0
1035	0
1036	0.206
1037	0
1038	-0.372
1039	-0.177
104	0
1040	-0.121
1041	0.0418

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: CNhs11197

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	4.95602e-4
MA0003.1	MA0003.1	0.379
MA0004.1	MA0004.1	0.342
MA0006.1	MA0006.1	0.92
MA0007.1	MA0007.1	0.513
MA0009.1	MA0009.1	0.269
MA0014.1	MA0014.1	0.247
MA0017.1	MA0017.1	0.619
MA0018.2	MA0018.2	0.0691
MA0019.1	MA0019.1	0.34
MA0024.1	MA0024.1	2.37613e-5
MA0025.1	MA0025.1	0.0137
MA0027.1	MA0027.1	0.745
MA0028.1	MA0028.1	1.22031e-6
MA0029.1	MA0029.1	0.053
MA0030.1	MA0030.1	0.741
MA0031.1	MA0031.1	0.254
MA0035.2	MA0035.2	0.37
MA0038.1	MA0038.1	0.979
MA0039.2	MA0039.2	0.316
MA0040.1	MA0040.1	0.91
MA0041.1	MA0041.1	0.32
MA0042.1	MA0042.1	0.922
MA0043.1	MA0043.1	0.228
MA0046.1	MA0046.1	1.35651e-17
MA0047.2	MA0047.2	0.481
MA0048.1	MA0048.1	0.645
MA0050.1	MA0050.1	2.97991e-6
MA0051.1	MA0051.1	3.75859e-5
MA0052.1	MA0052.1	0.00682
MA0055.1	MA0055.1	0.909
MA0057.1	MA0057.1	0.613
MA0058.1	MA0058.1	0.496
MA0059.1	MA0059.1	0.0179
MA0060.1	MA0060.1	0.00416
MA0061.1	MA0061.1	9.76286e-5
MA0062.2	MA0062.2	2.59171e-17
MA0065.2	MA0065.2	0.416
MA0066.1	MA0066.1	0.0175
MA0067.1	MA0067.1	0.578
MA0068.1	MA0068.1	0.87
MA0069.1	MA0069.1	0.896
MA0070.1	MA0070.1	0.414
MA0071.1	MA0071.1	0.423
MA0072.1	MA0072.1	8.69775e-7
MA0073.1	MA0073.1	0.783
MA0074.1	MA0074.1	0.931
MA0076.1	MA0076.1	3.92694e-9
MA0077.1	MA0077.1	0.179
MA0078.1	MA0078.1	0.549
MA0079.2	MA0079.2	0.0372
MA0080.2	MA0080.2	3.18617e-13
MA0081.1	MA0081.1	0.024
MA0083.1	MA0083.1	0.152
MA0084.1	MA0084.1	0.536
MA0087.1	MA0087.1	0.411
MA0088.1	MA0088.1	0.177
MA0090.1	MA0090.1	0.0677
MA0091.1	MA0091.1	0.0482
MA0092.1	MA0092.1	0.896
MA0093.1	MA0093.1	0.382
MA0099.2	MA0099.2	0.181
MA0100.1	MA0100.1	0.00868
MA0101.1	MA0101.1	2.49555e-4
MA0102.2	MA0102.2	0.557
MA0103.1	MA0103.1	1.5078e-4
MA0104.2	MA0104.2	0.13
MA0105.1	MA0105.1	1.10858e-7
MA0106.1	MA0106.1	0.697
MA0107.1	MA0107.1	3.34361e-4
MA0108.2	MA0108.2	0.0286
MA0111.1	MA0111.1	0.309
MA0112.2	MA0112.2	0.0155
MA0113.1	MA0113.1	0.734
MA0114.1	MA0114.1	0.32
MA0115.1	MA0115.1	0.419
MA0116.1	MA0116.1	0.00253
MA0117.1	MA0117.1	0.731
MA0119.1	MA0119.1	0.897
MA0122.1	MA0122.1	1
MA0124.1	MA0124.1	0.264
MA0125.1	MA0125.1	0.583
MA0131.1	MA0131.1	0.061
MA0135.1	MA0135.1	0.268
MA0136.1	MA0136.1	1.43845e-22
MA0137.2	MA0137.2	0.0293
MA0138.2	MA0138.2	5.3102e-5
MA0139.1	MA0139.1	0.175
MA0140.1	MA0140.1	0.566
MA0141.1	MA0141.1	0.321
MA0142.1	MA0142.1	0.873
MA0143.1	MA0143.1	0.235
MA0144.1	MA0144.1	0.337
MA0145.1	MA0145.1	0.391
MA0146.1	MA0146.1	0.531
MA0147.1	MA0147.1	0.0607
MA0148.1	MA0148.1	0.573
MA0149.1	MA0149.1	0.0459
MA0150.1	MA0150.1	0.327
MA0152.1	MA0152.1	0.908
MA0153.1	MA0153.1	1.32055e-8
MA0154.1	MA0154.1	0.0923
MA0155.1	MA0155.1	0.801
MA0156.1	MA0156.1	1.04672e-27
MA0157.1	MA0157.1	0.365
MA0159.1	MA0159.1	0.0891
MA0160.1	MA0160.1	0.266
MA0162.1	MA0162.1	0.39
MA0163.1	MA0163.1	9.71296e-4
MA0164.1	MA0164.1	0.886
MA0258.1	MA0258.1	0.0794
MA0259.1	MA0259.1	0.548

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: CNhs11197

Novel motif	Logo	P-value
1	1	0.176
10	10	0.0128
100	100	0.681
101	101	0.881
102	102	0.521
103	103	0.205
104	104	0.843
105	105	0.862
106	106	0.82
107	107	0.758
108	108	0.266
109	109	0.22
11	11	0.128
110	110	0.0425
111	111	0.786
112	112	0.275
113	113	0.463
114	114	0.858
115	115	0.485
116	116	0.761
117	117	6.22329e-4
118	118	0.344
119	119	0.291
12	12	0.647
120	120	0.218
121	121	0.301
122	122	0.573
123	123	0.611
124	124	0.825
125	125	0.105
126	126	0.63
127	127	0.734
128	128	0.74
129	129	0.222
13	13	0.00812
130	130	0.212
131	131	0.585
132	132	0.538
133	133	0.803
134	134	0.54
135	135	0.272
136	136	0.479
137	137	0.307
138	138	0.582
139	139	0.58
14	14	0.708
140	140	0.812
141	141	0.972
142	142	0.575
143	143	0.251
144	144	0.142
145	145	0.16
146	146	0.732
147	147	0.26
148	148	0.402
149	149	0.659
15	15	0.167
150	150	0.39
151	151	0.265
152	152	0.087
153	153	0.174
154	154	0.107
155	155	0.102
156	156	0.0329
157	157	0.724
158	158	0.0941
159	159	0.0217
160	160	0.811
161	161	0.605
162	162	0.551
163	163	0.862
164	164	0.145
165	165	0.199
166	166	0.429
167	167	0.132
168	168	0.301
169	169	0.253
17	17	0.616
18	18	0.909
19	19	0.654
2	2	0.0852
20	20	0.298
21	21	0.388
22	22	0.836
23	23	0.73
24	24	0.098
25	25	0.22
26	26	0.0401
27	27	0.479
28	28	0.226
29	29	0.0531
3	3	0.147
30	30	0.12
31	31	0.495
32	32	0.0961
33	33	0.304
34	34	0.991
35	35	0.101
36	36	0.174
37	37	0.164
38	38	0.239
39	39	0.926
4	4	0.871
40	40	0.588
41	41	0.96
42	42	0.0207
43	43	0.538
44	44	0.881
45	45	0.7
46	46	0.0982
47	47	0.309
48	48	0.157
49	49	0.215
5	5	0.318
50	50	0.85
51	51	0.935
52	52	0.146
53	53	0.962
54	54	0.236
55	55	0.381
56	56	0.926
57	57	0.26
58	58	0.259
59	59	0.743
6	6	0.216
60	60	0.839
61	61	0.0592
62	62	0.117
63	63	0.678
64	64	0.77
65	65	0.586
66	66	0.567
67	67	0.921
68	68	0.271
69	69	0.438
7	7	0.104
70	70	0.523
71	71	0.0258
72	72	0.517
73	73	0.495
74	74	0.851
75	75	0.0353
76	76	0.0847
77	77	0.266
78	78	0.0969
79	79	0.687
8	8	0.521
80	80	0.102
81	81	0.998
82	82	0.793
83	83	0.795
84	84	0.138
85	85	0.496
86	86	0.226
87	87	0.139
88	88	0.322
89	89	0.421
9	9	0.247
90	90	0.0515
91	91	0.676
92	92	0.669
93	93	0.93
94	94	0.311
95	95	0.247
96	96	0.0368
97	97	0.529
98	98	0.677
99	99	0.482

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: CNhs11197

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011401 mouse thymus- neonate N06 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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000312 (mouse neonate N6 sample)
0011401 (mouse thymus- neonate N06 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
-|DRA_sample_Accession=CAGE@DRS008983
+|DRA_sample_Accession=CAGE@SAMD00005698
-|accession_numbers=CAGE;DRX009120;DRR009994;DRZ001419;DRZ002802
+|accession_numbers=CAGE;DRX009120;DRR009994;DRZ001419;DRZ002802;DRZ012769;DRZ014152
 |ancestors_in_anatomy_facet=UBERON:0000468,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=
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:52096066..52096081,-!p2@Tcf7!2.66!553.09!Tcf7;;chr17:51971960..51971979,-!p1@Satb1!2.44!360.45!Satb1;;chr17:51971932..51971958,-!p2@Satb1!2.17!196.88!Satb1;;chr1:38721792..38721845,-!p1@Aff3!2.05!137.72!Aff3;;chr11:52095821..52095836,-!p3@Tcf7!1.98!94.30!Tcf7;;chr3:94181376..94181403,+!p2@Rorc!1.98!93.70!Rorc;;chr12:109242266..109242295,-!p1@Bcl11b!1.91!635.48!Bcl11b;;chr3:130815703..130815721,+!p2@Lef1!1.85!84.81!Lef1;;chr11:52096804..52096896,-!p1@Tcf7!1.77!447.08!Tcf7;;chr16:92826249..92826325,-!p1@Runx1!1.76!133.88!Runx1;;chr3:94181427..94181449,+!p3@Rorc!1.63!42.00!Rorc;;chr11:11590117..11590138,+!p4@Ikzf1!1.61!39.58!Ikzf1;;chr17:51971991..51972003,-!p4@Satb1!1.59!37.76!Satb1;;chr2:147190749..147190769,+!p1@Pax1!1.56!35.24!Pax1;;chr2:9800207..9800234,-!p1@Gata3!1.54!99.55!Gata3;;chr4:102787521..102787588,+!p4@Mier1!1.54!59.47!Mier1;;chr11:11590140..11590187,+!p3@Ikzf1!1.54!39.98!Ikzf1;;chr10:20880629..20880683,-!p1@Myb!1.52!89.96!Myb;;chr10:20880731..20880775,-!p2@Myb!1.52!66.13!Myb;;chr11:98407264..98407295,-!p1@Ikzf3!1.52!32.41!Ikzf3;;chr11:52095797..52095809,-!p5@Tcf7!1.51!31.00!Tcf7;;chr17:51965903..51965926,-!p5@Satb1!1.46!28.17!Satb1;;chr11:11584970..11585030,+!p2@Ikzf1!1.45!38.27!Ikzf1;;chr12:109241728..109241781,-!p2@Bcl11b!1.44!27.97!Bcl11b;;chr10:20880698..20880717,-!p3@Myb!1.43!40.59!Myb;;chr11:98407234..98407259,-!p2@Ikzf3!1.40!24.23!Ikzf3;;chr17:51972530..51972571,-!p7@Satb1!1.39!23.32!Satb1;;chr14:79915425..79915501,+!p1@Elf1!1.36!188.20!Elf1;;chr4:135728311..135728342,+!p3@E2f2!1.36!21.91!E2f2;;chr3:94181331..94181345,+!p4@Rorc!1.35!21.61!Rorc;;chr3:130813200..130813252,+!p1@Lef1!1.33!88.55!Lef1;;chr11:11586218..11586285,+!p1@Ikzf1!1.28!57.45!Ikzf1;;chr3:94181355..94181373,+!p5@Rorc!1.27!17.67!Rorc;;chr11:11585912..11585950,+!p6@Ikzf1!1.25!21.30!Ikzf1;;chr17:51972438..51972463,-!p8@Satb1!1.25!16.66!Satb1;;chr11:98826178..98826197,+!p7@Rara!1.23!16.15!Rara;;chr17:51972603..51972624,-!p9@Satb1!1.21!15.14!Satb1;;chr1:52065454..52065495,+!p1@Stat4!1.20!24.23!Stat4;;chr8:108583550..108583595,+!p2@Nfatc3!1.19!65.43!Nfatc3;;chr4:6917606..6917681,-!p1@Tox!1.19!59.97!Tox;;chr11:11585678..11585745,+!p5@Ikzf1!1.18!20.60!Ikzf1;;chr17:51972575..51972595,-!p13@Satb1!1.17!13.93!Satb1;;chr2:173044380..173044432,-!p1@Zbp1!1.14!30.59!Zbp1;;chr17:48025139..48025166,-!p8@Foxp4!1.13!14.74!Foxp4;;chr2:147190725..147190747,+!p2@Pax1!1.13!12.52!Pax1;;chr11:98407370..98407395,-!p3@Ikzf3!1.11!11.81!Ikzf3;;chr11:98407142..98407159,-!p5@Ikzf3!1.10!11.71!Ikzf3;;chr5:104182963..104182982,+!p5@Aff1!1.09!24.13!Aff1;;chr17:51965928..51965960,-!p10@Satb1!1.09!11.31!Satb1;;chr4:135728282..135728310,+!p4@E2f2!1.08!12.52!E2f2;;chr3:94181461..94181472,+!p6@Rorc!1.06!10.50!Rorc;;chr11:98407340..98407359,-!p4@Ikzf3!1.06!10.50!Ikzf3;;chr9:32503590..32503680,+!p1@Ets1!1.05!373.78!Ets1;;chr5:108155007..108155034,-!p1@Gfi1!1.05!10.20!Gfi1;;chr11:52096750..52096772,-!p4@Tcf7!1.03!15.25!Tcf7;;chr7:51787434..51787448,-!p1@Spib!1.03!13.93!Spib;;chr5:108494765..108494786,+!p2@Mtf2!1.03!13.13!Mtf2;;chr17:51952856..51952876,-!p12@Satb1!1.02!9.59!Satb1;;chr17:51965860..51965876,-!p14@Satb1!1.02!9.49!Satb1;;chr4:63064364..63064384,-!p1@Akna!1.01!27.56!Akna;;chr17:51972400..51972428,-!p11@Satb1!1.01!9.29!Satb1;;chr10:20881160..20881175,-!p4@Myb!1.01!9.29!Myb;;chr12:109241852..109241873,-!p4@Bcl11b!1.00!10.70!Bcl11b;;chr16:25801993..25802014,+!p1@Trp63!0.99!8.89!Trp63;;chr6:99216488..99216534,-!p2@Foxp1!0.97!24.13!Foxp1;;chr8:124984566..124984595,-!p1@Snai3!0.97!13.02!Snai3;;chr19:25746898..25746910,+!p1@Dmrt2!0.96!12.12!Dmrt2;;chr11:98407087..98407102,-!p11@Ikzf3!0.95!7.88!Ikzf3;;chr11:100800901..100800921,-!p4@Stat3!0.94!9.29!Stat3;;chr11:52096732..52096741,-!p6@Tcf7!0.94!7.67!Tcf7;;chr17:51951634..51951651,-!p6@Satb1!0.93!14.74!Satb1;;chr11:98338697..98338709,-!p9@Ikzf3!0.93!7.47!Ikzf3;;chr1:69732354..69732402,-!p1@Ikzf2!0.92!8.38!Ikzf2;;chr16:23988711..23988727,-!p1@Bcl6!0.91!88.65!Bcl6;;chr5:138186979..138187025,+!p4@Tsc22d4!0.91!27.46!Tsc22d4;;chr9:71959562..71959624,-!p3@Tcf12!0.91!25.44!Tcf12;;chr4:102787381..102787397,+!p9@Mier1!0.91!8.48!Mier1;;chr11:98407305..98407321,-!p6@Ikzf3!0.91!7.07!Ikzf3;;chr11:11590085..11590106,+!p7@Ikzf1!0.90!6.97!Ikzf1;;chr3:94181408..94181419,+!p7@Rorc!0.90!6.97!Rorc;;chr12:57796615..57796687,+!p1@Pax9!0.90!6.87!Pax9;;chr10:88145766..88145770,-!p1@Spic!0.89!9.09!Spic;;chr1:133904862..133904893,+!p6@Elk4!0.88!14.03!Elk4;;chr12:74147689..74147711,-!p1@Six1!0.86!14.24!Six1;;chr11:98407121..98407133,-!p10@Ikzf3!0.86!6.26!Ikzf3;;chr14:65568469..65568511,-!p2@Hmbox1!0.85!20.80!Hmbox1;;chr9:71958979..71959032,-!p4@Tcf12!0.85!7.88!Tcf12;;chr12:109241804..109241823,-!p5@Bcl11b!0.85!6.16!Bcl11b;;chr11:52074095..52074127,-!p8@Tcf7!0.85!6.16!Tcf7;;chr11:11590188..11590200,+!p8@Ikzf1!0.85!6.06!Ikzf1;;chr3:130813254..130813263,+!p4@Lef1!0.85!6.06!Lef1;;chr17:45692642..45692663,+!p1@Nfkbie!0.84!20.19!Nfkbie;;chr17:45692676..45692695,+!p2@Nfkbie!0.84!12.62!Nfkbie;;chr11:98407210..98407221,-!p7@Ikzf3!0.83!5.76!Ikzf3;;chr1:87495371..87495397,-!p1@Sp110!0.83!5.76!Sp110;;chr5:108155037..108155060,-!p2@Gfi1!0.83!5.76!Gfi1;;chr11:106134241..106134320,-!p2@Smarcd2!0.82!68.66!Smarcd2;;chr1:133904901..133904934,+!p3@Elk4!0.82!17.37!Elk4;;chr10:77506405..77506441,-!p1@Aire!0.82!5.65!Aire;;chr11:100683839..100683890,-!p2@Stat5b!0.81!13.53!Stat5b;;chr5:104183477..104183548,+!p6@Aff1!0.81!11.21!Aff1;;chr11:52070502..52070527,-!p7@Tcf7!0.80!5.35!Tcf7;;chr4:135728343..135728357,+!p9@E2f2!0.79!5.15!E2f2;;chr1:38721779..38721790,-!p6@Aff3!0.79!5.15!Aff3;;chr7:134169810..134169824,-!p7@Maz!0.78!20.60!Maz;;chr12:3891810..3891829,+!p2@Dnmt3a!0.78!8.08!Dnmt3a;;chr10:86956396..86956411,-!p1@Ascl1!0.78!8.08!Ascl1;;chr4:102792039..102792052,+!p7@Mier1!0.78!7.27!Mier1;;chr3:130815472..130815497,+!p6@Lef1!0.78!5.05!Lef1;;chr16:92697560..92697592,-!p2@Runx1!0.77!33.92!Runx1;;chr11:98407164..98407177,-!p8@Ikzf3!0.77!4.95!Ikzf3;;chr1:64579555..64579570,+!p3@Creb1!0.76!24.84!Creb1;;chr2:173044357..173044377,-!p2@Zbp1!0.76!7.17!Zbp1;;chr1:52065508..52065522,+!p2@Stat4!0.76!5.65!Stat4;;chr10:77506352..77506356,-!p2@Aire!0.76!4.75!Aire;;chr7:148514080..148514108,-!p4@Deaf1!0.74!10.20!Deaf1;;chr13:30841099..30841116,+!p1@Irf4!0.74!7.47!Irf4;;chr3:130813736..130813752,+!p3@Lef1!0.74!6.56!Lef1;;chr10:13685980..13686007,+!p6@Hivep2!0.74!5.76!Hivep2;;chr10:20881176..20881191,-!p6@Myb!0.74!4.54!Myb;;chr8:125921689..125921725,+!p3@Tcf25!0.74!4.54!Tcf25;;chr7:134169762..134169795,-!p3@Maz!0.73!44.02!Maz;;chr9:32348943..32349001,-!p1@Fli1!0.73!39.58!Fli1;;chr2:147190772..147190783,+!p3@Pax1!0.73!4.34!Pax1;;chr1:52176315..52176343,+!p1@Stat1!0.72!68.56!Stat1;;chr18:74375772..74375799,+!p2@Cxxc1!0.72!13.53!Cxxc1;;chr11:3190303..3190351,+!p3@Patz1!0.72!8.99!Patz1;;chr12:109242296..109242307,-!p3@Bcl11b!0.72!6.46!Bcl11b;;chr4:135728181..135728203,+!p2@E2f2!0.72!5.76!E2f2;;chr4:134676555..134676575,+!p2@Runx3!0.72!4.24!Runx3;;chrX:48559079..48559108,-!p2@Mbnl3!0.71!10.40!Mbnl3;;chr2:91077034..91077078,-!p2@Ddb2!0.71!10.00!Ddb2;;chr11:52096305..52096328,-!p11@Tcf7!0.71!4.14!Tcf7;;chr9:32349051..32349061,-!p5@Fli1!0.71!4.14!Fli1;;chr16:95924005..95924042,+!p2@Ets2!0.70!82.29!Ets2;;chr15:61816932..61816952,+!p2@Myc!0.70!37.76!Myc;;chr13:55431084..55431137,-!p1@Mxd3!0.70!35.34!Mxd3;;chr11:100721761..100721851,+!p1@Stat5a!0.70!33.52!Stat5a;;chr12:3891753..3891801,+!p4@Dnmt3a!0.70!6.87!Dnmt3a;;chr11:52070563..52070589,-!p9@Tcf7!0.70!4.04!Tcf7;;chr16:95924055..95924077,+!p1@Ets2!0.69!245.45!Ets2;;chr2:91077082..91077122,-!p1@Ddb2!0.69!27.16!Ddb2;;chr3:95021663..95021687,-!p3@Gabpb2!0.69!14.94!Gabpb2;;chrX:45807489..45807502,-!p2@Elf4!0.69!13.53!Elf4;;chr10:30375579..30375616,-!p3@Ncoa7!0.69!10.00!Ncoa7;;chr7:56136362..56136400,-!p1@E2f8!0.68!28.27!E2f8;;chr12:77470718..77470752,-!p4@Zbtb25!0.68!5.55!Zbtb25;;chr4:135736690..135736705,+!p6@E2f2!0.68!4.54!E2f2;;chr17:51972017..51972022,-!p17@Satb1!0.68!3.84!Satb1;;chr10:13686012..13686028,+!p8@Hivep2!0.68!3.84!Hivep2;;chr11:11590205..11590216,+!p9@Ikzf1!0.68!3.84!Ikzf1;;chr11:98826216..98826227,+!p10@Rara!0.68!3.84!Rara;;chr6:47544966..47545046,-!p1@Ezh2!0.67!88.14!Ezh2;;chr8:72676653..72676668,+!p4@2310045N01Rik,p4@Mef2b!0.67!3.63!Mef2b;;chr5:138187341..138187406,+!p3@Tsc22d4!0.66!44.43!Tsc22d4;;chr8:108160490..108160512,+!p2@Ctcf!0.66!34.03!Ctcf;;chrX:98449898..98449913,+!p2@Foxo4!0.66!12.92!Foxo4;;chr6:115803317..115803361,-!p2@Mbd4!0.66!9.89!Mbd4;;chr4:134708451..134708469,+!p1@Runx3!0.66!6.87!Runx3;;chr11:100711801..100711910,-!p1@Stat5b!0.65!55.63!Stat5b;;chr11:62272010..62272050,-!p2@Ncor1!0.65!12.52!Ncor1;;chrX:48558950..48559016,-!p1@Mbnl3!0.65!12.52!Mbnl3;;chr7:71083729..71083742,-!p4@Klf13!0.65!6.66!Klf13;;chr4:102792009..102792021,+!p6@Mier1!0.65!6.36!Mier1;;chr1:87546583..87546595,+!p1@Sp100!0.64!5.05!Sp100;;chr11:78200071..78200100,-!p1@Foxn1!0.64!3.33!Foxn1;;chr9:21420744..21420755,+!p3@Smarca4!0.63!10.80!Smarca4;;chr4:102792072..102792091,+!p5@Mier1!0.63!9.89!Mier1;;chrX:48559055..48559077,-!p6@Mbnl3!0.63!4.44!Mbnl3;;chr1:87546602..87546617,+!p2@Sp100!0.63!4.04!Sp100;;chr9:57684520..57684612,-!p1@Arid3b!0.62!32.92!Arid3b;;chr6:47545052..47545064,-!p2@Ezh2!0.62!6.87!Ezh2;;chr12:100802113..100802127,-!p5@Foxn3!0.62!4.34!Foxn3;;chr1:38721767..38721778,-!p5@Aff3!0.62!3.13!Aff3;;chr9:20757246..20757278,-!p1@Dnmt1!0.61!107.63!Dnmt1;;chr10:67000609..67000625,+!p1@Egr2!0.61!8.08!Egr2;;chr9:72122748..72122757,+!p4@Zfp280d!0.61!3.74!Zfp280d;;chr11:52070478..52070500,-!p10@Tcf7!0.61!3.03!Tcf7;;chr5:108494715..108494757,+!p1@Mtf2!0.60!54.12!Mtf2;;chr5:138187583..138187602,+!p6@Tsc22d4!0.60!6.16!Tsc22d4;;chr7:31206743..31206761,+!p1@Nfkbid!0.60!4.34!Nfkbid;;chr15:100430414..100430470,-!p1@Pou6f1!0.59!10.60!Pou6f1;;chr7:16986617..16986632,+!p2@Zc3h4!0.59!9.39!Zc3h4;;chr5:108494686..108494701,+!p3@Mtf2!0.59!4.44!Mtf2;;chr10:20881239..20881254,-!p5@Myb!0.59!2.93!Myb;;chr4:102791976..102792008,+!p2@Mier1!0.58!37.26!Mier1;;chr5:104121391..104121450,+!p3@Aff1!0.58!17.77!Aff1;;chrX:45947746..45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1!0.25!69.26!Smarce1;;chr4:34830168..34830213,-!p1@Zfp292!0.25!60.48!Zfp292;;chr5:38611720..38611799,+!p1@Lyar!0.25!42.91!Lyar;;chr2:28915759..28915807,+!p1@Ttf1!0.25!21.61!Ttf1;;chr9:22112085..22112138,-!p1@Zfp810!0.25!19.59!Zfp810;;chr4:133310237..133310293,-!p2@Arid1a!0.25!19.59!Arid1a;;chr4:87679232..87679277,-!p1@Mllt3!0.25!18.48!Mllt3;;chr17:4994286..4994373,+!p2@Arid1b!0.25!16.86!Arid1b;;chr4:128483347..128483411,-!p2@Zfp362!0.25!11.41!Zfp362;;chr2:72818459..72818528,-!p3@Sp3!0.25!11.21!Sp3;;chr13:96095150..96095184,+!p2@Zbed3!0.25!10.70!Zbed3;;chr6:133985993..133986029,+!p2@Etv6!0.25!9.69!Etv6;;chr11:23670953..23671028,-!p1@Rel!0.25!8.48!Rel;;chr13:67585161..67585205,-!p1@Zfp874b!0.25!7.67!Zfp874b;;chr9:96159665..96159680,+!p3@Tfdp2!0.25!6.56!Tfdp2;;chr12:77470507..77470572,-!p2@Zbtb25!0.25!5.55!Zbtb25;;chr5:107125838..107125858,-!p2@Zfp644!0.25!4.75!Zfp644;;chr19:26681865..26681900,+!p6@Smarca2!0.25!3.94!Smarca2;;chr7:30875418..30875454,-!p2@Zfp566,p2@Zfp82!0.25!3.74!Zfp566;;chr7:134550321..134550345,-!p2@Zfp764!0.25!2.83!Zfp764;;chr7:49761111..49761128,-!p2@ENSMUST00000174407,p2@uc009gmb.1!0.25!2.63!Zfp141;;chr4:108151497..108151514,+!p3@Zcchc11!0.25!2.42!Zcchc11;;chr4:48058129..48058179,+!p2@Nr4a3!0.25!2.22!Nr4a3;;chr7:88138313..88138368,+!p4@Zfp592!0.25!2.02!Zfp592;;chr7:56136974..56136989,-!p4@E2f8!0.25!1.82!E2f8;;chr4:63071717..63071736,-!p4@Akna!0.25!1.41!Akna;;chr14:32979290..32979309,+!p3@Gm6768,p3@Ncoa4!0.25!1.11!Ncoa4;;chr5:38611816..38611827,+!p4@Lyar!0.25!1.01!Lyar;;chr11:80196811..80196838,+!p1@Zfp207!0.24!271.90!Zfp207;;chr16:91044627..91044703,-!p1@Gcfc1!0.24!49.68!Gcfc1;;chr8:107821563..107821642,+!p1@E2f4!0.24!44.32!E2f4;;chr11:60034052..60034134,-!p2@Srebf1!0.24!36.45!Srebf1;;chr10:127080031..127080090,+!p1@Stat6!0.24!33.52!Stat6;;chr1:93309740..93309811,-!p1@Hes6!0.24!31.10!Hes6;;chr7:13595144..13595205,-!p1@Zbtb45!0.24!30.39!Zbtb45;;chr4:102787007..102787050,+!p1@Mier1!0.24!24.84!Mier1;;chr13:67654035..67654112,-!p1@Zfp748!0.24!22.62!Zfp748;;chr7:24866907..24866967,+!p1@LOC676710,p1@Zfp180!0.24!19.59!Zfp180;;chr3:152058955..152059023,+!p1@Gm8261,p1@Zzz3!0.24!19.39!Zzz3;;chr14:79880971..79880992,+!p2@Elf1!0.24!19.39!Elf1;;chr16:98073403..98073460,-!p1@Prdm15!0.24!11.81!Prdm15;;chr7:138554009..138554034,-!p1@Ikzf5!0.24!9.29!Ikzf5;;chr8:72520162..72520197,-!p4@Gatad2a!0.24!7.37!Gatad2a;;chr19:12870598..12870636,-!p1@U05342,p1@Zfp91!0.24!7.17!Zfp91;;chr19:28085485..28085544,-!p5@Rfx3!0.24!5.45!Rfx3;;chr14:65977459..65977489,+!p3@Zfp395!0.24!4.85!Zfp395;;chr10:79896690..79896746,-!p4@Tcf3!0.24!4.64!Tcf3;;chr3:87945895..87945946,+!p2@Mef2d!0.24!4.34!Mef2d;;chr12:77471463..77471495,+!p3@Zbtb1!0.24!3.94!Zbtb1;;chr8:83262929..83262957,-!p1@Smarca5!0.24!3.53!Smarca5;;chr3:9610074..9610086,-!p2@Zfp704!0.24!3.03!Zfp704;;chr18:76401789..76401814,+!p4@Smad2!0.24!2.73!Smad2;;chr4:133276779..133276796,-!p8@Arid1a!0.24!2.32!Arid1a;;chr13:96095124..96095144,+!p3@Zbed3!0.24!2.32!Zbed3;;chr7:30638614..30638628,-!p2@Zfp940!0.24!1.62!Zfp940;;chr8:72356384..72356434,+!p2@Pbx4!0.24!1.62!Pbx4;;chr12:77470573..77470585,-!p6@Zbtb25!0.24!1.51!Zbtb25;;chr14:52640315..52640328,-!p10@Zfp219!0.24!1.21!Zfp219;;chr5:22939909..22939948,+!p6@Mll5!0.24!1.21!Mll5;;chr2:153067233..153067236,-!p4@Plagl2!0.24!1.11!Plagl2;;chr9:44689360..44689406,-!p1@Mll1!0.23!57.45!Mll1;;chr1:64579394..64579433,+!p1@Creb1!0.23!55.23!Creb1;;chr2:165818125..165818167,+!p1@Ncoa3!0.23!40.49!Ncoa3;;chr3:19957802..19957857,+!p1@Hltf!0.23!26.45!Hltf;;chr12:85658052..85658097,+!p1@Zfp410!0.23!25.85!Zfp410;;chr17:27110106..27110164,+!p1@Ggnbp1,p1@Zbtb9!0.23!25.04!Zbtb9;;chr2:73730596..73730612,-!p3@Atf2,p3@LOC100047997!0.23!19.08!Atf2;;chr17:25152711..25152736,-!p1@Cramp1l!0.23!14.84!Cramp1l;;chr3:94819338..94819384,-!p1@Zfp687!0.23!13.83!Zfp687;;chr10:127707602..127707633,+!p1@Stat2!0.23!12.92!Stat2;;chr7:135019614..135019666,-!p1@Zfp668!0.23!12.12!Zfp668;;chr2:91489908..91489941,-!p1@Zfp408!0.23!11.81!Zfp408;;chr19:28085676..28085711,-!p2@Rfx3!0.23!8.68!Rfx3;;chr17:21587325..21587361,+!p1@Zfp51!0.23!8.68!Zfp51;;chr2:120996843..120996894,-!p1@Zscan29!0.23!8.68!Zscan29;;chr4:126698529..126698536,+!p2@Sfpq!0.23!6.36!Sfpq;;chr2:73730619..73730630,-!p4@Atf2,p4@LOC100047997!0.23!5.86!Atf2;;chr13:67370029..67370067,-!p1@Zfp458!0.23!5.86!Zfp458;;chr16:33380950..33380988,+!p2@Zfp148!0.23!5.55!Zfp148;;chr6:117813087..117813121,+!p1@Zfp239!0.23!5.15!Zfp239;;chr17:24592183..24592202,-!p2@E4f1!0.23!4.75!E4f1;;chr7:28764153..28764173,-!p2@Zfp780b!0.23!4.44!Zfp780b;;chr7:31742079..31742108,-!p4@LOC100504922,p4@Usf2!0.23!3.94!Usf2;;chr7:88138585..88138600,+!p2@Zfp592!0.23!3.63!Zfp592;;chr10:75495410..75495444,+!p2@Zfp280b!0.23!3.13!Zfp280b;;chr5:77543897..77543911,-!p2@Hopx!0.23!2.12!Hopx;;chr17:4995982..4995989,+!p9@Arid1b!0.23!1.82!Arid1b;;chr10:67375146..67375208,-!p2@Zfp365!0.23!1.51!Zfp365;;chr10:127080091..127080100,+!p4@Stat6!0.23!1.41!Stat6;;chr4:87679181..87679192,-!p10@Mllt3!0.23!1.41!Mllt3;;chr7:52253119..52253130,+!p4@Irf3!0.23!0.91!Irf3;;chr8:7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@@ Line 44: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11197
-|library_ids=CNhs11197
+|library_id_phase_based=2:CNhs11197
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;681
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;681
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N06.CNhs11197.681-26C4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N06.CNhs11197.681-26C4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N06.CNhs11197.681-26C4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N06.CNhs11197.681-26C4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N06.CNhs11197.681-26C4.mm9.nobarcode.rdna.fa.gz
 |name=thymus, neonate N06
 |namespace=FANTOM5
@@ Line 50: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11197,LSID747,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0642512698304775,0.0283282084746532,0.0521513359606335,0,0.571253824178281,0,0.219622058314777,0.00318192712730573,0,0,0,0.0931488495184322,0.0417740847988257,0,0,0,0,0,0.208557727612542,0,0.0399401115296209,0,0,0.0798802230592418,0,0,0,0,0,0,0.0208870423994129,0,0.423040093228024,0,0,0,0,0,0.0645656108127411,-0.0124666104554862,-0.00223962148901435,-0.550212904446669,-0.154957770644279,0.0417740847988257,0,0,0,0,0,0.0417740847988257,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.104478639039142,0,0.116401293378451,0,0.0798802230592418,0,0.0791593615905569,0.223780956264591,0.0476000591343852,0.0244720005602762,0,0.0474009912394705,-0.0760168881589905,0,0.0417740847988257,0,0,-0.175419617924082,-0.292791319929798,0.12685950706556,0.0208870423994129,0,0,0,0,0,-0.0893284091371433,-0.0483211737056921,-0.0649720740550266,0.0417740847988257,0,0,0,0
@@ Line 87: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:681-26C4;search_select_hide=table117:681-26C4
 }}

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FF:681-26C4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:19, 4 June 2020

CNhs11197

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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