FF:11818-124E9: Difference between revisions

Latest revision as of 18:22, 4 June 2020

Name:	CD4+CD25+ regulatory T cells, pool2 (Balb_cAJcl)
Species:	Mouse (Mus musculus)
Library ID:	CNhs13221
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	Balb/cAJcl
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	BLTreg
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		SAMD00004975

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13221		CAGE		DRX008790		DRR009662

Accession ID Mm9

Library id		BAM		CTSS
CNhs13221		DRZ001087		DRZ002472

Accession ID Mm10

Library id		BAM		CTSS
CNhs13221		DRZ012437		DRZ013822

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

CNhs13221

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0631
1002	-0.116
1003	-0.148
1004	0
1005	0.0998
1006	-0.143
1007	-0.199
1008	0
1009	-0.19
101	0.151
1010	0
1011	0.0347
1012	0.083
1013	-0.0691
1014	-0.0874
1015	-0.109
1016	-0.594
1017	0
1018	0
1019	0
102	0.799
1020	0.0527
1021	0
1022	-0.315
1023	0.0527
1024	-0.14
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.0989
103	-0.0887
1030	0
1031	-1.093
1032	-0.655
1033	0.522
1034	0
1035	0
1036	0.373
1037	0
1038	-0.184
1039	-0.181
104	0
1040	-0.121
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: CNhs13221

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	3.37776e-5
MA0003.1	MA0003.1	0.419
MA0004.1	MA0004.1	0.0505
MA0006.1	MA0006.1	0.609
MA0007.1	MA0007.1	0.446
MA0009.1	MA0009.1	0.65
MA0014.1	MA0014.1	0.815
MA0017.1	MA0017.1	0.706
MA0018.2	MA0018.2	2.00102e-5
MA0019.1	MA0019.1	0.917
MA0024.1	MA0024.1	0.721
MA0025.1	MA0025.1	0.734
MA0027.1	MA0027.1	0.75
MA0028.1	MA0028.1	6.97893e-8
MA0029.1	MA0029.1	0.427
MA0030.1	MA0030.1	0.248
MA0031.1	MA0031.1	0.00804
MA0035.2	MA0035.2	0.627
MA0038.1	MA0038.1	0.00785
MA0039.2	MA0039.2	0.541
MA0040.1	MA0040.1	0.239
MA0041.1	MA0041.1	0.0862
MA0042.1	MA0042.1	0.444
MA0043.1	MA0043.1	0.0223
MA0046.1	MA0046.1	9.58241e-10
MA0047.2	MA0047.2	0.161
MA0048.1	MA0048.1	0.3
MA0050.1	MA0050.1	2.13614e-10
MA0051.1	MA0051.1	5.99243e-7
MA0052.1	MA0052.1	0.0903
MA0055.1	MA0055.1	0.138
MA0057.1	MA0057.1	0.88
MA0058.1	MA0058.1	0.0407
MA0059.1	MA0059.1	0.0439
MA0060.1	MA0060.1	0.00526
MA0061.1	MA0061.1	1.54223e-11
MA0062.2	MA0062.2	2.5443e-24
MA0065.2	MA0065.2	0.932
MA0066.1	MA0066.1	0.111
MA0067.1	MA0067.1	0.0178
MA0068.1	MA0068.1	0.0102
MA0069.1	MA0069.1	0.622
MA0070.1	MA0070.1	0.784
MA0071.1	MA0071.1	0.801
MA0072.1	MA0072.1	0.0942
MA0073.1	MA0073.1	0.732
MA0074.1	MA0074.1	0.481
MA0076.1	MA0076.1	1.5439e-10
MA0077.1	MA0077.1	0.0717
MA0078.1	MA0078.1	0.645
MA0079.2	MA0079.2	0.0852
MA0080.2	MA0080.2	1.28881e-13
MA0081.1	MA0081.1	0.00164
MA0083.1	MA0083.1	0.341
MA0084.1	MA0084.1	0.677
MA0087.1	MA0087.1	0.829
MA0088.1	MA0088.1	0.998
MA0090.1	MA0090.1	0.0632
MA0091.1	MA0091.1	0.821
MA0092.1	MA0092.1	0.597
MA0093.1	MA0093.1	0.063
MA0099.2	MA0099.2	0.92
MA0100.1	MA0100.1	0.25
MA0101.1	MA0101.1	5.72993e-12
MA0102.2	MA0102.2	0.964
MA0103.1	MA0103.1	0.183
MA0104.2	MA0104.2	0.0711
MA0105.1	MA0105.1	4.364e-11
MA0106.1	MA0106.1	0.942
MA0107.1	MA0107.1	6.07129e-12
MA0108.2	MA0108.2	0.00199
MA0111.1	MA0111.1	0.293
MA0112.2	MA0112.2	0.292
MA0113.1	MA0113.1	0.143
MA0114.1	MA0114.1	0.111
MA0115.1	MA0115.1	0.853
MA0116.1	MA0116.1	0.0237
MA0117.1	MA0117.1	0.244
MA0119.1	MA0119.1	0.54
MA0122.1	MA0122.1	0.404
MA0124.1	MA0124.1	0.686
MA0125.1	MA0125.1	0.165
MA0131.1	MA0131.1	0.584
MA0135.1	MA0135.1	0.945
MA0136.1	MA0136.1	1.69552e-25
MA0137.2	MA0137.2	1.53488e-6
MA0138.2	MA0138.2	0.00179
MA0139.1	MA0139.1	0.416
MA0140.1	MA0140.1	0.18
MA0141.1	MA0141.1	0.731
MA0142.1	MA0142.1	0.26
MA0143.1	MA0143.1	0.586
MA0144.1	MA0144.1	0.00603
MA0145.1	MA0145.1	0.299
MA0146.1	MA0146.1	0.691
MA0147.1	MA0147.1	0.0338
MA0148.1	MA0148.1	0.143
MA0149.1	MA0149.1	0.185
MA0150.1	MA0150.1	0.933
MA0152.1	MA0152.1	0.932
MA0153.1	MA0153.1	6.53611e-5
MA0154.1	MA0154.1	0.126
MA0155.1	MA0155.1	0.588
MA0156.1	MA0156.1	3.68403e-29
MA0157.1	MA0157.1	0.00938
MA0159.1	MA0159.1	0.133
MA0160.1	MA0160.1	0.887
MA0162.1	MA0162.1	0.825
MA0163.1	MA0163.1	0.0197
MA0164.1	MA0164.1	0.262
MA0258.1	MA0258.1	0.148
MA0259.1	MA0259.1	0.184

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: CNhs13221

Novel motif	Logo	P-value
1	1	0.383
10	10	0.0343
100	100	0.54
101	101	0.895
102	102	0.507
103	103	0.644
104	104	0.845
105	105	0.659
106	106	0.684
107	107	0.472
108	108	0.577
109	109	0.291
11	11	0.336
110	110	0.0805
111	111	0.141
112	112	0.206
113	113	0.627
114	114	0.323
115	115	0.647
116	116	0.758
117	117	4.1361e-4
118	118	0.321
119	119	0.785
12	12	0.282
120	120	0.105
121	121	0.313
122	122	0.846
123	123	0.66
124	124	0.315
125	125	0.293
126	126	0.526
127	127	0.954
128	128	0.497
129	129	0.583
13	13	0.0889
130	130	0.808
131	131	0.765
132	132	0.993
133	133	0.821
134	134	0.514
135	135	0.848
136	136	0.273
137	137	0.327
138	138	0.558
139	139	0.401
14	14	0.725
140	140	0.668
141	141	0.251
142	142	0.328
143	143	2.66668e-4
144	144	0.382
145	145	0.224
146	146	0.987
147	147	0.365
148	148	0.165
149	149	0.135
15	15	0.12
150	150	0.796
151	151	0.249
152	152	0.499
153	153	0.372
154	154	0.306
155	155	0.104
156	156	0.114
157	157	0.939
158	158	0.0569
159	159	0.537
160	160	0.387
161	161	0.273
162	162	0.721
163	163	0.368
164	164	0.031
165	165	0.576
166	166	0.464
167	167	0.0936
168	168	0.63
169	169	0.889
17	17	0.671
18	18	0.391
19	19	0.0814
2	2	0.0386
20	20	0.0169
21	21	0.2
22	22	0.789
23	23	0.828
24	24	0.281
25	25	0.164
26	26	0.364
27	27	0.742
28	28	0.257
29	29	0.0417
3	3	0.293
30	30	0.0908
31	31	0.526
32	32	0.133
33	33	0.127
34	34	0.462
35	35	0.0582
36	36	0.0315
37	37	0.126
38	38	0.659
39	39	0.636
4	4	0.885
40	40	0.321
41	41	0.42
42	42	0.262
43	43	0.558
44	44	0.657
45	45	0.462
46	46	0.513
47	47	0.581
48	48	0.343
49	49	0.232
5	5	0.0428
50	50	0.49
51	51	0.794
52	52	0.106
53	53	0.685
54	54	0.59
55	55	0.543
56	56	0.854
57	57	0.905
58	58	0.331
59	59	0.809
6	6	0.729
60	60	0.961
61	61	0.217
62	62	0.0933
63	63	0.826
64	64	0.971
65	65	0.527
66	66	0.278
67	67	0.797
68	68	0.88
69	69	0.855
7	7	0.435
70	70	0.0124
71	71	0.0974
72	72	0.292
73	73	0.181
74	74	0.548
75	75	0.00563
76	76	0.0207
77	77	0.0516
78	78	0.19
79	79	0.795
8	8	0.583
80	80	0.233
81	81	0.728
82	82	0.311
83	83	0.0441
84	84	0.488
85	85	0.997
86	86	0.102
87	87	0.744
88	88	0.389
89	89	0.851
9	9	0.913
90	90	0.141
91	91	0.905
92	92	0.556
93	93	0.247
94	94	0.375
95	95	0.0712
96	96	0.278
97	97	0.498
98	98	0.534
99	99	0.0369

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: CNhs13221

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011455 CD4-positiveCD25-positive regulatory T cells (Balb_cAJcl) 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)
0000815 (regulatory T cell)
0000792 (CD4-positive, CD25-positive, alpha-beta regulatory T cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0011455 (CD4-positiveCD25-positive regulatory T cells (Balb_cAJcl) 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)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00004975
+|accession_numbers=CAGE;DRX008790;DRR009662;DRZ001087;DRZ002472;DRZ012437;DRZ013822
 |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:0000815,CL:0000792
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chrX:7156792..7156811,+!p1@Foxp3!2.96!916.78!Foxp3;;chr3:130815703..130815721,+!p2@Lef1!1.92!98.26!Lef1;;chr1:38721792..38721845,-!p1@Aff3!1.82!80.31!Aff3;;chr5:134720044..134720103,-!p6@Gtf2i!1.76!56.69!Gtf2i;;chr1:52065454..52065495,+!p1@Stat4!1.75!90.13!Stat4;;chr13:30841099..30841116,+!p1@Irf4!1.72!79.67!Irf4;;chr4:124805061..124805087,-!p1@Zc3h12a!1.71!151.33!Zc3h12a;;chr11:11590117..11590138,+!p4@Ikzf1!1.71!49.97!Ikzf1;;chr17:51971932..51971958,-!p2@Satb1!1.68!62.75!Satb1;;chr11:100683839..100683890,-!p2@Stat5b!1.67!102.91!Stat5b;;chr11:11590140..11590187,+!p3@Ikzf1!1.67!54.88!Ikzf1;;chr1:52065508..52065522,+!p2@Stat4!1.66!52.55!Stat4;;chr4:63064364..63064384,-!p1@Akna!1.65!124.35!Akna;;chr16:92826249..92826325,-!p1@Runx1!1.65!104.07!Runx1;;chr4:48058129..48058179,+!p2@Nr4a3!1.65!80.70!Nr4a3;;chr2:173044380..173044432,-!p1@Zbp1!1.59!87.67!Zbp1;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.59!47.78!Zbtb11;;chr6:99216488..99216534,-!p2@Foxp1!1.58!101.88!Foxp1;;chr12:109242266..109242295,-!p1@Bcl11b!1.55!273.48!Bcl11b;;chr11:98407264..98407295,-!p1@Ikzf3!1.55!34.09!Ikzf3;;chr2:9800207..9800234,-!p1@Gata3!1.54!100.07!Gata3;;chr10:30375579..30375616,-!p3@Ncoa7!1.51!72.44!Ncoa7;;chr11:98407234..98407259,-!p2@Ikzf3!1.48!29.44!Ikzf3;;chr12:87027663..87027678,+!p2@Batf!1.47!28.67!Batf;;chr11:52096066..52096081,-!p2@Tcf7!1.46!33.83!Tcf7;;chr7:19895384..19895399,-!p2@Fosb!1.44!37.32!Fosb;;chr8:87502608..87502623,-!p1@Junb!1.43!403.51!Junb;;chr7:19895354..19895369,-!p1@Fosb!1.43!35.51!Fosb;;chr12:86814833..86814846,+!p1@Fos!1.41!546.97!Fos;;chr17:51971960..51971979,-!p1@Satb1!1.39!31.51!Satb1;;chr11:53583544..53583559,+!p1@Irf1!1.37!358.19!Irf1;;chr11:11584970..11585030,+!p2@Ikzf1!1.36!30.99!Ikzf1;;chr4:48058016..48058032,+!p3@Nr4a3!1.33!34.35!Nr4a3;;chr9:32503590..32503680,+!p1@Ets1!1.32!692.36!Ets1;;chr1:87546583..87546595,+!p1@Sp100!1.31!27.25!Sp100;;chr8:74842952..74842970,+!p1@Klf2!1.30!1218.28!Klf2;;chrX:7156827..7156838,+!p2@Foxp3!1.30!19.11!Foxp3;;chr12:56593574..56593592,-!p1@Nfkbia!1.29!910.58!Nfkbia;;chr1:52176315..52176343,+!p1@Stat1!1.28!255.15!Stat1;;chr2:91077034..91077078,-!p2@Ddb2!1.27!39.00!Ddb2;;chr11:100683794..100683805,-!p4@Stat5b!1.26!17.17!Stat5b;;chr14:79915425..79915501,+!p1@Elf1!1.25!143.97!Elf1;;chr12:87027598..87027652,+!p1@Batf!1.25!38.48!Batf;;chr10:128082840..128082872,-!p1@Ikzf4!1.25!20.14!Ikzf4;;chr16:55822241..55822258,-!p1@Nfkbiz!1.23!484.60!Nfkbiz;;chr2:173044357..173044377,-!p2@Zbp1!1.23!23.11!Zbp1;;chr12:77470718..77470752,-!p4@Zbtb25!1.23!22.34!Zbtb25;;chr11:11585912..11585950,+!p6@Ikzf1!1.23!20.14!Ikzf1;;chr11:52096804..52096896,-!p1@Tcf7!1.21!121.89!Tcf7;;chr10:67000609..67000625,+!p1@Egr2!1.21!34.86!Egr2;;chr11:11585678..11585745,+!p5@Ikzf1!1.21!22.08!Ikzf1;;chr1:52065530..52065548,+!p3@Stat4!1.21!15.11!Stat4;;chr7:25917492..25917512,-!p1@Pou2f2!1.20!25.18!Pou2f2;;chr18:3281750..3281776,-!p2@Crem!1.19!29.44!Crem;;chr15:101097270..101097290,+!p1@Nr4a1!1.14!130.03!Nr4a1;;chr11:96880072..96880079,+!p1@Sp6!1.13!12.40!Sp6;;chr1:36364590..36364608,+!p1@Arid5a!1.12!122.93!Arid5a;;chrX:48499591..48499593,-!p3@Mbnl3!1.12!12.14!Mbnl3;;chr7:31206743..31206761,+!p1@Nfkbid!1.11!16.14!Nfkbid;;chr11:52095821..52095836,-!p3@Tcf7!1.10!11.49!Tcf7;;chr18:3337249..3337274,-!p17@Crem!1.09!11.36!Crem;;chr3:135354384..135354443,-!p1@Nfkb1!1.08!68.56!Nfkb1;;chr7:31208285..31208312,+!p3@Nfkbid!1.08!12.14!Nfkbid;;chr3:89191004..89191022,-!p4@Zbtb7b!1.08!10.98!Zbtb7b;;chr11:100721761..100721851,+!p1@Stat5a!1.07!80.19!Stat5a;;chr11:98407340..98407359,-!p4@Ikzf3!1.07!10.72!Ikzf3;;chr3:52072329..52072346,+!p1@Foxo1!1.06!160.37!Foxo1;;chr4:6917606..6917681,-!p1@Tox!1.05!43.26!Tox;;chr2:126501799..126501832,-!p4@Gabpb1!1.05!10.33!Gabpb1;;chr4:94718861..94718872,-!p2@Jun!1.04!76.31!Jun;;chr11:23670953..23671028,-!p1@Rel!1.04!56.81!Rel;;chr17:71201572..71201601,-!p10@Tgif1!1.04!9.94!Tgif1;;chr3:130813200..130813252,+!p1@Lef1!1.03!43.90!Lef1;;chr1:87497610..87497645,+!p1@Gm2427,p1@Sp140!1.03!9.81!Sp140;;chrX:7157626..7157635,+!p3@Foxp3!1.03!9.68!Foxp3;;chr11:98407142..98407159,-!p5@Ikzf3!1.02!9.56!Ikzf3;;chr18:5594197..5594228,+!p7@Zeb1!1.02!9.56!Zeb1;;chr4:124805092..124805135,-!p2@Zc3h12a!1.01!39.90!Zc3h12a;;chr4:48058047..48058062,+!p1@Nr4a3!1.01!14.33!Nr4a3;;chr1:69732354..69732402,-!p1@Ikzf2!1.01!10.46!Ikzf2;;chr3:89191054..89191070,-!p5@Zbtb7b!1.01!9.17!Zbtb7b;;chr11:98407370..98407395,-!p3@Ikzf3!1.01!9.17!Ikzf3;;chr4:32325688..32325777,+!p1@Bach2!1.00!80.44!Bach2;;chr17:45692642..45692663,+!p1@Nfkbie!1.00!29.57!Nfkbie;;chr6:99385340..99385362,-!p11@Foxp1!1.00!9.04!Foxp1;;chr8:108583550..108583595,+!p2@Nfatc3!0.99!40.16!Nfatc3;;chr10:13685585..13685645,+!p2@Hivep2!0.99!30.86!Hivep2;;chr18:3337339..3337397,-!p5@Crem!0.99!17.56!Crem;;chr1:87546602..87546617,+!p2@Sp100!0.99!10.46!Sp100;;chr11:11590085..11590106,+!p7@Ikzf1!0.98!8.65!Ikzf1;;chr6:99216375..99216395,-!p5@Foxp1!0.98!8.52!Foxp1;;chr5:108155007..108155034,-!p1@Gfi1!0.98!8.52!Gfi1;;chr15:102076652..102076679,-!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5605,-!p1@Zfp644!0.18!23.63!Zfp644;;chr1:75188717..75188804,+!p1@ENSMUST00000125384,p1@ENSMUST00000127625,p1@ENSMUST00000131788,p1@ENSMUST00000134233,p1@ENSMUST00000134378,p1@ENSMUST00000145459,p1@ENSMUST00000151887,p1@ENSMUST00000152233!0.18!18.08!Ankzf1;;chr17:24806629..24806672,+!p1@Zfp598!0.18!14.46!Zfp598;;chr1:64579364..64579389,+!p2@Creb1!0.18!11.62!Creb1;;chr7:135019614..135019666,-!p1@Zfp668!0.18!10.72!Zfp668;;chr13:67601387..67601448,-!p2@Zfp58!0.18!10.59!Zfp58;;chr18:84255841..84255883,-!p1@Tshz1!0.18!8.91!Tshz1;;chr5:9160908..9160912,-!p2@Dmtf1!0.18!4.91!Dmtf1;;chr8:4613182..4613207,+!p2@Zfp958!0.18!4.78!Zfp958;;chr10:114821532..114821565,-!p4@Thap2!0.18!4.13!Thap2;;chr13:67914714..67914768,+!p1@Zfp273!0.18!3.74!Zfp273;;chr13:67182439..67182491,-!p2@Zfp708!0.18!2.71!Zfp708;;chr1:95651388..95651434,-!p2@Thap4!0.18!2.45!Thap4;;chr7:30691543..30691586,-!p2@Zfp27!0.18!2.32!Zfp27;;chr17:51951634..51951651,-!p6@Satb1!0.18!1.81!Satb1;;chr13:44826650..44826661,+!p8@Jarid2!0.18!1.55!Jarid2;;chr13:59924173..59924194,-!p4@Zcchc6!0.18!1.55!Zcchc6;;chr5:92391948..92391968,+!p3@Thap6!0.18!1.29!Thap6;;chr12:85534690..85534708,-!p9@C130039O16Rik!0.18!1.03!C130039O16Rik;;chr4:142802570..142802581,-!p2@Prdm2!0.18!0.90!Prdm2;;chr5:104182943..104182954,+!p12@Aff1!0.18!0.90!Aff1;;chr10:67599450..67599456,-!p8@Arid5b!0.18!0.77!Arid5b;;chr10:67599461..67599470,-!p6@Arid5b!0.18!0.77!Arid5b;;chr11:98407087..98407102,-!p11@Ikzf3!0.18!0.52!Ikzf3;;chr10:66998213..66998240,+!p4@Egr2!0.18!0.52!Egr2;;chr11:98826178..98826197,+!p7@Rara!0.18!0.52!Rara;;chr11:11589947..11589950,+!p18@Ikzf1!0.18!0.52!Ikzf1;;chr11:23670799..23670808,-!p7@Rel!0.18!0.52!Rel;;chr11:52070563..52070589,-!p9@Tcf7!0.18!0.52!Tcf7;;chr11:97524329..97524348,+!p6@Mllt6!0.18!0.52!Mllt6;;chr11:100721425..100721430,+!p15@Stat5a!0.18!0.52!Stat5a;;chr11:23671199..23671210,-!p9@Rel!0.18!0.52!Rel;;chr12:109241791..109241802,-!p7@Bcl11b!0.18!0.52!Bcl11b;;chr12:109241971..109241982,-!p9@Bcl11b!0.18!0.52!Bcl11b;;chr10:67000934..67000943,+!p8@Egr2!0.18!0.52!Egr2;;chr5:38611199..38611209,+!p6@Lyar!0.18!0.52!Lyar;;chr8:77540128..77540145,+!p2@Hmgxb4!0.18!0.52!Hmgxb4;;chrX:137077530..137077533,-!p11@Tsc22d3!0.18!0.52!Tsc22d3;;chr7:31208447..31208496,+!p2@Nfkbid!0.18!0.52!Nfkbid;;chr7:31377960..31377973,-!p3@Zbtb32!0.18!0.52!Zbtb32;;chr9:113840426..113840435,+!p8@Ubp1!0.18!0.52!Ubp1;;chr17:34784066..34784067,+!p5@Atf6b!0.18!0.52!Atf6b;;chr16:91225808..91225824,+!p1@Olig2!0.18!0.52!Olig2;;chr18:5593345..5593349,+!p14@Zeb1!0.18!0.52!Zeb1;;chr17:51965928..51965960,-!p10@Satb1!0.18!0.52!Satb1;;chr2:56967381..56967386,-!p8@Nr4a2!0.18!0.52!Nr4a2;;chr2:56967316..56967327,-!p3@Nr4a2!0.18!0.52!Nr4a2;;chr12:78063165..78063227,-!p1@Max!0.17!112.60!Max;;chr11:95171500..95171527,-!p1@Myst2!0.17!82.51!Myst2;;chr6:108610610..108610676,+!p1@Bhlhe40!0.17!64.43!Bhlhe40;;chr12:41172341..41172385,-!p1@Zfp277!0.17!45.84!Zfp277;;chr2:18314363..18314465,-!p1@Dnajc1!0.17!32.54!Dnajc1;;chr7:30553587..30553661,+!p1@Zfp84!0.17!31.38!Zfp84;;chr5:53981912..53981942,+!p1@Rbpj!0.17!25.57!Rbpj;;chr13:21494557..21494617,-!p1@Zkscan3!0.17!24.02!Zkscan3;;chr9:20264394..20264448,-!p1@Zfp26!0.17!23.24!Zfp26;;chr16:95924005..95924042,+!p2@Ets2!0.17!23.24!Ets2;;chr4:119212257..119212303,+!p1@Foxj3!0.17!23.11!Foxj3;;chr6:83391606..83391658,-!p1@Tet3!0.17!22.08!Tet3;;chr1:173341474..173341513,+!p2@Usf1!0.17!17.69!Usf1;;chr3:152058955..152059023,+!p1@Gm8261,p1@Zzz3!0.17!16.01!Zzz3;;chr3:32409487..32409563,+!p1@Zfp639!0.17!9.04!Zfp639;;chr11:58717675..58717719,-!p1@Zfp39!0.17!8.65!Zfp39;;chr18:5334362..5334408,-!p1@Zfp438!0.17!4.91!Zfp438;;chr4:151401710..151401733,-!p2@Zbtb48!0.17!3.36!Zbtb48;;chr12:77471463..77471495,+!p3@Zbtb1!0.17!3.23!Zbtb1;;chr19:5637489..5637500,+!p5@Rela!0.17!2.58!Rela;;chr8:74405860..74405905,+!p2@Zfp709!0.17!2.20!Zfp709;;chr5:65194810..65194819,+!p9@Klf3!0.17!1.81!Klf3;;chrX:70587989..70588000,+!p3@Zfp275!0.17!1.81!Zfp275;;chr7:134169999..134170010,-!p13@Maz!0.17!1.42!Maz;;chr5:138188113..138188145,+!p9@Tsc22d4!0.17!1.29!Tsc22d4;;chr7:134592574..134592591,-!p2@Zfp689!0.17!1.16!Zfp689;;chr19:5423800..5423821,-!p5@Drap1!0.17!1.16!Drap1;;chr1:13364153..13364156,-!p5@Ncoa2!0.17!1.16!Ncoa2;;chr8:118230847..118230856,-!p8@Maf!0.17!1.03!Maf;;
@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011455
 |is_obsolete=
+|library_id=CNhs13221
+|library_id_phase_based=2:CNhs13221
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11818
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11818
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25%252b%2520regulatory%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13221.11818-124E9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25%252b%2520regulatory%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13221.11818-124E9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25%252b%2520regulatory%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13221.11818-124E9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25%252b%2520regulatory%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13221.11818-124E9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25%252b%2520regulatory%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13221.11818-124E9.mm9.nobarcode.rdna.fa.gz
 |name=CD4+CD25+ regulatory T cells, pool2 (Balb_cAJcl)
 |namespace=
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13221,LSID1005,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0.954514873996484,0.216328664154126,0,-0.0954651892342525,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.0877424031537146,0,0,0,0,0.427908384099143,0,0,0,0,0,0,0,0.0991834542533635,-0.198353492194396,0,0,0,0,0,0.0788762566460552,-0.0484504509168724,0.115573639790889,-0.984211366477826,-0.269868638010351,0.142192289944826,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.0391357935194999,0,-0.0596004204783735,0.0527413783866199,0.180840494114715,0,-0.0462936579359132,-0.257909278952766,-0.158091042771083,-0.0102220198035435,0,-0.0779220297779274,-0.0973736644748266,-0.00484194761633205,0.0527413783866199,0,-0.0680518321457894,-0.0429753863541584,0.0302286322973486,0.0633606951049186,0.0273527371326463,0,0,0,0,0,0.169344616312548,0.204892560252393,0.55884952469937,0,0,0,0.0997657817140535,0
 |rna_box=124
 |rna_catalog_number=
@@ Line 58: / Line 73: @@
 |rna_rin=
 |rna_sample_type=total RNA
-|rna_tube_id=124E9
+|rna_tube_id=1.24E+11
 |rna_weight_ug=1.48422
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
 |top_motifs=RUNX1..3:3.95875601555;BPTF:3.59419521239;NFKB1_REL_RELA:3.56294174228;ETS1,2:2.97135601212;PDX1:2.83764895623;ELF1,2,4:2.80953929924;ATF5_CREB3:2.77983707397;STAT5{A,B}:2.7729838326;ATF4:2.63639581913;NFATC1..3:2.62239866956;FOXO1,3,4:2.41295315349;SPI1:2.40233849742;CREB1:2.35789147636;STAT2,4,6:2.29785534898;ALX4:2.12399921035;SPIB:1.99824100086;FOX{D1,D2}:1.99023323795;PAX2:1.86035866883;DMAP1_NCOR{1,2}_SMARC:1.761275596;NFE2L1:1.67403944695;ELK1,4_GABP{A,B1}:1.65317622941;IRF1,2:1.57692117861;SPZ1:1.57291439605;IRF7:1.55567160433;YY1:1.34534247654;ZBTB16:1.23904405515;PAX8:1.17615283194;AIRE:1.16143667383;FOXD3:1.09714243112;ATF6:1.07099240873;TLX2:1.02919509149;TBX4,5:1.00077396016;NANOG{mouse}:0.950187410016;STAT1,3:0.942789032421;CDX1,2,4:0.846779263399;PPARG:0.806000171922;FOXM1:0.793373748224;FOX{I1,J2}:0.787368335319;JUN:0.714671928333;ZNF384:0.464907663956;EP300:0.446111827514;RFX2..5_RFXANK_RFXAP:0.444280266063;SREBF1,2:0.437443172003;RORA:0.428352691159;POU1F1:0.423573037259;MYB:0.402470053884;bHLH_family:0.350683774336;NRF1:0.294481053197;ALX1:0.292842641344;NFIX:0.267311012707;FOS_FOS{B,L1}_JUN{B,D}:0.255642538138;FOXQ1:0.185315447327;NKX2-2,8:0.180361224188;FOX{F1,F2,J1}:0.175139263957;NKX2-1,4:0.138126204175;POU2F1..3:0.125264747521;FOXP1:0.120906411484;CRX:0.0826343107564;ARID5B:0.0792462752557;TAL1_TCF{3,4,12}:0.0452017317945;ATF2:0.0182041728666;AHR_ARNT_ARNT2:-0.00313232062056;LEF1_TCF7_TCF7L1,2:-0.0394817737568;ZNF148:-0.0514389653962;AR:-0.0742722084975;HOX{A4,D4}:-0.0806848103422;HSF1,2:-0.0884950065331;FOXP3:-0.0911305621849;E2F1..5:-0.103132341587;ZEB1:-0.106680998329;NANOG:-0.123278669586;POU3F1..4:-0.123722981164;GATA6:-0.124341427168;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.173111001774;NFIL3:-0.178638394012;PAX4:-0.180372722739;PITX1..3:-0.215877482515;SOX2:-0.238709617649;PBX1:-0.290802981229;LMO2:-0.29825473853;OCT4_SOX2{dimer}:-0.301356367479;NKX6-1,2:-0.333257871955;CEBPA,B_DDIT3:-0.339641837942;NR1H4:-0.35083397218;SRF:-0.363968218237;SMAD1..7,9:-0.415798618863;EN1,2:-0.433785923673;NFY{A,B,C}:-0.44912654113;POU5F1:-0.45307292043;TGIF1:-0.466063062365;SNAI1..3:-0.488760897609;NR5A1,2:-0.498951560476;HOXA9_MEIS1:-0.530826805828;HLF:-0.535285832104;FOSL2:-0.540602541894;NKX3-1:-0.548549381619;EGR1..3:-0.558240556683;POU6F1:-0.563124670119;TEF:-0.56423053877;FOXN1:-0.568117750157;MEF2{A,B,C,D}:-0.575651210739;HOX{A5,B5}:-0.595660833505;HBP1_HMGB_SSRP1_UBTF:-0.632155005536;MYOD1:-0.632435398676;BACH2:-0.639236197295;EVI1:-0.642197173862;RFX1:-0.659832154807;HNF4A_NR2F1,2:-0.661918193717;ZFP161:-0.667123898559;SOX{8,9,10}:-0.682336687585;SOX17:-0.68537778508;NR6A1:-0.741078115056;RXRA_VDR{dimer}:-0.767620923856;PRRX1,2:-0.778924502635;HNF1A:-0.795281184249;ZNF143:-0.804956395506;MAFB:-0.822632547642;HIF1A:-0.830655777821;HMX1:-0.866105111227;T:-0.871183641827;CUX2:-0.871352914262;MED-1{core}:-0.872104105183;NHLH1,2:-0.902646974928;TFDP1:-0.915779874973;MTE{core}:-0.924079778419;GLI1..3:-0.925924829467;MZF1:-0.939462169578;TBP:-0.939480307405;RREB1:-0.982061734532;MYFfamily:-0.997184587147;LHX3,4:-1.01390165322;FOXL1:-1.02903735976;PAX1,9:-1.03475119103;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.03718865827;RBPJ:-1.03807248997;ZNF238:-1.04526702012;TFCP2:-1.04907966458;PAX6:-1.07842734589;ESRRA:-1.08218688516;GATA4:-1.1135508919;NFE2:-1.11845078787;HAND1,2:-1.12436545449;VSX1,2:-1.13755699762;NKX2-3_NKX2-5:-1.1558420027;REST:-1.16783684713;RXR{A,B,G}:-1.20008120022;IKZF2:-1.20223423942;HES1:-1.21491580971;TFAP2B:-1.23665585425;BREu{core}:-1.2944403839;SOX5:-1.30460875152;HMGA1,2:-1.30736051235;CDC5L:-1.31757571689;EBF1:-1.36903917328;MTF1:-1.40997687846;ZBTB6:-1.43064561092;TP53:-1.44797279482;FOXA2:-1.44853441091;PRDM1:-1.47474802634;GZF1:-1.52927568103;PATZ1:-1.54338711053;NFE2L2:-1.55656202543;NR3C1:-1.57789508481;ONECUT1,2:-1.60550565177;MAZ:-1.61165001927;DBP:-1.63932155257;NKX3-2:-1.67716432056;TFAP2{A,C}:-1.68442273938;ADNP_IRX_SIX_ZHX:-1.73731996482;GTF2I:-1.77991247229;HIC1:-1.82173281621;ZIC1..3:-1.86637463821;SP1:-1.8676283403;UFEwm:-1.88165588024;GFI1:-1.88779375558;TEAD1:-1.88967327815;KLF4:-1.9843303537;ESR1:-2.01760210534;TOPORS:-2.0307633047;XCPE1{core}:-2.04316575146;IKZF1:-2.14922961957;MYBL2:-2.20217301878;GCM1,2:-2.26156651343;PAX5:-2.31139146267;TFAP4:-2.43113358775;ZNF423:-2.5011150713;GTF2A1,2:-2.52515312072;GFI1B:-2.61406235217;TLX1..3_NFIC{dimer}:-2.61720451236
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11818-124E9;search_select_hide=table117:11818-124E9
 }}

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FF:11818-124E9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:22, 4 June 2020

CNhs13221

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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