FF:1393-42G2: Difference between revisions

Latest revision as of 19:05, 4 June 2020

Name:	thymus, neonate N30
Species:	Mouse (Mus musculus)
Library ID:	CNhs11132
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	thymus
dev stage	30 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		SAMD00006007

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11132		CAGE		DRX009125		DRR009999

Accession ID Mm9

Library id		BAM		CTSS
CNhs11132		DRZ001424		DRZ002807

Accession ID Mm10

Library id		BAM		CTSS
CNhs11132		DRZ012774		DRZ014157

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

CNhs11132

0	0
1	0
10	0
100	0
1000	-0.0115
1001	0.0738
1002	-0.0837
1003	-0.116
1004	0
1005	0.048
1006	-0.143
1007	0.159
1008	0
1009	-0.19
101	0.03
1010	0
1011	0.023
1012	0.567
1013	0.0207
1014	-0.0874
1015	-0.0323
1016	-0.379
1017	0
1018	0.167
1019	0
102	0.131
1020	0
1021	0
1022	-0.224
1023	0
1024	-0.103
1025	-0.0611
1026	0
1027	0
1028	0
1029	0.39
103	-0.0788
1030	0.048
1031	-0.757
1032	-0.429
1033	0.104
1034	0
1035	0
1036	0.0803
1037	0
1038	-0.301
1039	-0.0378
104	0
1040	-0.121
1041	0.048

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: CNhs11132

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	1.82127e-4
MA0003.1	MA0003.1	0.439
MA0004.1	MA0004.1	0.309
MA0006.1	MA0006.1	0.697
MA0007.1	MA0007.1	0.353
MA0009.1	MA0009.1	0.45
MA0014.1	MA0014.1	0.395
MA0017.1	MA0017.1	0.817
MA0018.2	MA0018.2	0.0994
MA0019.1	MA0019.1	0.492
MA0024.1	MA0024.1	0.0569
MA0025.1	MA0025.1	0.0144
MA0027.1	MA0027.1	0.662
MA0028.1	MA0028.1	3.64475e-6
MA0029.1	MA0029.1	0.205
MA0030.1	MA0030.1	0.768
MA0031.1	MA0031.1	0.0349
MA0035.2	MA0035.2	0.44
MA0038.1	MA0038.1	0.274
MA0039.2	MA0039.2	0.454
MA0040.1	MA0040.1	0.513
MA0041.1	MA0041.1	0.325
MA0042.1	MA0042.1	0.905
MA0043.1	MA0043.1	0.147
MA0046.1	MA0046.1	4.57227e-14
MA0047.2	MA0047.2	0.361
MA0048.1	MA0048.1	0.814
MA0050.1	MA0050.1	1.09854e-7
MA0051.1	MA0051.1	2.09528e-6
MA0052.1	MA0052.1	2.02474e-4
MA0055.1	MA0055.1	0.282
MA0057.1	MA0057.1	0.747
MA0058.1	MA0058.1	0.395
MA0059.1	MA0059.1	0.039
MA0060.1	MA0060.1	0.598
MA0061.1	MA0061.1	1.07682e-4
MA0062.2	MA0062.2	2.91989e-19
MA0065.2	MA0065.2	0.695
MA0066.1	MA0066.1	0.0125
MA0067.1	MA0067.1	0.308
MA0068.1	MA0068.1	0.523
MA0069.1	MA0069.1	0.954
MA0070.1	MA0070.1	0.6
MA0071.1	MA0071.1	0.397
MA0072.1	MA0072.1	3.88486e-6
MA0073.1	MA0073.1	0.752
MA0074.1	MA0074.1	0.914
MA0076.1	MA0076.1	2.45594e-8
MA0077.1	MA0077.1	0.0701
MA0078.1	MA0078.1	0.628
MA0079.2	MA0079.2	0.0546
MA0080.2	MA0080.2	7.0926e-14
MA0081.1	MA0081.1	0.0241
MA0083.1	MA0083.1	0.0555
MA0084.1	MA0084.1	0.545
MA0087.1	MA0087.1	0.344
MA0088.1	MA0088.1	0.429
MA0090.1	MA0090.1	0.0397
MA0091.1	MA0091.1	0.0722
MA0092.1	MA0092.1	0.957
MA0093.1	MA0093.1	0.308
MA0099.2	MA0099.2	0.12
MA0100.1	MA0100.1	0.0308
MA0101.1	MA0101.1	6.5061e-4
MA0102.2	MA0102.2	0.494
MA0103.1	MA0103.1	3.52092e-5
MA0104.2	MA0104.2	0.315
MA0105.1	MA0105.1	3.37347e-8
MA0106.1	MA0106.1	0.901
MA0107.1	MA0107.1	6.2943e-4
MA0108.2	MA0108.2	5.44483e-4
MA0111.1	MA0111.1	0.259
MA0112.2	MA0112.2	0.0128
MA0113.1	MA0113.1	0.517
MA0114.1	MA0114.1	0.321
MA0115.1	MA0115.1	0.691
MA0116.1	MA0116.1	0.004
MA0117.1	MA0117.1	0.858
MA0119.1	MA0119.1	0.966
MA0122.1	MA0122.1	0.952
MA0124.1	MA0124.1	0.395
MA0125.1	MA0125.1	0.401
MA0131.1	MA0131.1	0.307
MA0135.1	MA0135.1	0.201
MA0136.1	MA0136.1	6.94065e-24
MA0137.2	MA0137.2	0.1
MA0138.2	MA0138.2	2.53715e-4
MA0139.1	MA0139.1	0.179
MA0140.1	MA0140.1	0.756
MA0141.1	MA0141.1	0.384
MA0142.1	MA0142.1	0.41
MA0143.1	MA0143.1	0.288
MA0144.1	MA0144.1	0.422
MA0145.1	MA0145.1	0.679
MA0146.1	MA0146.1	0.323
MA0147.1	MA0147.1	0.192
MA0148.1	MA0148.1	0.429
MA0149.1	MA0149.1	0.0299
MA0150.1	MA0150.1	0.411
MA0152.1	MA0152.1	0.939
MA0153.1	MA0153.1	1.3443e-8
MA0154.1	MA0154.1	0.115
MA0155.1	MA0155.1	0.934
MA0156.1	MA0156.1	4.22736e-27
MA0157.1	MA0157.1	0.135
MA0159.1	MA0159.1	0.122
MA0160.1	MA0160.1	0.297
MA0162.1	MA0162.1	0.701
MA0163.1	MA0163.1	0.00413
MA0164.1	MA0164.1	0.9
MA0258.1	MA0258.1	0.045
MA0259.1	MA0259.1	0.889

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: CNhs11132

Novel motif	Logo	P-value
1	1	0.157
10	10	0.024
100	100	0.77
101	101	0.699
102	102	0.508
103	103	0.222
104	104	0.942
105	105	0.829
106	106	0.717
107	107	0.892
108	108	0.211
109	109	0.319
11	11	0.124
110	110	0.0836
111	111	0.744
112	112	0.15
113	113	0.33
114	114	0.386
115	115	0.448
116	116	0.984
117	117	4.70776e-4
118	118	0.154
119	119	0.234
12	12	0.672
120	120	0.218
121	121	0.433
122	122	0.978
123	123	0.412
124	124	0.683
125	125	0.152
126	126	0.556
127	127	0.84
128	128	0.533
129	129	0.184
13	13	0.0359
130	130	0.312
131	131	0.603
132	132	0.847
133	133	0.989
134	134	0.696
135	135	0.393
136	136	0.341
137	137	0.48
138	138	0.773
139	139	0.248
14	14	0.949
140	140	0.992
141	141	0.62
142	142	0.487
143	143	0.225
144	144	0.153
145	145	0.147
146	146	0.709
147	147	0.402
148	148	0.227
149	149	0.883
15	15	0.0829
150	150	0.471
151	151	0.0864
152	152	0.204
153	153	0.153
154	154	0.0962
155	155	0.0745
156	156	0.136
157	157	0.732
158	158	0.0841
159	159	0.0554
160	160	0.877
161	161	0.403
162	162	0.697
163	163	0.879
164	164	0.175
165	165	0.298
166	166	0.341
167	167	0.156
168	168	0.242
169	169	0.198
17	17	0.605
18	18	0.756
19	19	0.709
2	2	0.094
20	20	0.311
21	21	0.596
22	22	0.996
23	23	0.842
24	24	0.164
25	25	0.22
26	26	0.0564
27	27	0.314
28	28	0.113
29	29	0.117
3	3	0.103
30	30	0.161
31	31	0.6
32	32	0.131
33	33	0.479
34	34	0.883
35	35	0.0679
36	36	0.158
37	37	0.116
38	38	0.195
39	39	0.73
4	4	0.773
40	40	0.672
41	41	0.88
42	42	0.0272
43	43	0.405
44	44	0.887
45	45	0.85
46	46	0.129
47	47	0.394
48	48	0.216
49	49	0.131
5	5	0.224
50	50	0.714
51	51	0.832
52	52	0.152
53	53	0.995
54	54	0.41
55	55	0.444
56	56	0.652
57	57	0.302
58	58	0.182
59	59	0.721
6	6	0.2
60	60	0.985
61	61	0.0625
62	62	0.0797
63	63	0.672
64	64	0.832
65	65	0.405
66	66	0.436
67	67	0.787
68	68	0.622
69	69	0.38
7	7	0.136
70	70	0.198
71	71	0.0782
72	72	0.539
73	73	0.259
74	74	0.784
75	75	0.0111
76	76	0.0548
77	77	0.224
78	78	0.175
79	79	0.876
8	8	0.64
80	80	0.0769
81	81	0.87
82	82	0.605
83	83	0.761
84	84	0.137
85	85	0.929
86	86	0.129
87	87	0.143
88	88	0.415
89	89	0.371
9	9	0.268
90	90	0.0345
91	91	0.831
92	92	0.968
93	93	0.8
94	94	0.324
95	95	0.436
96	96	0.0166
97	97	0.546
98	98	0.602
99	99	0.435

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: CNhs11132

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011497 mouse thymus- neonate N30 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)
0000310 (mouse neonate N30 sample)
0011497 (mouse thymus- neonate N30 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@DRS008988
+|DRA_sample_Accession=CAGE@SAMD00006007
-|accession_numbers=CAGE;DRX009125;DRR009999;DRZ001424;DRZ002807
+|accession_numbers=CAGE;DRX009125;DRR009999;DRZ001424;DRZ002807;DRZ012774;DRZ014157
 |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!2.71!612.90!Tcf7;;chr17:51971960..51971979,-!p1@Satb1!2.57!491.23!Satb1;;chr17:51971932..51971958,-!p2@Satb1!2.43!361.62!Satb1;;chr1:38721792..38721845,-!p1@Aff3!2.27!226.86!Aff3;;chr3:94181376..94181403,+!p2@Rorc!2.12!129.38!Rorc;;chr12:109242266..109242295,-!p1@Bcl11b!2.00!772.91!Bcl11b;;chr11:52095821..52095836,-!p3@Tcf7!1.97!92.80!Tcf7;;chr11:52096804..52096896,-!p1@Tcf7!1.92!621.43!Tcf7;;chr4:102787521..102787588,+!p4@Mier1!1.84!120.03!Mier1;;chr3:130815703..130815721,+!p2@Lef1!1.81!77.14!Lef1;;chr3:94181427..94181449,+!p3@Rorc!1.81!64.05!Rorc;;chr17:51965903..51965926,-!p5@Satb1!1.81!63.70!Satb1;;chr16:92826249..92826325,-!p1@Runx1!1.77!137.45!Runx1;;chr11:11590117..11590138,+!p4@Ikzf1!1.76!55.98!Ikzf1;;chr11:52095797..52095809,-!p5@Tcf7!1.72!50.96!Tcf7;;chr11:98407264..98407295,-!p1@Ikzf3!1.67!45.47!Ikzf3;;chr10:20880731..20880775,-!p2@Myb!1.65!89.18!Myb;;chr11:11590140..11590187,+!p3@Ikzf1!1.63!49.56!Ikzf1;;chr17:51971991..51972003,-!p4@Satb1!1.62!40.32!Satb1;;chr17:51972438..51972463,-!p8@Satb1!1.58!37.17!Satb1;;chr2:9800207..9800234,-!p1@Gata3!1.53!97.48!Gata3;;chr10:20880629..20880683,-!p1@Myb!1.52!89.64!Myb;;chr11:98407234..98407259,-!p2@Ikzf3!1.52!32.14!Ikzf3;;chr11:11584970..11585030,+!p2@Ikzf1!1.51!44.53!Ikzf1;;chr12:109241728..109241781,-!p2@Bcl11b!1.51!33.19!Bcl11b;;chr2:147190749..147190769,+!p1@Pax1!1.51!31.56!Pax1;;chr17:51972530..51972571,-!p7@Satb1!1.50!30.39!Satb1;;chr14:79915425..79915501,+!p1@Elf1!1.49!251.05!Elf1;;chr11:11586218..11586285,+!p1@Ikzf1!1.47!87.89!Ikzf1;;chr17:51972400..51972428,-!p11@Satb1!1.47!28.52!Satb1;;chr17:51965928..51965960,-!p10@Satb1!1.46!27.58!Satb1;;chr4:6917606..6917681,-!p1@Tox!1.45!109.40!Tox;;chr11:11585912..11585950,+!p6@Ikzf1!1.44!33.66!Ikzf1;;chr3:130813200..130813252,+!p1@Lef1!1.43!112.67!Lef1;;chr3:94181331..94181345,+!p4@Rorc!1.42!25.25!Rorc;;chr10:20880698..20880717,-!p3@Myb!1.41!38.34!Myb;;chr11:11585678..11585745,+!p5@Ikzf1!1.41!36.00!Ikzf1;;chr8:108583550..108583595,+!p2@Nfatc3!1.39!102.27!Nfatc3;;chr1:52065454..52065495,+!p1@Stat4!1.39!38.10!Stat4;;chr17:51952856..51952876,-!p12@Satb1!1.38!23.14!Satb1;;chr3:94181355..94181373,+!p5@Rorc!1.37!22.44!Rorc;;chr9:32503590..32503680,+!p1@Ets1!1.34!735.51!Ets1;;chr4:63064364..63064384,-!p1@Akna!1.33!58.79!Akna;;chr11:100683839..100683890,-!p2@Stat5b!1.33!46.52!Stat5b;;chr17:51972603..51972624,-!p9@Satb1!1.29!18.58!Satb1;;chr3:94181461..94181472,+!p6@Rorc!1.29!18.35!Rorc;;chr17:51965860..51965876,-!p14@Satb1!1.28!18.00!Satb1;;chr12:109241852..109241873,-!p4@Bcl11b!1.27!21.15!Bcl11b;;chr2:173044380..173044432,-!p1@Zbp1!1.25!39.50!Zbp1;;chr11:98407142..98407159,-!p5@Ikzf3!1.25!16.95!Ikzf3;;chr6:99216488..99216534,-!p2@Foxp1!1.24!45.47!Foxp1;;chr5:104182963..104182982,+!p5@Aff1!1.23!33.43!Aff1;;chr11:98407370..98407395,-!p3@Ikzf3!1.21!15.08!Ikzf3;;chr11:98407340..98407359,-!p4@Ikzf3!1.18!14.14!Ikzf3;;chr3:94181408..94181419,+!p7@Rorc!1.18!14.03!Rorc;;chr17:51951634..51951651,-!p6@Satb1!1.17!26.30!Satb1;;chr8:124984566..124984595,-!p1@Snai3!1.17!21.27!Snai3;;chr1:69732354..69732402,-!p1@Ikzf2!1.17!15.54!Ikzf2;;chr9:71958979..71959032,-!p4@Tcf12!1.16!17.06!Tcf12;;chr4:135728311..135728342,+!p3@E2f2!1.16!13.56!E2f2;;chr11:98826178..98826197,+!p7@Rara!1.16!13.32!Rara;;chr11:52096750..52096772,-!p4@Tcf7!1.15!20.45!Tcf7;;chr11:100800901..100800921,-!p4@Stat3!1.15!15.43!Stat3;;chr16:23988711..23988727,-!p1@Bcl6!1.12!144.11!Bcl6;;chr7:51787434..51787448,-!p1@Spib!1.12!17.65!Spib;;chr17:51972575..51972595,-!p13@Satb1!1.12!12.04!Satb1;;chr10:20881160..20881175,-!p4@Myb!1.11!11.92!Myb;;chr11:11590085..11590106,+!p7@Ikzf1!1.10!11.45!Ikzf1;;chr10:13686012..13686028,+!p8@Hivep2!1.10!11.45!Hivep2;;chr17:45692642..45692663,+!p1@Nfkbie!1.08!35.06!Nfkbie;;chr5:108155007..108155034,-!p1@Gfi1!1.08!11.10!Gfi1;;chr2:147190725..147190747,+!p2@Pax1!1.07!10.87!Pax1;;chr16:25801993..25802014,+!p1@Trp63!1.07!10.64!Trp63;;chr1:64579555..64579570,+!p3@Creb1!1.05!48.50!Creb1;;chr4:102792039..102792052,+!p7@Mier1!1.05!14.61!Mier1;;chr17:48025139..48025166,-!p8@Foxp4!1.05!11.92!Foxp4;;chr11:52096732..52096741,-!p6@Tcf7!1.05!10.17!Tcf7;;chr11:98407305..98407321,-!p6@Ikzf3!1.05!10.17!Ikzf3;;chr1:133904901..133904934,+!p3@Elk4!1.01!27.47!Elk4;;chr1:133904862..133904893,+!p6@Elk4!1.01!19.28!Elk4;;chr10:13685980..13686007,+!p6@Hivep2!1.01!11.57!Hivep2;;chr4:102787381..102787397,+!p9@Mier1!1.01!10.99!Mier1;;chr1:38721779..38721790,-!p6@Aff3!1.01!9.35!Aff3;;chr3:130813254..130813263,+!p4@Lef1!1.01!9.23!Lef1;;chr4:134676555..134676575,+!p2@Runx3!1.00!9.00!Runx3;;chr9:71959562..71959624,-!p3@Tcf12!0.99!30.74!Tcf12;;chr1:87546583..87546595,+!p1@Sp100!0.99!12.74!Sp100;;chr10:88145766..88145770,-!p1@Spic!0.99!11.45!Spic;;chr10:67000609..67000625,+!p1@Egr2!0.98!20.10!Egr2;;chr10:20881176..20881191,-!p6@Myb!0.97!8.42!Myb;;chr11:98338697..98338709,-!p9@Ikzf3!0.96!8.06!Ikzf3;;chr12:77470718..77470752,-!p4@Zbtb25!0.95!11.22!Zbtb25;;chr11:98407121..98407133,-!p10@Ikzf3!0.95!7.95!Ikzf3;;chr19:25746898..25746910,+!p1@Dmrt2!0.94!11.57!Dmrt2;;chr15:100430414..100430470,-!p1@Pou6f1!0.93!24.31!Pou6f1;;chr11:98407210..98407221,-!p7@Ikzf3!0.93!7.60!Ikzf3;;chr1:87495371..87495397,-!p1@Sp110!0.93!7.60!Sp110;;chr4:102792009..102792021,+!p6@Mier1!0.92!12.62!Mier1;;chr3:130815472..130815497,+!p6@Lef1!0.92!7.25!Lef1;;chr11:98407087..98407102,-!p11@Ikzf3!0.92!7.25!Ikzf3;;chr12:109241804..109241823,-!p5@Bcl11b!0.91!7.13!Bcl11b;;chr7:148514080..148514108,-!p4@Deaf1!0.90!15.31!Deaf1;;chr5:104183477..104183548,+!p6@Aff1!0.90!14.14!Aff1;;chr9:72122748..72122757,+!p4@Zfp280d!0.90!8.30!Zfp280d;;chr5:138186979..138187025,+!p4@Tsc22d4!0.89!26.06!Tsc22d4;;chr14:65568469..65568511,-!p2@Hmbox1!0.89!23.02!Hmbox1;;chr11:100721761..100721851,+!p1@Stat5a!0.88!50.37!Stat5a;;chr7:71083729..71083742,-!p4@Klf13!0.88!11.92!Klf13;;chr1:52065508..52065522,+!p2@Stat4!0.88!7.95!Stat4;;chr11:98407164..98407177,-!p8@Ikzf3!0.88!6.66!Ikzf3;;chr11:52096305..52096328,-!p11@Tcf7!0.88!6.55!Tcf7;;chr15:100430393..100430410,-!p3@Pou6f1!0.88!6.55!Pou6f1;;chr11:106134241..106134320,-!p2@Smarcd2!0.87!76.79!Smarcd2;;chr4:102787067..102787080,+!p10@Mier1!0.87!8.18!Mier1;;chr4:135728282..135728310,+!p4@E2f2!0.87!7.25!E2f2;;chr5:134720044..134720103,-!p6@Gtf2i!0.87!6.43!Gtf2i;;chr1:52176315..52176343,+!p1@Stat1!0.86!95.61!Stat1;;chr2:91077034..91077078,-!p2@Ddb2!0.86!14.38!Ddb2;;chr17:45692676..45692695,+!p2@Nfkbie!0.86!13.21!Nfkbie;;chr2:173044357..173044377,-!p2@Zbp1!0.86!9.12!Zbp1;;chr9:32348943..32349001,-!p1@Fli1!0.85!52.36!Fli1;;chr8:108160826..108160879,+!p3@Ctcf!0.85!18.82!Ctcf;;chr1:133904946..133904974,+!p7@Elk4!0.85!9.58!Elk4;;chr10:77506352..77506356,-!p2@Aire!0.84!5.96!Aire;;chr11:52070502..52070527,-!p7@Tcf7!0.84!5.84!Tcf7;;chr10:77506405..77506441,-!p1@Aire!0.84!5.84!Aire;;chr6:99385340..99385362,-!p11@Foxp1!0.84!5.84!Foxp1;;chr5:108155037..108155060,-!p2@Gfi1!0.84!5.84!Gfi1;;chr2:91077082..91077122,-!p1@Ddb2!0.83!38.45!Ddb2;;chr13:30841099..30841116,+!p1@Irf4!0.83!9.23!Irf4;;chr11:11590188..11590200,+!p8@Ikzf1!0.82!5.61!Ikzf1;;chr9:57684520..57684612,-!p1@Arid3b!0.81!52.13!Arid3b;;chr5:34530519..34530545,-!p4@Mxd4!0.81!8.65!Mxd4;;chr7:31206743..31206761,+!p1@Nfkbid!0.81!7.71!Nfkbid;;chr7:120351014..120351109,+!p1@Arntl!0.80!79.36!Arntl;;chr10:86956396..86956411,-!p1@Ascl1!0.80!8.53!Ascl1;;chr16:95924005..95924042,+!p2@Ets2!0.79!99.58!Ets2;;chr11:100711801..100711910,-!p1@Stat5b!0.78!75.50!Stat5b;;chr5:104121391..104121450,+!p3@Aff1!0.78!28.52!Aff1;;chr9:21420744..21420755,+!p3@Smarca4!0.78!15.54!Smarca4;;chr1:87546602..87546617,+!p2@Sp100!0.78!6.08!Sp100;;chr2:147190772..147190783,+!p3@Pax1!0.78!5.03!Pax1;;chr4:102791976..102792008,+!p2@Mier1!0.77!59.26!Mier1;;chr17:31701800..31701818,+!p2@Pknox1!0.77!13.32!Pknox1;;chr12:3891753..3891801,+!p4@Dnmt3a!0.77!8.30!Dnmt3a;;chr12:109242296..109242307,-!p3@Bcl11b!0.77!7.36!Bcl11b;;chr12:100802113..100802127,-!p5@Foxn3!0.77!6.55!Foxn3;;chr5:138187466..138187477,+!p11@Tsc22d4!0.77!6.31!Tsc22d4;;chr14:79915521..79915539,+!p5@Elf1!0.77!5.96!Elf1;;chr7:71083748..71083819,-!p1@Klf13!0.76!177.19!Klf13;;chr7:87171047..87171078,+!p1@Zfp710!0.76!17.18!Zfp710;;chr10:30375579..30375616,-!p3@Ncoa7!0.76!11.92!Ncoa7;;chr12:74147689..74147711,-!p1@Six1!0.76!11.22!Six1;;chr5:138187583..138187602,+!p6@Tsc22d4!0.76!9.35!Tsc22d4;;chr9:32349051..32349061,-!p5@Fli1!0.76!4.79!Fli1;;chr17:51972017..51972022,-!p17@Satb1!0.76!4.79!Satb1;;chr5:104183219..104183236,+!p2@Aff1!0.75!34.83!Aff1;;chrX:45807489..45807502,-!p2@Elf4!0.75!15.54!Elf4;;chr4:134708451..134708469,+!p1@Runx3!0.75!8.65!Runx3;;chr17:51952537..51952552,-!p15@Satb1!0.75!5.03!Satb1;;chr17:51952893..51952904,-!p26@Satb1!0.75!4.68!Satb1;;chr11:11590205..11590216,+!p9@Ikzf1!0.75!4.68!Ikzf1;;chr5:138187341..138187406,+!p3@Tsc22d4!0.74!53.06!Tsc22d4;;chr19:26681929..26681987,+!p4@Smarca2!0.74!27.82!Smarca2;;chr11:3191741..3191769,+!p5@Patz1!0.74!5.96!Patz1;;chr16:92826338..92826347,-!p6@Runx1!0.74!4.56!Runx1;;chr6:99216375..99216395,-!p5@Foxp1!0.74!4.56!Foxp1;;chr17:51951383..51951409,-!p19@Satb1!0.74!4.44!Satb1;;chr15:101097270..101097290,+!p1@Nr4a1!0.73!50.49!Nr4a1;;chr7:134169810..134169824,-!p7@Maz!0.73!18.58!Maz;;chr11:52070563..52070589,-!p9@Tcf7!0.73!4.32!Tcf7;;chr17:51951662..51951670,-!p21@Satb1!0.73!4.32!Satb1;;chr11:52074095..52074127,-!p8@Tcf7!0.72!4.21!Tcf7;;chr18:80904854..80904919,-!p2@Nfatc1!0.71!56.10!Nfatc1;;chr1:38721767..38721778,-!p5@Aff3!0.71!4.09!Aff3;;chr12:109241897..109241915,-!p6@Bcl11b!0.71!4.09!Bcl11b;;chr8:108160490..108160512,+!p2@Ctcf!0.70!37.75!Ctcf;;chr4:102792072..102792091,+!p5@Mier1!0.70!11.80!Mier1;;chr12:100802129..100802145,-!p4@Foxn3!0.70!6.78!Foxn3;;chr12:57796615..57796687,+!p1@Pax9!0.70!3.97!Pax9;;chr4:124805061..124805087,-!p1@Zc3h12a!0.69!13.32!Zc3h12a;;chr9:72122773..72122820,+!p1@Zfp280d!0.68!116.53!Zfp280d;;chr12:100801772..100801861,-!p1@Foxn3!0.68!89.06!Foxn3;;chr11:3190303..3190351,+!p3@Patz1!0.68!8.18!Patz1;;chr5:138187411..138187422,+!p8@Tsc22d4!0.68!6.19!Tsc22d4;;chr10:13686074..13686090,+!p9@Hivep2!0.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@@ Line 44: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11132
+|library_id_phase_based=2:CNhs11132
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1393
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1393
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N30.CNhs11132.1393-42G2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N30.CNhs11132.1393-42G2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N30.CNhs11132.1393-42G2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N30.CNhs11132.1393-42G2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N30.CNhs11132.1393-42G2.mm9.nobarcode.rdna.fa.gz
 |name=thymus, neonate N30
 |namespace=FANTOM5
@@ Line 49: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11132,LSID735,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.0345054155136816,0.0325714374743968,0.109436157377901,0,0.82781937511823,0,0.226127425655438,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.299998172608195,0,0.0456142524280545,0,0,0,0,0,0,0,0,0,0.0240026547541851,0,0.575840573628427,0,0,0,0,0,0.0912561076269618,0,0.0544548556870812,-0.892982861621717,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0.05963719582802,0,0.130536619167171,0,0.0912297833919849,0.386038941953333,-0.0275544236039112,0.074102044785029,0,0.109338903243882,-0.059171715158786,0,0,0,0,-0.14376663205432,-0.336287961549896,0.180795324350766,0.091228504856109,0,0,0,0,0,-0.127876150727834,-0.0413975394273982,-0.158920440219759,0,0,0,0,0
@@ Line 86: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1393-42G2;search_select_hide=table117:1393-42G2
 }}

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FF:1393-42G2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:05, 4 June 2020

CNhs11132

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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