FF:11815-124E6: Difference between revisions

Latest revision as of 18:22, 4 June 2020

Name:	CD4+CD25-CD44- naive conventional T cells, antiCD3_CD28 stimulation, 06hr, pool1 (C57BL_6J)
Species:	Mouse (Mus musculus)
Library ID:	CNhs13218
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	blood
dev stage	NA
sex	NA
age	NA
cell type	T cell
cell line	NA
company	NA
collaboration	Morikawa (University of Kyoto)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	B6Ts3/28-6
catalog number	NA
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005830

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13218		CAGE		DRX008793		DRR009665

Accession ID Mm9

Library id		BAM		CTSS
CNhs13218		DRZ001090		DRZ002475

Accession ID Mm10

Library id		BAM		CTSS
CNhs13218		DRZ012440		DRZ013825

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

CNhs13218

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0749
1002	-0.116
1003	-0.087
1004	0
1005	0
1006	-0.436
1007	-0.122
1008	0
1009	-0.2
101	0.71
1010	0
1011	0.153
1012	0
1013	-0.331
1014	-0.0243
1015	0.212
1016	-0.61
1017	0
1018	0
1019	0
102	0.307
1020	0.128
1021	0
1022	-0.223
1023	0
1024	-0.307
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.115
103	-0.0887
1030	0
1031	-1.193
1032	-0.602
1033	0.661
1034	0
1035	0
1036	0.631
1037	0
1038	-0.481
1039	-0.348
104	0
1040	-0.216
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: CNhs13218

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0067
MA0003.1	MA0003.1	0.273
MA0004.1	MA0004.1	0.00463
MA0006.1	MA0006.1	0.137
MA0007.1	MA0007.1	0.346
MA0009.1	MA0009.1	0.924
MA0014.1	MA0014.1	0.73
MA0017.1	MA0017.1	0.244
MA0018.2	MA0018.2	0.00188
MA0019.1	MA0019.1	0.521
MA0024.1	MA0024.1	0.369
MA0025.1	MA0025.1	0.71
MA0027.1	MA0027.1	0.43
MA0028.1	MA0028.1	4.55556e-8
MA0029.1	MA0029.1	0.535
MA0030.1	MA0030.1	0.246
MA0031.1	MA0031.1	0.873
MA0035.2	MA0035.2	0.622
MA0038.1	MA0038.1	0.00635
MA0039.2	MA0039.2	0.0351
MA0040.1	MA0040.1	0.278
MA0041.1	MA0041.1	0.143
MA0042.1	MA0042.1	0.532
MA0043.1	MA0043.1	0.0386
MA0046.1	MA0046.1	1.16911e-9
MA0047.2	MA0047.2	0.844
MA0048.1	MA0048.1	0.0996
MA0050.1	MA0050.1	0.111
MA0051.1	MA0051.1	0.458
MA0052.1	MA0052.1	0.0737
MA0055.1	MA0055.1	0.00747
MA0057.1	MA0057.1	0.707
MA0058.1	MA0058.1	0.00283
MA0059.1	MA0059.1	6.4326e-7
MA0060.1	MA0060.1	1.93449e-10
MA0061.1	MA0061.1	5.04248e-5
MA0062.2	MA0062.2	1.33131e-17
MA0065.2	MA0065.2	0.133
MA0066.1	MA0066.1	0.194
MA0067.1	MA0067.1	0.0792
MA0068.1	MA0068.1	0.218
MA0069.1	MA0069.1	0.848
MA0070.1	MA0070.1	0.463
MA0071.1	MA0071.1	0.134
MA0072.1	MA0072.1	0.123
MA0073.1	MA0073.1	0.763
MA0074.1	MA0074.1	0.259
MA0076.1	MA0076.1	1.44856e-9
MA0077.1	MA0077.1	0.432
MA0078.1	MA0078.1	0.211
MA0079.2	MA0079.2	0.0259
MA0080.2	MA0080.2	9.31245e-8
MA0081.1	MA0081.1	0.00453
MA0083.1	MA0083.1	0.428
MA0084.1	MA0084.1	0.214
MA0087.1	MA0087.1	0.913
MA0088.1	MA0088.1	0.354
MA0090.1	MA0090.1	0.127
MA0091.1	MA0091.1	0.238
MA0092.1	MA0092.1	0.667
MA0093.1	MA0093.1	0.00678
MA0099.2	MA0099.2	0.0132
MA0100.1	MA0100.1	0.244
MA0101.1	MA0101.1	1.49296e-7
MA0102.2	MA0102.2	0.565
MA0103.1	MA0103.1	0.229
MA0104.2	MA0104.2	5.43602e-6
MA0105.1	MA0105.1	4.6811e-6
MA0106.1	MA0106.1	0.711
MA0107.1	MA0107.1	4.38625e-6
MA0108.2	MA0108.2	2.23758e-4
MA0111.1	MA0111.1	0.256
MA0112.2	MA0112.2	0.067
MA0113.1	MA0113.1	0.31
MA0114.1	MA0114.1	0.972
MA0115.1	MA0115.1	0.0397
MA0116.1	MA0116.1	0.0317
MA0117.1	MA0117.1	0.344
MA0119.1	MA0119.1	0.467
MA0122.1	MA0122.1	0.55
MA0124.1	MA0124.1	0.987
MA0125.1	MA0125.1	0.0709
MA0131.1	MA0131.1	0.23
MA0135.1	MA0135.1	0.334
MA0136.1	MA0136.1	8.7591e-18
MA0137.2	MA0137.2	2.4542e-4
MA0138.2	MA0138.2	0.0365
MA0139.1	MA0139.1	0.471
MA0140.1	MA0140.1	0.915
MA0141.1	MA0141.1	0.102
MA0142.1	MA0142.1	0.291
MA0143.1	MA0143.1	0.711
MA0144.1	MA0144.1	0.073
MA0145.1	MA0145.1	0.213
MA0146.1	MA0146.1	0.924
MA0147.1	MA0147.1	8.67113e-8
MA0148.1	MA0148.1	0.896
MA0149.1	MA0149.1	0.0678
MA0150.1	MA0150.1	0.0537
MA0152.1	MA0152.1	0.227
MA0153.1	MA0153.1	1.60579e-4
MA0154.1	MA0154.1	0.206
MA0155.1	MA0155.1	0.797
MA0156.1	MA0156.1	1.00072e-15
MA0157.1	MA0157.1	0.72
MA0159.1	MA0159.1	0.0913
MA0160.1	MA0160.1	0.133
MA0162.1	MA0162.1	0.775
MA0163.1	MA0163.1	0.00446
MA0164.1	MA0164.1	0.157
MA0258.1	MA0258.1	0.024
MA0259.1	MA0259.1	0.0107

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: CNhs13218

Novel motif	Logo	P-value
1	1	0.128
10	10	0.0433
100	100	0.527
101	101	0.608
102	102	0.386
103	103	0.429
104	104	0.477
105	105	0.525
106	106	0.521
107	107	0.687
108	108	0.821
109	109	0.147
11	11	0.135
110	110	0.026
111	111	0.00892
112	112	0.0772
113	113	0.924
114	114	0.0657
115	115	0.841
116	116	0.704
117	117	5.12485e-4
118	118	0.545
119	119	0.476
12	12	0.491
120	120	0.176
121	121	0.525
122	122	0.971
123	123	0.669
124	124	0.259
125	125	0.0755
126	126	0.131
127	127	0.558
128	128	0.44
129	129	0.423
13	13	0.0637
130	130	0.541
131	131	0.454
132	132	0.686
133	133	0.067
134	134	0.438
135	135	0.749
136	136	0.249
137	137	0.621
138	138	0.328
139	139	0.00777
14	14	0.196
140	140	0.098
141	141	0.475
142	142	0.28
143	143	0.0136
144	144	0.546
145	145	0.0301
146	146	0.857
147	147	0.792
148	148	0.252
149	149	0.491
15	15	0.157
150	150	0.768
151	151	0.703
152	152	0.214
153	153	0.177
154	154	0.419
155	155	0.321
156	156	0.0196
157	157	0.534
158	158	0.0166
159	159	0.925
160	160	0.781
161	161	0.0543
162	162	0.391
163	163	0.938
164	164	0.0135
165	165	0.307
166	166	0.065
167	167	0.021
168	168	0.82
169	169	0.703
17	17	0.521
18	18	0.0957
19	19	0.277
2	2	0.164
20	20	0.00557
21	21	0.124
22	22	0.772
23	23	0.49
24	24	0.517
25	25	0.192
26	26	0.0317
27	27	0.509
28	28	0.661
29	29	0.0207
3	3	0.307
30	30	0.112
31	31	0.814
32	32	0.543
33	33	0.173
34	34	0.364
35	35	0.0741
36	36	0.045
37	37	0.175
38	38	1
39	39	0.89
4	4	0.625
40	40	0.394
41	41	0.146
42	42	0.414
43	43	0.54
44	44	0.296
45	45	0.477
46	46	0.167
47	47	0.466
48	48	0.189
49	49	0.149
5	5	0.0903
50	50	0.751
51	51	0.939
52	52	0.231
53	53	0.727
54	54	0.842
55	55	0.41
56	56	0.932
57	57	0.364
58	58	0.32
59	59	0.975
6	6	0.767
60	60	0.76
61	61	0.144
62	62	0.0844
63	63	0.588
64	64	0.529
65	65	0.775
66	66	0.357
67	67	0.568
68	68	0.0895
69	69	0.645
7	7	0.31
70	70	0.00239
71	71	0.0106
72	72	0.451
73	73	0.251
74	74	0.811
75	75	0.0104
76	76	0.00696
77	77	0.518
78	78	0.0329
79	79	0.6
8	8	0.0832
80	80	0.242
81	81	0.677
82	82	0.158
83	83	0.268
84	84	0.414
85	85	0.919
86	86	0.193
87	87	0.96
88	88	0.449
89	89	0.626
9	9	0.978
90	90	0.0183
91	91	0.937
92	92	0.0735
93	93	0.158
94	94	0.208
95	95	0.182
96	96	0.0389
97	97	0.537
98	98	0.527
99	99	0.264

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: CNhs13218

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011446 CD4-positiveCD25-CD44- naive conventional T cells stimulated with alphaCD3_CD28 - 06hr- (C57BL_6J) 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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000791 (mature alpha-beta T cell)
0000084 (T cell)
0000789 (alpha-beta T cell)
0002419 (mature T cell)
0000624 (CD4-positive, alpha-beta T cell)
0000898 (naive T cell)
0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000363 (6 hr sample)
0000409 (T cell expansion sample)
0011446 (CD4-positiveCD25-CD44- naive conventional T cells stimulated with alphaCD3_CD28 - 06hr- (C57BL_6J) 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
CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)
CL:0000790 (immature alpha-beta T cell)
CL:0002425 (early T lineage precursor)
CL:0002427 (resting double-positive thymocyte)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005830
+|accession_numbers=CAGE;DRX008793;DRR009665;DRZ001090;DRZ002475;DRZ012440;DRZ013825
 |ancestors_in_anatomy_facet=
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002371,CL:0000542,CL:0000219,CL:0000738,CL:0002087,CL:0002242,CL:0000255,CL:0000791,CL:0000084,CL:0000789,CL:0002419,CL:0000624,CL:0000898,CL:0000895
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr13:30841099..30841116,+!p1@Irf4!2.97!1414.60!Irf4;;chr4:48058129..48058179,+!p2@Nr4a3!2.18!279.09!Nr4a3;;chr15:101097270..101097290,+!p1@Nr4a1!2.14!1324.20!Nr4a1;;chr7:31206743..31206761,+!p1@Nfkbid!2.08!158.72!Nfkbid;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.93!106.33!Zbtb11;;chr17:51971932..51971958,-!p2@Satb1!1.91!109.07!Satb1;;chr3:130815703..130815721,+!p2@Lef1!1.89!92.29!Lef1;;chr4:48058047..48058062,+!p1@Nr4a3!1.87!110.44!Nr4a3;;chr7:147129712..147129774,+!p1@Utf1!1.86!71.23!Utf1;;chr3:135354384..135354443,-!p1@Nfkb1!1.83!388.66!Nfkb1;;chr10:67000609..67000625,+!p1@Egr2!1.79!135.78!Egr2;;chr4:48058016..48058032,+!p3@Nr4a3!1.76!94.34!Nr4a3;;chr19:5447886..5447905,+!p1@Fosl1!1.76!57.19!Fosl1;;chr9:51021788..51021802,+!p1@Pou2af1!1.75!64.55!Pou2af1;;chr2:56967334..56967366,-!p1@Nr4a2!1.69!95.20!Nr4a2;;chr11:11590117..11590138,+!p4@Ikzf1!1.68!47.08!Ikzf1;;chr11:23670750..23670789,-!p2@Rel!1.64!78.59!Rel;;chr15:61816932..61816952,+!p2@Myc!1.60!308.71!Myc;;chr11:11590140..11590187,+!p3@Ikzf1!1.60!46.74!Ikzf1;;chr11:23670827..23670846,-!p3@Rel!1.59!37.84!Rel;;chr18:80909801..80909819,-!p1@Nfatc1!1.57!203.41!Nfatc1;;chr7:31208447..31208496,+!p2@Nfkbid!1.55!34.76!Nfkbid;;chr17:51971960..51971979,-!p1@Satb1!1.43!34.24!Satb1;;chr5:108155007..108155034,-!p1@Gfi1!1.43!25.85!Gfi1;;chr19:46379199..46379301,+!p1@Nfkb2!1.41!137.32!Nfkb2;;chr4:48058196..48058205,+!p4@Nr4a3!1.40!23.97!Nr4a3;;chr4:133801432..133801448,-!p3@Zfp593!1.36!33.22!Zfp593;;chr11:98407264..98407295,-!p1@Ikzf3!1.36!21.92!Ikzf3;;chr15:61817095..61817111,+!p1@Myc!1.32!1147.33!Myc;;chr5:53981592..53981616,+!p3@Rbpj!1.31!36.13!Rbpj;;chr11:11585678..11585745,+!p5@Ikzf1!1.30!27.57!Ikzf1;;chr10:66998241..66998263,+!p2@Egr2!1.30!19.01!Egr2;;chr19:5637528..5637548,+!p2@Rela!1.28!103.07!Rela;;chr18:3281750..3281776,-!p2@Crem!1.28!36.30!Crem;;chr17:71202822..71202877,-!p3@Tgif1!1.25!48.45!Tgif1;;chr11:11590085..11590106,+!p7@Ikzf1!1.25!16.61!Ikzf1;;chr11:98407234..98407259,-!p2@Ikzf3!1.23!15.92!Ikzf3;;chr6:99216488..99216534,-!p2@Foxp1!1.22!43.66!Foxp1;;chr11:11585912..11585950,+!p6@Ikzf1!1.20!19.01!Ikzf1;;chr11:11584970..11585030,+!p2@Ikzf1!1.19!20.89!Ikzf1;;chr11:23670953..23671028,-!p1@Rel!1.17!78.25!Rel;;chr11:52096066..52096081,-!p2@Tcf7!1.16!16.27!Tcf7;;chr5:108155037..108155060,-!p2@Gfi1!1.08!11.13!Gfi1;;chr14:70477113..70477173,+!p1@Egr3!1.08!11.13!Egr3;;chr4:48058252..48058261,+!p6@Nr4a3!1.08!10.96!Nr4a3;;chr16:92826249..92826325,-!p1@Runx1!1.07!26.37!Runx1;;chr16:55838757..55838774,-!p2@Nfkbiz!1.06!12.50!Nfkbiz;;chr1:52065508..52065522,+!p2@Stat4!1.06!12.50!Stat4;;chr11:52095821..52095836,-!p3@Tcf7!1.06!10.44!Tcf7;;chr7:147129777..147129814,+!p2@Utf1!1.06!10.44!Utf1;;chr7:20214704..20214800,-!p1@Relb!1.05!33.56!Relb;;chr19:46380235..46380277,+!p3@Nfkb2!1.04!21.92!Nfkb2;;chr4:124805061..124805087,-!p1@Zc3h12a!1.02!29.79!Zc3h12a;;chr7:31208400..31208427,+!p5@Nfkbid!1.02!9.59!Nfkbid;;chr4:32325688..32325777,+!p1@Bach2!1.01!81.84!Bach2;;chr12:56593574..56593592,-!p1@Nfkbia!1.00!474.96!Nfkbia;;chr17:71200529..71200556,-!p1@Tgif1!1.00!147.25!Tgif1;;chr19:38893646..38893732,-!p1@Noc3l!0.99!96.22!Noc3l;;chr11:100721761..100721851,+!p1@Stat5a!0.99!65.92!Stat5a;;chr8:107694661..107694713,+!p2@Cbfb!0.99!60.27!Cbfb;;chr10:13685585..13685645,+!p2@Hivep2!0.98!30.65!Hivep2;;chr10:66998213..66998240,+!p4@Egr2!0.98!8.56!Egr2;;chr11:11590188..11590200,+!p8@Ikzf1!0.97!8.39!Ikzf1;;chr17:51965903..51965926,-!p5@Satb1!0.96!8.05!Satb1;;chr4:48064149..48064169,+!p9@Nr4a3!0.96!8.05!Nr4a3;;chr1:38721792..38721845,-!p1@Aff3!0.95!10.10!Aff3;;chr1:52065454..52065495,+!p1@Stat4!0.94!13.01!Stat4;;chr17:51971991..51972003,-!p4@Satb1!0.94!7.70!Satb1;;chr8:87502608..87502623,-!p1@Junb!0.93!127.56!Junb;;chr11:102177921..102177960,-!p9@Ubtf!0.93!11.13!Ubtf;;chr7:31208285..31208312,+!p3@Nfkbid!0.93!8.39!Nfkbid;;chr1:193007123..193007139,-!p1@Atf3!0.92!42.29!Atf3;;chr17:71201096..71201114,-!p6@Tgif1!0.92!8.73!Tgif1;;chr12:77470718..77470752,-!p4@Zbtb25!0.91!10.27!Zbtb25;;chr12:109242266..109242295,-!p1@Bcl11b!0.90!60.78!Bcl11b;;chr7:29551464..29551487,-!p2@Nfkbib!0.90!27.74!Nfkbib;;chr2:9800207..9800234,-!p1@Gata3!0.90!22.26!Gata3;;chr7:31207408..31207450,+!p4@Nfkbid!0.90!11.64!Nfkbid;;chr4:48057987..48057996,+!p7@Nr4a3!0.90!8.22!Nr4a3;;chr18:35020854..35020869,+!p1@Egr1!0.88!265.90!Egr1;;chr15:57526345..57526392,+!p3@Zhx2!0.88!12.50!Zhx2;;chr4:134708451..134708469,+!p1@Runx3!0.87!11.64!Runx3;;chr5:53981578..53981590,+!p4@Rbpj!0.87!8.22!Rbpj;;chr5:134720044..134720103,-!p6@Gtf2i!0.86!6.16!Gtf2i;;chr17:45692642..45692663,+!p1@Nfkbie!0.85!20.55!Nfkbie;;chr1:13364202..13364263,-!p3@Ncoa2!0.83!17.81!Ncoa2;;chr8:81552528..81552553,+!p6@Zfp827!0.83!9.59!Zfp827;;chr11:52096804..52096896,-!p1@Tcf7!0.82!49.14!Tcf7;;chr2:126501197..126501245,-!p1@Gabpb1!0.82!45.72!Gabpb1;;chr4:48058102..48058110,+!p5@Nr4a3!0.82!6.34!Nr4a3;;chr4:48061898..48061935,+!p8@Nr4a3!0.82!5.65!Nr4a3;;chr4:48064302..48064316,+!p11@Nr4a3!0.82!5.65!Nr4a3;;chr1:52065530..52065548,+!p3@Stat4!0.82!5.65!Stat4;;chr7:138553839..138553860,-!p2@Ikzf5!0.82!5.65!Ikzf5;;chr7:25917459..25917474,-!p2@Pou2f2!0.81!5.48!Pou2f2;;chr6:98978245..98978289,-!p1@Foxp1!0.80!85.95!Foxp1;;chr3:89191004..89191022,-!p4@Zbtb7b!0.80!5.31!Zbtb7b;;chr4:133801494..133801519,-!p2@Zfp593!0.79!39.21!Zfp593;;chr18:3281725..3281740,-!p3@Crem!0.79!6.68!Crem;;chr10:67000811..67000822,+!p3@Egr2!0.79!5.14!Egr2;;chr4:133801453..133801492,-!p1@Zfp593!0.78!45.37!Zfp593;;chr4:48061952..48061964,+!p10@Nr4a3!0.78!4.97!Nr4a3;;chr4:48064251..48064268,+!p12@Nr4a3!0.78!4.97!Nr4a3;;chr11:100721640..100721658,+!p2@Stat5a!0.78!4.97!Stat5a;;chr1:36364590..36364608,+!p1@Arid5a!0.77!54.28!Arid5a;;chr8:108583550..108583595,+!p2@Nfatc3!0.77!23.80!Nfatc3;;chr16:92697560..92697592,-!p2@Runx1!0.76!32.87!Runx1;;chr4:124805092..124805135,-!p2@Zc3h12a!0.76!21.92!Zc3h12a;;chr11:102178005..102178022,-!p8@Ubtf!0.76!8.05!Ubtf;;chr3:135354375..135354381,-!p10@Nfkb1!0.76!5.99!Nfkb1;;chr19:46380433..46380451,+!p5@Nfkb2!0.76!4.79!Nfkb2;;chr17:51965928..51965960,-!p10@Satb1!0.76!4.79!Satb1;;chr6:99216375..99216395,-!p5@Foxp1!0.76!4.79!Foxp1;;chr11:11590205..11590216,+!p9@Ikzf1!0.76!4.79!Ikzf1;;chr7:52963182..52963199,+!p9@Dbp!0.76!4.79!Dbp;;chr16:55822241..55822258,-!p1@Nfkbiz!0.75!159.40!Nfkbiz;;chr8:123260252..123260264,+!p1@Irf8!0.75!35.61!Irf8;;chr10:127984472..127984504,-!p2@Zc3h10!0.74!15.92!Zc3h10;;chr17:71201050..71201078,-!p9@Tgif1!0.74!4.45!Tgif1;;chr5:38611720..38611799,+!p1@Lyar!0.73!131.32!Lyar;;chr7:133839456..133839523,+!p1@Bola2!0.72!235.08!Bola2;;chr10:30375579..30375616,-!p3@Ncoa7!0.72!10.96!Ncoa7;;chr7:20162663..20162678,+!p1@Zfp296!0.72!5.82!Zfp296;;chr7:29551488..29551529,-!p1@Nfkbib!0.71!149.99!Nfkbib;;chr13:29044875..29044928,-!p4@Sox4!0.71!5.82!Sox4;;chr4:133801418..133801425,-!p4@Zfp593!0.71!4.11!Zfp593;;chr15:80085920..80085941,+!p1@Atf4!0.70!528.72!Atf4;;chr4:63064364..63064384,-!p1@Akna!0.70!12.84!Akna;;chr3:135354452..135354475,-!p5@Nfkb1!0.70!11.13!Nfkb1;;chr17:45692676..45692695,+!p2@Nfkbie!0.70!8.90!Nfkbie;;chr2:56976467..56976482,-!p4@Nr4a2!0.70!4.97!Nr4a2;;chr5:111082367..111082441,-!p1@Noc4l!0.69!103.59!Noc4l;;chr5:32438831..32438878,+!p1@Fosl2!0.69!45.37!Fosl2;;chr11:100800901..100800921,-!p4@Stat3!0.69!4.79!Stat3;;chr2:126501799..126501832,-!p4@Gabpb1!0.69!3.94!Gabpb1;;chr10:79862089..79862129,-!p2@Mbd3!0.68!47.43!Mbd3;;chr19:5637501..5637517,+!p4@Rela!0.68!17.29!Rela;;chr2:128769696..128769712,-!p2@Zc3h8!0.68!13.36!Zc3h8;;chr18:5591389..5591406,+!p3@Zeb1!0.68!4.62!Zeb1;;chr19:46380399..46380417,+!p4@Nfkb2!0.68!3.77!Nfkb2;;chr11:23670799..23670808,-!p7@Rel!0.68!3.77!Rel;;chr6:99216360..99216372,-!p8@Foxp1!0.68!3.77!Foxp1;;chr4:6917606..6917681,-!p1@Tox!0.67!17.46!Tox;;chr11:11586218..11586285,+!p1@Ikzf1!0.67!13.18!Ikzf1;;chrX:34443339..34443348,-!p2@Nkrf!0.67!10.79!Nkrf;;chr2:153475210..153475252,+!p2@Dnmt3b!0.66!11.13!Dnmt3b;;chr3:135354349..135354371,-!p6@Nfkb1!0.66!8.05!Nfkb1;;chr5:38611816..38611827,+!p4@Lyar!0.66!4.11!Lyar;;chr11:100721732..100721742,+!p3@Stat5a!0.66!3.60!Stat5a;;chr2:156665551..156665562,+!p6@Tgif2!0.66!3.60!Tgif2;;chr19:47125313..47125405,-!p1@Pcgf6!0.65!86.98!Pcgf6;;chr13:67274092..67274140,+!p1@Rsl1!0.65!14.04!Rsl1;;chr7:30875418..30875454,-!p2@Zfp566,p2@Zfp82!0.65!10.96!Zfp566;;chr2:56976543..56976558,-!p2@Nr4a2!0.65!8.73!Nr4a2;;chr15:61818965..61819046,+!p3@Myc!0.65!6.68!Myc;;chr7:25917492..25917512,-!p1@Pou2f2!0.65!6.34!Pou2f2;;chr12:87027663..87027678,+!p2@Batf!0.65!3.42!Batf;;chr2:56967316..56967327,-!p3@Nr4a2!0.65!3.42!Nr4a2;;chr11:23670864..23670877,-!p5@Rel!0.65!3.42!Rel;;chrX:7156792..7156811,+!p1@Foxp3!0.65!3.42!Foxp3;;chr7:148514080..148514108,-!p4@Deaf1!0.64!7.88!Deaf1;;chr10:20880731..20880775,-!p2@Myb!0.64!7.70!Myb;;chr5:21290933..21291050,-!p1@Dnajc2!0.63!145.36!Dnajc2;;chr11:16908650..16908690,-!p1@Plek!0.63!23.46!Plek;;chr15:57526469..57526534,+!p1@Zhx2!0.63!13.53!Zhx2;;chr12:85560016..85560038,-!p6@C130039O16Rik!0.63!3.25!C130039O16Rik;;chr4:32325910..32325921,+!p8@Bach2!0.63!3.25!Bach2;;chr16:23988711..23988727,-!p1@Bcl6!0.62!44.17!Bcl6;;chr3:135354476..135354528,-!p2@Nfkb1!0.62!20.72!Nfkb1;;chr17:34169293..34169320,+!p3@Rxrb!0.62!11.13!Rxrb;;chr10:20880629..20880683,-!p1@Myb!0.62!10.44!Myb;;chr12:77471500..77471515,+!p2@Zbtb1!0.62!10.44!Zbtb1;;chr11:102177974..102177992,-!p17@Ubtf!0.62!4.11!Ubtf;;chr6:140571997..140572136,+!p1@Aebp2!0.61!85.95!Aebp2;;chr3:135354289..135354334,-!p3@Nfkb1!0.61!18.32!Nfkb1;;chr15:61818914..61818943,+!p7@Myc!0.61!3.94!Myc;;chr2:126501847..126501876,-!p5@Gabpb1!0.61!3.60!Gabpb1;;chr9:63559790..63559801,-!p14@Smad3!0.61!3.08!Smad3;;chr11:98407340..98407359,-!p4@Ikzf3!0.61!3.08!Ikzf3;;chr11:23671230..23671264,-!p6@Rel!0.61!3.08!Rel;;chr3:30993974..30994045,+!p1@Skil!0.60!99.99!Skil;;chr17:21626055..21626081,+!p2@Zfp53!0.60!5.48!Zfp53;;chr15:61819047..61819076,+!p5@Myc!0.60!3.77!Myc;;chr3:151873433..151873498,+!p1@Fubp1!0.59!464.51!Fubp1;;chr17:79336371..79336414,-!p1@Cebpz!0.59!168.14!Cebpz;;chr10:127080031..127080090,+!p1@Stat6!0.59!75.85!Stat6;;chr1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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011446
 |is_obsolete=
+|library_id=CNhs13218
+|library_id_phase_based=2:CNhs13218
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11815
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11815
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520antiCD3_CD28%2520stimulation%252c%252006hr%252c%2520pool1%2520%2528C57BL_6J%2529.CNhs13218.11815-124E6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520antiCD3_CD28%2520stimulation%252c%252006hr%252c%2520pool1%2520%2528C57BL_6J%2529.CNhs13218.11815-124E6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520antiCD3_CD28%2520stimulation%252c%252006hr%252c%2520pool1%2520%2528C57BL_6J%2529.CNhs13218.11815-124E6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520antiCD3_CD28%2520stimulation%252c%252006hr%252c%2520pool1%2520%2528C57BL_6J%2529.CNhs13218.11815-124E6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520antiCD3_CD28%2520stimulation%252c%252006hr%252c%2520pool1%2520%2528C57BL_6J%2529.CNhs13218.11815-124E6.mm9.nobarcode.rdna.fa.gz
 |name=CD4+CD25-CD44- naive conventional T cells, antiCD3_CD28 stimulation, 06hr, pool1 (C57BL_6J)
 |namespace=
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13218,LSID1005,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0.0686377264886741,0.127893569522672,0,-0.214011351775947,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.0767056428545931,0,0,0,0,0,0,0,0,0,0,0,0,0.0982656480056731,-0.289823798586864,0,0,0,0,-0.0530863716153007,-0.14537594073449,-0.168242538004918,0.311009235363191,-0.984211366477826,-0.269868638010351,0.306919693317858,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0.0356792840611419,0.180026585552633,0,-0.117389802908326,-0.0420516636022186,-0.158091042771083,-0.0424220352616197,0,-0.0497942419693087,-0.183050861297059,-0.0451856420005112,0,0,-0.169074896158238,-0.143748398718179,-0.0434572300765632,0.0490619746827648,0,0,0,0,0,0,-0.100467385632792,-0.246148129555495,0.33006239653353,0,0,0,0.127718011707044,0
 |rna_box=124
 |rna_catalog_number=
@@ Line 58: / Line 73: @@
 |rna_rin=
 |rna_sample_type=total RNA
-|rna_tube_id=124E6
+|rna_tube_id=1.24E+08
 |rna_weight_ug=4.37523
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
 |top_motifs=bHLH_family:4.27806574288;ELK1,4_GABP{A,B1}:3.29622530588;NFKB1_REL_RELA:3.0368120466;NFE2L1:2.73923889277;RUNX1..3:2.63761958163;ATF5_CREB3:2.63618719897;YY1:2.526062295;HIF1A:2.49296998598;SPZ1:2.44434719098;PAX8:2.37607860047;FOXP3:2.24279793077;ATF4:2.07283006779;AIRE:2.03848953424;ZBTB16:1.90959499916;PPARG:1.88418838333;ELF1,2,4:1.79536933758;STAT1,3:1.7826930518;STAT5{A,B}:1.77662816515;ALX4:1.76887533098;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.58038648192;CREB1:1.5436978613;NFE2:1.4773821359;HSF1,2:1.42531971049;AHR_ARNT_ARNT2:1.41720821976;ETS1,2:1.28133622296;HES1:1.24573701228;SPI1:1.2135001643;TBX4,5:1.20836556026;PDX1:1.17374287389;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.15781861508;SPIB:1.09885995158;NFATC1..3:1.08000704272;NANOG{mouse}:1.01452725455;CDX1,2,4:0.992848600045;NKX3-1:0.992688796684;ALX1:0.959450004025;CEBPA,B_DDIT3:0.95779428837;FOXD3:0.881731078867;RORA:0.87545093325;MYB:0.697209279301;FOS_FOS{B,L1}_JUN{B,D}:0.634652053773;CRX:0.605327503595;TLX2:0.552634498234;HLF:0.53585654989;STAT2,4,6:0.506019092742;JUN:0.501638657524;PITX1..3:0.453641243999;NR6A1:0.450366128346;NRF1:0.42860022145;IKZF2:0.424246891956;POU3F1..4:0.41525763824;BPTF:0.412566905183;FOSL2:0.405266677156;PAX2:0.400358514089;PAX4:0.370381928959;ATF2:0.344267377985;PAX6:0.338197131695;NANOG:0.322022757488;CUX2:0.263948563076;HOX{A5,B5}:0.257288719653;PAX1,9:0.201483690822;NKX6-1,2:0.191610732498;FOXQ1:0.187764300102;HMGA1,2:0.179679967179;EN1,2:0.151420477555;HOX{A4,D4}:0.134934474103;NKX2-2,8:0.121163147457;NFIX:0.0962077198221;ZNF384:0.0910553591698;IRF7:0.0795453480643;EP300:0.0739484972905;RFX2..5_RFXANK_RFXAP:0.0102665477761;EVI1:0.00513553043514;FOXP1:0.00503289177905;OCT4_SOX2{dimer}:-0.00762940323665;NFIL3:-0.0266292488552;IRF1,2:-0.0279763641331;NKX2-1,4:-0.0610109937943;SOX17:-0.0967022004744;RXRA_VDR{dimer}:-0.0994725564984;ZEB1:-0.126255745219;ARID5B:-0.142324396276;E2F1..5:-0.150384800815;SRF:-0.181910269547;DMAP1_NCOR{1,2}_SMARC:-0.206549452392;NR5A1,2:-0.209818022333;LHX3,4:-0.294369814267;VSX1,2:-0.297809883142;ZIC1..3:-0.304133626477;FOX{F1,F2,J1}:-0.329864718707;ZNF143:-0.343196813906;NR1H4:-0.348259662678;GATA6:-0.362737485876;HMX1:-0.37475795454;TAL1_TCF{3,4,12}:-0.385796924718;LMO2:-0.406052926758;RXR{A,B,G}:-0.433110353535;SNAI1..3:-0.436253456177;MYOD1:-0.440890840724;ATF6:-0.444735871248;NKX2-3_NKX2-5:-0.454483941874;POU6F1:-0.468231447617;TFDP1:-0.488929457724;ESRRA:-0.48963196895;BACH2:-0.490302513253;AR:-0.490916345603;MEF2{A,B,C,D}:-0.500408881894;UFEwm:-0.504448722572;RBPJ:-0.531103214932;PRRX1,2:-0.559507551655;ZFP161:-0.565096152849;TEF:-0.573930479475;HNF4A_NR2F1,2:-0.574501617097;TP53:-0.597875428197;NKX3-2:-0.601956747648;POU5F1:-0.604942766729;FOX{I1,J2}:-0.616914113469;PBX1:-0.621699095457;EGR1..3:-0.633444895969;FOX{D1,D2}:-0.642312262595;FOXA2:-0.642804082089;SOX2:-0.678509043182;HNF1A:-0.684062354872;KLF4:-0.691850907009;BREu{core}:-0.70171892602;FOXM1:-0.703542636058;POU1F1:-0.718999491281;ADNP_IRX_SIX_ZHX:-0.734827310798;MAFB:-0.760900959534;PRDM1:-0.782560349542;HAND1,2:-0.783856934917;FOXO1,3,4:-0.813449157629;ESR1:-0.840423291411;LEF1_TCF7_TCF7L1,2:-0.870253458983;SMAD1..7,9:-0.890438453548;TBP:-0.937193988191;MTE{core}:-0.93869689804;ONECUT1,2:-0.956118595878;HOXA9_MEIS1:-0.978117344467;RREB1:-0.981414138043;RFX1:-0.985661684349;POU2F1..3:-0.987375991942;NR3C1:-1.00949584099;MED-1{core}:-1.05583384762;REST:-1.06492083382;IKZF1:-1.17832447895;ZNF148:-1.22641747148;MZF1:-1.23355371805;ZBTB6:-1.26939356366;NHLH1,2:-1.29762224151;ZNF238:-1.31312941751;GLI1..3:-1.37397243822;HBP1_HMGB_SSRP1_UBTF:-1.40044858407;TFAP2B:-1.40254153893;TFCP2:-1.40793988998;GZF1:-1.43552306821;TGIF1:-1.487271121;FOXN1:-1.50028854138;GCM1,2:-1.5143779432;NFE2L2:-1.52209440305;TEAD1:-1.55706908433;CDC5L:-1.60571795851;DBP:-1.60632729581;MYFfamily:-1.65525713129;SOX{8,9,10}:-1.66455981985;GATA4:-1.68812366229;SOX5:-1.6952575371;FOXL1:-1.71962328264;PAX5:-1.78163646853;HIC1:-1.81997913439;SREBF1,2:-1.83872432186;GFI1B:-1.87840932453;TFAP2{A,C}:-1.90219656468;TOPORS:-1.90871214918;T:-1.9115835318;NFY{A,B,C}:-1.94473792193;GTF2I:-2.00797428668;MYBL2:-2.03389864945;MAZ:-2.08313453337;PATZ1:-2.19843069761;TFAP4:-2.26416493512;GTF2A1,2:-2.34234236337;MTF1:-2.37850984412;ZNF423:-2.39979684322;GFI1:-2.58829369125;TLX1..3_NFIC{dimer}:-2.61597559713;EBF1:-2.68538747653;SP1:-3.31393482679;XCPE1{core}:-3.59382810729
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11815-124E6;search_select_hide=table117:11815-124E6
 }}

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FF:11815-124E6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:22, 4 June 2020

CNhs13218

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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