FF:713-19D3: Difference between revisions

Latest revision as of 19:19, 4 June 2020

Name:	thymus, neonate N07
Species:	Mouse (Mus musculus)
Library ID:	CNhs11211
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	thymus
dev stage	7 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		SAMD00005656

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11211		CAGE		DRX009121		DRR009995

Accession ID Mm9

Library id		BAM		CTSS
CNhs11211		DRZ001420		DRZ002803

Accession ID Mm10

Library id		BAM		CTSS
CNhs11211		DRZ012770		DRZ014153

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

CNhs11211

0	0
1	0
10	0
100	0
1000	-0.00631
1001	0.0876
1002	-0.0186
1003	-0.107
1004	0
1005	0
1006	-0.143
1007	0.135
1008	0
1009	-0.101
101	0.127
1010	0
1011	0.056
1012	0.463
1013	-0.135
1014	-0.0874
1015	0.0415
1016	-0.33
1017	0
1018	0.0319
1019	0
102	0.0319
1020	0
1021	0.0319
1022	-0.226
1023	0
1024	-0.0861
1025	-0.0611
1026	0
1027	-0.0278
1028	0
1029	0.389
103	-0.0605
1030	0.0616
1031	-0.629
1032	-0.463
1033	0
1034	0
1035	0
1036	0.219
1037	0
1038	-0.305
1039	-0.131
104	0
1040	-0.0865
1041	0.0319

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: CNhs11211

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00371
MA0003.1	MA0003.1	0.244
MA0004.1	MA0004.1	0.255
MA0006.1	MA0006.1	0.932
MA0007.1	MA0007.1	0.375
MA0009.1	MA0009.1	0.519
MA0014.1	MA0014.1	0.2
MA0017.1	MA0017.1	0.676
MA0018.2	MA0018.2	0.0595
MA0019.1	MA0019.1	0.156
MA0024.1	MA0024.1	4.4207e-6
MA0025.1	MA0025.1	0.00791
MA0027.1	MA0027.1	0.53
MA0028.1	MA0028.1	3.84657e-7
MA0029.1	MA0029.1	0.0787
MA0030.1	MA0030.1	0.936
MA0031.1	MA0031.1	0.176
MA0035.2	MA0035.2	0.402
MA0038.1	MA0038.1	0.998
MA0039.2	MA0039.2	0.263
MA0040.1	MA0040.1	0.986
MA0041.1	MA0041.1	0.303
MA0042.1	MA0042.1	0.987
MA0043.1	MA0043.1	0.204
MA0046.1	MA0046.1	2.74959e-15
MA0047.2	MA0047.2	0.505
MA0048.1	MA0048.1	0.603
MA0050.1	MA0050.1	3.59826e-6
MA0051.1	MA0051.1	3.16333e-5
MA0052.1	MA0052.1	1.36674e-4
MA0055.1	MA0055.1	0.948
MA0057.1	MA0057.1	0.727
MA0058.1	MA0058.1	0.406
MA0059.1	MA0059.1	0.0127
MA0060.1	MA0060.1	0.00587
MA0061.1	MA0061.1	2.9366e-4
MA0062.2	MA0062.2	3.25436e-18
MA0065.2	MA0065.2	0.541
MA0066.1	MA0066.1	0.0155
MA0067.1	MA0067.1	0.475
MA0068.1	MA0068.1	0.848
MA0069.1	MA0069.1	0.844
MA0070.1	MA0070.1	0.526
MA0071.1	MA0071.1	0.359
MA0072.1	MA0072.1	1.57721e-6
MA0073.1	MA0073.1	0.751
MA0074.1	MA0074.1	0.886
MA0076.1	MA0076.1	2.96056e-9
MA0077.1	MA0077.1	0.178
MA0078.1	MA0078.1	0.619
MA0079.2	MA0079.2	0.0254
MA0080.2	MA0080.2	8.23782e-13
MA0081.1	MA0081.1	0.0367
MA0083.1	MA0083.1	0.0124
MA0084.1	MA0084.1	0.37
MA0087.1	MA0087.1	0.349
MA0088.1	MA0088.1	0.279
MA0090.1	MA0090.1	0.0491
MA0091.1	MA0091.1	0.0712
MA0092.1	MA0092.1	0.994
MA0093.1	MA0093.1	0.308
MA0099.2	MA0099.2	0.062
MA0100.1	MA0100.1	0.00462
MA0101.1	MA0101.1	5.92615e-4
MA0102.2	MA0102.2	0.4
MA0103.1	MA0103.1	1.9694e-4
MA0104.2	MA0104.2	0.089
MA0105.1	MA0105.1	7.31932e-7
MA0106.1	MA0106.1	0.858
MA0107.1	MA0107.1	0.001
MA0108.2	MA0108.2	2.74993e-4
MA0111.1	MA0111.1	0.33
MA0112.2	MA0112.2	0.0457
MA0113.1	MA0113.1	0.77
MA0114.1	MA0114.1	0.265
MA0115.1	MA0115.1	0.738
MA0116.1	MA0116.1	0.00577
MA0117.1	MA0117.1	0.749
MA0119.1	MA0119.1	0.846
MA0122.1	MA0122.1	0.965
MA0124.1	MA0124.1	0.329
MA0125.1	MA0125.1	0.404
MA0131.1	MA0131.1	0.054
MA0135.1	MA0135.1	0.151
MA0136.1	MA0136.1	4.04598e-21
MA0137.2	MA0137.2	0.123
MA0138.2	MA0138.2	1.18861e-5
MA0139.1	MA0139.1	0.205
MA0140.1	MA0140.1	0.656
MA0141.1	MA0141.1	0.484
MA0142.1	MA0142.1	0.746
MA0143.1	MA0143.1	0.293
MA0144.1	MA0144.1	0.534
MA0145.1	MA0145.1	0.261
MA0146.1	MA0146.1	0.345
MA0147.1	MA0147.1	0.0373
MA0148.1	MA0148.1	0.512
MA0149.1	MA0149.1	0.0345
MA0150.1	MA0150.1	0.415
MA0152.1	MA0152.1	0.645
MA0153.1	MA0153.1	7.26973e-8
MA0154.1	MA0154.1	0.36
MA0155.1	MA0155.1	0.941
MA0156.1	MA0156.1	1.40276e-25
MA0157.1	MA0157.1	0.325
MA0159.1	MA0159.1	0.14
MA0160.1	MA0160.1	0.275
MA0162.1	MA0162.1	0.557
MA0163.1	MA0163.1	9.30226e-4
MA0164.1	MA0164.1	0.688
MA0258.1	MA0258.1	0.0994
MA0259.1	MA0259.1	0.394

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: CNhs11211

Novel motif	Logo	P-value
1	1	0.245
10	10	0.0144
100	100	0.641
101	101	0.886
102	102	0.44
103	103	0.181
104	104	0.942
105	105	0.749
106	106	0.94
107	107	0.724
108	108	0.217
109	109	0.361
11	11	0.166
110	110	0.0922
111	111	0.807
112	112	0.256
113	113	0.404
114	114	0.852
115	115	0.438
116	116	0.809
117	117	4.99026e-4
118	118	0.128
119	119	0.344
12	12	0.6
120	120	0.277
121	121	0.335
122	122	0.725
123	123	0.635
124	124	0.975
125	125	0.0708
126	126	0.35
127	127	0.784
128	128	0.655
129	129	0.162
13	13	0.0126
130	130	0.33
131	131	0.469
132	132	0.662
133	133	0.846
134	134	0.581
135	135	0.433
136	136	0.396
137	137	0.341
138	138	0.694
139	139	0.549
14	14	0.692
140	140	0.728
141	141	0.95
142	142	0.691
143	143	0.236
144	144	0.177
145	145	0.121
146	146	0.842
147	147	0.328
148	148	0.288
149	149	0.647
15	15	0.112
150	150	0.363
151	151	0.246
152	152	0.0337
153	153	0.199
154	154	0.0639
155	155	0.0961
156	156	0.0448
157	157	0.663
158	158	0.0702
159	159	0.022
160	160	0.889
161	161	0.442
162	162	0.635
163	163	0.965
164	164	0.126
165	165	0.335
166	166	0.226
167	167	0.18
168	168	0.206
169	169	0.589
17	17	0.681
18	18	0.774
19	19	0.512
2	2	0.0493
20	20	0.228
21	21	0.435
22	22	0.749
23	23	0.525
24	24	0.16
25	25	0.192
26	26	0.0231
27	27	0.487
28	28	0.235
29	29	0.0632
3	3	0.164
30	30	0.152
31	31	0.432
32	32	0.095
33	33	0.377
34	34	0.918
35	35	0.0958
36	36	0.144
37	37	0.285
38	38	0.439
39	39	0.974
4	4	0.901
40	40	0.499
41	41	0.928
42	42	0.0256
43	43	0.629
44	44	0.956
45	45	0.628
46	46	0.11
47	47	0.444
48	48	0.199
49	49	0.207
5	5	0.273
50	50	0.771
51	51	0.897
52	52	0.147
53	53	0.907
54	54	0.254
55	55	0.469
56	56	0.904
57	57	0.24
58	58	0.26
59	59	0.6
6	6	0.27
60	60	0.803
61	61	0.0649
62	62	0.132
63	63	0.677
64	64	0.766
65	65	0.863
66	66	0.653
67	67	0.745
68	68	0.342
69	69	0.551
7	7	0.129
70	70	0.412
71	71	0.0419
72	72	0.576
73	73	0.644
74	74	0.74
75	75	0.0238
76	76	0.0248
77	77	0.133
78	78	0.141
79	79	0.72
8	8	0.458
80	80	0.105
81	81	0.931
82	82	0.92
83	83	0.944
84	84	0.176
85	85	0.534
86	86	0.357
87	87	0.118
88	88	0.312
89	89	0.297
9	9	0.331
90	90	0.0306
91	91	0.594
92	92	0.618
93	93	0.829
94	94	0.326
95	95	0.373
96	96	0.0293
97	97	0.502
98	98	0.503
99	99	0.307

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: CNhs11211

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011407 mouse thymus- neonate N07 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)
0000313 (mouse neonate N7 sample)
0011407 (mouse thymus- neonate N07 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@SAMD00005656
-|accession_numbers=CAGE;DRX009121;DRR009995;DRZ001420;DRZ002803
+|accession_numbers=CAGE;DRX009121;DRR009995;DRZ001420;DRZ002803;DRZ012770;DRZ014153
 |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=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:52096066..52096081,-!p2@Tcf7!2.65!533.98!Tcf7;;chr17:51971960..51971979,-!p1@Satb1!2.41!334.47!Satb1;;chr17:51971932..51971958,-!p2@Satb1!2.16!194.63!Satb1;;chr1:38721792..38721845,-!p1@Aff3!2.03!130.85!Aff3;;chr3:94181376..94181403,+!p2@Rorc!1.94!85.89!Rorc;;chr12:109242266..109242295,-!p1@Bcl11b!1.90!617.50!Bcl11b;;chr11:52096804..52096896,-!p1@Tcf7!1.89!585.19!Tcf7;;chr11:52095821..52095836,-!p3@Tcf7!1.85!70.42!Tcf7;;chr3:130815703..130815721,+!p2@Lef1!1.70!58.68!Lef1;;chr16:92826249..92826325,-!p1@Runx1!1.69!113.47!Runx1;;chr3:94181427..94181449,+!p3@Rorc!1.64!42.45!Rorc;;chr2:147190749..147190769,+!p1@Pax1!1.59!37.95!Pax1;;chr11:11590117..11590138,+!p4@Ikzf1!1.58!36.81!Ikzf1;;chr11:52095797..52095809,-!p5@Tcf7!1.54!33.53!Tcf7;;chr11:98407264..98407295,-!p1@Ikzf3!1.53!33.15!Ikzf3;;chr2:9800207..9800234,-!p1@Gata3!1.51!92.74!Gata3;;chr17:51971991..51972003,-!p4@Satb1!1.51!31.40!Satb1;;chr10:20880731..20880775,-!p2@Myb!1.50!62.34!Myb;;chr4:102787521..102787588,+!p4@Mier1!1.49!53.12!Mier1;;chr11:11584970..11585030,+!p2@Ikzf1!1.48!41.30!Ikzf1;;chr11:11590140..11590187,+!p3@Ikzf1!1.48!34.98!Ikzf1;;chr10:20880629..20880683,-!p1@Myb!1.47!79.86!Myb;;chr17:51965903..51965926,-!p5@Satb1!1.47!28.20!Satb1;;chr4:135728311..135728342,+!p3@E2f2!1.43!26.14!E2f2;;chr11:11585912..11585950,+!p6@Ikzf1!1.42!32.08!Ikzf1;;chr17:51972530..51972571,-!p7@Satb1!1.41!24.77!Satb1;;chr3:130813200..130813252,+!p1@Lef1!1.39!101.74!Lef1;;chr12:109241728..109241781,-!p2@Bcl11b!1.37!24.01!Bcl11b;;chr3:94181331..94181345,+!p4@Rorc!1.37!22.63!Rorc;;chr10:20880698..20880717,-!p3@Myb!1.35!33.23!Myb;;chr11:11585678..11585745,+!p5@Ikzf1!1.32!28.73!Ikzf1;;chr11:98407234..98407259,-!p2@Ikzf3!1.31!19.43!Ikzf3;;chr17:51972603..51972624,-!p9@Satb1!1.30!19.13!Satb1;;chr14:79915425..79915501,+!p1@Elf1!1.29!160.11!Elf1;;chr17:48025139..48025166,-!p8@Foxp4!1.27!20.50!Foxp4;;chr17:51972438..51972463,-!p8@Satb1!1.27!17.45!Satb1;;chr11:11586218..11586285,+!p1@Ikzf1!1.22!49.53!Ikzf1;;chr3:94181461..94181472,+!p6@Rorc!1.22!15.47!Rorc;;chr1:52065454..52065495,+!p1@Stat4!1.21!25.00!Stat4;;chr8:108583550..108583595,+!p2@Nfatc3!1.20!66.68!Nfatc3;;chr4:6917606..6917681,-!p1@Tox!1.20!60.89!Tox;;chr4:135728282..135728310,+!p4@E2f2!1.20!16.61!E2f2;;chr3:94181355..94181373,+!p5@Rorc!1.20!14.94!Rorc;;chr17:51952856..51952876,-!p12@Satb1!1.19!14.48!Satb1;;chr17:51972400..51972428,-!p11@Satb1!1.19!14.33!Satb1;;chr5:104182963..104182982,+!p5@Aff1!1.18!29.49!Aff1;;chr4:63064364..63064384,-!p1@Akna!1.13!36.12!Akna;;chr2:147190725..147190747,+!p2@Pax1!1.13!12.57!Pax1;;chr9:32503590..32503680,+!p1@Ets1!1.11!426.61!Ets1;;chr12:109241852..109241873,-!p4@Bcl11b!1.11!14.17!Bcl11b;;chr11:98407370..98407395,-!p3@Ikzf3!1.11!11.81!Ikzf3;;chr8:124984566..124984595,-!p1@Snai3!1.09!17.53!Snai3;;chr11:52096750..52096772,-!p4@Tcf7!1.09!17.45!Tcf7;;chr17:51965928..51965960,-!p10@Satb1!1.09!11.43!Satb1;;chr11:98407142..98407159,-!p5@Ikzf3!1.09!11.20!Ikzf3;;chr11:98826178..98826197,+!p7@Rara!1.08!11.13!Rara;;chr5:108494765..108494786,+!p2@Mtf2!1.07!14.48!Mtf2;;chr10:20881160..20881175,-!p4@Myb!1.07!10.82!Myb;;chr5:108155007..108155034,-!p1@Gfi1!1.07!10.67!Gfi1;;chr16:25801993..25802014,+!p1@Trp63!1.06!10.36!Trp63;;chr17:51972575..51972595,-!p13@Satb1!1.06!10.36!Satb1;;chr11:100800901..100800921,-!p4@Stat3!1.03!11.66!Stat3;;chr2:173044380..173044432,-!p1@Zbp1!1.02!22.71!Zbp1;;chr11:98407340..98407359,-!p4@Ikzf3!1.01!9.30!Ikzf3;;chr17:51965860..51965876,-!p14@Satb1!1.01!9.22!Satb1;;chr11:52096732..52096741,-!p6@Tcf7!1.01!9.14!Tcf7;;chr3:94181408..94181419,+!p7@Rorc!0.99!8.69!Rorc;;chr9:71959562..71959624,-!p3@Tcf12!0.97!29.42!Tcf12;;chr11:98338697..98338709,-!p9@Ikzf3!0.97!8.31!Ikzf3;;chr17:45692642..45692663,+!p1@Nfkbie!0.96!26.52!Nfkbie;;chr4:135728181..135728203,+!p2@E2f2!0.96!10.75!E2f2;;chr9:71958979..71959032,-!p4@Tcf12!0.96!10.36!Tcf12;;chr5:138186979..138187025,+!p4@Tsc22d4!0.95!29.87!Tsc22d4;;chr19:25746898..25746910,+!p1@Dmrt2!0.95!11.96!Dmrt2;;chr6:99216488..99216534,-!p2@Foxp1!0.94!22.71!Foxp1;;chr7:148514080..148514108,-!p4@Deaf1!0.93!16.38!Deaf1;;chr12:57796615..57796687,+!p1@Pax9!0.93!7.47!Pax9;;chr16:23988711..23988727,-!p1@Bcl6!0.92!89.54!Bcl6;;chr4:102787381..102787397,+!p9@Mier1!0.92!8.69!Mier1;;chr10:20881176..20881191,-!p6@Myb!0.91!7.16!Myb;;chr11:98407305..98407321,-!p6@Ikzf3!0.91!7.09!Ikzf3;;chr5:108155037..108155060,-!p2@Gfi1!0.90!7.01!Gfi1;;chr11:98407121..98407133,-!p10@Ikzf3!0.89!6.71!Ikzf3;;chr7:51787434..51787448,-!p1@Spib!0.88!9.75!Spib;;chr3:130813254..130813263,+!p4@Lef1!0.88!6.55!Lef1;;chr1:133904862..133904893,+!p6@Elk4!0.86!13.34!Elk4;;chr17:51951634..51951651,-!p6@Satb1!0.86!12.35!Satb1;;chr1:69732354..69732402,-!p1@Ikzf2!0.86!7.09!Ikzf2;;chr11:52074095..52074127,-!p8@Tcf7!0.86!6.17!Tcf7;;chr4:102792039..102792052,+!p7@Mier1!0.85!8.76!Mier1;;chr11:98407087..98407102,-!p11@Ikzf3!0.85!6.10!Ikzf3;;chr11:106134241..106134320,-!p2@Smarcd2!0.84!72.85!Smarcd2;;chr5:104183477..104183548,+!p6@Aff1!0.83!11.89!Aff1;;chr12:77470718.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chr2:9800094..9800108,-!p3@Gata3!0.47!1.98!Gata3;;chr11:98826125..98826141,+!p12@Rara!0.47!1.98!Rara;;chr7:28645585..28645659,+!p1@Zfp607!0.46!24.77!Zfp607;;chr2:72818459..72818528,-!p3@Sp3!0.46!18.82!Sp3;;chr2:84877605..84877687,+!p3@Ssrp1!0.46!15.32!Ssrp1;;chr10:62328186..62328219,-!p1@Tet1!0.46!15.17!Tet1;;chr10:127707562..127707597,+!p2@Stat2!0.46!12.80!Stat2;;chr14:52634412..52634500,-!p2@Zfp219!0.46!11.51!Zfp219;;chrX:132420488..132420517,+!p4@Bhlhb9!0.46!10.75!Bhlhb9;;chrX:132420525..132420558,+!p3@Bhlhb9!0.46!10.59!Bhlhb9;;chr7:134170541..134170569,-!p9@Maz!0.46!9.60!Maz;;chr10:79896347..79896358,-!p2@Tcf3!0.46!8.84!Tcf3;;chr15:102301130..102301147,+!p3@Pcbp2!0.46!7.47!Pcbp2;;chr7:4947697..4947718,-!p2@Zfp579!0.46!7.16!Zfp579;;chr6:51382677..51382783,+!p1@Nfe2l3!0.46!6.10!Nfe2l3;;chr19:46380235..46380277,+!p3@Nfkb2!0.46!4.95!Nfkb2;;chr15:88582079..88582091,+!p1@Gm15583,p1@Zbed4!0.46!3.73!Zbed4;;chr9:21420812..21420815,+!p6@Smarca4!0.46!3.28!Smarca4;;chr15:61817095..61817111,+!p1@Myc!0.45!151.27!Myc;;chr8:108160409..108160489,+!p1@Ctcf!0.45!146.39!Ctcf;;chr3:103772250..103772317,+!p1@Phtf1!0.45!49.23!Phtf1;;chr6:128312937..128313076,+!p1@Foxm1!0.45!35.36!Foxm1;;chr2:128793119..128793179,+!p1@Zc3h6!0.45!20.80!Zc3h6;;chr2:168415815..168415872,-!p1@Nfatc2!0.45!13.49!Nfatc2;;chr13:67461490..67461531,-!p1@Zfp595,p1@Zfp953!0.45!9.83!Zfp953;;chr7:4947724..4947743,-!p3@Zfp579!0.45!5.11!Zfp579;;chr19:28085997..28086028,-!p7@Rfx3!0.45!4.04!Rfx3;;chr9:71959508..71959519,-!p15@Tcf12!0.45!1.83!Tcf12;;chr5:138187195..138187255,+!p1@Tsc22d4!0.44!107.60!Tsc22d4;;chr13:48608763..48608821,-!p1@Zfp169!0.44!38.71!Hkr1;;chr12:77470507..77470572,-!p2@Zbtb25!0.44!9.07!Zbtb25;;chr1:133904217..133904250,+!p5@Elk4!0.44!7.39!Elk4;;chr11:49016816..49016846,+!p2@Zfp62!0.44!6.55!Zfp62;;chr11:69749320..69749345,+!p2@Ybx2!0.44!3.43!Ybx2;;chr11:106993203..106993214,-!p5@Bptf!0.44!3.28!Bptf;;chr5:108494686..108494701,+!p3@Mtf2!0.44!2.82!Mtf2;;chr7:134169459..134169468,-!p15@Maz!0.44!2.67!Maz;;chr7:147129777..147129814,+!p2@Utf1!0.44!1.75!Utf1;;chr6:99385340..99385362,-!p11@Foxp1!0.44!1.75!Foxp1;;chr10:20862857..20862868,-!p7@Myb!0.44!1.75!Myb;;chr17:48025131..48025138,-!p15@Foxp4!0.44!1.75!Foxp4;;chr17:48025117..48025122,-!p16@Foxp4!0.44!1.75!Foxp4;;chr6:120314411..120314466,+!p2@Kdm5a!0.43!16.99!Kdm5a;;chr17:45570660..45570694,-!p1@Cdc5l!0.43!16.16!Cdc5l;;chr2:153475178..153475196,+!p1@Dnmt3b!0.43!4.50!Dnmt3b;;chr12:109241832..109241843,-!p11@Bcl11b!0.43!1.68!Bcl11b;;chr12:77471524..77471607,+!p1@Zbtb1!0.42!30.18!Zbtb1;;chr16:87699149..87699204,+!p2@Bach1!0.42!18.82!Bach1;;chr4:102787317..102787364,+!p3@Mier1!0.42!13.11!Mier1;;chr7:135020324..135020368,-!p4@Zfp668!0.42!6.40!Zfp668;;chr6:124959131..124959160,+!p4@Zfp384!0.42!5.94!Zfp384;;chr17:32506357..32506377,-!p3@Wiz!0.42!4.27!Wiz;;chr7:56136349..56136360,-!p5@E2f8!0.42!2.29!E2f8;;chr9:43013917..43013968,-!p1@Pou2f3!0.42!1.60!Pou2f3;;chr4:102789824..102789856,+!p19@Mier1!0.42!1.60!Mier1;;chr3:130815455..130815467,+!p10@Lef1!0.42!1.60!Lef1;;chr11:100800869..100800880,-!p6@Stat3!0.42!1.60!Stat3;;chr1:15795720..15795756,+!p1@Terf1!0.41!67.52!Terf1;;chr13:44826722..44826742,+!p1@Jarid2!0.41!36.88!Jarid2;;chr5:34163344..34163484,+!p1@Whsc1!0.41!36.27!Whsc1;;chr8:123260252..123260264,+!p1@Irf8!0.41!15.85!Irf8;;chr10:82226833..82226864,-!p3@Nfyb!0.41!11.43!Nfyb;;chr5:65194602..65194613,+!p3@Klf3!0.41!9.75!Klf3;;chr14:65977459..65977489,+!p3@Zfp395!0.41!7.70!Zfp395;;chr17:47278081..47278103,+!p1@Trerf1!0.41!4.72!Trerf1;;chr3:9610233..9610247,-!p4@Zfp704!0.41!2.59!Zfp704;;chr13:64254437..64254453,-!p4@Zfp367!0.41!2.44!Zfp367;;chr5:125538905..125538910,-!p4@Ncor2!0.41!2.21!Ncor2;;chr5:77695390..77695414,+!p2@Rest!0.41!2.21!Rest;;chr18:70728080..70728160,+!p2@Mbd2!0.40!43.82!Mbd2;;chr17:35653725..35653780,-!p1@Tcf19!0.40!37.72!Tcf19;;chr12:119539843..119539899,-!p1@Sp4!0.40!11.81!Sp4;;chr19:28085586..28085622,-!p3@Rfx3!0.40!9.22!Rfx3;;chr1:13362515..13362538,-!p2@Ncoa2!0.40!7.24!Ncoa2;;chr18:3337612..3337644,-!p8@Crem!0.40!3.73!Crem;;chr7:56136402..56136420,-!p3@E2f8!0.40!3.43!E2f8;;chr9:51021788..51021802,+!p1@Pou2af1!0.40!1.98!Pou2af1;;chr11:98407448..98407455,-!p12@Ikzf3!0.40!1.52!Ikzf3;;chr12:109241411..109241422,-!p8@Bcl11b!0.40!1.52!Bcl11b;;chr9:20385951..20386032,+!p1@Zfp846!0.39!17.60!Zfp846;;chr5:146041333..146041379,+!p@chr5:146041333..146041379,+!0.39!16.84!Zfp498;;chr3:95021853..95021911,-!p1@Gabpb2!0.39!16.46!Gabpb2;;chr4:128483347..128483411,-!p2@Zfp362!0.39!16.31!Zfp362;;chr17:25325325..25325363,+!p1@Unkl!0.39!15.77!Unkl;;chr13:96095150..96095184,+!p2@Zbed3!0.39!15.01!Zbed3;;chr7:134170660..134170711,-!p6@Maz!0.39!12.04!Maz;;chr10:20032330..20032345,+!p3@Bclaf1!0.39!10.14!Bclaf1;;chr5:104121453..104121479,+!p4@Aff1!0.39!9.53!Aff1;;chr8:72520139..72520157,-!p6@Gatad2a!0.39!8.23!Gatad2a;;chr6:47785748..47785776,+!p3@Zfp398!0.39!7.77!Zfp398;;chr1:64579440..64579451,+!p4@Creb1!0.39!7.09!Creb1;;chr10:79896328..79896339,-!p3@Tcf3!0.39!7.01!Tcf3;;chr1:52176378..52176401,+!p3@Stat1!0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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11211
-|library_id_phase_based=1:CNhs11211
+|library_id_phase_based=2:CNhs11211
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;713
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;713
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N07.CNhs11211.713-19D3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N07.CNhs11211.713-19D3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N07.CNhs11211.713-19D3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N07.CNhs11211.713-19D3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N07.CNhs11211.713-19D3.mm9.nobarcode.rdna.fa.gz
 |name=thymus, neonate N07
 |namespace=FANTOM5
@@ Line 51: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11211,LSID747,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.111939930704693,0.0158889756001152,0,0.031895734489288,0.751941990806014,0,0.132666381893857,0,0.0308041899510522,0,0,0.00507848872506521,0,0,0,0,0,0,0.271278224794984,0,0.0447088645608033,0,0,0,0,0,0,0,0,0,0.0447088645608033,0,0.268656240097819,0,0,0,0,0,0.160062829409683,-0.0289887960841883,0.00105826376082696,-0.719800915471967,-0.180450908888745,0,0,0,0,0,0,0,0,0,0,0,0.031895734489288,-0.00439716766133594,0,0,0,0,0.0187614248192296,0,0.111992617453481,0.0894177291216067,0.346217756059235,0,0.104659508828286,0.174727708469149,0.106319408234777,0.117007851131524,0,0.0285249404470723,-0.0576539277958799,0,0.0616083799021044,0,-0.00531120513120255,-0.0725408676462296,-0.313863665906317,0.106837358489769,0,0,0,0,0,0,-0.164592999154703,-0.221682036935015,-0.183752944400766,0,0,0,0,0
@@ Line 88: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:713-19D3;search_select_hide=table117:713-19D3
 }}

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FF:713-19D3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:19, 4 June 2020

CNhs11211

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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