FF:11820-124F2: Difference between revisions

Latest revision as of 18:22, 4 June 2020

Name:	CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool2 (Balb_cAJcl)
Species:	Mouse (Mus musculus)
Library ID:	CNhs13226
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	BLTsPI-2
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		SAMD00004704

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13226		CAGE		DRX008792		DRR009664

Accession ID Mm9

Library id		BAM		CTSS
CNhs13226		DRZ001089		DRZ002474

Accession ID Mm10

Library id		BAM		CTSS
CNhs13226		DRZ012439		DRZ013824

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

CNhs13226

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0668
1002	-0.116
1003	-0.14
1004	0
1005	-0.101
1006	-0.436
1007	-0.246
1008	0
1009	-0.19
101	0.657
1010	0
1011	0.0913
1012	0
1013	-0.183
1014	-0.0851
1015	0.176
1016	-0.448
1017	0
1018	0
1019	0
102	0.836
1020	0.037
1021	0
1022	-0.296
1023	0.167
1024	-0.14
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.0989
103	-0.0887
1030	0
1031	-1.056
1032	-0.717
1033	0.929
1034	0
1035	0
1036	0.583
1037	0
1038	-0.183
1039	-0.482
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: CNhs13226

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0123
MA0003.1	MA0003.1	0.132
MA0004.1	MA0004.1	0.0237
MA0006.1	MA0006.1	0.189
MA0007.1	MA0007.1	0.939
MA0009.1	MA0009.1	0.648
MA0014.1	MA0014.1	0.91
MA0017.1	MA0017.1	0.137
MA0018.2	MA0018.2	2.07019e-9
MA0019.1	MA0019.1	0.94
MA0024.1	MA0024.1	0.92
MA0025.1	MA0025.1	0.173
MA0027.1	MA0027.1	0.744
MA0028.1	MA0028.1	0.00249
MA0029.1	MA0029.1	0.934
MA0030.1	MA0030.1	0.961
MA0031.1	MA0031.1	0.326
MA0035.2	MA0035.2	0.892
MA0038.1	MA0038.1	0.0248
MA0039.2	MA0039.2	0.132
MA0040.1	MA0040.1	0.96
MA0041.1	MA0041.1	0.0585
MA0042.1	MA0042.1	0.0987
MA0043.1	MA0043.1	2.05521e-4
MA0046.1	MA0046.1	5.92568e-11
MA0047.2	MA0047.2	0.667
MA0048.1	MA0048.1	0.265
MA0050.1	MA0050.1	1.28568e-4
MA0051.1	MA0051.1	0.00394
MA0052.1	MA0052.1	0.532
MA0055.1	MA0055.1	0.157
MA0057.1	MA0057.1	0.829
MA0058.1	MA0058.1	0.00664
MA0059.1	MA0059.1	3.67959e-4
MA0060.1	MA0060.1	0.00516
MA0061.1	MA0061.1	5.00318e-11
MA0062.2	MA0062.2	5.74142e-11
MA0065.2	MA0065.2	0.385
MA0066.1	MA0066.1	0.614
MA0067.1	MA0067.1	9.17826e-4
MA0068.1	MA0068.1	7.04658e-4
MA0069.1	MA0069.1	0.679
MA0070.1	MA0070.1	0.95
MA0071.1	MA0071.1	0.631
MA0072.1	MA0072.1	0.158
MA0073.1	MA0073.1	0.522
MA0074.1	MA0074.1	0.583
MA0076.1	MA0076.1	0.00342
MA0077.1	MA0077.1	0.798
MA0078.1	MA0078.1	0.5
MA0079.2	MA0079.2	0.326
MA0080.2	MA0080.2	4.44885e-10
MA0081.1	MA0081.1	8.28542e-4
MA0083.1	MA0083.1	0.619
MA0084.1	MA0084.1	0.341
MA0087.1	MA0087.1	0.889
MA0088.1	MA0088.1	0.0725
MA0090.1	MA0090.1	0.0295
MA0091.1	MA0091.1	0.877
MA0092.1	MA0092.1	0.0846
MA0093.1	MA0093.1	0.0243
MA0099.2	MA0099.2	1.90857e-6
MA0100.1	MA0100.1	0.263
MA0101.1	MA0101.1	1.39184e-15
MA0102.2	MA0102.2	0.401
MA0103.1	MA0103.1	0.553
MA0104.2	MA0104.2	1.26819e-4
MA0105.1	MA0105.1	1.50427e-6
MA0106.1	MA0106.1	0.582
MA0107.1	MA0107.1	6.78646e-16
MA0108.2	MA0108.2	0.475
MA0111.1	MA0111.1	0.409
MA0112.2	MA0112.2	0.389
MA0113.1	MA0113.1	0.952
MA0114.1	MA0114.1	0.00388
MA0115.1	MA0115.1	0.268
MA0116.1	MA0116.1	0.97
MA0117.1	MA0117.1	0.0353
MA0119.1	MA0119.1	0.0251
MA0122.1	MA0122.1	0.632
MA0124.1	MA0124.1	0.483
MA0125.1	MA0125.1	0.114
MA0131.1	MA0131.1	0.526
MA0135.1	MA0135.1	0.88
MA0136.1	MA0136.1	1.50298e-16
MA0137.2	MA0137.2	0.00564
MA0138.2	MA0138.2	2.57295e-4
MA0139.1	MA0139.1	0.212
MA0140.1	MA0140.1	0.721
MA0141.1	MA0141.1	0.524
MA0142.1	MA0142.1	0.585
MA0143.1	MA0143.1	0.226
MA0144.1	MA0144.1	0.183
MA0145.1	MA0145.1	0.0226
MA0146.1	MA0146.1	0.958
MA0147.1	MA0147.1	7.41537e-6
MA0148.1	MA0148.1	0.622
MA0149.1	MA0149.1	0.246
MA0150.1	MA0150.1	0.0778
MA0152.1	MA0152.1	0.0654
MA0153.1	MA0153.1	5.21671e-6
MA0154.1	MA0154.1	0.739
MA0155.1	MA0155.1	0.336
MA0156.1	MA0156.1	1.56159e-14
MA0157.1	MA0157.1	0.259
MA0159.1	MA0159.1	0.679
MA0160.1	MA0160.1	0.971
MA0162.1	MA0162.1	0.0189
MA0163.1	MA0163.1	0.748
MA0164.1	MA0164.1	0.0466
MA0258.1	MA0258.1	0.849
MA0259.1	MA0259.1	0.0203

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: CNhs13226

Novel motif	Logo	P-value
1	1	0.972
10	10	0.228
100	100	0.474
101	101	0.463
102	102	0.434
103	103	0.16
104	104	0.493
105	105	0.425
106	106	0.215
107	107	0.971
108	108	0.77
109	109	0.722
11	11	0.702
110	110	0.407
111	111	0.129
112	112	0.296
113	113	0.91
114	114	0.975
115	115	0.462
116	116	0.543
117	117	2.80937e-4
118	118	0.66
119	119	0.899
12	12	0.295
120	120	0.162
121	121	0.373
122	122	0.981
123	123	0.648
124	124	0.221
125	125	0.579
126	126	0.452
127	127	0.502
128	128	0.191
129	129	0.513
13	13	0.259
130	130	0.461
131	131	0.305
132	132	0.612
133	133	0.196
134	134	0.454
135	135	0.253
136	136	0.954
137	137	0.872
138	138	0.976
139	139	0.143
14	14	0.0871
140	140	0.992
141	141	0.847
142	142	0.562
143	143	0.0167
144	144	0.36
145	145	0.192
146	146	0.854
147	147	0.662
148	148	0.244
149	149	0.115
15	15	0.486
150	150	1
151	151	0.973
152	152	0.673
153	153	0.467
154	154	0.165
155	155	0.22
156	156	0.00111
157	157	0.983
158	158	0.0143
159	159	0.714
160	160	0.119
161	161	0.322
162	162	0.203
163	163	0.767
164	164	0.0701
165	165	0.807
166	166	0.0774
167	167	0.133
168	168	0.709
169	169	0.212
17	17	0.921
18	18	0.29
19	19	0.0105
2	2	0.00773
20	20	0.00328
21	21	0.167
22	22	0.356
23	23	0.683
24	24	0.533
25	25	0.357
26	26	0.55
27	27	0.122
28	28	0.421
29	29	0.251
3	3	0.984
30	30	0.12
31	31	0.444
32	32	0.0509
33	33	0.223
34	34	0.298
35	35	0.278
36	36	0.157
37	37	0.371
38	38	0.446
39	39	0.589
4	4	0.788
40	40	0.914
41	41	0.151
42	42	0.787
43	43	0.686
44	44	0.728
45	45	0.32
46	46	0.883
47	47	0.646
48	48	0.794
49	49	0.696
5	5	0.205
50	50	0.635
51	51	0.658
52	52	0.497
53	53	0.641
54	54	0.564
55	55	0.992
56	56	0.757
57	57	0.63
58	58	0.74
59	59	0.428
6	6	0.654
60	60	0.458
61	61	0.243
62	62	0.264
63	63	0.699
64	64	0.592
65	65	0.791
66	66	0.668
67	67	0.621
68	68	0.157
69	69	0.523
7	7	0.689
70	70	0.0204
71	71	0.235
72	72	0.818
73	73	0.369
74	74	0.668
75	75	0.042
76	76	0.0327
77	77	0.02
78	78	0.0608
79	79	0.857
8	8	0.989
80	80	0.415
81	81	0.877
82	82	0.803
83	83	0.243
84	84	0.284
85	85	0.582
86	86	0.129
87	87	0.423
88	88	0.544
89	89	0.322
9	9	0.819
90	90	0.524
91	91	0.554
92	92	0.622
93	93	0.258
94	94	0.486
95	95	0.482
96	96	0.567
97	97	0.502
98	98	0.852
99	99	0.0483

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: CNhs13226

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011449 CD4-positiveCD25-CD44- naive conventional T cells stimulated with PMA an ionomycin- 02hr- (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)
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)
0000359 (2 hr sample)
0000409 (T cell expansion sample)
0011449 (CD4-positiveCD25-CD44- naive conventional T cells stimulated with PMA an ionomycin- 02hr- (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)
CL:0002425 (early T lineage precursor)
CL:0002427 (resting double-positive thymocyte)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002370,UBERON:0000483,UBERON:0002530,UBERON:0002384,UBERON:0006562,UBERON:0000974,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0000077,UBERON:0002368,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005911,UBERON:0004921,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0005291,UBERON:0003929,UBERON:0000072,UBERON:0004807,UBERON:0003104,UBERON:0004177,UBERON:0005057,UBERON:0005058,UBERON:0001048,UBERON:0000925,UBERON:0003408,UBERON:0006598,UBERON:0003351,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0000065,UBERON:0001004,UBERON:0000153,UBERON:0007811,UBERON:0002390,UBERON:0007026,UBERON:0001041,UBERON:0000949,UBERON:0001557,UBERON:0001042,UBERON:0002193,UBERON:0002405,UBERON:0009113,UBERON:0008814,UBERON:0009142,UBERON:0003081,UBERON:0003295,UBERON:0009722,UBERON:0006595,UBERON:0006603,UBERON:0009145,UBERON:0005562,UBERON:0003061,UBERON:0007690
+|DRA_sample_Accession=CAGE@SAMD00004704
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000723,CL:0000048,CL:0000988,CL:0000548,CL:0000034,CL:0002032,CL:0000012,CL:0002320,CL:0000063,CL:0002371,CL:0000542,CL:0000219,CL:0000004,CL:0000134,CL:0000738,CL:0002087,CL:0000255,CL:0000791,CL:0000084,CL:0000789,CL:0002420,CL:0002419,CL:0000624,CL:0000893,CL:0002489,CL:0000790,CL:0000838,CL:0002031,CL:0000827,CL:0000898,CL:0000037,CL:0000809,CL:0000810,CL:0000566,CL:0000837,CL:0000895,CL:0000051,CL:0000808,CL:0000894,CL:0000806,CL:0000807,CL:0000805,CL:0002425,CL:0002436,CL:0002427,CL:0002428,CL:0002429,CL:0002433,CL:0002431,CL:0002432
+|accession_numbers=CAGE;DRX008792;DRR009664;DRZ001089;DRZ002474;DRZ012439;DRZ013824
+|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
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000350,FF:0000359,FF:0000409,FF:0011449
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr13:30841099..30841116,+!p1@Irf4!3.36!3518.93!Irf4;;chr7:31206743..31206761,+!p1@Nfkbid!3.34!2910.83!Nfkbid;;chr15:101097270..101097290,+!p1@Nr4a1!3.02!10019.83!Nr4a1;;chr4:48058047..48058062,+!p1@Nr4a3!2.96!1362.02!Nr4a3;;chr7:31208447..31208496,+!p2@Nfkbid!2.85!708.98!Nfkbid;;chr4:48058129..48058179,+!p2@Nr4a3!2.80!1161.66!Nr4a3;;chr10:67000609..67000625,+!p1@Egr2!2.70!1114.38!Egr2;;chr2:56967334..56967366,-!p1@Nr4a2!2.69!954.75!Nr4a2;;chr7:31208400..31208427,+!p5@Nfkbid!2.55!355.54!Nfkbid;;chr17:51971932..51971958,-!p2@Satb1!2.52!439.34!Satb1;;chr11:23670750..23670789,-!p2@Rel!2.45!517.05!Rel;;chr11:23670827..23670846,-!p3@Rel!2.38!238.51!Rel;;chr7:31208285..31208312,+!p3@Nfkbid!2.37!257.71!Nfkbid;;chr4:48058016..48058032,+!p3@Nr4a3!2.33!347.12!Nr4a3;;chr14:70477113..70477173,+!p1@Egr3!2.31!202.23!Egr3;;chr15:61816932..61816952,+!p2@Myc!2.29!1516.04!Myc;;chr3:135354384..135354443,-!p1@Nfkb1!2.28!1090.51!Nfkb1;;chr17:51971960..51971979,-!p1@Satb1!2.17!195.68!Satb1;;chr12:56593574..56593592,-!p1@Nfkbia!2.10!6008.67!Nfkbia;;chr12:86814833..86814846,+!p1@Fos!2.09!2642.35!Fos;;chr18:80909801..80909819,-!p1@Nfatc1!2.09!685.34!Nfatc1;;chr3:130815703..130815721,+!p2@Lef1!2.07!140.67!Lef1;;chr5:108155007..108155034,-!p1@Gfi1!2.05!111.88!Gfi1;;chr12:85560016..85560038,-!p6@C130039O16Rik!2.04!107.44!C130039O16Rik;;chr11:11590140..11590187,+!p3@Ikzf1!2.02!123.35!Ikzf1;;chr4:48058196..48058205,+!p4@Nr4a3!2.01!101.58!Nr4a3;;chr11:23670953..23671028,-!p1@Rel!1.97!495.51!Rel;;chr4:124805061..124805087,-!p1@Zc3h12a!1.96!269.17!Zc3h12a;;chr7:19895384..19895399,-!p2@Fosb!1.96!125.69!Fosb;;chr11:11590117..11590138,+!p4@Ikzf1!1.92!82.86!Ikzf1;;chr12:87027663..87027678,+!p2@Batf!1.91!80.99!Batf;;chr11:23670864..23670877,-!p5@Rel!1.90!79.35!Rel;;chr1:52065508..52065522,+!p2@Stat4!1.89!89.65!Stat4;;chr18:3281750..3281776,-!p2@Crem!1.88!148.40!Crem;;chr16:92826249..92826325,-!p1@Runx1!1.87!172.97!Runx1;;chr19:46380433..46380451,+!p5@Nfkb2!1.87!72.33!Nfkb2;;chr15:79178060..79178074,+!p2@Maff!1.86!92.46!Maff;;chr10:67000811..67000822,+!p3@Egr2!1.86!70.92!Egr2;;chr1:193007123..193007139,-!p1@Atf3!1.85!373.33!Atf3;;chr15:57526345..57526392,+!p3@Zhx2!1.85!124.05!Zhx2;;chr7:19895354..19895369,-!p1@Fosb!1.85!94.80!Fosb;;chr8:87502608..87502623,-!p1@Junb!1.83!1010.22!Junb;;chr16:55822241..55822258,-!p1@Nfkbiz!1.82!1892.41!Nfkbiz;;chr16:55838757..55838774,-!p2@Nfkbiz!1.82!76.54!Nfkbiz;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.78!75.37!Zbtb11;;chr11:52096066..52096081,-!p2@Tcf7!1.78!70.92!Tcf7;;chr4:48058252..48058261,+!p6@Nr4a3!1.77!57.81!Nr4a3;;chr11:23670933..23670942,-!p4@Rel!1.76!57.11!Rel;;chr15:61817095..61817111,+!p1@Myc!1.75!3048.69!Myc;;chr10:66998241..66998263,+!p2@Egr2!1.74!54.30!Egr2;;chr19:5447886..5447905,+!p1@Fosl1!1.74!54.07!Fosl1;;chr15:79177964..79177986,+!p1@Maff!1.72!170.16!Maff;;chr7:31207408..31207450,+!p4@Nfkbid!1.72!81.92!Nfkbid;;chr11:100721640..100721658,+!p2@Stat5a!1.72!51.03!Stat5a;;chr19:5637528..5637548,+!p2@Rela!1.71!279.71!Rela;;chr7:31208431..31208442,+!p6@Nfkbid!1.71!50.32!Nfkbid;;chr19:46380399..46380417,+!p4@Nfkb2!1.71!50.09!Nfkb2;;chr1:52065530..52065548,+!p3@Stat4!1.68!47.28!Stat4;;chr11:23670799..23670808,-!p7@Rel!1.67!45.64!Rel;;chr10:13686815..13686846,+!p3@Hivep2!1.66!96.20!Hivep2;;chr9:51021788..51021802,+!p1@Pou2af1!1.66!53.37!Pou2af1;;chr13:112476433..112476448,+!p2@Mier3!1.65!80.52!Mier3;;chr2:126501799..126501832,-!p4@Gabpb1!1.65!43.30!Gabpb1;;chr11:52095821..52095836,-!p3@Tcf7!1.64!43.07!Tcf7;;chr4:63064364..63064384,-!p1@Akna!1.62!114.46!Akna;;chr11:98407264..98407295,-!p1@Ikzf3!1.62!40.26!Ikzf3;;chr9:32503336..32503360,+!p4@Ets1!1.61!40.03!Ets1;;chr18:3281725..3281740,-!p3@Crem!1.60!48.69!Crem;;chr19:46379199..46379301,+!p1@Nfkb2!1.59!205.74!Nfkb2;;chr6:99216488..99216534,-!p2@Foxp1!1.59!102.99!Foxp1;;chr4:134708451..134708469,+!p1@Runx3!1.59!66.24!Runx3;;chr15:79178013..79178028,+!p3@Maff!1.59!49.15!Maff;;chr15:79178029..79178044,+!p4@Maff!1.59!46.34!Maff;;chr17:45692676..45692695,+!p2@Nfkbie!1.58!72.56!Nfkbie;;chr11:98821858..98821907,+!p6@Rara!1.58!59.45!Rara;;chr11:100721761..100721851,+!p1@Stat5a!1.57!253.96!Stat5a;;chr2:9800207..9800234,-!p1@Gata3!1.57!106.03!Gata3;;chr5:22939909..22939948,+!p6@Mll5!1.57!46.58!Mll5;;chr4:6917606..6917681,-!p1@Tox!1.55!140.44!Tox;;chr7:147129712..147129774,+!p1@Utf1!1.55!34.88!Utf1;;chr4:48064149..48064169,+!p9@Nr4a3!1.55!34.41!Nr4a3;;chr11:100683839..100683890,-!p2@Stat5b!1.54!76.54!Stat5b;;chr12:109241728..109241781,-!p2@Bcl11b!1.54!36.28!Bcl11b;;chr18:35020854..35020869,+!p1@Egr1!1.53!1202.62!Egr1;;chr7:20214704..20214800,-!p1@Relb!1.53!105.33!Relb;;chr11:11584970..11585030,+!p2@Ikzf1!1.53!46.58!Ikzf1;;chr19:5447692..5447711,+!p2@Fosl1!1.52!32.30!Fosl1;;chr15:61818965..61819046,+!p3@Myc!1.51!53.83!Myc;;chr17:71200529..71200556,-!p1@Tgif1!1.50!467.89!Tgif1;;chr4:48061952..48061964,+!p10@Nr4a3!1.50!30.90!Nr4a3;;chr5:32438831..32438878,+!p1@Fosl2!1.49!292.58!Fosl2;;chr12:86815639..86815664,+!p2@Fos!1.48!29.49!Fos;;chr2:56967316..56967327,-!p3@Nr4a2!1.48!29.02!Nr4a2;;chr15:61819047..61819076,+!p5@Myc!1.47!34.41!Myc;;chr12:25257141..25257173,+!p1@Grhl1!1.46!56.18!Grhl1;;chr11:11585678..11585745,+!p5@Ikzf1!1.46!39.79!Ikzf1;;chr11:11585912..11585950,+!p6@Ikzf1!1.46!35.58!Ikzf1;;chr4:48061898..48061935,+!p8@Nr4a3!1.46!27.85!Nr4a3;;chr15:57526469..57526534,+!p1@Zhx2!1.45!94.80!Zhx2;;chr17:45692642..45692663,+!p1@Nfkbie!1.45!84.73!Nfkbie;;chr5:32438894..32438908,+!p2@Fosl2!1.45!55.71!Fosl2;;chr17:51965903..51965926,-!p5@Satb1!1.45!27.15!Satb1;;chr17:51971991..51972003,-!p4@Satb1!1.44!26.68!Satb1;;chr7:29551464..29551487,-!p2@Nfkbib!1.43!97.37!Nfkbib;;chr4:48064251..48064268,+!p12@Nr4a3!1.43!25.75!Nr4a3;;chr4:48057987..48057996,+!p7@Nr4a3!1.42!29.49!Nr4a3;;chr4:48064302..48064316,+!p11@Nr4a3!1.42!25.51!Nr4a3;;chr5:138187466..138187477,+!p11@Tsc22d4!1.40!29.96!Tsc22d4;;chr18:75527009..75527027,+!p1@Smad7!1.39!470.70!Smad7;;chr11:98821937..98821987,+!p4@Rara!1.39!51.03!Rara;;chr1:38721792..38721845,-!p1@Aff3!1.39!29.49!Aff3;;chr2:91076997..91077012,-!p4@Ddb2!1.38!23.17!Ddb2;;chr11:96976641..96976646,-!p1@Tbx21!1.38!22.94!Tbx21;;chr3:135354375..135354381,-!p10@Nfkb1!1.37!27.15!Nfkb1;;chr4:48058102..48058110,+!p5@Nr4a3!1.37!25.28!Nr4a3;;chr11:100721732..100721742,+!p3@Stat5a!1.37!22.70!Stat5a;;chr11:98407234..98407259,-!p2@Ikzf3!1.37!22.70!Ikzf3;;chr11:11590085..11590106,+!p7@Ikzf1!1.37!22.24!Ikzf1;;chr4:32325688..32325777,+!p1@Bach2!1.36!185.15!Bach2;;chr12:85534957..85535017,-!p2@C130039O16Rik!1.36!106.50!C130039O16Rik;;chr1:92949999..92950097,+!p1@Lrrfip1!1.35!540.69!Lrrfip1;;chr19:46380235..46380277,+!p3@Nfkb2!1.35!45.41!Nfkb2;;chr3:133207214..133207228,-!p2@Tet2!1.35!25.98!Tet2;;chr1:92950128..92950139,+!p4@Lrrfip1!1.34!20.83!Lrrfip1;;chr5:108155037..108155060,-!p2@Gfi1!1.34!20.83!Gfi1;;chr3:130813200..130813252,+!p1@Lef1!1.33!89.88!Lef1;;chr2:126501847..126501876,-!p5@Gabpb1!1.33!23.17!Gabpb1;;chr11:11590188..11590200,+!p8@Ikzf1!1.33!20.60!Ikzf1;;chr10:13685585..13685645,+!p2@Hivep2!1.32!67.41!Hivep2;;chr12:77470718..77470752,-!p4@Zbtb25!1.32!28.09!Zbtb25;;chr17:51972530..51972571,-!p7@Satb1!1.32!19.90!Satb1;;chr7:31208324..31208333,+!p7@Nfkbid!1.31!19.19!Nfkbid;;chr11:52096804..52096896,-!p1@Tcf7!1.30!150.27!Tcf7;;chr17:71202822..71202877,-!p3@Tgif1!1.30!55.01!Tgif1;;chr4:63064279..63064293,-!p7@Akna!1.30!18.73!Akna;;chr8:123260252..123260264,+!p1@Irf8!1.29!127.80!Irf8;;chr4:124805092..124805135,-!p2@Zc3h12a!1.29!77.71!Zc3h12a;;chr4:32325955..32325971,+!p3@Bach2!1.29!24.11!Bach2;;chr12:85560051..85560070,-!p11@C130039O16Rik!1.29!18.49!C130039O16Rik;;chr12:109242266..109242295,-!p1@Bcl11b!1.28!147.23!Bcl11b;;chr5:104182754..104182777,+!p11@Aff1!1.27!19.43!Aff1;;chr11:23671230..23671264,-!p6@Rel!1.27!17.79!Rel;;chr11:53583544..53583559,+!p1@Irf1!1.26!283.22!Irf1;;chr1:138521574..138521597,+!p3@Zfp281!1.26!40.49!Zfp281;;chr7:31208381..31208390,+!p8@Nfkbid!1.26!17.32!Nfkbid;;chr3:135354349..135354371,-!p6@Nfkb1!1.25!33.94!Nfkb1;;chr7:71083729..71083742,-!p4@Klf13!1.25!29.26!Klf13;;chr1:64579145..64579168,+!p6@Creb1!1.25!16.85!Creb1;;chr19:46380462..46380471,+!p11@Nfkb2!1.25!16.85!Nfkb2;;chr7:147129777..147129814,+!p2@Utf1!1.25!16.62!Utf1;;chr13:44826937..44826952,+!p2@Jarid2!1.24!224.47!Jarid2;;chrX:98449898..98449913,+!p2@Foxo4!1.24!51.49!Foxo4;;chr11:62271274..62271337,-!p4@Ncor1!1.24!23.87!Ncor1;;chr10:66998213..66998240,+!p4@Egr2!1.24!16.38!Egr2;;chr12:81213989..81214006,-!p1@Zfp36l1!1.23!798.63!Zfp36l1;;chr13:44826694..44826710,+!p3@Jarid2!1.23!172.27!Jarid2;;chr15:61818593..61818614,+!p4@Myc!1.23!27.15!Myc;;chr5:104182694..104182724,+!p8@Aff1!1.23!19.66!Aff1;;chr17:51965928..51965960,-!p10@Satb1!1.23!16.15!Satb1;;chr4:48063649..48063653,+!p14@Nr4a3!1.23!15.92!Nr4a3;;chr3:52072329..52072346,+!p1@Foxo1!1.22!230.55!Foxo1;;chr10:44178521..44178557,-!p1@Prdm1!1.22!27.85!Prdm1;;chr13:44829403..44829438,+!p11@Jarid2!1.22!18.02!Jarid2;;chr12:87027598..87027652,+!p1@Batf!1.21!34.41!Batf;;chr13:44826722..44826742,+!p1@Jarid2!1.20!233.83!Jarid2;;chr11:11586218..11586285,+!p1@Ikzf1!1.20!47.52!Ikzf1;;chr15:100430393..100430410,-!p3@Pou6f1!1.20!14.75!Pou6f1;;chr17:71201572..71201601,-!p10@Tgif1!1.20!14.75!Tgif1;;chr19:46380374..46380397,+!p7@Nfkb2!1.20!14.75!Nfkb2;;chr12:119540395..119540415,-!p5@Sp4!1.19!22.00!Sp4;;chr1:133903955..133903969,+!p10@Elk4!1.19!18.26!Elk4;;chr12:25257176..25257190,+!p3@Grhl1!1.19!16.38!Grhl1;;chr3:30993974..30994045,+!p1@Skil!1.18!390.42!Skil;;chr11:98798983..98799049,+!p1@Rara!1.18!348.05!Rara;;chr5:53981592..53981616,+!p3@Rbpj!1.18!26.92!Rbpj;;chr17:71201096..71201114,-!p6@Tgif1!1.18!16.38!Tgif1;;chr15:57526394..57526404,+!p8@Zhx2!1.18!15.68!Zhx2;;chr13:42147384..42147441,+!p1@Hivep1!1.17!128.50!Hivep1;;chr4:133801432..133801448,-!p3@Zfp593!1.17!20.83!Zfp593;;chr15:61818914..61818943,+!p7@Myc!1.17!16.85!Myc;;chr7:31210290..31210308,+!p10@Nfkbid!1.17!13.81!Nfkbid;;chr8:74842952..74842970,+!p1@Klf2!1.16!898.34!Klf2;;chr16:23988711..23988727,-!p1@Bcl6!1.15!153.08!Bcl6;;chr18:75527030..75527055,+!p2@Sma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+|ffid_belonging_in_development=CL:0000134,CL:0000051,CL:0000790,CL:0002425,CL:0002427
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011449
 |is_obsolete=
+|library_id=CNhs13226
+|library_id_phase_based=2:CNhs13226
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11820
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11820
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25-CD44-%2520naive%2520conventional%2520T%2520cells%252c%2520PMA%2520and%2520ionomycin%2520stimulation%252c%252002hr%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13226.11820-124F2.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%2520PMA%2520and%2520ionomycin%2520stimulation%252c%252002hr%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13226.11820-124F2.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%2520PMA%2520and%2520ionomycin%2520stimulation%252c%252002hr%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13226.11820-124F2.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%2520PMA%2520and%2520ionomycin%2520stimulation%252c%252002hr%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13226.11820-124F2.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%2520PMA%2520and%2520ionomycin%2520stimulation%252c%252002hr%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13226.11820-124F2.mm9.nobarcode.rdna.fa.gz
 |name=CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool2 (Balb_cAJcl)
 |namespace=
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13226,LSID1005,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
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 |rna_box=124
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=4.40626
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
 |top_motifs=NFKB1_REL_RELA:5.46529720824;ATF4:4.38342448979;ATF5_CREB3:4.25735638358;NFATC1..3:3.87920364287;NFE2L1:3.80482773942;SPZ1:3.80466451654;RUNX1..3:3.58986533379;CREB1:3.52507916189;FOXP3:3.26908399123;AIRE:3.12828141939;bHLH_family:2.67915316537;ALX4:2.560184551;NANOG{mouse}:2.51256324647;STAT5{A,B}:2.39870300357;PAX2:2.37304254953;STAT1,3:2.34677381476;TBX4,5:2.24361241637;ZBTB16:2.05875920214;ETS1,2:2.01488922568;FOS_FOS{B,L1}_JUN{B,D}:2.01277834021;FOSL2:1.88442489356;HIF1A:1.8815113182;SPI1:1.74844879301;PPARG:1.72875179691;NFE2:1.71441282046;PDX1:1.66723444196;SPIB:1.52716461248;ELF1,2,4:1.52455796953;CRX:1.51803499089;TLX2:1.47002674788;JUN:1.42507839235;HSF1,2:1.41395009302;ELK1,4_GABP{A,B1}:1.38754974544;HES1:1.36368148773;PAX8:1.35581587987;HMX1:1.30170906303;BPTF:1.24404397015;AHR_ARNT_ARNT2:1.21008461759;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.20557527579;RORA:1.1543420093;PAX4:1.07322319596;STAT2,4,6:1.01987308483;YY1:0.999720966624;ZNF384:0.993646678547;IRF7:0.961436652112;NR1H4:0.958585151275;MTE{core}:0.84020048956;ATF6:0.840126116473;EGR1..3:0.829148125319;EP300:0.814736486163;IRF1,2:0.800245329426;BACH2:0.762993912183;ATF2:0.76227498265;DMAP1_NCOR{1,2}_SMARC:0.718396883425;CEBPA,B_DDIT3:0.665342805225;FOX{D1,D2}:0.653481831699;FOXN1:0.640828935529;MYB:0.594826891601;IKZF2:0.524306810572;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.485284159339;ALX1:0.459887948427;EVI1:0.30994229002;NKX3-1:0.306532489351;FOXD3:0.280453370012;NR6A1:0.245841629101;PITX1..3:0.231738276056;TFDP1:0.221151583388;RFX2..5_RFXANK_RFXAP:0.218558297932;MAFB:0.213325585373;HLF:0.139480359995;NANOG:0.127588456686;SRF:0.124394492441;FOXM1:0.112860528527;HOX{A5,B5}:0.0757870617959;NKX6-1,2:0.0604406485991;HMGA1,2:0.0470729213834;POU3F1..4:0.0436366329204;E2F1..5:0.041817128621;FOXP1:0.026888304532;NRF1:0.0249466727007;MYOD1:0.0228151872821;NKX2-1,4:-0.0837622378798;SMAD1..7,9:-0.0943404858122;ZNF148:-0.102826851788;ZIC1..3:-0.128863260949;SOX17:-0.150076280015;TFAP2B:-0.155595968183;TBP:-0.171185041467;HOX{A4,D4}:-0.206232439355;ZFP161:-0.265108991584;GATA6:-0.27528907055;SOX2:-0.285034406516;NFIL3:-0.327701272157;MED-1{core}:-0.331155902542;SNAI1..3:-0.351701101537;RREB1:-0.352595571569;RXR{A,B,G}:-0.362892961154;OCT4_SOX2{dimer}:-0.389770836528;FOXQ1:-0.3924307417;MEF2{A,B,C,D}:-0.407612571127;POU6F1:-0.409845427792;TP53:-0.412862261742;NR5A1,2:-0.417917433025;MZF1:-0.437875037428;LEF1_TCF7_TCF7L1,2:-0.444541928186;POU5F1:-0.457999428863;EN1,2:-0.458289763762;LMO2:-0.463239865904;RXRA_VDR{dimer}:-0.473826303171;CDX1,2,4:-0.479012891027;FOX{F1,F2,J1}:-0.488127856254;CUX2:-0.489932511547;CDC5L:-0.4906615689;PAX1,9:-0.504170117094;FOXL1:-0.51646467646;HBP1_HMGB_SSRP1_UBTF:-0.521225904605;GLI1..3:-0.527614395186;TAL1_TCF{3,4,12}:-0.5681818791;AR:-0.59390114564;PAX5:-0.62348345794;POU2F1..3:-0.628823351483;FOX{I1,J2}:-0.63233572629;ZEB1:-0.639370755609;NFIX:-0.676277566316;SP1:-0.681816540776;FOXO1,3,4:-0.683935161658;ZNF143:-0.685297902605;HNF1A:-0.715605723799;NKX2-2,8:-0.72448789736;MAZ:-0.729026985306;RBPJ:-0.730667806384;HNF4A_NR2F1,2:-0.738402363067;ESRRA:-0.764118981166;NFE2L2:-0.80039088387;NHLH1,2:-0.822494742511;UFEwm:-0.859868493966;VSX1,2:-0.863680567233;LHX3,4:-0.873694415436;MYFfamily:-0.89316808101;ZBTB6:-0.907634911557;BREu{core}:-0.908195840088;HOXA9_MEIS1:-0.946698959782;NFY{A,B,C}:-0.999741852594;FOXA2:-1.0386553079;REST:-1.03931693398;TFCP2:-1.04443486477;TGIF1:-1.0550724659;KLF4:-1.05719266512;PRDM1:-1.06068501888;ESR1:-1.07410745122;POU1F1:-1.07534690362;ARID5B:-1.08698856754;PBX1:-1.09596717954;NKX2-3_NKX2-5:-1.1128185582;TEF:-1.14318357472;RFX1:-1.154991569;NKX3-2:-1.19978154892;GCM1,2:-1.20214458761;PAX6:-1.21386525567;GZF1:-1.24694680943;HAND1,2:-1.34938641221;ZNF238:-1.3534122882;MTF1:-1.36337784832;PRRX1,2:-1.3680505279;SREBF1,2:-1.38740425773;SOX{8,9,10}:-1.39930750025;T:-1.43336877203;IKZF1:-1.4703320256;TFAP2{A,C}:-1.50932474791;GATA4:-1.51540099029;PATZ1:-1.53092491785;HIC1:-1.65785421138;GTF2A1,2:-1.67621170419;DBP:-1.77300711527;ADNP_IRX_SIX_ZHX:-1.77969821922;GTF2I:-1.79497261577;SOX5:-1.82330649516;ONECUT1,2:-1.84784459381;TEAD1:-1.88630439129;TOPORS:-1.90020611972;MYBL2:-1.995965657;EBF1:-2.23507167739;XCPE1{core}:-2.24617319568;NR3C1:-2.29882582042;TFAP4:-2.30936405468;GFI1B:-2.79760142976;GFI1:-2.87243582194;TLX1..3_NFIC{dimer}:-3.01850076725;ZNF423:-3.38977131832
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11820-124F2;search_select_hide=table117:11820-124F2
 }}

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FF:11820-124F2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:22, 4 June 2020

CNhs13226

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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