FF:11845-124H9: Difference between revisions

Latest revision as of 18:23, 4 June 2020

Name:	GP2+ M cell, pool1
Species:	Mouse (Mus musculus)
Library ID:	CNhs13228
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	Balb/c
tissue	ileum
dev stage	adult
sex	male
age	NA
cell type	M cell
cell line	NA
company	NA
collaboration	Shinji Fukuda (RCAI)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	M cell_a
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		SAMD00004773

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13228		CAGE		DRX008765		DRR009637

Accession ID Mm9

Library id		BAM		CTSS
CNhs13228		DRZ001062		DRZ002447

Accession ID Mm10

Library id		BAM		CTSS
CNhs13228		DRZ012412		DRZ013797

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

CNhs13228

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0749
1002	-0.116
1003	-0.175
1004	0
1005	1.179
1006	-0.264
1007	-0.0374
1008	1.218
1009	-0.177
101	-0.344
1010	0
1011	-0.337
1012	0
1013	0.348
1014	-0.0874
1015	-0.428
1016	-0.594
1017	0
1018	0.518
1019	0
102	0
1020	0
1021	0
1022	-0.0704
1023	0
1024	-0.307
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.176
103	-0.0887
1030	0
1031	-0.911
1032	1.065
1033	0
1034	0
1035	0
1036	-0.0428
1037	0
1038	-0.0166
1039	0.00176
104	0
1040	-0.728
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: CNhs13228

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0107
MA0003.1	MA0003.1	0.387
MA0004.1	MA0004.1	0.845
MA0006.1	MA0006.1	0.0771
MA0007.1	MA0007.1	0.284
MA0009.1	MA0009.1	0.0663
MA0014.1	MA0014.1	0.0541
MA0017.1	MA0017.1	4.20677e-29
MA0018.2	MA0018.2	0.207
MA0019.1	MA0019.1	0.0535
MA0024.1	MA0024.1	4.97107e-4
MA0025.1	MA0025.1	0.933
MA0027.1	MA0027.1	0.895
MA0028.1	MA0028.1	0.0769
MA0029.1	MA0029.1	0.901
MA0030.1	MA0030.1	0.635
MA0031.1	MA0031.1	0.195
MA0035.2	MA0035.2	6.97773e-6
MA0038.1	MA0038.1	0.517
MA0039.2	MA0039.2	5.01859e-6
MA0040.1	MA0040.1	0.0777
MA0041.1	MA0041.1	0.278
MA0042.1	MA0042.1	0.286
MA0043.1	MA0043.1	0.665
MA0046.1	MA0046.1	1.37008e-49
MA0047.2	MA0047.2	0.0231
MA0048.1	MA0048.1	0.358
MA0050.1	MA0050.1	0.00136
MA0051.1	MA0051.1	4.56306e-5
MA0052.1	MA0052.1	0.594
MA0055.1	MA0055.1	0.256
MA0057.1	MA0057.1	0.0752
MA0058.1	MA0058.1	0.948
MA0059.1	MA0059.1	0.736
MA0060.1	MA0060.1	0.222
MA0061.1	MA0061.1	0.00521
MA0062.2	MA0062.2	3.44942e-4
MA0065.2	MA0065.2	1.94103e-16
MA0066.1	MA0066.1	0.126
MA0067.1	MA0067.1	0.714
MA0068.1	MA0068.1	0.0766
MA0069.1	MA0069.1	0.741
MA0070.1	MA0070.1	0.289
MA0071.1	MA0071.1	0.042
MA0072.1	MA0072.1	0.683
MA0073.1	MA0073.1	0.829
MA0074.1	MA0074.1	0.167
MA0076.1	MA0076.1	0.204
MA0077.1	MA0077.1	0.448
MA0078.1	MA0078.1	0.892
MA0079.2	MA0079.2	0.482
MA0080.2	MA0080.2	4.3483e-5
MA0081.1	MA0081.1	0.805
MA0083.1	MA0083.1	0.396
MA0084.1	MA0084.1	0.138
MA0087.1	MA0087.1	0.295
MA0088.1	MA0088.1	0.451
MA0090.1	MA0090.1	0.462
MA0091.1	MA0091.1	0.253
MA0092.1	MA0092.1	0.404
MA0093.1	MA0093.1	0.908
MA0099.2	MA0099.2	1.30744e-11
MA0100.1	MA0100.1	0.886
MA0101.1	MA0101.1	6.14946e-5
MA0102.2	MA0102.2	0.642
MA0103.1	MA0103.1	1.47984e-6
MA0104.2	MA0104.2	0.118
MA0105.1	MA0105.1	0.157
MA0106.1	MA0106.1	0.287
MA0107.1	MA0107.1	7.56356e-5
MA0108.2	MA0108.2	6.25441e-4
MA0111.1	MA0111.1	0.424
MA0112.2	MA0112.2	0.00268
MA0113.1	MA0113.1	0.936
MA0114.1	MA0114.1	2.75589e-34
MA0115.1	MA0115.1	1.55177e-16
MA0116.1	MA0116.1	0.388
MA0117.1	MA0117.1	0.243
MA0119.1	MA0119.1	0.0821
MA0122.1	MA0122.1	0.816
MA0124.1	MA0124.1	0.468
MA0125.1	MA0125.1	0.92
MA0131.1	MA0131.1	0.556
MA0135.1	MA0135.1	0.392
MA0136.1	MA0136.1	6.21259e-8
MA0137.2	MA0137.2	0.017
MA0138.2	MA0138.2	0.868
MA0139.1	MA0139.1	0.201
MA0140.1	MA0140.1	0.147
MA0141.1	MA0141.1	8.01488e-8
MA0142.1	MA0142.1	0.071
MA0143.1	MA0143.1	0.233
MA0144.1	MA0144.1	0.00173
MA0145.1	MA0145.1	0.00795
MA0146.1	MA0146.1	0.14
MA0147.1	MA0147.1	0.156
MA0148.1	MA0148.1	0.0239
MA0149.1	MA0149.1	0.0187
MA0150.1	MA0150.1	0.00498
MA0152.1	MA0152.1	0.133
MA0153.1	MA0153.1	9.61844e-42
MA0154.1	MA0154.1	0.0444
MA0155.1	MA0155.1	0.812
MA0156.1	MA0156.1	3.03693e-4
MA0157.1	MA0157.1	0.836
MA0159.1	MA0159.1	1.56802e-4
MA0160.1	MA0160.1	6.87295e-6
MA0162.1	MA0162.1	0.68
MA0163.1	MA0163.1	0.589
MA0164.1	MA0164.1	0.995
MA0258.1	MA0258.1	0.0614
MA0259.1	MA0259.1	0.557

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: CNhs13228

Novel motif	Logo	P-value
1	1	0.178
10	10	0.304
100	100	0.867
101	101	0.958
102	102	0.799
103	103	0.52
104	104	0.88
105	105	0.0859
106	106	0.0128
107	107	0.126
108	108	0.597
109	109	0.0469
11	11	0.13
110	110	0.393
111	111	0.216
112	112	0.0177
113	113	0.22
114	114	0.12
115	115	0.488
116	116	0.095
117	117	0.0564
118	118	0.541
119	119	0.141
12	12	0.74
120	120	0.64
121	121	0.378
122	122	0.72
123	123	0.134
124	124	0.242
125	125	0.716
126	126	0.0476
127	127	0.167
128	128	0.176
129	129	0.15
13	13	7.56184e-5
130	130	0.938
131	131	0.795
132	132	0.6
133	133	0.473
134	134	0.752
135	135	0.152
136	136	0.0387
137	137	0.977
138	138	0.347
139	139	0.093
14	14	0.63
140	140	0.842
141	141	0.108
142	142	0.754
143	143	0.237
144	144	0.236
145	145	0.112
146	146	0.234
147	147	0.588
148	148	1
149	149	0.844
15	15	0.129
150	150	0.347
151	151	0.799
152	152	0.0231
153	153	0.683
154	154	0.644
155	155	0.256
156	156	0.19
157	157	0.439
158	158	0.444
159	159	0.71
160	160	0.799
161	161	0.595
162	162	0.99
163	163	0.0778
164	164	0.096
165	165	0.129
166	166	0.595
167	167	0.997
168	168	0.942
169	169	0.0341
17	17	0.0304
18	18	0.979
19	19	0.325
2	2	0.706
20	20	0.361
21	21	0.968
22	22	0.256
23	23	0.268
24	24	0.611
25	25	0.463
26	26	0.021
27	27	0.921
28	28	0.269
29	29	0.155
3	3	0.154
30	30	0.282
31	31	0.854
32	32	0.198
33	33	0.208
34	34	0.857
35	35	0.849
36	36	0.647
37	37	0.0325
38	38	0.409
39	39	0.418
4	4	0.432
40	40	0.221
41	41	0.126
42	42	0.712
43	43	0.316
44	44	0.123
45	45	0.375
46	46	0.478
47	47	0.471
48	48	0.25
49	49	0.318
5	5	0.666
50	50	0.455
51	51	0.562
52	52	0.112
53	53	0.499
54	54	0.319
55	55	0.529
56	56	0.534
57	57	0.892
58	58	0.217
59	59	0.163
6	6	0.674
60	60	0.0294
61	61	0.436
62	62	0.204
63	63	0.123
64	64	0.702
65	65	0.279
66	66	0.813
67	67	0.583
68	68	0.125
69	69	0.931
7	7	0.0844
70	70	0.00307
71	71	0.21
72	72	0.293
73	73	0.0222
74	74	0.931
75	75	0.0261
76	76	0.939
77	77	0.0597
78	78	0.0296
79	79	0.868
8	8	0.389
80	80	0.886
81	81	0.906
82	82	0.0595
83	83	0.423
84	84	0.0673
85	85	0.117
86	86	0.11
87	87	0.0177
88	88	0.278
89	89	0.309
9	9	0.994
90	90	0.511
91	91	0.652
92	92	0.459
93	93	0.242
94	94	0.816
95	95	0.0043
96	96	0.64
97	97	0.914
98	98	0.447
99	99	0.35

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: CNhs13228

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011159 mouse GP2-positive M cell 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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000473 (defensive cell)
0000255 (eukaryotic cell)
0000627 (transporting cell)
0000682 (M cell of gut)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0011159 (mouse GP2-positive M cell 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@SAMD00004773
+|accession_numbers=CAGE;DRX008765;DRR009637;DRZ001062;DRZ002447;DRZ012412;DRZ013797
 |ancestors_in_anatomy_facet=
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000012,CL:0000063,CL:0000066,CL:0002371,CL:0000004,CL:0000255,CL:0000473,CL:0000627,CL:0000682
+|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000473,CL:0000255,CL:0000627,CL:0000682
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0011159
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:80555320..80555378,-!p1@Creb3l3!2.84!792.44!Creb3l3;;chr7:51787434..51787448,-!p1@Spib!2.65!623.04!Spib;;chr3:3634145..3634161,+!p1@Hnf4g!2.46!288.84!Hnf4g;;chr2:163372884..163372904,+!p1@Hnf4a!2.34!215.91!Hnf4a;;chr6:86619104..86619119,-!p1@Mxd1!2.30!1497.60!Mxd1;;chr5:148118639..148118715,-!p1@Cdx2!2.05!110.25!Cdx2;;chr16:38294860..38294924,-!p1@Nr1i2!1.83!67.19!Nr1i2;;chr1:193007123..193007139,-!p1@Atf3!1.82!346.26!Atf3;;chr1:137155026..137155042,-!p1@Elf3!1.81!350.86!Elf3;;chr10:88969376..88969395,-!p1@Nr1h4!1.81!63.17!Nr1h4;;chr2:163332558..163332596,+!p2@Hnf4a!1.73!52.26!Hnf4a;;chr2:180069370..180069409,-!p1@Gata5!1.70!57.42!Gata5;;chr18:61195865..61195880,-!p1@Cdx1!1.70!48.81!Cdx1;;chr12:86814833..86814846,+!p1@Fos!1.69!1038.21!Fos;;chr18:61195843..61195864,-!p2@Cdx1!1.67!45.36!Cdx1;;chr14:63864056..63864102,-!p1@Gata4!1.65!74.65!Gata4;;chr4:122673187..122673201,+!p2@Mycl1!1.61!68.91!Mycl1;;chr8:77396591..77396639,+!p1@Isx!1.56!35.60!Isx;;chr4:124805061..124805087,-!p1@Zc3h12a!1.55!102.79!Zc3h12a;;chr6:39068163..39068176,-!p2@Parp12!1.54!61.44!Parp12;;chr10:80555398..80555409,-!p2@Creb3l3!1.52!32.16!Creb3l3;;chr2:133377954..133377973,+!p1@Bmp2!1.51!96.47!Bmp2;;chr5:120121169..120121171,+!p4@Tbx3!1.50!53.40!Tbx3;;chr5:115421065..115421088,-!p1@Hnf1a!1.50!30.43!Hnf1a;;chr17:25707623..25707639,-!p1@Sox8!1.45!112.55!Sox8;;chr1:173144100..173144138,+!p2@Nr1i3!1.45!26.99!Nr1i3;;chr3:3508024..3508069,+!p2@Hnf4g!1.44!26.41!Hnf4g;;chr19:5560600..5560617,-!p1@Ovol1!1.43!31.58!Ovol1;;chr8:87502608..87502623,-!p1@Junb!1.41!381.29!Junb;;chr1:194979315..194979359,+!p1@Irf6!1.40!141.84!Irf6;;chr11:53583544..53583559,+!p1@Irf1!1.37!357.75!Irf1;;chr5:135582751..135582788,+!p1@Mlxipl!1.36!84.99!Mlxipl;;chr19:6996243..6996293,-!p1@Esrra!1.34!222.23!Esrra;;chr15:97738692..97738747,-!p1@Vdr!1.33!108.53!Vdr;;chr1:39250584..39250643,+!p1@Npas2!1.32!97.05!Npas2;;chr8:77397190..77397202,+!p5@Isx!1.32!20.10!Isx;;chr7:20213752..20213778,-!p2@Relb!1.32!20.10!Relb;;chr18:64499674..64499696,+!p1@Onecut2!1.31!33.31!Onecut2;;chr5:148118840..148118857,-!p2@Cdx2!1.29!18.38!Cdx2;;chr14:99697871..99697934,+!p1@Klf5!1.28!343.96!Klf5;;chr12:56593574..56593592,-!p1@Nfkbia!1.26!859.05!Nfkbia;;chr7:19895354..19895369,-!p1@Fosb!1.25!22.97!Fosb;;chr10:80555285..80555291,-!p4@Creb3l3!1.25!16.65!Creb3l3;;chr7:19895384..19895399,-!p2@Fosb!1.22!21.82!Fosb;;chr10:80555299..80555306,-!p3@Creb3l3!1.22!15.50!Creb3l3;;chr15:79177964..79177986,+!p1@Maff!1.21!52.26!Maff;;chr7:20214704..20214800,-!p1@Relb!1.21!49.96!Relb;;chr8:77397492..77397514,+!p3@Isx!1.20!14.93!Isx;;chr8:77397095..77397127,+!p2@Isx!1.20!14.93!Isx;;chr2:163372869..163372882,+!p3@Hnf4a!1.20!14.93!Hnf4a;;chr12:78063146..78063159,-!p2@Max!1.19!37.33!Max;;chr19:46380235..46380277,+!p3@Nfkb2!1.19!31.01!Nfkb2;;chr8:125778192..125778217,+!p2@Zfp276!1.17!39.05!Zfp276;;chr4:133109285..133109308,+!p1@Nr0b2!1.17!13.78!Nr0b2;;chr12:58646974..58647003,-!p1@Foxa1!1.15!17.80!Foxa1;;chr14:76887526..76887555,+!p10@Tsc22d1!1.15!13.21!Tsc22d1;;chr11:70500401..70500460,-!p3@Camta2!1.15!13.21!Camta2;;chr15:35225845..35225867,+!p1@Osr2!1.13!31.58!Osr2;;chr8:87643578..87643593,-!p1@Zfp791!1.13!25.84!Zfp791;;chr17:27865882..27865901,-!p1@Spdef!1.13!12.63!Spdef;;chr1:194979361..194979373,+!p2@Irf6!1.12!16.65!Irf6;;chr8:77396650..77396662,+!p4@Isx!1.12!12.06!Isx;;chr7:19608891..19608895,-!p1@Foxa3!1.11!15.50!Foxa3;;chr18:64499706..64499721,+!p2@Onecut2!1.09!16.08!Onecut2;;chr18:35020854..35020869,+!p1@Egr1!1.08!426.08!Egr1;;chr4:55545337..55545357,-!p1@Klf4!1.08!164.23!Klf4;;chr7:134519473..134519502,-!p3@Zfp747!1.08!14.93!Zfp747;;chr3:94176733..94176794,+!p1@Rorc!1.07!83.26!Rorc;;chr7:29551464..29551487,-!p2@Nfkbib!1.07!41.92!Nfkbib;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.07!13.78!Zbtb11;;chr19:53384910..53384937,+!p3@Mxi1!1.06!29.86!Mxi1;;chr2:173044380..173044432,-!p1@Zbp1!1.06!25.27!Zbp1;;chr7:148452314..148452329,-!p1@Irf7!1.05!72.35!Irf7;;chr2:28477452..28477483,-!p1@Gfi1b!1.05!12.63!Gfi1b;;chr6:37391910..37391928,-!p3@Creb3l2!1.05!11.48!Creb3l2;;chr9:31720843..31720888,-!p1@Barx2!1.05!11.48!Barx2;;chr19:46379199..46379301,+!p1@Nfkb2!1.04!57.42!Nfkb2;;chr6:39068181..39068206,-!p3@Parp12!1.04!20.67!Parp12;;chr2:173044357..173044377,-!p2@Zbp1!1.04!14.36!Zbp1;;chr5:148118792..148118806,-!p3@Cdx2!1.03!9.76!Cdx2;;chr5:148118614..148118625,-!p4@Cdx2!1.03!9.76!Cdx2;;chr4:148178459..148178482,+!p4@Casz1!1.03!9.76!Casz1;;chr16:55822241..55822258,-!p1@Nfkbiz!1.02!296.30!Nfkbiz;;chr7:20408047..20408125,-!p1@Bcl3!1.02!110.25!Bcl3;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.01!26.99!Tfcp2l1;;chr5:140267510..140267555,+!p2@Mafk!1.01!22.40!Mafk;;chr10:44178521..44178557,-!p1@Prdm1!1.01!16.65!Prdm1;;chr7:31206743..31206761,+!p1@Nfkbid!1.01!12.63!Nfkbid;;chr6:86619130..86619158,-!p2@Mxd1!1.00!133.22!Mxd1;;chr3:135354384..135354443,-!p1@Nfkb1!1.00!55.70!Nfkb1;;chr13:5860776..5860796,+!p1@Klf6!0.98!211.89!Klf6;;chr5:140267476..140267493,+!p1@Mafk!0.96!47.09!Mafk;;chr6:64679112..64679126,+!p1@Atoh1!0.96!8.04!Atoh1;;chr2:103123925..103123959,-!p3@Ehf!0.96!8.04!Ehf;;chr19:6996294..6996324,-!p2@Esrra!0.95!53.98!Esrra;;chr8:123260252..123260264,+!p1@Irf8!0.94!56.27!Irf8;;chr18:36953486..36953503,+!p2@Zmat2!0.94!13.21!Zmat2;;chr10:44178493..44178520,-!p3@Prdm1!0.94!10.91!Prdm1;;chr7:134519511..134519534,-!p2@Zfp747!0.93!14.36!Zfp747;;chr10:44178474..44178487,-!p4@Prdm1!0.93!10.91!Prdm1;;chr10:44178375..44178390,-!p2@Prdm1!0.93!10.34!Prdm1;;chr5:148118809..148118832,-!p5@Cdx2!0.93!7.47!Cdx2;;chr19:5560570..5560582,-!p2@Ovol1!0.93!7.47!Ovol1;;chr3:128916868..128916890,+!p1@Pitx2!0.92!10.34!Pitx2;;chr11:100948597..100948637,+!p1@Mlx!0.91!177.44!Mlx;;chr1:135320989..135321043,-!p1@Sox13!0.91!82.69!Sox13;;chr8:118231678..118231692,-!p2@Maf!0.91!67.19!Maf;;chr10:80600749..80600766,+!p2@Zbtb7a!0.91!38.47!Zbtb7a;;chr4:94718861..94718872,-!p2@Jun!0.90!53.98!Jun;;chr19:55816546..55816556,+!p3@Tcf7l2!0.90!27.56!Tcf7l2;;chr3:89197057..89197114,-!p1@Zbtb7b!0.90!24.69!Zbtb7b;;chr18:11052485..11052508,+!p2@Gata6!0.90!20.10!Gata6;;chr3:87329568..87329589,+!p2@Etv3!0.90!9.76!Etv3;;chr19:53384985..53385042,+!p1@Mxi1!0.88!212.47!Mxi1;;chr13:112476433..112476448,+!p2@Mier3!0.87!12.63!Mier3;;chr9:63869890..63869908,-!p6@Smad6!0.87!8.61!Smad6;;chr11:98636508..98636524,-!p3@Nr1d1!0.87!8.04!Nr1d1;;chr4:43575544..43575565,+!p2@Creb3!0.86!38.47!Creb3;;chr1:189433521..189433548,+!p5@Esrrg!0.86!6.32!Esrrg;;chr7:29551488..29551529,-!p1@Nfkbib!0.85!205.58!Nfkbib;;chr2:152561980..152561997,+!p1@Id1!0.85!188.35!Id1;;chr5:120121020..120121049,+!p1@Tbx3!0.85!39.05!Tbx3;;chr17:45692642..45692663,+!p1@Nfkbie!0.85!20.67!Nfkbie;;chr13:30076280..30076334,-!p3@E2f3!0.85!18.95!E2f3;;chr6:39068210..39068251,-!p1@Parp12!0.84!29.29!Parp12;;chr11:98636400..98636418,-!p4@Nr1d1!0.84!8.04!Nr1d1;;chr1:135320962..135320981,-!p2@Sox13!0.83!20.67!Sox13;;chr5:32438894..32438908,+!p2@Fosl2!0.83!12.63!Fosl2;;chr9:31720903..31720918,-!p2@Barx2!0.83!5.74!Barx2;;chr7:20214018..20214024,-!p4@Relb!0.83!5.74!Relb;;chr8:73222425..73222444,+!p2@Jund!0.83!5.74!Jund;;chr1:173144144..173144176,+!p1@Nr1i3!0.83!5.74!Nr1i3;;chr8:79426176..79426275,+!p1@Nr3c2!0.82!29.86!Nr3c2;;chr5:76733981..76734018,-!p3@Clock!0.82!12.63!Clock;;chr4:94718879..94718898,-!p1@Jun!0.80!414.02!Jun;;chr4:124805092..124805135,-!p2@Zc3h12a!0.80!24.12!Zc3h12a;;chr12:85657780..85657815,+!p2@Zfp410!0.80!14.93!Zfp410;;chr7:87170879..87170914,+!p2@Zfp710!0.80!13.21!Zfp710;;chr2:91035197..91035237,-!p1@Nr1h3!0.80!11.48!Nr1h3;;chr18:11052642..11052659,+!p1@Gata6!0.79!28.14!Gata6;;chr3:89197216..89197258,-!p3@Zbtb7b!0.79!11.48!Zbtb7b;;chr17:28409136..28409150,+!p3@Ppard!0.79!5.17!Ppard;;chr2:180069640..180069660,-!p4@Gata5!0.79!5.17!Gata5;;chr1:189432634..189432643,+!p8@Esrrg!0.79!5.17!Esrrg;;chr1:194979383..194979393,+!p3@Irf6!0.79!5.17!Irf6;;chr2:166888058..166888105,-!p2@Znfx1!0.78!17.23!Znfx1;;chr5:65194752..65194769,+!p1@Klf3!0.77!179.73!Klf3;;chr15:85566051..85566080,+!p4@Ppara!0.77!5.74!Ppara;;chr2:103143336..103143367,-!p1@Ehf!0.76!8.04!Ehf;;chr5:32438831..32438878,+!p1@Fosl2!0.75!52.83!Fosl2;;chr15:25914114..25914128,+!p2@Zfp622!0.75!20.67!Zfp622;;chr14:63890519..63890539,-!p3@Gata4!0.75!4.59!Gata4;;chr2:28477422..28477433,-!p2@Gfi1b!0.75!4.59!Gfi1b;;chr2:180069410..180069421,-!p3@Gata5!0.75!4.59!Gata5;;chr1:165219345..165219366,-!p7@Prrx1!0.75!4.59!Prrx1;;chr10:126727842..126727859,+!p1@Ddit3!0.74!142.98!Ddit3;;chr19:46380172..46380231,+!p2@Nfkb2!0.74!34.45!Nfkb2;;chr17:45692676..45692695,+!p2@Nfkbie!0.74!9.76!Nfkbie;;chr3:30993616..30993634,+!p3@Skil!0.74!8.61!Skil;;chr2:91035254..91035271,-!p3@Nr1h3!0.74!5.74!Nr1h3;;chr8:118231705..118231722,-!p3@Maf!0.73!39.05!Maf;;chr18:75527009..75527027,+!p1@Smad7!0.72!99.92!Smad7;;chr17:48061381..48061399,-!p1@Foxp4!0.72!53.98!Foxp4;;chr10:80813050..80813114,-!p2@Hmg20b!0.72!51.68!Hmg20b;;chr7:20162663..20162678,+!p1@Zfp296!0.72!5.74!Zfp296;;chr1:194979301..194979310,+!p4@Irf6!0.72!5.17!Irf6;;chr10:80598209..80598236,+!p4@Zbtb7a!0.71!7.47!Zbtb7a;;chr11:53164556..53164567,+!p5@Aff4!0.71!6.89!Aff4;;chr4:148178559..148178603,+!p1@Casz1!0.70!12.63!Casz1;;chr5:148081686..148081715,+!p1@Pdx1!0.70!4.02!Pdx1;;chr2:147871627..147871641,-!p1@Foxa2!0.70!4.02!Foxa2;;chr14:63864337..63864381,-!p6@Gata4!0.70!4.02!Gata4;;chr4:135699731..135699747,+!p1@Id3!0.69!508.77!Id3;;chr2:160192793..160192809,-!p1@Mafb!0.69!66.61!Mafb;;chr4:135700687..135700719,+!p2@Id3!0.69!6.32!Id3;;chr10:107769168..107769215,+!p1@Pawr!0.68!43.64!Pawr;;chr6:140572352..140572382,+!p3@Aebp2!0.68!9.19!Aebp2;;chr15:79178060..79178074,+!p2@Maff!0.68!5.17!Maff;;chr3:87329494..87329565,+!p1@Etv3!0.67!64.31!Etv3;;chrX:7339938..7339963,+!p1@Tfe3!0.67!21.25!Tfe3;;chr18:11052606..11052633,+!p4@Gata6!0.67!10.34!Gata6;;chr11:98636531..98636559,-!p1@Nr1d1!0.66!23.54!Nr1d1;;chr4:148275237..148275311,+!p2@Casz1!0.66!16.65!Casz1;;chr18:36441119..36441158,+!p2@Pura!0.66!9.76!Pura;;chr11:96690797..96690813,-!p1@Nfe2l1!0.65!77.52!Nfe2l1;;chr14:79880971..79880992,+!p2@Elf1!0.65!51.68!Elf1;;chr8:72519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@@ Line 38: / Line 43: @@
 |is_a=EFO:0002091;;FF:0011159
 |is_obsolete=
+|library_id=CNhs13228
+|library_id_phase_based=2:CNhs13228
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11845
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11845
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool1.CNhs13228.11845-124H9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool1.CNhs13228.11845-124H9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool1.CNhs13228.11845-124H9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool1.CNhs13228.11845-124H9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool1.CNhs13228.11845-124H9.mm9.nobarcode.rdna.fa.gz
 |name=GP2+ M cell, pool1
 |namespace=
@@ Line 43: / Line 59: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13228,LSID1006,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0192612331825155,0,0,0,0,0,-0.26739664021754,0,0,0,0,-0.0843392403965415,0,0,0,0,0.166064033233336,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.361354066008304,0,0.518109443993596,0,0,-0.0165688761441002,-0.0432586922624896,-0.138920890718558,0.255752287044959,-0.984211366477826,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.154221771232853,0,-0.0321622022929229,0,0,-0.0487672192730093,-0.243225778194271,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.0871481873453718,-0.276660860310968,0,0,-0.0762446085579826,0.0737342952798195,-0.0778054367469735,-0.0788315948399074,0,0,0,0,0,0.197068726315728,-0.0814866010703366,-0.589157811726724,0.0462309289978455,0,0,0,0,0
 |rna_box=124
 |rna_catalog_number=
@@ Line 58: / Line 75: @@
 |rna_weight_ug=0.242
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 96: @@
 |top_motifs=HNF4A_NR2F1,2:2.77303766355;ESRRA:2.49954644943;ZEB1:2.49721700943;FOSL2:2.2325571069;SNAI1..3:2.07926963894;NFIX:2.00495677301;NFKB1_REL_RELA:1.92496756384;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.91286050426;FOXN1:1.77599875436;PAX2:1.74891519397;HNF1A:1.69302014902;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.59514729383;FOS_FOS{B,L1}_JUN{B,D}:1.57026821866;ATF6:1.55552986322;PPARG:1.52186621335;PDX1:1.46328262062;TBX4,5:1.42613697568;ATF4:1.37232582159;AR:1.35381199831;NR1H4:1.32557718022;BACH2:1.32542714889;ARID5B:1.32279243254;NR6A1:1.31465691907;STAT2,4,6:1.31423399554;FOXM1:1.2353604311;IRF1,2:1.22101959411;HES1:1.220253854;STAT5{A,B}:1.07002893638;ADNP_IRX_SIX_ZHX:1.05954634034;ATF5_CREB3:1.0056236643;TP53:1.00169137497;ELK1,4_GABP{A,B1}:0.980673121628;LMO2:0.944106248548;DMAP1_NCOR{1,2}_SMARC:0.935341347423;SP1:0.922110035585;GTF2A1,2:0.898669821796;NR5A1,2:0.840359990908;ZBTB6:0.796361014842;FOX{I1,J2}:0.74820090282;MYOD1:0.702511620048;PAX8:0.664837499781;LHX3,4:0.621922512449;XCPE1{core}:0.620902637861;VSX1,2:0.602554292714;HLF:0.596480819364;ZNF148:0.561010368734;NKX6-1,2:0.556025798378;CREB1:0.533667416034;FOXL1:0.524729526574;TBP:0.457861544723;EBF1:0.393479259784;POU2F1..3:0.365128792992;bHLH_family:0.333729736648;SPI1:0.320306671698;TLX1..3_NFIC{dimer}:0.294243541461;CDX1,2,4:0.272491642441;FOX{D1,D2}:0.262900417351;T:0.262595993359;ESR1:0.261141850335;ETS1,2:0.166004440157;YY1:0.142683568265;ONECUT1,2:0.126779885737;TFCP2:0.103805552956;STAT1,3:0.0700725701604;RORA:0.0249305373602;FOXA2:0.0238427546198;JUN:-0.00936752285102;ELF1,2,4:-0.0139081678754;GATA6:-0.0635679119921;NFE2:-0.0661185558487;IRF7:-0.0675318191526;RUNX1..3:-0.140683921895;CRX:-0.152213995527;ALX4:-0.166395683676;MAFB:-0.190836128815;ZNF423:-0.208329000972;NFY{A,B,C}:-0.218047888357;TAL1_TCF{3,4,12}:-0.24614834704;FOXO1,3,4:-0.247015514342;CUX2:-0.247465759084;MYB:-0.281573013439;HBP1_HMGB_SSRP1_UBTF:-0.297609348367;SREBF1,2:-0.332834978495;SRF:-0.342499066372;NFE2L2:-0.350763398675;RXRA_VDR{dimer}:-0.354367194171;LEF1_TCF7_TCF7L1,2:-0.419370900697;OCT4_SOX2{dimer}:-0.442058941025;NANOG:-0.44856390947;HOX{A4,D4}:-0.457196626625;NANOG{mouse}:-0.461738934789;TEAD1:-0.488665975522;POU6F1:-0.49112405513;FOXQ1:-0.545223521819;TFAP4:-0.557371111788;MED-1{core}:-0.586049756915;TFAP2B:-0.586827544498;MEF2{A,B,C,D}:-0.614376221077;PAX6:-0.639643794902;GFI1B:-0.66224630027;PRRX1,2:-0.683123494871;EP300:-0.701265218188;FOX{F1,F2,J1}:-0.718201074172;HSF1,2:-0.726203029026;REST:-0.727399125617;NKX2-1,4:-0.730746721601;RFX1:-0.778439199422;POU3F1..4:-0.784377767259;RXR{A,B,G}:-0.78464473458;GFI1:-0.830728273121;TFAP2{A,C}:-0.841265354337;MAZ:-0.852628601988;PBX1:-0.862161626719;CDC5L:-0.906486734805;PAX5:-0.939081710425;SMAD1..7,9:-0.946365774313;NFIL3:-0.966222339564;ZFP161:-0.985894650218;FOXP3:-0.985926078206;SOX17:-0.988428166237;MYFfamily:-1.00240463481;E2F1..5:-1.0142535231;HIF1A:-1.02441142543;NKX3-2:-1.03033687726;POU5F1:-1.04053881929;SPIB:-1.0418031704;BPTF:-1.06856340368;NKX2-2,8:-1.07456251583;AHR_ARNT_ARNT2:-1.07651769921;ZNF143:-1.08129959103;EGR1..3:-1.08609881672;HOXA9_MEIS1:-1.11920148288;HIC1:-1.12621500659;NKX2-3_NKX2-5:-1.12745472356;SPZ1:-1.13550745497;SOX5:-1.16223685176;GZF1:-1.16936230005;NRF1:-1.17331927977;EVI1:-1.20234283944;TGIF1:-1.21373487077;CEBPA,B_DDIT3:-1.21477741476;NFE2L1:-1.23170485905;DBP:-1.24487396793;SOX{8,9,10}:-1.25691480182;ZNF238:-1.25963221854;RFX2..5_RFXANK_RFXAP:-1.27993472642;TLX2:-1.31743866793;MTE{core}:-1.3348323019;HOX{A5,B5}:-1.33911267179;SOX2:-1.33929058772;BREu{core}:-1.34256303681;GTF2I:-1.36291299867;MTF1:-1.36798601374;NHLH1,2:-1.37156716645;MYBL2:-1.41896663232;UFEwm:-1.48298077174;PITX1..3:-1.50102830422;ATF2:-1.52948686021;MZF1:-1.53458983574;PATZ1:-1.5401118106;AIRE:-1.55779833987;ALX1:-1.57720430897;HMX1:-1.63074890353;ZNF384:-1.69453134835;TOPORS:-1.71015045312;ZBTB16:-1.72928445812;GLI1..3:-1.76693922169;GCM1,2:-1.77625640575;HAND1,2:-1.7822804448;GATA4:-1.78963628305;NR3C1:-1.83853849648;POU1F1:-1.84545277138;IKZF1:-1.85500725461;PRDM1:-1.86424930955;KLF4:-1.87590933546;NFATC1..3:-1.88633517285;PAX1,9:-1.91110200348;ZIC1..3:-1.91828669252;FOXD3:-1.95365953329;RBPJ:-1.95717487802;RREB1:-1.96459361961;TFDP1:-1.96506614969;PAX4:-1.99822589448;NKX3-1:-2.07384880996;FOXP1:-2.12686372632;HMGA1,2:-2.21819527022;EN1,2:-2.21835704952;TEF:-2.4360587035;IKZF2:-2.48284004211
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11845-124H9;search_select_hide=table117:11845-124H9
 }}

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FF:11845-124H9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:23, 4 June 2020

CNhs13228

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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