FF:12162-128H2: Difference between revisions

Latest revision as of 18:32, 4 June 2020

Name:	MC1+Gr1+ myeloid-derived suppressor cells control, donor2 (0127 PBS)
Species:	Mouse (Mus musculus)
Library ID:	CNhs12541
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	bone marrow
dev stage	NA
sex	NA
age	NA
cell type	stem cell
cell line	NA
company	NA
collaboration	Hozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	total RNA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004836

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12541		CAGE		DRX008776		DRR009648

Accession ID Mm9

Library id		BAM		CTSS
CNhs12541		DRZ001073		DRZ002458

Accession ID Mm10

Library id		BAM		CTSS
CNhs12541		DRZ012423		DRZ013808

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

CNhs12541

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0749
1002	-0.116
1003	-0.175
1004	0
1005	1.123
1006	-0.143
1007	-0.0237
1008	0
1009	-0.2
101	-0.449
1010	0
1011	-0.108
1012	0
1013	-0.0308
1014	-0.0874
1015	-0.328
1016	-0.594
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.0487
1022	-0.315
1023	0.811
1024	-0.0899
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.115
103	-0.0887
1030	0
1031	-0.911
1032	-0.951
1033	-0.0665
1034	0
1035	0
1036	0.0433
1037	0
1038	-0.612
1039	-0.595
104	0
1040	-0.333
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: CNhs12541

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	7.11289e-13
MA0003.1	MA0003.1	0.88
MA0004.1	MA0004.1	0.548
MA0006.1	MA0006.1	0.216
MA0007.1	MA0007.1	0.377
MA0009.1	MA0009.1	0.672
MA0014.1	MA0014.1	0.242
MA0017.1	MA0017.1	0.34
MA0018.2	MA0018.2	0.0637
MA0019.1	MA0019.1	0.718
MA0024.1	MA0024.1	0.208
MA0025.1	MA0025.1	0.0203
MA0027.1	MA0027.1	0.657
MA0028.1	MA0028.1	9.84036e-4
MA0029.1	MA0029.1	0.612
MA0030.1	MA0030.1	0.855
MA0031.1	MA0031.1	0.0304
MA0035.2	MA0035.2	0.613
MA0038.1	MA0038.1	0.0357
MA0039.2	MA0039.2	0.0693
MA0040.1	MA0040.1	0.0817
MA0041.1	MA0041.1	0.351
MA0042.1	MA0042.1	0.92
MA0043.1	MA0043.1	1.37283e-4
MA0046.1	MA0046.1	4.89705e-10
MA0047.2	MA0047.2	0.0341
MA0048.1	MA0048.1	0.197
MA0050.1	MA0050.1	5.86115e-5
MA0051.1	MA0051.1	9.88993e-4
MA0052.1	MA0052.1	0.0359
MA0055.1	MA0055.1	0.261
MA0057.1	MA0057.1	0.833
MA0058.1	MA0058.1	0.726
MA0059.1	MA0059.1	0.441
MA0060.1	MA0060.1	0.0608
MA0061.1	MA0061.1	0.00546
MA0062.2	MA0062.2	1.10006e-15
MA0065.2	MA0065.2	0.18
MA0066.1	MA0066.1	0.0947
MA0067.1	MA0067.1	0.0096
MA0068.1	MA0068.1	0.19
MA0069.1	MA0069.1	0.486
MA0070.1	MA0070.1	0.23
MA0071.1	MA0071.1	0.221
MA0072.1	MA0072.1	0.0867
MA0073.1	MA0073.1	0.705
MA0074.1	MA0074.1	0.475
MA0076.1	MA0076.1	5.51876e-4
MA0077.1	MA0077.1	0.151
MA0078.1	MA0078.1	0.759
MA0079.2	MA0079.2	0.378
MA0080.2	MA0080.2	7.90603e-16
MA0081.1	MA0081.1	2.124e-4
MA0083.1	MA0083.1	0.833
MA0084.1	MA0084.1	0.798
MA0087.1	MA0087.1	0.431
MA0088.1	MA0088.1	0.696
MA0090.1	MA0090.1	0.0482
MA0091.1	MA0091.1	0.724
MA0092.1	MA0092.1	0.498
MA0093.1	MA0093.1	0.539
MA0099.2	MA0099.2	0.00144
MA0100.1	MA0100.1	0.061
MA0101.1	MA0101.1	0.0295
MA0102.2	MA0102.2	1.12191e-9
MA0103.1	MA0103.1	0.725
MA0104.2	MA0104.2	0.0567
MA0105.1	MA0105.1	4.9047e-5
MA0106.1	MA0106.1	0.719
MA0107.1	MA0107.1	0.0094
MA0108.2	MA0108.2	0.0571
MA0111.1	MA0111.1	0.469
MA0112.2	MA0112.2	3.44388e-4
MA0113.1	MA0113.1	0.348
MA0114.1	MA0114.1	0.835
MA0115.1	MA0115.1	0.443
MA0116.1	MA0116.1	7.67015e-4
MA0117.1	MA0117.1	0.109
MA0119.1	MA0119.1	0.441
MA0122.1	MA0122.1	0.564
MA0124.1	MA0124.1	0.738
MA0125.1	MA0125.1	0.0224
MA0131.1	MA0131.1	0.807
MA0135.1	MA0135.1	0.418
MA0136.1	MA0136.1	8.83747e-30
MA0137.2	MA0137.2	0.115
MA0138.2	MA0138.2	0.146
MA0139.1	MA0139.1	0.559
MA0140.1	MA0140.1	0.914
MA0141.1	MA0141.1	0.218
MA0142.1	MA0142.1	0.136
MA0143.1	MA0143.1	0.184
MA0144.1	MA0144.1	0.129
MA0145.1	MA0145.1	0.243
MA0146.1	MA0146.1	0.0873
MA0147.1	MA0147.1	0.0487
MA0148.1	MA0148.1	0.103
MA0149.1	MA0149.1	0.315
MA0150.1	MA0150.1	8.40448e-6
MA0152.1	MA0152.1	0.334
MA0153.1	MA0153.1	0.00828
MA0154.1	MA0154.1	0.0294
MA0155.1	MA0155.1	0.895
MA0156.1	MA0156.1	4.12708e-25
MA0157.1	MA0157.1	0.0986
MA0159.1	MA0159.1	0.0145
MA0160.1	MA0160.1	0.212
MA0162.1	MA0162.1	0.571
MA0163.1	MA0163.1	0.0246
MA0164.1	MA0164.1	0.648
MA0258.1	MA0258.1	0.00517
MA0259.1	MA0259.1	0.362

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: CNhs12541

Novel motif	Logo	P-value
1	1	0.172
10	10	0.0492
100	100	0.756
101	101	0.766
102	102	0.488
103	103	0.317
104	104	0.635
105	105	0.427
106	106	0.0339
107	107	0.623
108	108	0.855
109	109	0.0686
11	11	0.0897
110	110	0.251
111	111	0.527
112	112	0.0405
113	113	0.72
114	114	0.0611
115	115	0.797
116	116	0.954
117	117	7.35746e-4
118	118	0.461
119	119	0.328
12	12	0.499
120	120	0.0431
121	121	0.393
122	122	0.412
123	123	0.441
124	124	0.7
125	125	0.157
126	126	0.39
127	127	0.306
128	128	0.0848
129	129	0.35
13	13	0.113
130	130	0.623
131	131	0.935
132	132	0.827
133	133	0.0357
134	134	0.833
135	135	0.506
136	136	0.561
137	137	0.041
138	138	0.327
139	139	0.0519
14	14	0.295
140	140	0.657
141	141	0.571
142	142	0.00475
143	143	0.00204
144	144	0.791
145	145	0.123
146	146	0.882
147	147	0.748
148	148	0.158
149	149	0.917
15	15	0.0463
150	150	0.339
151	151	0.176
152	152	0.258
153	153	0.175
154	154	0.947
155	155	0.551
156	156	0.863
157	157	0.791
158	158	0.022
159	159	0.574
160	160	0.939
161	161	0.132
162	162	0.609
163	163	0.26
164	164	0.04
165	165	0.16
166	166	0.717
167	167	0.808
168	168	0.298
169	169	0.00918
17	17	0.172
18	18	0.131
19	19	0.41
2	2	0.403
20	20	0.0551
21	21	0.505
22	22	0.359
23	23	0.107
24	24	0.239
25	25	0.266
26	26	0.125
27	27	0.746
28	28	0.0973
29	29	0.026
3	3	0.0665
30	30	0.448
31	31	0.711
32	32	0.915
33	33	0.261
34	34	0.811
35	35	0.463
36	36	0.1
37	37	0.0863
38	38	0.294
39	39	0.823
4	4	0.639
40	40	0.176
41	41	0.0127
42	42	0.265
43	43	0.109
44	44	0.793
45	45	0.811
46	46	0.311
47	47	0.336
48	48	0.241
49	49	0.0764
5	5	0.131
50	50	0.675
51	51	0.736
52	52	0.927
53	53	0.805
54	54	0.633
55	55	0.629
56	56	0.26
57	57	0.709
58	58	0.178
59	59	0.468
6	6	0.781
60	60	0.225
61	61	0.269
62	62	0.0788
63	63	0.645
64	64	0.584
65	65	0.245
66	66	0.741
67	67	0.206
68	68	0.772
69	69	0.393
7	7	0.139
70	70	0.0492
71	71	0.053
72	72	0.27
73	73	0.042
74	74	0.0595
75	75	0.00481
76	76	0.213
77	77	0.935
78	78	0.11
79	79	0.874
8	8	0.466
80	80	0.0523
81	81	0.503
82	82	0.414
83	83	0.228
84	84	0.765
85	85	0.116
86	86	0.0657
87	87	0.278
88	88	0.533
89	89	0.722
9	9	0.508
90	90	0.154
91	91	0.466
92	92	0.393
93	93	0.235
94	94	0.0671
95	95	0.0217
96	96	0.777
97	97	0.94
98	98	0.331
99	99	0.128

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: CNhs12541

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000002 in vivo cell sample
FF:0000103 mouse 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)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (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
NA

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00004836
+|accession_numbers=CAGE;DRX008776;DRR009648;DRZ001073;DRZ002458;DRZ012423;DRZ013808
 |ancestors_in_anatomy_facet=
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001
 |comment=Previously. MDSC (MC1-positiveGr1-positive) control, rep2 (0127 PBS). TODO: full classification
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr6:86619104..86619119,-!p1@Mxd1!2.34!1657.07!Mxd1;;chr14:55330976..55330990,-!p1@Cebpe!2.24!172.81!Cebpe;;chr2:90936901..90936945,+!p1@Sfpi1!2.18!752.03!Sfpi1;;chr12:86814833..86814846,+!p1@Fos!2.17!3202.80!Fos;;chr15:103085802..103085817,-!p4@Nfe2!2.16!178.96!Nfe2;;chr15:103085660..103085681,-!p1@Nfe2!2.08!173.49!Nfe2;;chr11:16908650..16908690,-!p1@Plek!2.06!653.67!Plek;;chr11:11586218..11586285,+!p1@Ikzf1!2.05!338.11!Ikzf1;;chr2:90936947..90936977,+!p2@Sfpi1!2.05!214.48!Sfpi1;;chr5:92391466..92391471,+!p2@Thap6!2.01!144.81!Thap6;;chr13:59923965..59924003,-!p2@Zcchc6!1.88!89.48!Zcchc6;;chr2:90936978..90937023,+!p3@Sfpi1!1.87!134.56!Sfpi1;;chr14:55330957..55330971,-!p2@Cebpe!1.85!70.35!Cebpe;;chr2:90922554..90922575,+!p4@Sfpi1!1.84!119.53!Sfpi1;;chr4:63064364..63064384,-!p1@Akna!1.80!174.86!Akna;;chr8:87502608..87502623,-!p1@Junb!1.74!834.68!Junb;;chr4:124805061..124805087,-!p1@Zc3h12a!1.69!143.44!Zc3h12a;;chr19:5447692..5447711,+!p2@Fosl1!1.69!47.81!Fosl1;;chr15:103085864..103085876,-!p5@Nfe2!1.69!47.81!Nfe2;;chr11:100683839..100683890,-!p2@Stat5b!1.68!107.24!Stat5b;;chr1:52065508..52065522,+!p2@Stat4!1.64!49.86!Stat4;;chr6:86619130..86619158,-!p2@Mxd1!1.61!534.82!Mxd1;;chr1:52065454..52065495,+!p1@Stat4!1.61!64.89!Stat4;;chr16:92826249..92826325,-!p1@Runx1!1.55!81.97!Runx1;;chr16:15887371..15887385,+!p1@Cebpd!1.52!1036.86!Cebpd;;chr8:87225329..87225396,+!p1@Lyl1!1.52!116.12!Lyl1;;chr12:78063057..78063070,-!p3@Max!1.52!66.26!Max;;chr1:87546583..87546595,+!p1@Sp100!1.52!45.08!Sp100;;chr12:78063032..78063043,-!p4@Max!1.50!41.67!Max;;chr2:90922519..90922544,+!p6@Sfpi1!1.50!34.15!Sfpi1;;chr11:120491440..120491474,-!p3@Mafg!1.47!41.67!Mafg;;chr15:103085690..103085710,-!p3@Nfe2!1.46!30.05!Nfe2;;chr16:55822241..55822258,-!p1@Nfkbiz!1.45!799.16!Nfkbiz;;chr19:37509324..37509337,+!p1@Hhex!1.44!179.64!Hhex;;chr12:78063146..78063159,-!p2@Max!1.43!65.57!Max;;chr17:33766353..33766393,+!p2@Zfp414!1.39!63.52!Zfp414;;chr2:90936867..90936874,+!p7@Sfpi1!1.37!22.54!Sfpi1;;chr5:32438831..32438878,+!p1@Fosl2!1.36!219.26!Fosl2;;chr5:32438894..32438908,+!p2@Fosl2!1.35!44.40!Fosl2;;chr11:120491830..120491851,-!p10@Mafg!1.33!20.49!Mafg;;chr1:186556410..186556424,-!p1@Hlx!1.30!58.06!Hlx;;chr18:35020615..35020641,+!p2@Egr1!1.30!22.54!Egr1;;chr9:32348943..32349001,-!p1@Fli1!1.27!140.71!Fli1;;chr8:74842952..74842970,+!p1@Klf2!1.25!1099.70!Klf2;;chrX:137077653..137077669,-!p3@Tsc22d3!1.25!73.77!Tsc22d3;;chr15:25914114..25914128,+!p2@Zfp622!1.25!66.94!Zfp622;;chr7:19895354..19895369,-!p1@Fosb!1.25!23.22!Fosb;;chr2:90936886..90936898,+!p5@Sfpi1!1.25!19.81!Sfpi1;;chrX:137077716..137077734,-!p1@Tsc22d3!1.24!114.75!Tsc22d3;;chr8:125778192..125778217,+!p2@Zfp276!1.24!45.76!Zfp276;;chr12:86940338..86940357,+!p1@Jdp2!1.21!147.54!Jdp2;;chr13:5860872..5860883,+!p3@Klf6!1.21!30.05!Klf6;;chr19:37511197..37511206,+!p3@Hhex!1.20!15.03!Hhex;;chr13:5860776..5860796,+!p1@Klf6!1.19!339.47!Klf6;;chr10:79389784..79389833,+!p1@Arid3a!1.19!75.82!Arid3a;;chr12:87027598..87027652,+!p1@Batf!1.19!33.47!Batf;;chr4:63064395..63064410,-!p2@Akna!1.18!24.59!Akna;;chr2:167514456..167514473,+!p1@Cebpb!1.17!605.86!Cebpb;;chr14:98568532..98568561,-!p4@Dach1!1.17!21.17!Dach1;;chr15:103085821..103085828,-!p6@Nfe2!1.17!13.66!Nfe2;;chr1:87497610..87497645,+!p1@Gm2427,p1@Sp140!1.17!13.66!Sp140;;chr2:173044380..173044432,-!p1@Zbp1!1.16!32.10!Zbp1;;chr5:140267510..140267555,+!p2@Mafk!1.15!30.74!Mafk;;chr2:120996813..120996829,-!p2@Zscan29!1.15!21.86!Zscan29;;chr16:23988711..23988727,-!p1@Bcl6!1.14!150.27!Bcl6;;chr19:53384910..53384937,+!p3@Mxi1!1.14!36.20!Mxi1;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!1.14!20.49!Ncoa4;;chr10:80870405..80870428,-!p4@Nfic!1.12!32.79!Nfic;;chrX:137077608..137077619,-!p6@Tsc22d3!1.12!16.39!Tsc22d3;;chr14:55331234..55331245,-!p4@Cebpe!1.12!12.29!Cebpe;;chr7:87170879..87170914,+!p2@Zfp710!1.11!28.00!Zfp710;;chr12:56593574..56593592,-!p1@Nfkbia!1.08!568.29!Nfkbia;;chr18:3337249..3337274,-!p17@Crem!1.08!10.93!Crem;;chr7:148452314..148452329,-!p1@Irf7!1.07!75.14!Irf7;;chr1:36364590..36364608,+!p1@Arid5a!1.06!106.56!Arid5a;;chr1:92949999..92950097,+!p1@Lrrfip1!1.05!274.58!Lrrfip1;;chr5:31262571..31262582,-!p4@Preb!1.05!12.29!Preb;;chr1:52065530..52065548,+!p3@Stat4!1.05!10.25!Stat4;;chr15:103085858..103085863,-!p11@Nfe2!1.05!10.25!Nfe2;;chr14:55331167..55331204,-!p3@Cebpe!1.05!10.25!Cebpe;;chr1:52176315..52176343,+!p1@Stat1!1.04!145.49!Stat1;;chr7:31206743..31206761,+!p1@Nfkbid!1.04!13.66!Nfkbid;;chr19:26681226..26681299,+!p7@Smarca2!1.03!23.22!Smarca2;;chr11:11585678..11585745,+!p5@Ikzf1!1.03!14.34!Ikzf1;;chr16:95680889..95680991,-!p1@Erg!1.02!79.23!Erg;;chr11:53583544..53583559,+!p1@Irf1!1.01!157.78!Irf1;;chr4:135728581..135728668,+!p1@E2f2!1.01!45.08!E2f2;;chr5:138187195..138187255,+!p1@Tsc22d4!1.00!392.75!Tsc22d4;;chrX:45807329..45807370,-!p1@Elf4!1.00!64.89!Elf4;;chr5:22940353..22940372,+!p3@Mll5!0.99!17.08!Mll5;;chr17:51972530..51972571,-!p7@Satb1!0.99!8.88!Satb1;;chr19:53384985..53385042,+!p1@Mxi1!0.98!268.44!Mxi1;;chr18:3337339..3337397,-!p5@Crem!0.96!16.39!Crem;;chrX:137077682..137077692,-!p5@Tsc22d3!0.96!12.98!Tsc22d3;;chr8:108582687..108582734,+!p4@Nfatc3!0.96!8.20!Nfatc3;;chr4:134708909..134708939,+!p3@Runx3!0.96!8.20!Runx3;;chr11:98822093..98822104,+!p16@Rara!0.96!8.20!Rara;;chr5:108155037..108155060,-!p2@Gfi1!0.96!8.20!Gfi1;;chr5:92391970..92391984,+!p5@Thap6!0.96!8.20!Thap6;;chr11:23670953..23671028,-!p1@Rel!0.94!45.76!Rel;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.94!10.93!Carhsp1;;chr11:98822047..98822072,+!p9@Rara!0.93!7.51!Rara;;chr18:35020854..35020869,+!p1@Egr1!0.92!294.39!Egr1;;chr10:127080031..127080090,+!p1@Stat6!0.92!163.93!Stat6;;chr2:169956656..169956684,-!p1@Zfp217!0.92!51.91!Zfp217;;chr8:72520139..72520157,-!p6@Gatad2a!0.91!29.37!Gatad2a;;chr13:53076382..53076393,-!p2@Nfil3!0.91!11.61!Nfil3;;chr7:19895384..19895399,-!p2@Fosb!0.91!10.25!Fosb;;chr17:45692642..45692663,+!p1@Nfkbie!0.90!23.22!Nfkbie;;chr3:89197216..89197258,-!p3@Zbtb7b!0.90!15.03!Zbtb7b;;chr16:3872286..3872315,-!p3@Zfp597!0.90!13.66!Zfp597;;chr14:79915425..79915501,+!p1@Elf1!0.89!63.52!Elf1;;chr8:87225670..87225697,+!p2@Lyl1!0.89!20.49!Lyl1;;chr12:113917014..113917034,+!p1@Zbtb42!0.89!12.29!Zbtb42;;chr11:62272200..62272221,-!p11@Ncor1!0.89!6.83!Ncor1;;chr3:89191054..89191070,-!p5@Zbtb7b!0.89!6.83!Zbtb7b;;chr15:103083199..103083215,-!p8@Nfe2!0.89!6.83!Nfe2;;chr18:80904854..80904919,-!p2@Nfatc1!0.88!82.65!Nfatc1;;chr18:83080255..83080277,+!p4@Zfp516!0.88!17.08!Zfp516;;chr11:100800671..100800770,-!p1@Stat3!0.87!219.94!Stat3;;chr7:20408047..20408125,-!p1@Bcl3!0.87!77.87!Bcl3;;chr5:92391948..92391968,+!p3@Thap6!0.87!10.25!Thap6;;chr10:41995430..41995458,-!p3@Foxo3!0.86!17.08!Foxo3;;chrX:137077636..137077647,-!p7@Tsc22d3!0.86!7.51!Tsc22d3;;chr17:88840082..88840127,+!p1@Foxn2!0.85!45.76!Foxn2;;chr7:31208285..31208312,+!p3@Nfkbid!0.85!6.83!Nfkbid;;chr19:46378880..46378896,+!p8@Nfkb2!0.85!6.15!Nfkb2;;chr16:92826232..92826245,-!p4@Runx1!0.85!6.15!Runx1;;chr11:98822081..98822092,+!p14@Rara!0.85!6.15!Rara;;chr6:99385340..99385362,-!p11@Foxp1!0.85!6.15!Foxp1;;chr15:101097270..101097290,+!p1@Nr4a1!0.84!64.89!Nr4a1;;chr4:124805092..124805135,-!p2@Zc3h12a!0.84!26.64!Zc3h12a;;chr16:55973950..55973977,+!p4@Rpl24,p4@Zbtb11!0.83!28.69!Zbtb11;;chr3:135354349..135354371,-!p6@Nfkb1!0.83!12.29!Nfkb1;;chr12:85559762..85559778,-!p5@C130039O16Rik!0.83!9.56!C130039O16Rik;;chr4:94718861..94718872,-!p2@Jun!0.82!45.76!Jun;;chr7:49761065..49761106,-!p1@ENSMUST00000174407,p1@uc009gmb.1!0.82!32.79!Zfp141;;chr7:71083729..71083742,-!p4@Klf13!0.82!10.25!Klf13;;chr11:98821858..98821907,+!p6@Rara!0.82!9.56!Rara;;chr2:72817045..72817123,-!p1@Sp3!0.81!192.62!Sp3;;chr13:59924433..59924504,-!p1@Zcchc6!0.81!131.83!Zcchc6;;chr14:98568502..98568516,-!p7@Dach1!0.81!5.46!Dach1;;chr14:56223010..56223067,+!p1@Irf9!0.80!45.08!Irf9;;chr13:67461490..67461531,-!p1@Zfp595,p1@Zfp953!0.80!23.22!Zfp953;;chr18:83080305..83080335,+!p2@Zfp516!0.80!17.76!Zfp516;;chr2:126501847..126501876,-!p5@Gabpb1!0.80!6.15!Gabpb1;;chr12:85559785..85559840,-!p1@C130039O16Rik!0.79!75.14!C130039O16Rik;;chr18:55152206..55152251,-!p1@Zfp608!0.79!53.96!Zfp608;;chr17:88840054..88840081,+!p2@Foxn2!0.79!47.13!Foxn2;;chr17:47873985..47874056,+!p1@Tfeb!0.79!45.76!Tfeb;;chr5:145962698..145962742,-!p1@Zkscan14!0.79!25.96!Zkscan14;;chrX:48558950..48559016,-!p1@Mbnl3!0.79!17.76!Mbnl3;;chr5:138187181..138187192,+!p5@Tsc22d4!0.79!14.34!Tsc22d4;;chr9:32503590..32503680,+!p1@Ets1!0.78!201.50!Ets1;;chr1:170362273..170362317,-!p1@Pbx1!0.78!156.42!Pbx1;;chr14:99697871..99697934,+!p1@Klf5!0.78!109.97!Klf5;;chr12:72116953..72117050,+!p1@Arid4a!0.78!66.26!Arid4a;;chr11:98821749..98821799,+!p2@Rara!0.78!34.15!Rara;;chr18:83080278..83080293,+!p5@Zfp516!0.78!12.29!Zfp516;;chr11:70501599..70501634,-!p2@Camta2,p2@LOC100048818!0.78!10.93!Camta2;;chr2:173044357..173044377,-!p2@Zbp1!0.78!7.51!Zbp1;;chr4:135728181..135728203,+!p2@E2f2!0.78!6.83!E2f2;;chr16:95924055..95924077,+!p1@Ets2!0.77!291.66!Ets2;;chr18:39650303..39650371,-!p1@Nr3c1!0.77!61.47!Nr3c1;;chr8:72663098..72663160,-!p2@LOC100048268,p2@Rfxank!0.77!26.64!Rfxank;;chr11:100800641..100800669,-!p3@Stat3!0.77!8.88!Stat3;;chr17:44873393..44873418,-!p4@Runx2!0.77!8.88!Runx2;;chr17:51971932..51971958,-!p2@Satb1!0.77!6.83!Satb1;;chr8:47825107..47825145,+!p1@Irf2!0.76!208.33!Irf2;;chr16:23988686..23988693,-!p2@Bcl6!0.76!10.25!Bcl6;;chr17:45692676..45692695,+!p2@Nfkbie!0.76!10.25!Nfkbie;;chr15:25914138..25914146,+!p4@Zfp622!0.76!8.20!Zfp622;;chr8:87425854..87425891,+!p1@Klf1!0.76!4.78!Klf1;;chr2:126501799..126501832,-!p4@Gabpb1!0.76!4.78!Gabpb1;;chr13:53076396..53076452,-!p1@Nfil3!0.75!90.85!Nfil3;;chr2:91490176..91490193,-!p2@Zfp408!0.75!6.15!Zfp408;;chr18:70727922..70728052,+!p1@Mbd2!0.74!178.96!Mbd2;;chr5:65194752..65194769,+!p1@Klf3!0.74!168.71!Klf3;;chr10:127080091..127080100,+!p4@Stat6!0.74!6.83!Stat6;;chr1:64167972..64168026,-!p1@Klf7!0.73!116.80!Klf7;;chr11:106134241..106134320,-!p2@Smarcd2!0.72!54.64!Smarcd2;;chr13:5860749..5860772,+!p2@Klf6!0.72!46.45!Klf6;;chr9:576845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1.37!Arid5a;;chr1:136456791..136456810,+!p1@Kdm5b!0.31!65.57!Kdm5b;;chr6:120314112..120314181,+!p1@Kdm5a!0.31!35.52!Kdm5a;;chr1:162836503..162836591,+!p1@Rc3h1!0.31!32.10!Rc3h1;;chr15:102034070..102034124,+!p1@Zfp740!0.31!30.74!Zfp740;;chr11:4604645..4604705,+!p1@Zmat5!0.31!23.91!Zmat5;;chr17:28314075..28314159,+!p1@Zfp523!0.31!21.86!Zfp523;;chr8:27268658..27268724,+!p1@Thap1!0.31!21.86!Thap1;;chr18:39649430..39649522,-!p2@Nr3c1!0.31!17.76!Nr3c1;;chr2:91489908..91489941,-!p1@Zfp408!0.31!14.34!Zfp408;;chr10:5959061..5959104,+!p2@Zbtb2!0.31!6.83!Zbtb2;;chr3:89197057..89197114,-!p1@Zbtb7b!0.31!5.46!Zbtb7b;;chr15:100058660..100058711,+!p1@Gm1862,p2@Atf1!0.31!5.46!Atf1;;chr13:30076280..30076334,-!p3@E2f3!0.31!4.78!E2f3;;chr1:170361826..170361844,-!p9@Pbx1!0.31!3.42!Pbx1;;chr1:92950099..92950109,+!p3@Lrrfip1!0.31!1.37!Lrrfip1;;chr4:48057987..48057996,+!p7@Nr4a3!0.31!1.37!Nr4a3;;chr11:5420973..5420992,+!p1@Xbp1!0.30!192.62!Xbp1;;chr8:72498266..72498306,-!p3@Gatad2a!0.30!11.61!Gatad2a;;chr17:21587325..21587361,+!p1@Zfp51!0.30!10.25!Zfp51;;chr13:67585161..67585205,-!p1@Zfp874b!0.30!8.88!Zfp874b;;chr2:37278526..37278575,-!p2@Rc3h2!0.30!6.83!Rc3h2;;chr11:102178937..102178956,-!p5@Ubtf!0.30!4.78!Ubtf;;chr16:55973899..55973913,+!p7@Rpl24,p7@Zbtb11!0.30!3.42!Zbtb11;;chr6:134780163..134780197,+!p2@Crebl2!0.30!3.42!Crebl2;;chr5:65194709..65194716,+!p10@Klf3!0.30!2.73!Klf3;;chr2:168032516..168032525,-!p5@Adnp!0.30!2.05!Adnp;;chr12:86939657..86939685,+!p6@Jdp2!0.30!1.37!Jdp2;;chr16:4213951..4213995,-!p@chr16:4213951..4213995,-!0.29!49.18!Crebbp;;chr11:98798983..98799049,+!p1@Rara!0.29!44.40!Rara;;chr16:3744089..3744145,+!p1@Zfp263!0.29!36.20!Zfp263;;chr2:37278415..37278478,-!p1@Rc3h2!0.29!15.03!Rc3h2;;chr5:145992626..145992652,+!p2@Zfp655!0.29!11.61!Zfp655;;chr6:124959683..124959735,+!p2@Zfp384!0.29!9.56!Zfp384;;chr6:39068210..39068251,-!p1@Parp12!0.29!7.51!Parp12;;chr17:21520689..21520730,+!p1@Zfp677!0.29!5.46!Zfp677;;chr4:151401710..151401733,-!p2@Zbtb48!0.29!4.78!Zbtb48;;chr9:21420610..21420621,+!p5@Smarca4!0.29!4.78!Smarca4;;chr16:3744162..3744180,+!p2@Zfp263!0.29!4.10!Zfp263;;chr1:64167550..64167618,-!p4@Klf7!0.29!4.10!Klf7;;chr5:104183477..104183548,+!p6@Aff1!0.29!2.73!Aff1;;chr16:95923651..95923701,+!p3@Ets2!0.29!2.05!Ets2;;chr2:28477452..28477483,-!p1@Gfi1b!0.29!1.37!Gfi1b;;chr1:13364477..13364492,-!p6@Ncoa2!0.29!1.37!Ncoa2;;chr18:73863393..73863460,-!p1@Smad4!0.28!154.37!Smad4;;chr7:29551488..29551529,-!p1@Nfkbib!0.28!55.33!Nfkbib;;chr3:30993974..30994045,+!p1@Skil!0.28!47.81!Skil;;chr1:13364108..13364150,-!p1@Ncoa2!0.28!37.57!Ncoa2;;chr3:19957802..19957857,+!p1@Hltf!0.28!30.05!Hltf;;chr5:123844791..123844835,+!p1@Mlxip!0.28!29.37!Mlxip;;chrX:98728131..98728214,+!p1@Taf1!0.28!24.59!Taf1;;chr18:84758883..84758919,-!p1@Zfp407!0.28!18.44!Zfp407;;chr6:124959279..124959335,+!p1@Zfp384!0.28!16.39!Zfp384;;chr1:138521528..138521572,+!p1@Zfp281!0.28!9.56!Zfp281;;chr7:148513599..148513636,-!p3@Deaf1!0.28!6.15!Deaf1;;chr2:166888058..166888105,-!p2@Znfx1!0.28!4.78!Znfx1;;chr10:85379814..85379844,-!p2@Prdm4!0.28!3.42!Prdm4;;chr8:87225702..87225726,+!p3@Lyl1!0.28!2.73!Lyl1;;chr7:74517748..74517757,-!p3@Mef2a!0.28!2.73!Mef2a;;chr4:133310214..133310231,-!p11@Arid1a!0.28!2.05!Arid1a;;chr15:50721211..50721234,-!p6@Trps1!0.28!2.05!Trps1;;chr5:65203599..65203617,+!p8@Klf3!0.28!2.05!Klf3;;chr5:125538905..125538910,-!p4@Ncor2!0.28!1.37!Ncor2;;chr11:11585912..11585950,+!p6@Ikzf1!0.28!1.37!Ikzf1;;chr4:102787067..102787080,+!p10@Mier1!0.28!1.37!Mier1;;chr5:104182694..104182724,+!p8@Aff1!0.28!1.37!Aff1;;chr10:116661536..116661555,-!p1@Yeats4!0.27!96.31!Yeats4;;chr18:5591866..5591900,+!p1@Zeb1!0.27!40.98!Zeb1;;chr19:41557122..41557178,+!p1@Lcor!0.27!34.84!Lcor;;chr15:38230448..38230470,-!p1@Klf10!0.27!34.84!Klf10;;chr5:53981912..53981942,+!p1@Rbpj!0.27!32.10!Rbpj;;chrX:91368426..91368498,-!p1@Zfx!0.27!30.05!Zfx;;chr17:33766023..33766059,+!p1@Zfp414!0.27!25.27!Zfp414;;chr1:75188717..75188804,+!p1@ENSMUST00000125384,p1@ENSMUST00000127625,p1@ENSMUST00000131788,p1@ENSMUST00000134233,p1@ENSMUST00000134378,p1@ENSMUST00000145459,p1@ENSMUST00000151887,p1@ENSMUST00000152233!0.27!22.54!Ankzf1;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.27!17.08!Camta2;;chr17:25152711..25152736,-!p1@Cramp1l!0.27!16.39!Cramp1l;;chr10:126726055..126726091,-!p2@Mbd6!0.27!12.98!Mbd6;;chr3:95021853..95021911,-!p1@Gabpb2!0.27!12.29!Gabpb2;;chr11:100721761..100721851,+!p1@Stat5a!0.27!11.61!Stat5a;;chr10:20032330..20032345,+!p3@Bclaf1!0.27!7.51!Bclaf1;;chr12:119539902..119539931,-!p2@Sp4!0.27!5.46!Sp4;;chr1:133904217..133904250,+!p5@Elk4!0.27!4.78!Elk4;;chr7:20214704..20214800,-!p1@Relb!0.27!4.78!Relb;;chr11:53164533..53164548,+!p4@Aff4!0.27!4.10!Aff4;;chr11:120494669..120494688,-!p2@Mafg!0.27!3.42!Mafg;;chr15:88582079..88582091,+!p1@Gm15583,p1@Zbed4!0.27!2.05!Zbed4;;chr17:69733108..69733129,+!p3@Zfp161!0.27!2.05!Zfp161;;chr4:102792009..102792021,+!p6@Mier1!0.27!2.05!Mier1;;chr15:50721239..50721260,-!p9@Trps1!0.27!2.05!Trps1;;chr13:31650026..31650045,+!p2@Foxq1!0.27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@@ Line 39: / Line 43: @@
 |is_a=EFO:0002091;;FF:0000002;;FF:0000103
 |is_obsolete=
+|library_id=CNhs12541
+|library_id_phase_based=2:CNhs12541
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12162
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12162
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/MC1%252bGr1%252b%2520myeloid-derived%2520suppressor%2520cells%2520control%252c%2520donor2%2520%25280127%2520PBS%2529.CNhs12541.12162-128H2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/MC1%252bGr1%252b%2520myeloid-derived%2520suppressor%2520cells%2520control%252c%2520donor2%2520%25280127%2520PBS%2529.CNhs12541.12162-128H2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/MC1%252bGr1%252b%2520myeloid-derived%2520suppressor%2520cells%2520control%252c%2520donor2%2520%25280127%2520PBS%2529.CNhs12541.12162-128H2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/MC1%252bGr1%252b%2520myeloid-derived%2520suppressor%2520cells%2520control%252c%2520donor2%2520%25280127%2520PBS%2529.CNhs12541.12162-128H2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/MC1%252bGr1%252b%2520myeloid-derived%2520suppressor%2520cells%2520control%252c%2520donor2%2520%25280127%2520PBS%2529.CNhs12541.12162-128H2.mm9.nobarcode.rdna.fa.gz
 |name=MC1+Gr1+ myeloid-derived suppressor cells control, donor2 (0127 PBS)
 |namespace=FANTOM5
@@ Line 44: / Line 59: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12541,LSID920,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.135340578492333,0,0,0,0,-0.0843392403965415,0,0,0,0,0.113047926555807,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0,0.203604095621833,0,0,0,0,0,0.145813631227802,-0.125454696333107,0.337638420816111,-0.984211366477826,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,1.05098580917212,0,0,-0.0176486388949804,0,0,0,-0.0285678456024198,-0.0845548042277737,-0.158091042771083,-0.140687683267293,0,0,-0.119676394854555,0,0,0,-0.0783284673749465,0.382918179983341,-0.369819027628957,-0.0788315948399074,0,0,0,0,0,0,-0.0901223798974778,-0.236961238279846,-0.082787283189959,0,0,0,0,0
 |rna_box=128
 |rna_catalog_number=
@@ Line 59: / Line 75: @@
 |rna_weight_ug=0.597
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 79: / Line 96: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12162-128H2;search_select_hide=table117:12162-128H2
 }}

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FF:12162-128H2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:32, 4 June 2020

CNhs12541

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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