FF:11853-124I8: Difference between revisions

Latest revision as of 18:23, 4 June 2020

Name:	CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool2
Species:	Mouse (Mus musculus)
Library ID:	CNhs13210
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	enterocyte
cell line	NA
company	NA
collaboration	Shinji Fukuda (RCAI)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	RANKL_Ephigh_b
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		SAMD00005805

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13210		CAGE		DRX008789		DRR009661

Accession ID Mm9

Library id		BAM		CTSS
CNhs13210		DRZ001086		DRZ002471

Accession ID Mm10

Library id		BAM		CTSS
CNhs13210		DRZ012436		DRZ013821

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

CNhs13210

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0749
1002	-0.116
1003	-0.156
1004	0
1005	1.167
1006	-0.344
1007	0.0296
1008	2.264
1009	-0.19
101	-0.0219
1010	0
1011	-0.337
1012	0
1013	0.238
1014	-0.0874
1015	-0.206
1016	-0.378
1017	0
1018	0.606
1019	0
102	0
1020	0
1021	0.409
1022	-0.0704
1023	0
1024	-0.18
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.0989
103	-0.0861
1030	0
1031	-1.026
1032	0.577
1033	0.0913
1034	0
1035	0
1036	-0.0104
1037	0
1038	0.0677
1039	-0.0327
104	0
1040	-0.564
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: CNhs13210

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.103
MA0003.1	MA0003.1	0.287
MA0004.1	MA0004.1	0.517
MA0006.1	MA0006.1	0.0969
MA0007.1	MA0007.1	0.323
MA0009.1	MA0009.1	0.0895
MA0014.1	MA0014.1	0.0378
MA0017.1	MA0017.1	3.36802e-23
MA0018.2	MA0018.2	0.02
MA0019.1	MA0019.1	0.186
MA0024.1	MA0024.1	0.754
MA0025.1	MA0025.1	0.695
MA0027.1	MA0027.1	0.49
MA0028.1	MA0028.1	0.00977
MA0029.1	MA0029.1	0.91
MA0030.1	MA0030.1	0.653
MA0031.1	MA0031.1	0.452
MA0035.2	MA0035.2	1.17015e-5
MA0038.1	MA0038.1	0.495
MA0039.2	MA0039.2	5.8337e-6
MA0040.1	MA0040.1	0.274
MA0041.1	MA0041.1	0.192
MA0042.1	MA0042.1	0.286
MA0043.1	MA0043.1	0.129
MA0046.1	MA0046.1	4.26875e-45
MA0047.2	MA0047.2	0.00168
MA0048.1	MA0048.1	0.141
MA0050.1	MA0050.1	0.00262
MA0051.1	MA0051.1	1.12068e-4
MA0052.1	MA0052.1	0.181
MA0055.1	MA0055.1	0.0496
MA0057.1	MA0057.1	0.0624
MA0058.1	MA0058.1	0.601
MA0059.1	MA0059.1	0.409
MA0060.1	MA0060.1	0.228
MA0061.1	MA0061.1	7.7545e-5
MA0062.2	MA0062.2	1.55812e-5
MA0065.2	MA0065.2	3.52239e-12
MA0066.1	MA0066.1	0.398
MA0067.1	MA0067.1	0.583
MA0068.1	MA0068.1	0.194
MA0069.1	MA0069.1	0.686
MA0070.1	MA0070.1	0.121
MA0071.1	MA0071.1	0.1
MA0072.1	MA0072.1	0.491
MA0073.1	MA0073.1	0.778
MA0074.1	MA0074.1	0.527
MA0076.1	MA0076.1	0.0574
MA0077.1	MA0077.1	0.196
MA0078.1	MA0078.1	0.393
MA0079.2	MA0079.2	0.658
MA0080.2	MA0080.2	2.58896e-5
MA0081.1	MA0081.1	0.75
MA0083.1	MA0083.1	0.76
MA0084.1	MA0084.1	0.305
MA0087.1	MA0087.1	0.263
MA0088.1	MA0088.1	0.243
MA0090.1	MA0090.1	0.678
MA0091.1	MA0091.1	0.718
MA0092.1	MA0092.1	0.832
MA0093.1	MA0093.1	0.577
MA0099.2	MA0099.2	6.51633e-8
MA0100.1	MA0100.1	0.691
MA0101.1	MA0101.1	3.36269e-8
MA0102.2	MA0102.2	0.435
MA0103.1	MA0103.1	8.97431e-9
MA0104.2	MA0104.2	0.972
MA0105.1	MA0105.1	0.0527
MA0106.1	MA0106.1	0.198
MA0107.1	MA0107.1	5.19768e-8
MA0108.2	MA0108.2	3.08393e-5
MA0111.1	MA0111.1	0.508
MA0112.2	MA0112.2	0.0461
MA0113.1	MA0113.1	0.816
MA0114.1	MA0114.1	1.65353e-27
MA0115.1	MA0115.1	7.85144e-12
MA0116.1	MA0116.1	0.341
MA0117.1	MA0117.1	0.441
MA0119.1	MA0119.1	0.281
MA0122.1	MA0122.1	0.964
MA0124.1	MA0124.1	0.42
MA0125.1	MA0125.1	0.856
MA0131.1	MA0131.1	0.867
MA0135.1	MA0135.1	0.167
MA0136.1	MA0136.1	7.90358e-10
MA0137.2	MA0137.2	0.00324
MA0138.2	MA0138.2	0.729
MA0139.1	MA0139.1	0.224
MA0140.1	MA0140.1	0.103
MA0141.1	MA0141.1	3.38426e-5
MA0142.1	MA0142.1	0.139
MA0143.1	MA0143.1	0.0514
MA0144.1	MA0144.1	5.37654e-4
MA0145.1	MA0145.1	0.0302
MA0146.1	MA0146.1	0.222
MA0147.1	MA0147.1	0.781
MA0148.1	MA0148.1	0.00129
MA0149.1	MA0149.1	0.0162
MA0150.1	MA0150.1	0.0488
MA0152.1	MA0152.1	0.057
MA0153.1	MA0153.1	1.58466e-35
MA0154.1	MA0154.1	0.174
MA0155.1	MA0155.1	0.555
MA0156.1	MA0156.1	1.73224e-5
MA0157.1	MA0157.1	0.799
MA0159.1	MA0159.1	1.23679e-4
MA0160.1	MA0160.1	1.53059e-4
MA0162.1	MA0162.1	0.913
MA0163.1	MA0163.1	0.36
MA0164.1	MA0164.1	0.565
MA0258.1	MA0258.1	0.186
MA0259.1	MA0259.1	0.976

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: CNhs13210

Novel motif	Logo	P-value
1	1	0.239
10	10	0.186
100	100	0.627
101	101	0.552
102	102	0.977
103	103	0.91
104	104	0.942
105	105	0.408
106	106	0.0116
107	107	0.151
108	108	0.543
109	109	0.0423
11	11	0.219
110	110	0.433
111	111	0.271
112	112	0.0515
113	113	0.0875
114	114	0.311
115	115	0.821
116	116	0.0962
117	117	0.0151
118	118	0.707
119	119	0.208
12	12	0.341
120	120	0.487
121	121	0.247
122	122	0.907
123	123	0.0673
124	124	0.0829
125	125	0.296
126	126	0.00505
127	127	0.277
128	128	0.143
129	129	0.407
13	13	1.17612e-5
130	130	0.864
131	131	0.581
132	132	0.808
133	133	0.627
134	134	0.706
135	135	0.0305
136	136	7.02375e-4
137	137	0.501
138	138	0.541
139	139	0.523
14	14	0.877
140	140	0.857
141	141	0.312
142	142	0.486
143	143	0.292
144	144	0.056
145	145	0.0622
146	146	0.265
147	147	0.907
148	148	0.804
149	149	0.514
15	15	0.259
150	150	0.422
151	151	0.716
152	152	0.0167
153	153	0.462
154	154	0.855
155	155	0.461
156	156	0.0539
157	157	0.359
158	158	0.813
159	159	0.685
160	160	0.575
161	161	0.668
162	162	0.596
163	163	0.251
164	164	0.0998
165	165	0.193
166	166	0.522
167	167	0.494
168	168	0.422
169	169	0.0849
17	17	0.0428
18	18	0.695
19	19	0.564
2	2	0.823
20	20	0.261
21	21	0.61
22	22	0.537
23	23	0.995
24	24	0.494
25	25	0.388
26	26	0.00505
27	27	0.802
28	28	0.567
29	29	0.0376
3	3	0.292
30	30	0.463
31	31	0.726
32	32	0.555
33	33	0.207
34	34	0.787
35	35	0.945
36	36	0.365
37	37	0.0575
38	38	0.714
39	39	0.483
4	4	0.152
40	40	0.124
41	41	0.159
42	42	0.746
43	43	0.639
44	44	0.246
45	45	0.525
46	46	0.339
47	47	0.615
48	48	0.316
49	49	0.898
5	5	0.9
50	50	0.656
51	51	0.897
52	52	0.177
53	53	0.332
54	54	0.618
55	55	0.838
56	56	0.566
57	57	0.871
58	58	0.39
59	59	0.476
6	6	0.927
60	60	0.0313
61	61	0.252
62	62	0.329
63	63	0.218
64	64	0.915
65	65	0.508
66	66	0.578
67	67	0.635
68	68	0.13
69	69	0.964
7	7	0.0664
70	70	0.0204
71	71	0.115
72	72	0.411
73	73	0.012
74	74	0.206
75	75	0.0129
76	76	0.643
77	77	0.0533
78	78	0.0575
79	79	1
8	8	0.267
80	80	0.663
81	81	0.632
82	82	0.449
83	83	0.842
84	84	0.149
85	85	0.224
86	86	0.102
87	87	0.00129
88	88	0.186
89	89	0.43
9	9	0.837
90	90	0.24
91	91	0.824
92	92	0.918
93	93	0.143
94	94	0.735
95	95	0.00553
96	96	0.854
97	97	0.724
98	98	0.664
99	99	0.47

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: CNhs13210

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011445 CD326-positive+ enterocyte isolated from mice- treated with RANKL- day03

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)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0000239 (brush border epithelial cell)
0000677 (gut absorptive cell)
0000212 (absorptive cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0000584 (enterocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000160 (intestine)
0000483 (epithelium)
0001242 (intestinal mucosa)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0005911 (endo-epithelium)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0000485 (simple columnar epithelium)
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004808 (gastrointestinal system epithelium)
0001277 (intestinal epithelium)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000383 (3 days sample)
0000627 (RANK ligand treatment sample)
0011445 (CD326-positive+ enterocyte isolated from mice- treated with RANKL- day03)

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:0000223 (endodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005805
+|accession_numbers=CAGE;DRX008789;DRR009661;DRZ001086;DRZ002471;DRZ012436;DRZ013821
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000483,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0005911,UBERON:0004923,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0000490,UBERON:0001262,UBERON:0004786,UBERON:0000485,UBERON:0003350,UBERON:0003929,UBERON:0004808,UBERON:0001277,UBERON:0010317,UBERON:0001555,UBERON:0005409
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000075,CL:0000066,CL:0002371,CL:0002563,CL:0000255,CL:0000239,CL:0000677,CL:0000212,CL:0002076,CL:0002251,CL:0000584
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr7:51787434..51787448,-!p1@Spib!2.73!757.61!Spib;;chr2:163332558..163332596,+!p2@Hnf4a!2.24!174.51!Hnf4a;;chr10:80555320..80555378,-!p1@Creb3l3!2.09!139.70!Creb3l3;;chr17:27865882..27865901,-!p1@Spdef!2.05!110.03!Spdef;;chr3:3634145..3634161,+!p1@Hnf4g!2.04!109.33!Hnf4g;;chr1:137155026..137155042,-!p1@Elf3!1.95!487.78!Elf3;;chr18:61195865..61195880,-!p1@Cdx1!1.90!77.79!Cdx1;;chr6:64679112..64679126,+!p1@Atoh1!1.85!70.55!Atoh1;;chr5:148118639..148118715,-!p1@Cdx2!1.84!67.51!Cdx2;;chr7:19608891..19608895,-!p1@Foxa3!1.83!85.50!Foxa3;;chr6:86619104..86619119,-!p1@Mxd1!1.71!387.56!Mxd1;;chr2:163372884..163372904,+!p1@Hnf4a!1.68!46.96!Hnf4a;;chr8:77396591..77396639,+!p1@Isx!1.66!44.62!Isx;;chr1:193007123..193007139,-!p1@Atf3!1.65!234.55!Atf3;;chr2:79296783..79296801,-!p1@Neurod1!1.65!43.22!Neurod1;;chr3:3508024..3508069,+!p2@Hnf4g!1.63!41.58!Hnf4g;;chr12:86814833..86814846,+!p1@Fos!1.61!881.65!Fos;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.60!48.59!Zbtb11;;chr18:61195843..61195864,-!p2@Cdx1!1.60!38.78!Cdx1;;chr5:135582751..135582788,+!p1@Mlxipl!1.58!143.20!Mlxipl;;chr4:124805061..124805087,-!p1@Zc3h12a!1.54!101.62!Zc3h12a;;chr2:103143336..103143367,-!p1@Ehf!1.53!52.80!Ehf;;chr14:63864056..63864102,-!p1@Gata4!1.52!54.20!Gata4;;chr10:88969376..88969395,-!p1@Nr1h4!1.52!31.77!Nr1h4;;chr16:38294860..38294924,-!p1@Nr1i2!1.51!31.30!Nr1i2;;chr18:64499674..64499696,+!p1@Onecut2!1.50!51.63!Onecut2;;chr12:58646974..58647003,-!p1@Foxa1!1.44!35.28!Foxa1;;chr4:122673187..122673201,+!p2@Mycl1!1.43!44.85!Mycl1;;chr7:19895354..19895369,-!p1@Fosb!1.43!35.28!Fosb;;chr2:180069370..180069409,-!p1@Gata5!1.43!30.60!Gata5;;chr18:64499706..64499721,+!p2@Onecut2!1.42!35.04!Onecut2;;chr19:5560600..5560617,-!p1@Ovol1!1.41!29.67!Ovol1;;chr7:19895384..19895399,-!p2@Fosb!1.40!34.11!Fosb;;chr2:133377954..133377973,+!p1@Bmp2!1.36!68.92!Bmp2;;chr14:99697871..99697934,+!p1@Klf5!1.32!382.89!Klf5;;chr17:25707623..25707639,-!p1@Sox8!1.32!83.63!Sox8;;chr18:35020854..35020869,+!p1@Egr1!1.30!700.37!Egr1;;chr5:115421065..115421088,-!p1@Hnf1a!1.30!19.16!Hnf1a;;chr10:61595830..61595846,+!p1@Neurog3!1.29!18.46!Neurog3;;chr5:148118840..148118857,-!p2@Cdx2!1.27!17.75!Cdx2;;chr2:103123925..103123959,-!p3@Ehf!1.26!17.05!Ehf;;chr5:120121169..120121171,+!p4@Tbx3!1.25!30.14!Tbx3;;chr2:103143315..103143328,-!p2@Ehf!1.23!15.89!Ehf;;chr1:194979315..194979359,+!p1@Irf6!1.22!92.98!Irf6;;chr10:20880629..20880683,-!p1@Myb!1.22!44.15!Myb;;chr17:28409136..28409150,+!p3@Ppard!1.20!14.95!Ppard;;chr9:43013917..43013968,-!p1@Pou2f3!1.20!14.95!Pou2f3;;chr19:46380235..46380277,+!p3@Nfkb2!1.18!30.60!Nfkb2;;chr12:56593574..56593592,-!p1@Nfkbia!1.15!659.72!Nfkbia;;chr19:46379199..46379301,+!p1@Nfkb2!1.15!74.29!Nfkb2;;chr15:97738692..97738747,-!p1@Vdr!1.13!67.75!Vdr;;chr5:148118792..148118806,-!p3@Cdx2!1.13!12.62!Cdx2;;chr8:77396650..77396662,+!p4@Isx!1.13!12.38!Isx;;chr8:87502608..87502623,-!p1@Junb!1.12!196.70!Junb;;chr2:146047829..146047847,+!p1@Insm1!1.12!22.19!Insm1;;chr3:90046995..90047031,-!p2@Creb3l4!1.12!15.42!Creb3l4;;chr4:87452180..87452196,-!p3@Mllt3!1.10!22.89!Mllt3;;chr2:28477452..28477483,-!p1@Gfi1b!1.10!14.48!Gfi1b;;chr8:77397492..77397514,+!p3@Isx!1.10!11.45!Isx;;chr4:87452200..87452229,-!p2@Mllt3!1.09!24.06!Mllt3;;chr7:20214704..20214800,-!p1@Relb!1.08!35.98!Relb;;chr10:67000609..67000625,+!p1@Egr2!1.08!25.46!Egr2;;chr5:144951153..144951203,+!p1@Bhlha15!1.08!16.12!Bhlha15;;chr11:53583544..53583559,+!p1@Irf1!1.06!174.51!Irf1;;chr15:79177964..79177986,+!p1@Maff!1.05!35.51!Maff;;chr4:148178559..148178603,+!p1@Casz1!1.05!29.90!Casz1;;chr7:20408047..20408125,-!p1@Bcl3!1.04!114.70!Bcl3;;chr2:147871627..147871641,-!p1@Foxa2!1.04!10.05!Foxa2;;chr1:39250584..39250643,+!p1@Npas2!1.02!48.83!Npas2;;chr7:20213752..20213778,-!p2@Relb!1.01!9.34!Relb;;chr6:39068163..39068176,-!p2@Parp12!1.00!17.29!Parp12;;chr3:128916868..128916890,+!p1@Pitx2!1.00!12.38!Pitx2;;chr15:101097270..101097290,+!p1@Nr4a1!0.99!91.58!Nr4a1;;chr7:20162663..20162678,+!p1@Zfp296!0.99!11.68!Zfp296;;chr19:5447692..5447711,+!p2@Fosl1!0.99!8.88!Fosl1;;chr11:70500401..70500460,-!p3@Camta2!0.98!8.64!Camta2;;chr8:77397095..77397127,+!p2@Isx!0.98!8.64!Isx;;chr7:31206743..31206761,+!p1@Nfkbid!0.97!11.45!Nfkbid;;chr10:51397572..51397595,+!p1@Rfx6!0.96!8.18!Rfx6;;chr7:150155143..150155156,-!p1@Ascl2!0.94!7.71!Ascl2;;chr16:55822241..55822258,-!p1@Nfkbiz!0.93!244.59!Nfkbiz;;chr13:44825008..44825066,+!p5@Jarid2!0.93!15.18!Jarid2;;chr19:6996243..6996293,-!p1@Esrra!0.92!83.17!Esrra;;chr7:148452314..148452329,-!p1@Irf7!0.92!52.56!Irf7;;chr19:55816546..55816556,+!p3@Tcf7l2!0.90!27.33!Tcf7l2;;chr1:173144100..173144138,+!p2@Nr1i3!0.90!7.01!Nr1i3;;chr5:148118614..148118625,-!p4@Cdx2!0.89!6.77!Cdx2;;chr3:128918394..128918413,+!p5@Pitx2!0.89!6.77!Pitx2;;chr3:94176733..94176794,+!p1@Rorc!0.87!53.03!Rorc;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.87!19.39!Tfcp2l1;;chr18:11052606..11052633,+!p4@Gata6!0.87!16.82!Gata6;;chr1:194979361..194979373,+!p2@Irf6!0.87!8.88!Irf6;;chr2:163372869..163372882,+!p3@Hnf4a!0.86!6.31!Hnf4a;;chr14:76887526..76887555,+!p10@Tsc22d1!0.86!6.31!Tsc22d1;;chr18:11052642..11052659,+!p1@Gata6!0.84!32.00!Gata6;;chr15:35225845..35225867,+!p1@Osr2!0.84!15.65!Osr2;;chr7:87170879..87170914,+!p2@Zfp710!0.84!14.25!Zfp710;;chr2:173044357..173044377,-!p2@Zbp1!0.84!8.64!Zbp1;;chr5:148118809..148118832,-!p5@Cdx2!0.84!5.84!Cdx2;;chr10:107769168..107769215,+!p1@Pawr!0.82!61.67!Pawr;;chr3:135354384..135354443,-!p1@Nfkb1!0.82!36.68!Nfkb1;;chr8:73222425..73222444,+!p2@Jund!0.82!5.61!Jund;;chr10:80555398..80555409,-!p2@Creb3l3!0.82!5.61!Creb3l3;;chr8:125778192..125778217,+!p2@Zfp276!0.80!16.12!Zfp276;;chr4:94718861..94718872,-!p2@Jun!0.79!41.82!Jun;;chr10:80600749..80600766,+!p2@Zbtb7a!0.79!29.20!Zbtb7a;;chr2:173044380..173044432,-!p1@Zbp1!0.79!13.08!Zbp1;;chr1:189432634..189432643,+!p8@Esrrg!0.79!5.14!Esrrg;;chr17:45692676..45692695,+!p2@Nfkbie!0.77!10.51!Nfkbie;;chr8:77397190..77397202,+!p5@Isx!0.77!4.91!Isx;;chr19:10315179..10315241,-!p1@Gm98!0.75!53.50!Gm98;;chr19:5560570..5560582,-!p2@Ovol1!0.75!4.67!Ovol1;;chr3:3508005..3508021,+!p3@Hnf4g!0.75!4.67!Hnf4g;;chr18:36953486..36953503,+!p2@Zmat2!0.74!7.94!Zmat2;;chr5:77524250..77524300,-!p1@Hopx!0.73!99.52!Hopx;;chr17:45692642..45692663,+!p1@Nfkbie!0.73!15.18!Nfkbie;;chr11:106128936..106128955,-!p4@Smarcd2!0.73!5.14!Smarcd2;;chr3:51144740..51144743,-!p7@Elf2!0.72!7.48!Elf2;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.72!6.31!Carhsp1;;chr4:148178459..148178482,+!p4@Casz1!0.72!4.21!Casz1;;chr8:123260252..123260264,+!p1@Irf8!0.71!32.47!Irf8;;chr5:140267510..140267555,+!p2@Mafk!0.71!10.51!Mafk;;chr2:152561980..152561997,+!p1@Id1!0.70!132.69!Id1;;chr13:5860776..5860796,+!p1@Klf6!0.70!109.33!Klf6;;chr17:34784073..34784118,+!p2@Atf6b!0.70!18.22!Atf6b;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!0.70!10.75!Hmga1;;chr10:127095407..127095440,+!p3@Stat6!0.70!5.14!Stat6;;chr14:63890519..63890539,-!p3@Gata4!0.70!3.97!Gata4;;chr4:94718879..94718898,-!p1@Jun!0.69!324.02!Jun;;chr4:55545337..55545357,-!p1@Klf4!0.69!65.18!Klf4;;chr8:79426176..79426275,+!p1@Nr3c2!0.69!21.73!Nr3c2;;chr17:48061381..48061399,-!p1@Foxp4!0.68!49.76!Foxp4;;chr5:77524231..77524245,-!p3@Hopx!0.68!10.51!Hopx;;chr18:35020615..35020641,+!p2@Egr1!0.68!4.67!Egr1;;chr4:135728581..135728668,+!p1@E2f2!0.67!19.86!E2f2;;chr4:124805092..124805135,-!p2@Zc3h12a!0.67!17.75!Zc3h12a;;chr10:107769219..107769226,+!p5@Pawr!0.67!4.67!Pawr;;chr11:96690797..96690813,-!p1@Nfe2l1!0.66!80.13!Nfe2l1;;chr3:89197057..89197114,-!p1@Zbtb7b!0.66!13.78!Zbtb7b;;chr4:122673278..122673336,+!p1@Mycl1!0.66!12.62!Mycl1;;chr10:30375579..30375616,-!p3@Ncoa7!0.66!9.34!Ncoa7;;chr10:107769229..107769238,+!p3@Pawr!0.66!5.37!Pawr;;chrX:90531838..90531861,+!p1@Arx!0.66!4.67!Arx;;chr4:148178529..148178548,+!p3@Casz1!0.65!9.11!Casz1;;chr6:115310872..115310899,+!p2@Pparg!0.65!6.54!Pparg;;chr15:37162834..37162849,+!p2@Grhl2!0.65!4.21!Grhl2;;chr9:31720843..31720888,-!p1@Barx2!0.65!3.97!Barx2;;chr5:148081686..148081715,+!p1@Pdx1!0.65!3.50!Pdx1;;chr3:90046983..90046994,-!p6@Creb3l4!0.65!3.50!Creb3l4;;chr11:96153767..96153822,+!p1@Hoxb6!0.64!5.61!Hoxb6;;chr11:98636400..98636418,-!p4@Nr1d1!0.64!4.67!Nr1d1;;chr8:124806048..124806094,+!p1@Zfpm1!0.63!35.28!Zfpm1;;chr11:83664334..83664353,+!p2@Hnf1b!0.63!3.27!Hnf1b;;chr5:115420882..115420896,-!p3@Hnf1a!0.63!3.27!Hnf1a;;chr11:100948597..100948637,+!p1@Mlx!0.62!89.94!Mlx;;chr13:55932591..55932622,-!p1@Pitx1!0.62!3.97!Pitx1;;chr1:138846047..138846074,-!p5@Nr5a2!0.62!3.50!Nr5a2;;chr7:35904304..35904320,+!p1@Cebpa!0.61!75.22!Cebpa;;chr17:48061584..48061601,-!p2@Foxp4!0.61!23.83!Foxp4;;chr13:112476264..112476282,+!p3@Mier3!0.61!4.67!Mier3;;chr2:180069410..180069421,-!p3@Gata5!0.61!3.04!Gata5;;chr2:105509045..105509071,+!p1@Pax6!0.61!3.04!Pax6;;chr1:6720216..6720232,+!p1@St18!0.61!3.04!St18;;chr1:138857076..138857105,-!p1@Nr5a2!0.61!3.04!Nr5a2;;chr7:138697803..138697813,+!p1@Hmx2!0.61!3.04!Hmx2;;chr10:80555299..80555306,-!p3@Creb3l3!0.61!3.04!Creb3l3;;chr19:46380172..46380231,+!p2@Nfkb2!0.60!24.30!Nfkb2;;chr17:27693746..27693759,+!p6@Hmga1-rs1,p7@Hmga1!0.60!6.54!Hmga1;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.60!5.14!Ncoa4;;chr6:86619130..86619158,-!p2@Mxd1!0.59!51.16!Mxd1;;chr2:162880387..162880413,+!p1@Mybl2!0.59!21.96!Mybl2;;chr8:73905344..73905381,-!p2@Nr2f6!0.59!7.94!Nr2f6;;chr15:37162796..37162828,+!p1@Grhl2!0.59!5.37!Grhl2;;chr3:87329568..87329589,+!p2@Etv3!0.59!4.21!Etv3;;chr14:79915425..79915501,+!p1@Elf1!0.58!30.60!Elf1;;chr15:25914114..25914128,+!p2@Zfp622!0.58!13.55!Zfp622;;chr13:55932739..55932756,-!p5@Pitx1!0.58!2.80!Pitx1;;chr2:180069423..180069434,-!p2@Gata5!0.58!2.80!Gata5;;chr5:29805118..29805137,-!p1@Mnx1!0.58!2.80!Mnx1;;chr19:46380399..46380417,+!p4@Nfkb2!0.58!2.80!Nfkb2;;chr10:80555285..80555291,-!p4@Creb3l3!0.58!2.80!Creb3l3;;chr5:76733981..76734018,-!p3@Clock!0.57!6.54!Clock;;chr5:77543897..77543911,-!p2@Hopx!0.57!5.84!Hopx;;chr10:80599248..80599261,+!p3@Zbtb7a!0.57!5.37!Zbtb7a;;chr7:134376558..134376587,+!p2@Zfp553!0.57!5.14!Zfp553;;chr14:52634651..52634678,-!p7@Z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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011445
 |is_obsolete=
+|library_id=CNhs13210
+|library_id_phase_based=2:CNhs13210
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11853
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11853
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool2.CNhs13210.11853-124I8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool2.CNhs13210.11853-124I8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool2.CNhs13210.11853-124I8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool2.CNhs13210.11853-124I8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool2.CNhs13210.11853-124I8.mm9.nobarcode.rdna.fa.gz
 |name=CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool2
 |namespace=
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13210,LSID1004,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0345471955650915,0,0,0,0,0,-0.297597425870067,0,0,0,0,-0.0843392403965415,0,0,0,0,0.0455894054315693,0,-0.191893350882575,0,0,0,0.0911788108631387,0,0,0,0,0,0,0,0,0.0455894054315693,-0.391925990773456,0,0.420828164225892,0,0.0911788108631387,-0.0052454066426001,-0.163733320064257,-0.0644077607709621,-0.0124638809378825,-0.984211366477826,-0.0392057077178569,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.123649846467701,0,-0.0153651003045395,0,0,-0.0316393102377815,-0.210777516709381,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.0797400615313424,-0.0880345464377128,0,0,-0.0843999432013821,0.010432418936116,0.294772478279816,-0.0788315948399074,0,0,0,0,0,0.420828164225892,0.239903167028717,0.165452757619591,0.670077207741203,0,0,0,0,0
 |rna_box=124
 |rna_catalog_number=
@@ Line 61: / Line 76: @@
 |rna_weight_ug=1.3101
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11853-124I8;search_select_hide=table117:11853-124I8
 }}

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FF:11853-124I8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:23, 4 June 2020

CNhs13210

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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