FF:11847-124I2: Difference between revisions

Latest revision as of 18:23, 4 June 2020

Name:	GP2+ M cell, pool3
Species:	Mouse (Mus musculus)
Library ID:	CNhs13240
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_c
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		SAMD00005004

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13240		CAGE		DRX008767		DRR009639

Accession ID Mm9

Library id		BAM		CTSS
CNhs13240		DRZ001064		DRZ002449

Accession ID Mm10

Library id		BAM		CTSS
CNhs13240		DRZ012414		DRZ013799

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

CNhs13240

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0749
1002	-0.116
1003	-0.123
1004	0
1005	1.131
1006	-0.364
1007	0.0188
1008	1.884
1009	-0.157
101	-0.137
1010	0
1011	-0.337
1012	0
1013	0.368
1014	-0.0874
1015	-0.258
1016	-0.465
1017	0
1018	0.648
1019	0
102	0
1020	0
1021	0
1022	-0.0931
1023	0
1024	-0.291
1025	-0.00155
1026	0
1027	-0.048
1028	0
1029	-0.0912
103	-0.0887
1030	0
1031	-0.961
1032	0.872
1033	0.00952
1034	0
1035	0
1036	-0.186
1037	0
1038	-0.0435
1039	0.0748
104	0
1040	-0.79
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: CNhs13240

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.034
MA0003.1	MA0003.1	0.338
MA0004.1	MA0004.1	0.657
MA0006.1	MA0006.1	0.105
MA0007.1	MA0007.1	0.322
MA0009.1	MA0009.1	0.132
MA0014.1	MA0014.1	0.0594
MA0017.1	MA0017.1	2.5709e-27
MA0018.2	MA0018.2	0.266
MA0019.1	MA0019.1	0.067
MA0024.1	MA0024.1	0.0334
MA0025.1	MA0025.1	0.739
MA0027.1	MA0027.1	0.908
MA0028.1	MA0028.1	0.00967
MA0029.1	MA0029.1	0.862
MA0030.1	MA0030.1	0.746
MA0031.1	MA0031.1	0.488
MA0035.2	MA0035.2	1.35321e-5
MA0038.1	MA0038.1	0.685
MA0039.2	MA0039.2	5.58813e-6
MA0040.1	MA0040.1	0.0843
MA0041.1	MA0041.1	0.231
MA0042.1	MA0042.1	0.278
MA0043.1	MA0043.1	0.552
MA0046.1	MA0046.1	1.85992e-55
MA0047.2	MA0047.2	0.0153
MA0048.1	MA0048.1	0.211
MA0050.1	MA0050.1	2.88541e-4
MA0051.1	MA0051.1	2.3227e-5
MA0052.1	MA0052.1	0.24
MA0055.1	MA0055.1	0.13
MA0057.1	MA0057.1	0.0538
MA0058.1	MA0058.1	0.71
MA0059.1	MA0059.1	0.874
MA0060.1	MA0060.1	0.419
MA0061.1	MA0061.1	0.00104
MA0062.2	MA0062.2	5.08219e-6
MA0065.2	MA0065.2	6.99639e-15
MA0066.1	MA0066.1	0.132
MA0067.1	MA0067.1	0.812
MA0068.1	MA0068.1	0.101
MA0069.1	MA0069.1	0.779
MA0070.1	MA0070.1	0.158
MA0071.1	MA0071.1	0.068
MA0072.1	MA0072.1	0.83
MA0073.1	MA0073.1	0.972
MA0074.1	MA0074.1	0.297
MA0076.1	MA0076.1	0.041
MA0077.1	MA0077.1	0.365
MA0078.1	MA0078.1	0.701
MA0079.2	MA0079.2	0.447
MA0080.2	MA0080.2	7.24917e-6
MA0081.1	MA0081.1	0.739
MA0083.1	MA0083.1	0.227
MA0084.1	MA0084.1	0.185
MA0087.1	MA0087.1	0.263
MA0088.1	MA0088.1	0.207
MA0090.1	MA0090.1	0.623
MA0091.1	MA0091.1	0.298
MA0092.1	MA0092.1	0.607
MA0093.1	MA0093.1	0.702
MA0099.2	MA0099.2	1.06378e-11
MA0100.1	MA0100.1	0.903
MA0101.1	MA0101.1	2.32481e-6
MA0102.2	MA0102.2	0.602
MA0103.1	MA0103.1	3.14102e-7
MA0104.2	MA0104.2	0.441
MA0105.1	MA0105.1	0.0585
MA0106.1	MA0106.1	0.313
MA0107.1	MA0107.1	1.47958e-6
MA0108.2	MA0108.2	6.72333e-4
MA0111.1	MA0111.1	0.454
MA0112.2	MA0112.2	0.00298
MA0113.1	MA0113.1	0.738
MA0114.1	MA0114.1	7.61666e-32
MA0115.1	MA0115.1	1.20966e-16
MA0116.1	MA0116.1	0.245
MA0117.1	MA0117.1	0.351
MA0119.1	MA0119.1	0.122
MA0122.1	MA0122.1	0.877
MA0124.1	MA0124.1	0.611
MA0125.1	MA0125.1	0.998
MA0131.1	MA0131.1	0.93
MA0135.1	MA0135.1	0.176
MA0136.1	MA0136.1	3.32226e-11
MA0137.2	MA0137.2	0.00282
MA0138.2	MA0138.2	0.981
MA0139.1	MA0139.1	0.151
MA0140.1	MA0140.1	0.131
MA0141.1	MA0141.1	1.93406e-6
MA0142.1	MA0142.1	0.0451
MA0143.1	MA0143.1	0.121
MA0144.1	MA0144.1	7.38099e-4
MA0145.1	MA0145.1	0.0132
MA0146.1	MA0146.1	0.101
MA0147.1	MA0147.1	0.558
MA0148.1	MA0148.1	0.016
MA0149.1	MA0149.1	0.0282
MA0150.1	MA0150.1	0.0119
MA0152.1	MA0152.1	0.165
MA0153.1	MA0153.1	1.27712e-45
MA0154.1	MA0154.1	0.0503
MA0155.1	MA0155.1	0.85
MA0156.1	MA0156.1	3.39389e-6
MA0157.1	MA0157.1	0.738
MA0159.1	MA0159.1	5.20485e-4
MA0160.1	MA0160.1	4.31782e-5
MA0162.1	MA0162.1	0.64
MA0163.1	MA0163.1	0.275
MA0164.1	MA0164.1	0.834
MA0258.1	MA0258.1	0.0558
MA0259.1	MA0259.1	0.841

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: CNhs13240

Novel motif	Logo	P-value
1	1	0.172
10	10	0.205
100	100	0.895
101	101	0.69
102	102	0.85
103	103	0.465
104	104	0.969
105	105	0.193
106	106	0.0197
107	107	0.142
108	108	0.651
109	109	0.0345
11	11	0.143
110	110	0.404
111	111	0.155
112	112	0.0284
113	113	0.164
114	114	0.213
115	115	0.892
116	116	0.0915
117	117	0.027
118	118	0.589
119	119	0.143
12	12	0.654
120	120	0.442
121	121	0.247
122	122	0.995
123	123	0.0974
124	124	0.108
125	125	0.592
126	126	0.0665
127	127	0.235
128	128	0.22
129	129	0.19
13	13	3.16139e-5
130	130	0.871
131	131	0.897
132	132	0.743
133	133	0.493
134	134	0.958
135	135	0.103
136	136	0.00744
137	137	0.81
138	138	0.265
139	139	0.188
14	14	0.751
140	140	0.882
141	141	0.153
142	142	0.988
143	143	0.146
144	144	0.166
145	145	0.148
146	146	0.24
147	147	0.792
148	148	0.839
149	149	0.857
15	15	0.117
150	150	0.421
151	151	0.985
152	152	0.0268
153	153	0.85
154	154	0.742
155	155	0.366
156	156	0.0715
157	157	0.409
158	158	0.661
159	159	0.714
160	160	0.872
161	161	0.805
162	162	0.551
163	163	0.061
164	164	0.0963
165	165	0.153
166	166	0.647
167	167	0.771
168	168	0.938
169	169	0.0262
17	17	0.0401
18	18	0.85
19	19	0.297
2	2	0.846
20	20	0.308
21	21	0.981
22	22	0.276
23	23	0.539
24	24	0.456
25	25	0.455
26	26	0.0126
27	27	0.995
28	28	0.34
29	29	0.0798
3	3	0.196
30	30	0.353
31	31	0.923
32	32	0.257
33	33	0.195
34	34	0.881
35	35	0.968
36	36	0.581
37	37	0.0254
38	38	0.429
39	39	0.386
4	4	0.202
40	40	0.214
41	41	0.134
42	42	0.75
43	43	0.311
44	44	0.152
45	45	0.365
46	46	0.408
47	47	0.417
48	48	0.224
49	49	0.445
5	5	0.738
50	50	0.387
51	51	0.677
52	52	0.164
53	53	0.458
54	54	0.43
55	55	0.503
56	56	0.5
57	57	0.844
58	58	0.274
59	59	0.246
6	6	0.65
60	60	0.031
61	61	0.303
62	62	0.227
63	63	0.0951
64	64	0.722
65	65	0.296
66	66	0.826
67	67	0.479
68	68	0.0769
69	69	0.957
7	7	0.0651
70	70	0.0142
71	71	0.169
72	72	0.256
73	73	0.0226
74	74	0.663
75	75	0.0171
76	76	0.733
77	77	0.0558
78	78	0.0195
79	79	0.803
8	8	0.334
80	80	0.913
81	81	0.973
82	82	0.16
83	83	0.533
84	84	0.123
85	85	0.149
86	86	0.151
87	87	0.00562
88	88	0.259
89	89	0.281
9	9	0.979
90	90	0.311
91	91	0.925
92	92	0.562
93	93	0.23
94	94	0.745
95	95	0.00213
96	96	0.979
97	97	0.813
98	98	0.509
99	99	0.42

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: CNhs13240

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@SAMD00005004
+|accession_numbers=CAGE;DRX008767;DRR009639;DRZ001064;DRZ002449;DRZ012414;DRZ013799
 |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=chr7:51787434..51787448,-!p1@Spib!2.81!915.54!Spib;;chr10:80555320..80555378,-!p1@Creb3l3!2.62!478.56!Creb3l3;;chr3:3634145..3634161,+!p1@Hnf4g!2.38!237.02!Hnf4g;;chr2:163372884..163372904,+!p1@Hnf4a!2.21!159.45!Hnf4a;;chr6:86619104..86619119,-!p1@Mxd1!2.07!896.14!Mxd1;;chr5:148118639..148118715,-!p1@Cdx2!2.04!109.03!Cdx2;;chr2:163332558..163332596,+!p2@Hnf4a!1.99!97.82!Hnf4a;;chr1:137155026..137155042,-!p1@Elf3!1.88!410.69!Elf3;;chr16:38294860..38294924,-!p1@Nr1i2!1.82!65.07!Nr1i2;;chr8:77396591..77396639,+!p1@Isx!1.77!57.53!Isx;;chr18:61195865..61195880,-!p1@Cdx1!1.76!56.24!Cdx1;;chr10:88969376..88969395,-!p1@Nr1h4!1.71!50.20!Nr1h4;;chr4:124805061..124805087,-!p1@Zc3h12a!1.63!124.76!Zc3h12a;;chr17:27865882..27865901,-!p1@Spdef!1.63!41.80!Spdef;;chr14:63864056..63864102,-!p1@Gata4!1.61!67.66!Gata4;;chr1:193007123..193007139,-!p1@Atf3!1.57!193.28!Atf3;;chr17:25707623..25707639,-!p1@Sox8!1.55!141.35!Sox8;;chr2:180069370..180069409,-!p1@Gata5!1.55!40.29!Gata5;;chr12:86814833..86814846,+!p1@Fos!1.54!741.22!Fos;;chr18:61195843..61195864,-!p2@Cdx1!1.53!33.18!Cdx1;;chr3:3508024..3508069,+!p2@Hnf4g!1.53!33.18!Hnf4g;;chr4:122673187..122673201,+!p2@Mycl1!1.50!53.22!Mycl1;;chr5:115421065..115421088,-!p1@Hnf1a!1.45!27.36!Hnf1a;;chr2:133377954..133377973,+!p1@Bmp2!1.42!78.22!Bmp2;;chr5:135582751..135582788,+!p1@Mlxipl!1.41!96.53!Mlxipl;;chr7:19608891..19608895,-!p1@Foxa3!1.41!31.67!Foxa3;;chr10:80555398..80555409,-!p2@Creb3l3!1.41!24.99!Creb3l3;;chr6:64679112..64679126,+!p1@Atoh1!1.41!24.78!Atoh1;;chr19:5560600..5560617,-!p1@Ovol1!1.36!26.72!Ovol1;;chr1:173144100..173144138,+!p2@Nr1i3!1.36!21.76!Nr1i3;;chr7:19895384..19895399,-!p2@Fosb!1.35!30.38!Fosb;;chr5:120121169..120121171,+!p4@Tbx3!1.34!36.85!Tbx3;;chr2:28477452..28477483,-!p1@Gfi1b!1.34!25.64!Gfi1b;;chr1:194979315..194979359,+!p1@Irf6!1.30!112.48!Irf6;;chr5:148118840..148118857,-!p2@Cdx2!1.30!19.18!Cdx2;;chr7:20213752..20213778,-!p2@Relb!1.29!18.32!Relb;;chr8:87502608..87502623,-!p1@Junb!1.27!277.74!Junb;;chr18:64499674..64499696,+!p1@Onecut2!1.27!29.95!Onecut2;;chr14:99697871..99697934,+!p1@Klf5!1.26!328.38!Klf5;;chr11:53583544..53583559,+!p1@Irf1!1.26!278.60!Irf1;;chr15:97738692..97738747,-!p1@Vdr!1.26!91.79!Vdr;;chr19:46380235..46380277,+!p3@Nfkb2!1.25!35.98!Nfkb2;;chr7:19895354..19895369,-!p1@Fosb!1.25!23.06!Fosb;;chr8:77397095..77397127,+!p2@Isx!1.25!16.59!Isx;;chr6:39068163..39068176,-!p2@Parp12!1.23!29.74!Parp12;;chr7:20214704..20214800,-!p1@Relb!1.22!49.99!Relb;;chr8:77397492..77397514,+!p3@Isx!1.22!15.73!Isx;;chr12:56593574..56593592,-!p1@Nfkbia!1.21!763.85!Nfkbia;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.21!19.39!Zbtb11;;chr2:103123925..103123959,-!p3@Ehf!1.20!14.87!Ehf;;chr12:58646974..58647003,-!p1@Foxa1!1.19!19.61!Foxa1;;chr8:77396650..77396662,+!p4@Isx!1.18!14.01!Isx;;chr19:46379199..46379301,+!p1@Nfkb2!1.17!77.14!Nfkb2;;chr8:125778192..125778217,+!p2@Zfp276!1.17!39.22!Zfp276;;chr7:20408047..20408125,-!p1@Bcl3!1.16!151.91!Bcl3;;chr18:64499706..64499721,+!p2@Onecut2!1.15!18.53!Onecut2;;chr7:31206743..31206761,+!p1@Nfkbid!1.15!17.88!Nfkbid;;chr2:163372869..163372882,+!p3@Hnf4a!1.15!13.14!Hnf4a;;chr19:6996243..6996293,-!p1@Esrra!1.12!132.95!Esrra;;chr2:103143336..103143367,-!p1@Ehf!1.10!18.96!Ehf;;chr1:39250584..39250643,+!p1@Npas2!1.08!55.59!Npas2;;chr15:79177964..79177986,+!p1@Maff!1.08!38.57!Maff;;chr15:35225845..35225867,+!p1@Osr2!1.07!27.36!Osr2;;chr2:173044380..173044432,-!p1@Zbp1!1.07!25.86!Zbp1;;chr14:76887526..76887555,+!p10@Tsc22d1!1.07!10.77!Tsc22d1;;chr10:80555299..80555306,-!p3@Creb3l3!1.05!10.34!Creb3l3;;chr5:148118792..148118806,-!p3@Cdx2!1.05!10.34!Cdx2;;chr7:148452314..148452329,-!p1@Irf7!1.04!70.24!Irf7;;chr8:77397190..77397202,+!p5@Isx!1.04!9.91!Isx;;chr2:173044357..173044377,-!p2@Zbp1!1.03!14.22!Zbp1;;chr1:194979361..194979373,+!p2@Irf6!1.03!13.14!Irf6;;chr11:70500401..70500460,-!p3@Camta2!1.03!9.70!Camta2;;chr7:20162663..20162678,+!p1@Zfp296!1.02!12.71!Zfp296;;chr10:80555285..80555291,-!p4@Creb3l3!1.02!9.48!Creb3l3;;chr18:35020854..35020869,+!p1@Egr1!1.01!361.78!Egr1;;chr2:147871627..147871641,-!p1@Foxa2!1.01!9.27!Foxa2;;chr3:94176733..94176794,+!p1@Rorc!0.98!68.09!Rorc;;chr3:3508005..3508021,+!p3@Hnf4g!0.98!8.62!Hnf4g;;chr3:135354384..135354443,-!p1@Nfkb1!0.97!52.57!Nfkb1;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.97!24.78!Tfcp2l1;;chr2:79296783..79296801,-!p1@Neurod1!0.97!8.40!Neurod1;;chr5:148118809..148118832,-!p5@Cdx2!0.97!8.40!Cdx2;;chr7:87170879..87170914,+!p2@Zfp710!0.93!18.10!Zfp710;;chr3:128918394..128918413,+!p5@Pitx2!0.93!7.54!Pitx2;;chr4:94718861..94718872,-!p2@Jun!0.92!56.67!Jun;;chr19:55816546..55816556,+!p3@Tcf7l2!0.92!29.09!Tcf7l2;;chr10:20880629..20880683,-!p1@Myb!0.92!21.98!Myb;;chr7:134519473..134519502,-!p3@Zfp747!0.92!10.13!Zfp747;;chr16:55822241..55822258,-!p1@Nfkbiz!0.90!227.11!Nfkbiz;;chr8:87643578..87643593,-!p1@Zfp791!0.90!14.87!Zfp791;;chr5:140267510..140267555,+!p2@Mafk!0.88!16.38!Mafk;;chr11:98636400..98636418,-!p4@Nr1d1!0.87!8.62!Nr1d1;;chr13:5860776..5860796,+!p1@Klf6!0.86!161.82!Klf6;;chr3:89197057..89197114,-!p1@Zbtb7b!0.86!22.41!Zbtb7b;;chr3:90046995..90047031,-!p2@Creb3l4!0.86!7.97!Creb3l4;;chr4:133109285..133109308,+!p1@Nr0b2!0.86!6.25!Nr0b2;;chr4:148178459..148178482,+!p4@Casz1!0.86!6.25!Casz1;;chr10:61595830..61595846,+!p1@Neurog3!0.86!6.25!Neurog3;;chr2:152561980..152561997,+!p1@Id1!0.85!186.17!Id1;;chr12:78063146..78063159,-!p2@Max!0.84!16.38!Max;;chr9:31720843..31720888,-!p1@Barx2!0.84!6.68!Barx2;;chr6:37391910..37391928,-!p3@Creb3l2!0.84!6.68!Creb3l2;;chr4:55545337..55545357,-!p1@Klf4!0.83!91.79!Klf4;;chr17:45692642..45692663,+!p1@Nfkbie!0.83!19.39!Nfkbie;;chr13:112476433..112476448,+!p2@Mier3!0.83!11.20!Mier3;;chr3:128916868..128916890,+!p1@Pitx2!0.83!8.19!Pitx2;;chr5:148118614..148118625,-!p4@Cdx2!0.83!5.82!Cdx2;;chr19:53384910..53384937,+!p3@Mxi1!0.82!16.81!Mxi1;;chr4:87452180..87452196,-!p3@Mllt3!0.82!11.42!Mllt3;;chr3:87329568..87329589,+!p2@Etv3!0.82!7.97!Etv3;;chr14:63890519..63890539,-!p3@Gata4!0.82!5.60!Gata4;;chr19:5447692..5447711,+!p2@Fosl1!0.81!5.39!Fosl1;;chr8:77397026..77397036,+!p6@Isx!0.81!5.39!Isx;;chr8:123260252..123260264,+!p1@Irf8!0.80!40.94!Irf8;;chr4:148178559..148178603,+!p1@Casz1!0.80!16.38!Casz1;;chr18:11052642..11052659,+!p1@Gata6!0.79!28.23!Gata6;;chr17:45692676..45692695,+!p2@Nfkbie!0.79!10.99!Nfkbie;;chr18:36953486..36953503,+!p2@Zmat2!0.79!9.05!Zmat2;;chr1:173144144..173144176,+!p1@Nr1i3!0.79!5.17!Nr1i3;;chr2:28477422..28477433,-!p2@Gfi1b!0.79!5.17!Gfi1b;;chr11:100948597..100948637,+!p1@Mlx!0.78!130.58!Mlx;;chr10:44178521..44178557,-!p1@Prdm1!0.78!9.48!Prdm1;;chr17:34784073..34784118,+!p2@Atf6b!0.77!21.33!Atf6b;;chr7:29551464..29551487,-!p2@Nfkbib!0.77!20.69!Nfkbib;;chr18:11052606..11052633,+!p4@Gata6!0.77!13.14!Gata6;;chr7:150155143..150155156,-!p1@Ascl2!0.77!4.96!Ascl2;;chr10:67000609..67000625,+!p1@Egr2!0.76!11.85!Egr2;;chr2:91035197..91035237,-!p1@Nr1h3!0.76!10.56!Nr1h3;;chr19:5560570..5560582,-!p2@Ovol1!0.76!4.74!Ovol1;;chr14:63890545..63890560,-!p5@Gata4!0.76!4.74!Gata4;;chr8:118231678..118231692,-!p2@Maf!0.75!46.11!Maf;;chr19:6996294..6996324,-!p2@Esrra!0.75!34.04!Esrra;;chr5:76733981..76734018,-!p3@Clock!0.75!10.56!Clock;;chr6:86619130..86619158,-!p2@Mxd1!0.74!71.75!Mxd1;;chr19:46380172..46380231,+!p2@Nfkb2!0.74!34.04!Nfkb2;;chr13:112476264..112476282,+!p3@Mier3!0.74!6.68!Mier3;;chr2:103143315..103143328,-!p2@Ehf!0.74!4.52!Ehf;;chr1:194979383..194979393,+!p3@Irf6!0.74!4.52!Irf6;;chr7:20214018..20214024,-!p4@Relb!0.74!4.52!Relb;;chr9:31720903..31720918,-!p2@Barx2!0.74!4.52!Barx2;;chr7:29551488..29551529,-!p1@Nfkbib!0.73!156.86!Nfkbib;;chr4:43575544..43575565,+!p2@Creb3!0.73!28.44!Creb3;;chr4:87452200..87452229,-!p2@Mllt3!0.73!10.13!Mllt3;;chr8:73222425..73222444,+!p2@Jund!0.73!4.31!Jund;;chr17:28409136..28409150,+!p3@Ppard!0.73!4.31!Ppard;;chr10:80600749..80600766,+!p2@Zbtb7a!0.72!24.56!Zbtb7a;;chr3:89197216..89197258,-!p3@Zbtb7b!0.72!9.48!Zbtb7b;;chr11:96690797..96690813,-!p1@Nfe2l1!0.71!89.42!Nfe2l1;;chr5:144951153..144951203,+!p1@Bhlha15!0.71!6.25!Bhlha15;;chr1:138857048..138857071,-!p2@Nr5a2!0.71!4.09!Nr5a2;;chr11:98636508..98636524,-!p3@Nr1d1!0.70!5.17!Nr1d1;;chr2:91035254..91035271,-!p3@Nr1h3!0.70!5.17!Nr1h3;;chr17:48061381..48061399,-!p1@Foxp4!0.69!50.64!Foxp4;;chr2:75543089..75543122,-!p3@Nfe2l2!0.69!3.88!Nfe2l2;;chr4:94718879..94718898,-!p1@Jun!0.68!318.25!Jun;;chr5:140267476..140267493,+!p1@Mafk!0.68!24.35!Mafk;;chr10:107769168..107769215,+!p1@Pawr!0.67!43.09!Pawr;;chr6:39068210..39068251,-!p1@Parp12!0.67!19.39!Parp12;;chr3:128918433..128918448,+!p8@Pitx2!0.67!3.66!Pitx2;;chr12:85657780..85657815,+!p2@Zfp410!0.66!10.56!Zfp410;;chr13:44825008..44825066,+!p5@Jarid2!0.66!7.76!Jarid2;;chr10:80598209..80598236,+!p4@Zbtb7a!0.66!6.46!Zbtb7a;;chr5:120121020..120121049,+!p1@Tbx3!0.65!24.35!Tbx3;;chr18:11052485..11052508,+!p2@Gata6!0.65!10.99!Gata6;;chr13:112476296..112476308,+!p4@Mier3!0.65!4.09!Mier3;;chr9:43013917..43013968,-!p1@Pou2f3!0.65!3.45!Pou2f3;;chr5:32438831..32438878,+!p1@Fosl2!0.64!40.94!Fosl2;;chr11:98636531..98636559,-!p1@Nr1d1!0.64!22.19!Nr1d1;;chrX:7339938..7339963,+!p1@Tfe3!0.64!19.82!Tfe3;;chr4:148178529..148178548,+!p3@Casz1!0.64!8.83!Casz1;;chr10:127095407..127095440,+!p3@Stat6!0.64!4.31!Stat6;;chr19:53384985..53385042,+!p1@Mxi1!0.63!119.37!Mxi1;;chr4:124805092..124805135,-!p2@Zc3h12a!0.63!16.16!Zc3h12a;;chr7:134519511..134519534,-!p2@Zfp747!0.63!6.68!Zfp747;;chr2:146047829..146047847,+!p1@Insm1!0.63!6.46!Insm1;;chr12:113917014..113917034,+!p1@Zbtb42!0.63!6.25!Zbtb42;;chr1:189432634..189432643,+!p8@Esrrg!0.63!3.23!Esrrg;;chr12:86940338..86940357,+!p1@Jdp2!0.62!37.06!Jdp2;;chr15:101097270..101097290,+!p1@Nr4a1!0.61!37.71!Nr4a1;;chr8:79426176..79426275,+!p1@Nr3c2!0.61!17.88!Nr3c2;;chr2:166888058..166888105,-!p2@Znfx1!0.61!11.42!Znfx1;;chr4:135700687..135700719,+!p2@Id3!0.61!5.17!Id3;;chr8:47825203..47825225,+!p3@Irf2!0.61!4.31!Irf2;;chr4:122673278..122673336,+!p1@Mycl1!0.60!10.99!Mycl1;;chr5:104182694..104182724,+!p8@Aff1!0.60!3.88!Aff1;;chr5:148081686..148081715,+!p1@Pdx1!0.60!3.02!Pdx1;;chr18:644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@@ Line 36: / Line 41: @@
 |has_quality=
 |id=FF:11847-124I2
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011159
+|is_a=EFO:0002091;;FF:0011159
+|is_obsolete=
+|library_id=CNhs13240
+|library_id_phase_based=2:CNhs13240
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11847
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11847
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool3.CNhs13240.11847-124I2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool3.CNhs13240.11847-124I2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool3.CNhs13240.11847-124I2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool3.CNhs13240.11847-124I2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/GP2%252b%2520M%2520cell%252c%2520pool3.CNhs13240.11847-124I2.mm9.nobarcode.rdna.fa.gz
 |name=GP2+ M cell, pool3
 |namespace=
@@ Line 42: / Line 59: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13240,LSID1006,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0399845102340345,0,0,0,0,0,-0.122659156874358,0,0,0,0,-0.0843392403965415,0,0,0,0,0.21758520505126,0,-0.107148666299371,0,0,0,0.0847446845832032,0,0,0,0,0,0,0,0,0,-0.473678107740828,0,0.269952836963617,0,0,-0.0225657046614366,-0.166950383204225,-0.118590711954571,-0.00597650371040759,-0.984211366477826,-0.0533296672743855,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.317524407219623,0,-0.0528854793444415,0,0,-0.0411443860784561,-0.243225778194271,-0.310650657339386,-0.158091042771083,-0.12457533531859,0,0,-0.0858970819747225,-0.168217616753428,0,0,-0.0621689862148087,-0.0336839106622675,-0.235543518438072,0.00591308974329573,0,0,0,0,0,0.269952836963617,-0.139280638245452,-0.866705311942785,-0.092454241457989,0,0,0,0,0
 |rna_box=124
 |rna_catalog_number=
@@ Line 57: / Line 75: @@
 |rna_weight_ug=0.9834
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 95: @@
 |sample_tissue=ileum
 |top_motifs=ZEB1:2.6863348467;HNF4A_NR2F1,2:2.52998773865;NFKB1_REL_RELA:2.15677212293;SNAI1..3:2.09441164058;FOSL2:2.09246698317;ESRRA:2.03860094931;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.96564828493;NR6A1:1.78904560529;TBX4,5:1.76831738912;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.76379610421;HNF1A:1.72352542438;NFIX:1.67387810048;FOXN1:1.62491329954;NR1H4:1.56869611447;PPARG:1.51724619174;ARID5B:1.47309170227;FOXM1:1.26494319529;STAT5{A,B}:1.23323876032;FOS_FOS{B,L1}_JUN{B,D}:1.19195806093;IRF1,2:1.15883904237;ELK1,4_GABP{A,B1}:1.13069628858;PAX2:1.06723586622;AR:1.06711008653;bHLH_family:1.05298236249;ATF6:1.04602050232;MYOD1:1.04476382573;BACH2:0.938986423012;ATF5_CREB3:0.921852940052;HES1:0.90837977147;STAT1,3:0.897697791502;ADNP_IRX_SIX_ZHX:0.895073514077;ATF4:0.894192177389;LMO2:0.860866933643;STAT2,4,6:0.834564031253;PAX8:0.830020413075;TP53:0.827540805081;PDX1:0.809579504571;FOX{I1,J2}:0.77078755672;DMAP1_NCOR{1,2}_SMARC:0.744056257357;SP1:0.724401241739;NR5A1,2:0.685305457938;YY1:0.681472524471;LHX3,4:0.572860910485;GTF2A1,2:0.478397905171;XCPE1{core}:0.457723633032;TBP:0.440837198946;T:0.429398274496;CREB1:0.408574426035;HLF:0.405404021363;ONECUT1,2:0.385794315256;ZBTB6:0.363744577638;SPI1:0.358999564319;ZNF148:0.306845152427;ELF1,2,4:0.294433041148;VSX1,2:0.291908416662;ETS1,2:0.233858663062;POU2F1..3:0.231966532459;FOXL1:0.189819016911;TLX1..3_NFIC{dimer}:0.140223736954;ALX4:0.128952610371;EBF1:0.0996539539557;IRF7:0.089257946165;FOXA2:0.0694082225088;NFE2:0.0605208853016;ESR1:0.0170583004495;GATA6:0.0142175520479;NFY{A,B,C}:0.00479813419885;NKX6-1,2:-0.0361747825078;RXRA_VDR{dimer}:-0.0406616151526;MYB:-0.0477333011598;PAX6:-0.0660820777632;NFE2L2:-0.0796003733787;FOX{D1,D2}:-0.10022915273;CDX1,2,4:-0.101389723243;JUN:-0.125313754215;TFCP2:-0.143134001693;FOXO1,3,4:-0.14798480354;CRX:-0.178118715025;CUX2:-0.204558457166;POU1F1:-0.22977454009;NANOG:-0.249626848293;HIF1A:-0.250491573033;LEF1_TCF7_TCF7L1,2:-0.319343018562;RUNX1..3:-0.348751437994;GFI1:-0.366802526202;ZNF423:-0.395908195388;E2F1..5:-0.415181658625;SRF:-0.41970962792;ZNF143:-0.434514822653;TFAP4:-0.454728007856;OCT4_SOX2{dimer}:-0.456479703551;HSF1,2:-0.466631846437;MAFB:-0.473718515724;TEAD1:-0.531812270104;POU5F1:-0.556157188958;SREBF1,2:-0.572601636997;RORA:-0.5736358251;HBP1_HMGB_SSRP1_UBTF:-0.584428565662;NKX3-2:-0.624273098348;FOX{F1,F2,J1}:-0.648738632128;MED-1{core}:-0.657188263932;SOX17:-0.659382386282;FOXQ1:-0.662651203663;GFI1B:-0.676901970131;MEF2{A,B,C,D}:-0.687917913344;RFX1:-0.714223425751;EP300:-0.719733199073;HOX{A4,D4}:-0.723659684592;REST:-0.731563347078;TAL1_TCF{3,4,12}:-0.743987657703;NRF1:-0.749226017416;NFE2L1:-0.750179032033;POU6F1:-0.759270607737;TLX2:-0.842341550413;PRRX1,2:-0.846839198648;PAX5:-0.861564054512;NANOG{mouse}:-0.869911574033;AHR_ARNT_ARNT2:-0.878096089582;NFIL3:-0.918366004039;TFAP2B:-0.925278676968;TFAP2{A,C}:-0.946801581107;RFX2..5_RFXANK_RFXAP:-0.948242850788;SOX{8,9,10}:-0.967063316921;SPIB:-0.968266080707;ZFP161:-0.969678465257;HIC1:-0.979200189485;PAX1,9:-0.99047785731;CEBPA,B_DDIT3:-0.993452221101;HMX1:-1.00178634278;MAZ:-1.00727136502;POU3F1..4:-1.00823410962;GZF1:-1.02971914936;RXR{A,B,G}:-1.03064758261;HOX{A5,B5}:-1.03818486821;EGR1..3:-1.07693792047;CDC5L:-1.0903950925;SPZ1:-1.09407181163;SOX2:-1.10708318577;UFEwm:-1.13067594041;MYFfamily:-1.16468202476;PBX1:-1.17655157618;NKX2-3_NKX2-5:-1.17753975916;MTF1:-1.19578206037;NR3C1:-1.22209994289;FOXP3:-1.24402799888;BPTF:-1.24463637043;NHLH1,2:-1.24887056074;AIRE:-1.251390335;ATF2:-1.28446355332;TGIF1:-1.28722660447;GTF2I:-1.30991825906;HAND1,2:-1.31689544547;SMAD1..7,9:-1.31907249425;PITX1..3:-1.32111535534;DBP:-1.32180130034;NKX2-1,4:-1.3227270207;EVI1:-1.3396214147;BREu{core}:-1.34171992262;ZBTB16:-1.34220135273;GCM1,2:-1.37195560335;MTE{core}:-1.39833174264;NKX2-2,8:-1.413660994;MYBL2:-1.42646063722;TOPORS:-1.4354321779;RBPJ:-1.44511166048;SOX5:-1.45432008808;KLF4:-1.46601217384;ZNF384:-1.48404153085;HOXA9_MEIS1:-1.50276979574;ZNF238:-1.52359505133;PATZ1:-1.54126298287;TFDP1:-1.55675587225;MZF1:-1.60852194889;PRDM1:-1.75207823002;RREB1:-1.76865261167;GLI1..3:-1.80578530994;ZIC1..3:-1.83364749674;ALX1:-1.8759950111;GATA4:-1.91080652894;NFATC1..3:-1.91644227014;PAX4:-1.93531104423;HMGA1,2:-1.97028040267;IKZF1:-1.99965231551;FOXD3:-2.05470497939;FOXP1:-2.12142480437;EN1,2:-2.14254822203;NKX3-1:-2.22253773716;TEF:-2.26365819271;IKZF2:-2.26866314872
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11847-124I2;search_select_hide=table117:11847-124I2
 }}

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FF:11847-124I2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:23, 4 June 2020

CNhs13240

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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