FF:11852-124I7: Difference between revisions

Latest revision as of 18:23, 4 June 2020

Name:	CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool1
Species:	Mouse (Mus musculus)
Library ID:	CNhs13236
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_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		SAMD00004708

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13236		CAGE		DRX008764		DRR009636

Accession ID Mm9

Library id		BAM		CTSS
CNhs13236		DRZ001061		DRZ002446

Accession ID Mm10

Library id		BAM		CTSS
CNhs13236		DRZ012411		DRZ013796

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

CNhs13236

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0749
1002	-0.116
1003	-0.175
1004	0
1005	1.1
1006	-0.19
1007	0.182
1008	1.638
1009	-0.19
101	-0.0436
1010	0
1011	-0.337
1012	0
1013	0.266
1014	-0.0874
1015	-0.166
1016	-0.465
1017	0
1018	0.4
1019	0
102	0
1020	0
1021	0
1022	-0.0704
1023	0
1024	-0.14
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.148
103	-0.0887
1030	0
1031	-1.067
1032	0.661
1033	0.102
1034	0
1035	0
1036	0.0598
1037	0
1038	0.081
1039	0.0257
104	0
1040	-0.603
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: CNhs13236

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0696
MA0003.1	MA0003.1	0.476
MA0004.1	MA0004.1	0.371
MA0006.1	MA0006.1	0.0724
MA0007.1	MA0007.1	0.216
MA0009.1	MA0009.1	0.121
MA0014.1	MA0014.1	0.0335
MA0017.1	MA0017.1	9.16996e-22
MA0018.2	MA0018.2	8.37433e-5
MA0019.1	MA0019.1	0.0842
MA0024.1	MA0024.1	0.999
MA0025.1	MA0025.1	0.173
MA0027.1	MA0027.1	0.403
MA0028.1	MA0028.1	5.86277e-4
MA0029.1	MA0029.1	0.966
MA0030.1	MA0030.1	0.224
MA0031.1	MA0031.1	0.217
MA0035.2	MA0035.2	8.46445e-6
MA0038.1	MA0038.1	0.944
MA0039.2	MA0039.2	1.06561e-5
MA0040.1	MA0040.1	0.145
MA0041.1	MA0041.1	0.181
MA0042.1	MA0042.1	0.272
MA0043.1	MA0043.1	0.00349
MA0046.1	MA0046.1	1.20228e-54
MA0047.2	MA0047.2	1.00082e-4
MA0048.1	MA0048.1	0.121
MA0050.1	MA0050.1	0.00466
MA0051.1	MA0051.1	4.56543e-5
MA0052.1	MA0052.1	0.765
MA0055.1	MA0055.1	0.0254
MA0057.1	MA0057.1	0.0557
MA0058.1	MA0058.1	0.444
MA0059.1	MA0059.1	0.855
MA0060.1	MA0060.1	0.00361
MA0061.1	MA0061.1	9.78695e-5
MA0062.2	MA0062.2	1.74093e-9
MA0065.2	MA0065.2	1.54978e-10
MA0066.1	MA0066.1	0.468
MA0067.1	MA0067.1	0.317
MA0068.1	MA0068.1	0.219
MA0069.1	MA0069.1	0.755
MA0070.1	MA0070.1	0.362
MA0071.1	MA0071.1	0.126
MA0072.1	MA0072.1	0.787
MA0073.1	MA0073.1	0.998
MA0074.1	MA0074.1	0.478
MA0076.1	MA0076.1	0.00483
MA0077.1	MA0077.1	0.0813
MA0078.1	MA0078.1	0.396
MA0079.2	MA0079.2	0.1
MA0080.2	MA0080.2	4.43844e-6
MA0081.1	MA0081.1	0.431
MA0083.1	MA0083.1	0.752
MA0084.1	MA0084.1	0.197
MA0087.1	MA0087.1	0.257
MA0088.1	MA0088.1	0.545
MA0090.1	MA0090.1	0.439
MA0091.1	MA0091.1	0.393
MA0092.1	MA0092.1	0.68
MA0093.1	MA0093.1	0.406
MA0099.2	MA0099.2	1.80478e-9
MA0100.1	MA0100.1	0.626
MA0101.1	MA0101.1	2.25768e-10
MA0102.2	MA0102.2	0.98
MA0103.1	MA0103.1	9.5557e-9
MA0104.2	MA0104.2	0.75
MA0105.1	MA0105.1	0.713
MA0106.1	MA0106.1	0.586
MA0107.1	MA0107.1	4.803e-9
MA0108.2	MA0108.2	3.04079e-6
MA0111.1	MA0111.1	0.261
MA0112.2	MA0112.2	0.507
MA0113.1	MA0113.1	0.567
MA0114.1	MA0114.1	9.30992e-32
MA0115.1	MA0115.1	1.39109e-11
MA0116.1	MA0116.1	0.517
MA0117.1	MA0117.1	0.228
MA0119.1	MA0119.1	0.522
MA0122.1	MA0122.1	0.677
MA0124.1	MA0124.1	0.482
MA0125.1	MA0125.1	0.758
MA0131.1	MA0131.1	0.77
MA0135.1	MA0135.1	0.0987
MA0136.1	MA0136.1	2.87744e-11
MA0137.2	MA0137.2	0.00646
MA0138.2	MA0138.2	0.298
MA0139.1	MA0139.1	0.592
MA0140.1	MA0140.1	0.263
MA0141.1	MA0141.1	2.47823e-4
MA0142.1	MA0142.1	0.0696
MA0143.1	MA0143.1	0.0454
MA0144.1	MA0144.1	5.94089e-4
MA0145.1	MA0145.1	0.0303
MA0146.1	MA0146.1	0.0826
MA0147.1	MA0147.1	0.891
MA0148.1	MA0148.1	6.30158e-4
MA0149.1	MA0149.1	0.0333
MA0150.1	MA0150.1	0.0189
MA0152.1	MA0152.1	0.192
MA0153.1	MA0153.1	6.99264e-35
MA0154.1	MA0154.1	0.66
MA0155.1	MA0155.1	0.372
MA0156.1	MA0156.1	2.9341e-7
MA0157.1	MA0157.1	0.931
MA0159.1	MA0159.1	0.00102
MA0160.1	MA0160.1	1.01971e-4
MA0162.1	MA0162.1	0.619
MA0163.1	MA0163.1	0.342
MA0164.1	MA0164.1	0.842
MA0258.1	MA0258.1	0.701
MA0259.1	MA0259.1	0.997

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: CNhs13236

Novel motif	Logo	P-value
1	1	0.485
10	10	0.546
100	100	0.82
101	101	0.45
102	102	0.882
103	103	0.5
104	104	0.992
105	105	0.205
106	106	0.00365
107	107	0.132
108	108	0.566
109	109	0.0631
11	11	0.357
110	110	0.729
111	111	0.598
112	112	0.0759
113	113	0.0584
114	114	0.965
115	115	0.675
116	116	0.357
117	117	0.0189
118	118	0.866
119	119	0.289
12	12	0.691
120	120	0.547
121	121	0.142
122	122	0.984
123	123	0.0339
124	124	0.0146
125	125	0.512
126	126	0.00707
127	127	0.216
128	128	0.185
129	129	0.462
13	13	1.08586e-5
130	130	0.629
131	131	0.625
132	132	0.784
133	133	0.477
134	134	0.954
135	135	0.0616
136	136	2.79329e-4
137	137	0.739
138	138	0.316
139	139	0.524
14	14	0.89
140	140	0.665
141	141	0.804
142	142	0.652
143	143	0.0602
144	144	0.0259
145	145	0.226
146	146	0.25
147	147	0.814
148	148	0.882
149	149	0.431
15	15	0.353
150	150	0.497
151	151	0.437
152	152	0.0052
153	153	0.345
154	154	0.558
155	155	0.658
156	156	0.0522
157	157	0.348
158	158	0.43
159	159	0.884
160	160	0.2
161	161	0.798
162	162	0.624
163	163	0.143
164	164	0.247
165	165	0.289
166	166	0.407
167	167	0.942
168	168	0.692
169	169	0.225
17	17	0.0579
18	18	0.379
19	19	0.832
2	2	0.863
20	20	0.238
21	21	0.577
22	22	0.497
23	23	0.856
24	24	0.636
25	25	0.548
26	26	0.0271
27	27	0.751
28	28	0.403
29	29	0.106
3	3	0.59
30	30	0.327
31	31	0.558
32	32	0.916
33	33	0.252
34	34	0.849
35	35	0.773
36	36	0.894
37	37	0.0808
38	38	0.655
39	39	0.543
4	4	0.194
40	40	0.257
41	41	0.146
42	42	0.804
43	43	0.96
44	44	0.554
45	45	0.298
46	46	0.656
47	47	0.796
48	48	0.414
49	49	0.726
5	5	0.783
50	50	0.557
51	51	0.909
52	52	0.138
53	53	0.362
54	54	0.587
55	55	0.609
56	56	0.786
57	57	0.406
58	58	0.512
59	59	0.632
6	6	0.966
60	60	0.0317
61	61	0.326
62	62	0.47
63	63	0.257
64	64	0.927
65	65	0.547
66	66	0.514
67	67	0.394
68	68	0.331
69	69	0.473
7	7	0.088
70	70	0.135
71	71	0.684
72	72	0.347
73	73	0.00457
74	74	0.351
75	75	0.0246
76	76	0.941
77	77	0.0632
78	78	0.0413
79	79	0.645
8	8	0.765
80	80	0.886
81	81	0.463
82	82	0.765
83	83	0.944
84	84	0.0798
85	85	0.406
86	86	0.133
87	87	3.85332e-4
88	88	0.202
89	89	0.606
9	9	0.809
90	90	0.992
91	91	0.35
92	92	0.489
93	93	0.142
94	94	0.503
95	95	6.11299e-5
96	96	0.828
97	97	0.754
98	98	0.775
99	99	0.91

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: CNhs13236

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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000160,UBERON:0000483,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0000062,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005911,UBERON:0004923,UBERON:0004921,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0005291,UBERON:0001262,UBERON:0004786,UBERON:0000485,UBERON:0003350,UBERON:0003929,UBERON:0004808,UBERON:0001277,UBERON:0000925,UBERON:0006598,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0005409,UBERON:0007026,UBERON:0006595
+|DRA_sample_Accession=CAGE@SAMD00004708
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000012,CL:0002321,CL:0000063,CL:0000075,CL:0000066,CL:0002371,CL:0000220,CL:0000004,CL:0002563,CL:0000255,CL:0000239,CL:0000677,CL:0000212,CL:0002076,CL:0002251,CL:0000584,CL:0000223
+|accession_numbers=CAGE;DRX008764;DRR009636;DRZ001061;DRZ002446;DRZ012411;DRZ013796
+|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
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000350,FF:0000383,FF:0000627,FF:0011445
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr7:51787434..51787448,-!p1@Spib!2.49!431.28!Spib;;chr2:163332558..163332596,+!p2@Hnf4a!2.23!169.22!Hnf4a;;chr10:80555320..80555378,-!p1@Creb3l3!2.17!170.90!Creb3l3;;chr18:61195865..61195880,-!p1@Cdx1!2.03!106.77!Cdx1;;chr17:27865882..27865901,-!p1@Spdef!2.02!102.91!Spdef;;chr3:3634145..3634161,+!p1@Hnf4g!1.99!97.71!Hnf4g;;chr1:137155026..137155042,-!p1@Elf3!1.92!448.57!Elf3;;chr2:163372884..163372904,+!p1@Hnf4a!1.87!73.70!Hnf4a;;chr5:148118639..148118715,-!p1@Cdx2!1.82!65.31!Cdx2;;chr7:19608891..19608895,-!p1@Foxa3!1.80!80.75!Foxa3;;chr1:193007123..193007139,-!p1@Atf3!1.79!323.00!Atf3;;chr6:64679112..64679126,+!p1@Atoh1!1.77!58.09!Atoh1;;chr6:86619104..86619119,-!p1@Mxd1!1.76!439.34!Mxd1;;chr8:77396591..77396639,+!p1@Isx!1.73!52.21!Isx;;chr5:135582751..135582788,+!p1@Mlxipl!1.69!182.99!Mlxipl;;chr12:86814833..86814846,+!p1@Fos!1.67!1004.09!Fos;;chr18:61195843..61195864,-!p2@Cdx1!1.63!41.30!Cdx1;;chr4:122673187..122673201,+!p2@Mycl1!1.62!71.52!Mycl1;;chr3:3508024..3508069,+!p2@Hnf4g!1.62!40.79!Hnf4g;;chr7:19895384..19895399,-!p2@Fosb!1.57!50.20!Fosb;;chr14:63864056..63864102,-!p1@Gata4!1.56!59.43!Gata4;;chr2:79296783..79296801,-!p1@Neurod1!1.55!34.08!Neurod1;;chr4:124805061..124805087,-!p1@Zc3h12a!1.52!95.86!Zc3h12a;;chr18:64499674..64499696,+!p1@Onecut2!1.49!51.04!Onecut2;;chr16:38294860..38294924,-!p1@Nr1i2!1.48!29.38!Nr1i2;;chr2:103143336..103143367,-!p1@Ehf!1.47!45.33!Ehf;;chr7:19895354..19895369,-!p1@Fosb!1.47!39.12!Fosb;;chr5:115421065..115421088,-!p1@Hnf1a!1.46!27.70!Hnf1a;;chr12:58646974..58647003,-!p1@Foxa1!1.45!35.76!Foxa1;;chr10:88969376..88969395,-!p1@Nr1h4!1.44!26.36!Nr1h4;;chr18:64499706..64499721,+!p2@Onecut2!1.43!36.43!Onecut2;;chr19:5560600..5560617,-!p1@Ovol1!1.43!31.73!Ovol1;;chr18:35020854..35020869,+!p1@Egr1!1.38!840.07!Egr1;;chr9:43013917..43013968,-!p1@Pou2f3!1.38!23.17!Pou2f3;;chr10:20880629..20880683,-!p1@Myb!1.34!59.60!Myb;;chr2:180069370..180069409,-!p1@Gata5!1.34!24.51!Gata5;;chr14:99697871..99697934,+!p1@Klf5!1.33!392.00!Klf5;;chr8:87502608..87502623,-!p1@Junb!1.30!296.64!Junb;;chr5:148118840..148118857,-!p2@Cdx2!1.29!18.63!Cdx2;;chr17:25707623..25707639,-!p1@Sox8!1.28!76.55!Sox8;;chr7:31206743..31206761,+!p1@Nfkbid!1.28!24.85!Nfkbid;;chr2:133377954..133377973,+!p1@Bmp2!1.27!55.40!Bmp2;;chr2:103123925..103123959,-!p3@Ehf!1.23!15.95!Ehf;;chr19:46379199..46379301,+!p1@Nfkb2!1.22!87.30!Nfkb2;;chr4:87452180..87452196,-!p3@Mllt3!1.22!30.55!Mllt3;;chr1:194979315..194979359,+!p1@Irf6!1.21!92.17!Irf6;;chr19:46380235..46380277,+!p3@Nfkb2!1.21!32.90!Nfkb2;;chr2:103143315..103143328,-!p2@Ehf!1.20!14.94!Ehf;;chr10:61595830..61595846,+!p1@Neurog3!1.20!14.77!Neurog3;;chr8:77396650..77396662,+!p4@Isx!1.19!14.44!Isx;;chr7:20214704..20214800,-!p1@Relb!1.17!44.99!Relb;;chr5:120121169..120121171,+!p4@Tbx3!1.16!24.17!Tbx3;;chr2:28477452..28477483,-!p1@Gfi1b!1.16!16.62!Gfi1b;;chr12:56593574..56593592,-!p1@Nfkbia!1.15!663.96!Nfkbia;;chr2:147871627..147871641,-!p1@Foxa2!1.15!13.09!Foxa2;;chr5:148118792..148118806,-!p3@Cdx2!1.14!12.93!Cdx2;;chr19:5447692..5447711,+!p2@Fosl1!1.14!12.76!Fosl1;;chr15:101097270..101097290,+!p1@Nr4a1!1.12!123.73!Nr4a1;;chr4:87452200..87452229,-!p2@Mllt3!1.12!25.85!Mllt3;;chr7:20408047..20408125,-!p1@Bcl3!1.11!133.46!Bcl3;;chr2:146047829..146047847,+!p1@Insm1!1.10!20.82!Insm1;;chr3:128916868..128916890,+!p1@Pitx2!1.10!16.12!Pitx2;;chr15:97738692..97738747,-!p1@Vdr!1.09!61.95!Vdr;;chr15:79177964..79177986,+!p1@Maff!1.09!38.95!Maff;;chr3:90046995..90047031,-!p2@Creb3l4!1.06!13.09!Creb3l4;;chr10:67000609..67000625,+!p1@Egr2!1.05!23.84!Egr2;;chr17:28409136..28409150,+!p3@Ppard!1.04!10.07!Ppard;;chr10:80555398..80555409,-!p2@Creb3l3!1.02!9.40!Creb3l3;;chr4:148178559..148178603,+!p1@Casz1!1.01!26.69!Casz1;;chr6:39068163..39068176,-!p2@Parp12!1.01!17.46!Parp12;;chr11:53583544..53583559,+!p1@Irf1!1.00!152.94!Irf1;;chr4:94718861..94718872,-!p2@Jun!1.00!68.33!Jun;;chr3:135354384..135354443,-!p1@Nfkb1!1.00!56.74!Nfkb1;;chr15:35225845..35225867,+!p1@Osr2!1.00!23.34!Osr2;;chr10:51397572..51397595,+!p1@Rfx6!0.99!8.73!Rfx6;;chr8:77397095..77397127,+!p2@Isx!0.99!8.73!Isx;;chr7:20162663..20162678,+!p1@Zfp296!0.98!11.42!Zfp296;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.97!24.68!Tfcp2l1;;chr2:163372869..163372882,+!p3@Hnf4a!0.97!8.39!Hnf4a;;chr1:173144100..173144138,+!p2@Nr1i3!0.97!8.23!Nr1i3;;chr5:148118809..148118832,-!p5@Cdx2!0.97!8.23!Cdx2;;chr11:70500401..70500460,-!p3@Camta2!0.95!7.89!Camta2;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!0.94!9.90!Zbtb11;;chr7:87170879..87170914,+!p2@Zfp710!0.92!17.63!Zfp710;;chr19:6996243..6996293,-!p1@Esrra!0.91!81.59!Esrra;;chr3:94176733..94176794,+!p1@Rorc!0.91!58.09!Rorc;;chr1:39250584..39250643,+!p1@Npas2!0.90!36.77!Npas2;;chr5:140267510..140267555,+!p2@Mafk!0.90!16.96!Mafk;;chr7:150155143..150155156,-!p1@Ascl2!0.90!6.88!Ascl2;;chr16:55822241..55822258,-!p1@Nfkbiz!0.89!220.93!Nfkbiz;;chr7:20213752..20213778,-!p2@Relb!0.88!6.55!Relb;;chr8:77397492..77397514,+!p3@Isx!0.88!6.55!Isx;;chr7:148452314..148452329,-!p1@Irf7!0.87!46.67!Irf7;;chr18:11052642..11052659,+!p1@Gata6!0.86!33.41!Gata6;;chr17:48061381..48061399,-!p1@Foxp4!0.85!73.53!Foxp4;;chr19:10315179..10315241,-!p1@Gm98!0.85!67.49!Gm98;;chr14:76887526..76887555,+!p10@Tsc22d1!0.85!6.04!Tsc22d1;;chr4:94718879..94718898,-!p1@Jun!0.84!453.95!Jun;;chr1:194979361..194979373,+!p2@Irf6!0.84!8.23!Irf6;;chr8:73222425..73222444,+!p2@Jund!0.84!5.88!Jund;;chr5:144951153..144951203,+!p1@Bhlha15!0.83!8.56!Bhlha15;;chr7:138697803..138697813,+!p1@Hmx2!0.82!5.54!Hmx2;;chr3:3508005..3508021,+!p3@Hnf4g!0.82!5.54!Hnf4g;;chr10:107769168..107769215,+!p1@Pawr!0.81!59.43!Pawr;;chr10:30375579..30375616,-!p3@Ncoa7!0.81!13.77!Ncoa7;;chr18:35020615..35020641,+!p2@Egr1!0.81!6.72!Egr1;;chr3:128918394..128918413,+!p5@Pitx2!0.80!5.37!Pitx2;;chr13:5860776..5860796,+!p1@Klf6!0.79!136.49!Klf6;;chr13:44825008..44825066,+!p5@Jarid2!0.79!10.74!Jarid2;;chr1:138857048..138857071,-!p2@Nr5a2!0.79!5.20!Nr5a2;;chr19:55816546..55816556,+!p3@Tcf7l2!0.78!20.48!Tcf7l2;;chr5:76733981..76734018,-!p3@Clock!0.78!11.42!Clock;;chr1:189432634..189432643,+!p8@Esrrg!0.78!5.04!Esrrg;;chr3:135354452..135354475,-!p5@Nfkb1!0.76!12.93!Nfkb1;;chr2:173044380..173044432,-!p1@Zbp1!0.76!12.26!Zbp1;;chr19:5560570..5560582,-!p2@Ovol1!0.76!4.70!Ovol1;;chr5:77524250..77524300,-!p1@Hopx!0.75!102.91!Hopx;;chr8:123260252..123260264,+!p1@Irf8!0.75!35.93!Irf8;;chr18:11052606..11052633,+!p4@Gata6!0.75!12.59!Gata6;;chr8:124806048..124806094,+!p1@Zfpm1!0.74!46.00!Zfpm1;;chr17:45692676..45692695,+!p2@Nfkbie!0.73!9.40!Nfkbie;;chr3:51144740..51144743,-!p7@Elf2!0.73!7.72!Elf2;;chr7:20214018..20214024,-!p4@Relb!0.73!4.36!Relb;;chr2:152561980..152561997,+!p1@Id1!0.72!139.34!Id1;;chr4:55545337..55545357,-!p1@Klf4!0.72!70.68!Klf4;;chr2:173044357..173044377,-!p2@Zbp1!0.72!6.38!Zbp1;;chr10:107769229..107769238,+!p3@Pawr!0.72!6.21!Pawr;;chr2:28477422..28477433,-!p2@Gfi1b!0.72!4.20!Gfi1b;;chr17:48061584..48061601,-!p2@Foxp4!0.71!29.88!Foxp4;;chr10:80600749..80600766,+!p2@Zbtb7a!0.71!24.17!Zbtb7a;;chr15:37162796..37162828,+!p1@Grhl2!0.71!7.39!Grhl2;;chr3:89197057..89197114,-!p1@Zbtb7b!0.70!14.94!Zbtb7b;;chr13:112476433..112476448,+!p2@Mier3!0.70!8.23!Mier3;;chr11:106128936..106128955,-!p4@Smarcd2!0.70!4.70!Smarcd2;;chr8:77397190..77397202,+!p5@Isx!0.70!4.03!Isx;;chr5:29805118..29805137,-!p1@Mnx1!0.70!4.03!Mnx1;;chr5:148118614..148118625,-!p4@Cdx2!0.70!4.03!Cdx2;;chr1:194979383..194979393,+!p3@Irf6!0.70!4.03!Irf6;;chr8:125778192..125778217,+!p2@Zfp276!0.69!12.09!Zfp276;;chr5:77524231..77524245,-!p3@Hopx!0.69!10.58!Hopx;;chr10:20880698..20880717,-!p3@Myb!0.69!6.55!Myb;;chr14:63890545..63890560,-!p5@Gata4!0.69!3.86!Gata4;;chr14:63890519..63890539,-!p3@Gata4!0.69!3.86!Gata4;;chr1:64579145..64579168,+!p6@Creb1!0.69!3.86!Creb1;;chr8:79426176..79426275,+!p1@Nr3c2!0.68!21.49!Nr3c2;;chr4:148178529..148178548,+!p3@Casz1!0.68!9.74!Casz1;;chr19:46380172..46380231,+!p2@Nfkb2!0.66!28.04!Nfkb2;;chr4:148178459..148178482,+!p4@Casz1!0.66!3.53!Casz1;;chr5:115420882..115420896,-!p3@Hnf1a!0.66!3.53!Hnf1a;;chr12:109242266..109242295,-!p1@Bcl11b!0.65!33.74!Bcl11b;;chr17:48061409..48061431,-!p4@Foxp4!0.65!21.32!Foxp4;;chr10:80598968..80599012,+!p5@Zbtb7a!0.65!4.70!Zbtb7a;;chr11:96690797..96690813,-!p1@Nfe2l1!0.64!76.22!Nfe2l1;;chr17:34784073..34784118,+!p2@Atf6b!0.64!15.44!Atf6b;;chr10:127095407..127095440,+!p3@Stat6!0.64!4.36!Stat6;;chr18:64499879..64499895,+!p3@Onecut2!0.64!3.36!Onecut2;;chr17:28409059..28409076,+!p6@Ppard!0.64!3.36!Ppard;;chr3:30039329..30039355,-!p5@Mecom!0.64!3.36!Mecom;;chr5:148081722..148081744,+!p2@Pdx1!0.64!3.36!Pdx1;;chr9:31720903..31720918,-!p2@Barx2!0.64!3.36!Barx2;;chr5:140267476..140267493,+!p1@Mafk!0.63!21.66!Mafk;;chr4:124805092..124805135,-!p2@Zc3h12a!0.63!16.12!Zc3h12a;;chr7:35904304..35904320,+!p1@Cebpa!0.62!77.90!Cebpa;;chr6:86619130..86619158,-!p2@Mxd1!0.62!53.89!Mxd1;;chr6:39068210..39068251,-!p1@Parp12!0.62!17.29!Parp12;;chr17:27693788..27693803,+!p3@Hmga1,p4@Hmga1-rs1!0.62!16.62!Hmga1;;chr17:45692642..45692663,+!p1@Nfkbie!0.62!11.75!Nfkbie;;chr11:49016816..49016846,+!p2@Zfp62!0.62!10.58!Zfp62;;chr17:27693746..27693759,+!p6@Hmga1-rs1,p7@Hmga1!0.62!6.88!Hmga1;;chr15:37162834..37162849,+!p2@Grhl2!0.62!3.86!Grhl2;;chr11:100948597..100948637,+!p1@Mlx!0.60!86.29!Mlx;;chr6:134780234..134780288,+!p1@Crebl2!0.60!11.08!Crebl2;;chr1:57029281..57029326,-!p1@Satb2!0.60!5.04!Satb2;;chr4:135700687..135700719,+!p2@Id3!0.60!5.04!Id3;;chr5:65194752..65194769,+!p1@Klf3!0.59!119.03!Klf3;;chr8:73905344..73905381,-!p2@Nr2f6!0.59!7.89!Nr2f6;;chr8:87643578..87643593,-!p1@Zfp791!0.59!6.72!Zfp791;;chr5:77543897..77543911,-!p2@Hopx!0.59!6.21!Hopx;;chr10:80599248..80599261,+!p3@Zbtb7a!0.59!5.71!Zbtb7a;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.59!4.36!Carhsp1;;chr1:138846047..138846074,-!p5@Nr5a2!0.59!3.19!Nr5a2;;chr1:6720216..6720232,+!p1@St18!0.59!2.85!St18;;chr1:173144144..173144176,+!p1@Nr1i3!0.59!2.85!Nr1i3;;chr1:189432881..189432903,+!p2@Esrrg!0.59!2.85!Esrrg;;chr5:148081686..148081715,+!p1@Pdx1!0.59!2.85!Pdx1;;chr10:80555299..80555306,-!p3@Creb3l3!0.59!2.85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+|ffid_belonging_in_development=CL:0000223
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:11852-124I7
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011445
+|is_a=EFO:0002091;;FF:0011445
+|is_obsolete=
+|library_id=CNhs13236
+|library_id_phase_based=2:CNhs13236
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11852
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11852
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13236.11852-124I7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13236.11852-124I7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13236.11852-124I7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13236.11852-124I7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13236.11852-124I7.mm9.nobarcode.rdna.fa.gz
 |name=CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool1
 |namespace=
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13236,LSID1006,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.029223976606799,0,0,0,0,0,-0.276434002531768,0,0,0,0,-0.0843392403965415,0,0,0,0,0.168745095309481,0,-0.191893350882575,0,0,0,0.177143239467161,0,0,0,0,0,0,0,0,0,-0.432694831611214,0,0.125727960712818,0,0,0,-0.146458745139417,-0.0417740847988257,0.0425780786368599,-0.984211366477826,0.0327383742419235,0.0673979504369913,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.0245509953541166,0,-0.067832585094378,0,0,-0.0396184795268791,-0.209526802975775,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0106106503149601,-0.0520772115234336,0,0,0,-0.0256051161023511,0.025731228218839,-0.470186920027752,-0.0788315948399074,0,0,0,0,0,0.525084968573582,-0.172288662866041,-0.874389214599442,-0.181231382497818,0,0,0,0,0
 |rna_box=124
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=0.77
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=ileum
 |top_motifs=ZEB1:2.65959715237;bHLH_family:2.36785221318;NFKB1_REL_RELA:2.0670877321;SNAI1..3:1.9320324786;FOXN1:1.80950946337;TBX4,5:1.71141453503;HNF4A_NR2F1,2:1.70495364101;NFIX:1.70268791743;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.58853607891;PDX1:1.52373841418;FOSL2:1.5082739975;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.46556991161;HNF1A:1.37877986219;PPARG:1.33910438055;ESRRA:1.30509801088;ATF4:1.26815592582;ATF5_CREB3:1.23659206508;MYOD1:1.21731278706;AR:1.11445117954;SP1:1.08127113658;STAT5{A,B}:1.07640337304;CREB1:1.06628895018;HES1:1.0362276891;ELK1,4_GABP{A,B1}:1.02165968415;ATF6:1.00126799691;ONECUT1,2:0.978278231305;LMO2:0.950352456599;STAT1,3:0.935653270764;ADNP_IRX_SIX_ZHX:0.931171115175;POU2F1..3:0.885600120619;FOX{I1,J2}:0.871726580964;PAX8:0.791841245986;FOS_FOS{B,L1}_JUN{B,D}:0.773764069256;BACH2:0.771147668354;FOXM1:0.74636661322;IRF1,2:0.728271346932;GTF2A1,2:0.711010700907;XCPE1{core}:0.702951972899;TP53:0.669932819124;LHX3,4:0.663270860071;NFY{A,B,C}:0.661349250128;NR1H4:0.636390708561;PAX2:0.632108492751;NR6A1:0.621949526991;FOXA2:0.590701922733;ARID5B:0.48327800248;YY1:0.472715854198;NANOG:0.470040535033;POU5F1:0.436847468128;TBP:0.340222319221;VSX1,2:0.30407609211;OCT4_SOX2{dimer}:0.292254331493;STAT2,4,6:0.288913929658;DMAP1_NCOR{1,2}_SMARC:0.288429599708;NR5A1,2:0.260831865554;JUN:0.259346762609;T:0.187043916556;GATA6:0.171096066545;MYB:0.163436766025;E2F1..5:0.150934571023;ETS1,2:0.146644585695;SPI1:0.146375075027;FOX{D1,D2}:0.129909669897;ELF1,2,4:0.113964113075;FOXL1:0.0970195599995;ZBTB6:0.0886355331978;EBF1:0.0834490987994;HLF:0.0701311989505;ZNF148:0.067190833714;RXRA_VDR{dimer}:0.0494501293781;POU6F1:0.0331614831394;NFE2L2:0.0248540995306;ALX4:-0.00064294945495;ZNF143:-0.00537457974144;TLX1..3_NFIC{dimer}:-0.0158376306788;LEF1_TCF7_TCF7L1,2:-0.0425860841502;NFE2:-0.055800624437;NANOG{mouse}:-0.0857450540283;POU1F1:-0.0977230312277;CRX:-0.105512302556;MED-1{core}:-0.106904231277;SOX17:-0.125417577474;SRF:-0.135393278373;CDX1,2,4:-0.141612937572;IRF7:-0.147075374943;PAX6:-0.15158159008;TFCP2:-0.17447811872;FOX{F1,F2,J1}:-0.233598804963;TFAP2B:-0.260442825759;FOXQ1:-0.26321738442;PAX5:-0.288083640694;GFI1B:-0.291426182756;TLX2:-0.30636122831;ESR1:-0.32168378916;RORA:-0.349124659131;HMX1:-0.366994979237;HOX{A4,D4}:-0.383166265149;RUNX1..3:-0.385175850223;EP300:-0.386003756701;SOX{8,9,10}:-0.389443490083;HIC1:-0.391297693466;NKX6-1,2:-0.396252459919;TEAD1:-0.40110638067;TFAP4:-0.404069765747;AHR_ARNT_ARNT2:-0.421149539374;TFDP1:-0.444159339441;CUX2:-0.444347988705;RFX1:-0.449954155474;MAFB:-0.487121421199;GFI1:-0.488144226375;NRF1:-0.501492758925;BREu{core}:-0.501542055915;HSF1,2:-0.508611443435;EGR1..3:-0.529444819402;MEF2{A,B,C,D}:-0.540993625034;HIF1A:-0.556394260783;AIRE:-0.563806577225;REST:-0.566727084906;FOXO1,3,4:-0.587809741238;TFAP2{A,C}:-0.594954618552;ZFP161:-0.597672720367;TAL1_TCF{3,4,12}:-0.625127888039;HBP1_HMGB_SSRP1_UBTF:-0.653902183447;RFX2..5_RFXANK_RFXAP:-0.663332754134;NFIL3:-0.69666579777;MAZ:-0.720222039227;SREBF1,2:-0.750854457698;POU3F1..4:-0.769479110955;BPTF:-0.800959555721;MTF1:-0.805299235495;NKX2-3_NKX2-5:-0.821552142135;SOX2:-0.843660469269;ATF2:-0.845279651792;NFE2L1:-0.849083901667;CEBPA,B_DDIT3:-0.856729087155;NR3C1:-0.868258639508;GTF2I:-0.882403713938;DBP:-0.886753970664;MTE{core}:-0.90876440714;PBX1:-0.925175259042;PAX1,9:-0.94016394442;PRRX1,2:-0.946978243692;GCM1,2:-0.960159806864;SPIB:-0.971159926658;RXR{A,B,G}:-0.97570317105;RBPJ:-0.992954112416;TGIF1:-1.02134540274;CDC5L:-1.05230032886;ZNF423:-1.06982089045;NHLH1,2:-1.0708614734;GLI1..3:-1.09081022916;HOX{A5,B5}:-1.09610972235;MYFfamily:-1.14331285783;SPZ1:-1.23171536918;PATZ1:-1.2775981188;MZF1:-1.28142735641;RREB1:-1.28435103171;NKX2-1,4:-1.29771228463;ZNF384:-1.29787899448;KLF4:-1.30130624326;PITX1..3:-1.30375455515;FOXD3:-1.31789934735;ZBTB16:-1.31849733389;EN1,2:-1.33226479864;ZNF238:-1.34469488124;NKX3-2:-1.45516743327;ZIC1..3:-1.48155547236;PRDM1:-1.48243250018;FOXP3:-1.49317956651;SMAD1..7,9:-1.49451560388;UFEwm:-1.5008903747;SOX5:-1.51595039117;HAND1,2:-1.53736369855;TOPORS:-1.5534435588;MYBL2:-1.56469997718;NFATC1..3:-1.57735680689;NKX2-2,8:-1.58219365646;HOXA9_MEIS1:-1.71149505035;EVI1:-1.71315076568;GZF1:-1.73612560789;TEF:-1.79490511571;ALX1:-1.87622387707;IKZF1:-1.91398913064;GATA4:-1.95393344299;NKX3-1:-1.99622644248;PAX4:-1.99750169724;HMGA1,2:-2.08288007689;IKZF2:-2.11951757558;FOXP1:-2.13239070179
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11852-124I7;search_select_hide=table117:11852-124I7
 }}

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FF:11852-124I7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:23, 4 June 2020

CNhs13236

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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