FF:12228-129F5: Difference between revisions

Latest revision as of 18:35, 4 June 2020

Name:	Lgr5 positive intestinal stem cells, pool1
Species:	Mouse (Mus musculus)
Library ID:	CNhs12555
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	small intestine
dev stage	NA
sex	male
age	NA
cell type	stem cell
cell line	NA
company	NA
collaboration	Marc van de Wetering
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	NA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005052

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12555		CAGE		DRX008769		DRR009641

Accession ID Mm9

Library id		BAM		CTSS
CNhs12555		DRZ001066		DRZ002451

Accession ID Mm10

Library id		BAM		CTSS
CNhs12555		DRZ012416		DRZ013801

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

CNhs12555

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0668
1002	-0.116
1003	-0.109
1004	0
1005	0.11
1006	-0.143
1007	-0.0809
1008	0.883
1009	-0.19
101	0.13
1010	0
1011	-0.298
1012	0
1013	-0.136
1014	-0.0874
1015	-0.143
1016	-0.426
1017	0
1018	0.437
1019	0
102	0
1020	0
1021	0
1022	0.218
1023	0
1024	-0.172
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.176
103	-0.0887
1030	0
1031	-1.033
1032	0.431
1033	0.575
1034	0
1035	0
1036	0.452
1037	0
1038	-0.12
1039	0.103
104	0
1040	-0.811
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: CNhs12555

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.368
MA0003.1	MA0003.1	0.798
MA0004.1	MA0004.1	0.0111
MA0006.1	MA0006.1	0.962
MA0007.1	MA0007.1	0.141
MA0009.1	MA0009.1	0.172
MA0014.1	MA0014.1	0.0615
MA0017.1	MA0017.1	2.12026e-13
MA0018.2	MA0018.2	1.46134e-5
MA0019.1	MA0019.1	0.625
MA0024.1	MA0024.1	4.53992e-5
MA0025.1	MA0025.1	0.025
MA0027.1	MA0027.1	0.224
MA0028.1	MA0028.1	1.80788e-9
MA0029.1	MA0029.1	0.12
MA0030.1	MA0030.1	0.389
MA0031.1	MA0031.1	0.109
MA0035.2	MA0035.2	6.67734e-4
MA0038.1	MA0038.1	0.174
MA0039.2	MA0039.2	1.31569e-4
MA0040.1	MA0040.1	0.123
MA0041.1	MA0041.1	0.135
MA0042.1	MA0042.1	0.436
MA0043.1	MA0043.1	6.61037e-6
MA0046.1	MA0046.1	5.84292e-42
MA0047.2	MA0047.2	5.83788e-4
MA0048.1	MA0048.1	0.0138
MA0050.1	MA0050.1	0.0122
MA0051.1	MA0051.1	0.00668
MA0052.1	MA0052.1	0.0921
MA0055.1	MA0055.1	4.4324e-5
MA0057.1	MA0057.1	0.198
MA0058.1	MA0058.1	0.00862
MA0059.1	MA0059.1	0.00188
MA0060.1	MA0060.1	6.38026e-9
MA0061.1	MA0061.1	0.156
MA0062.2	MA0062.2	1.83612e-12
MA0065.2	MA0065.2	1.60445e-6
MA0066.1	MA0066.1	0.81
MA0067.1	MA0067.1	0.218
MA0068.1	MA0068.1	0.923
MA0069.1	MA0069.1	0.425
MA0070.1	MA0070.1	0.503
MA0071.1	MA0071.1	0.0274
MA0072.1	MA0072.1	0.672
MA0073.1	MA0073.1	0.878
MA0074.1	MA0074.1	0.797
MA0076.1	MA0076.1	5.82987e-9
MA0077.1	MA0077.1	0.279
MA0078.1	MA0078.1	0.361
MA0079.2	MA0079.2	0.289
MA0080.2	MA0080.2	0.00234
MA0081.1	MA0081.1	0.862
MA0083.1	MA0083.1	0.154
MA0084.1	MA0084.1	0.0585
MA0087.1	MA0087.1	0.167
MA0088.1	MA0088.1	0.0193
MA0090.1	MA0090.1	0.595
MA0091.1	MA0091.1	0.24
MA0092.1	MA0092.1	0.179
MA0093.1	MA0093.1	0.0124
MA0099.2	MA0099.2	0.0741
MA0100.1	MA0100.1	0.073
MA0101.1	MA0101.1	0.00875
MA0102.2	MA0102.2	0.675
MA0103.1	MA0103.1	5.32734e-6
MA0104.2	MA0104.2	0.0211
MA0105.1	MA0105.1	0.128
MA0106.1	MA0106.1	0.43
MA0107.1	MA0107.1	0.044
MA0108.2	MA0108.2	0.361
MA0111.1	MA0111.1	0.464
MA0112.2	MA0112.2	0.176
MA0113.1	MA0113.1	0.312
MA0114.1	MA0114.1	2.09187e-15
MA0115.1	MA0115.1	5.01733e-9
MA0116.1	MA0116.1	0.082
MA0117.1	MA0117.1	0.884
MA0119.1	MA0119.1	0.607
MA0122.1	MA0122.1	0.238
MA0124.1	MA0124.1	0.692
MA0125.1	MA0125.1	0.59
MA0131.1	MA0131.1	0.0951
MA0135.1	MA0135.1	0.436
MA0136.1	MA0136.1	3.12593e-11
MA0137.2	MA0137.2	9.20984e-5
MA0138.2	MA0138.2	0.0748
MA0139.1	MA0139.1	0.129
MA0140.1	MA0140.1	0.484
MA0141.1	MA0141.1	6.27359e-4
MA0142.1	MA0142.1	0.108
MA0143.1	MA0143.1	0.3
MA0144.1	MA0144.1	0.00805
MA0145.1	MA0145.1	0.809
MA0146.1	MA0146.1	0.154
MA0147.1	MA0147.1	0.00744
MA0148.1	MA0148.1	8.08488e-4
MA0149.1	MA0149.1	0.00797
MA0150.1	MA0150.1	0.564
MA0152.1	MA0152.1	0.456
MA0153.1	MA0153.1	5.83854e-30
MA0154.1	MA0154.1	0.88
MA0155.1	MA0155.1	0.477
MA0156.1	MA0156.1	1.20242e-7
MA0157.1	MA0157.1	0.551
MA0159.1	MA0159.1	0.00201
MA0160.1	MA0160.1	5.42802e-4
MA0162.1	MA0162.1	0.955
MA0163.1	MA0163.1	0.0156
MA0164.1	MA0164.1	0.805
MA0258.1	MA0258.1	0.382
MA0259.1	MA0259.1	0.136

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: CNhs12555

Novel motif	Logo	P-value
1	1	0.42
10	10	0.0665
100	100	0.273
101	101	0.327
102	102	0.885
103	103	0.515
104	104	0.938
105	105	0.486
106	106	0.438
107	107	0.946
108	108	0.509
109	109	0.0503
11	11	0.337
110	110	0.122
111	111	0.35
112	112	0.142
113	113	0.0526
114	114	0.52
115	115	0.395
116	116	0.829
117	117	0.0077
118	118	0.485
119	119	0.937
12	12	0.834
120	120	0.769
121	121	0.308
122	122	0.847
123	123	0.0304
124	124	0.0304
125	125	0.105
126	126	0.00355
127	127	0.753
128	128	0.835
129	129	0.916
13	13	3.09425e-7
130	130	0.241
131	131	0.828
132	132	0.33
133	133	0.462
134	134	0.262
135	135	0.0712
136	136	0.00466
137	137	0.424
138	138	0.461
139	139	0.319
14	14	0.724
140	140	0.985
141	141	0.366
142	142	0.911
143	143	0.0346
144	144	0.0176
145	145	0.0218
146	146	0.437
147	147	0.8
148	148	0.52
149	149	0.231
15	15	0.338
150	150	0.508
151	151	0.767
152	152	0.5
153	153	0.918
154	154	0.814
155	155	0.871
156	156	0.215
157	157	0.407
158	158	0.309
159	159	0.833
160	160	0.981
161	161	0.711
162	162	0.224
163	163	0.695
164	164	0.147
165	165	0.238
166	166	0.721
167	167	0.263
168	168	0.805
169	169	0.158
17	17	0.204
18	18	0.151
19	19	0.77
2	2	0.25
20	20	0.0776
21	21	0.771
22	22	0.999
23	23	0.27
24	24	0.0885
25	25	0.127
26	26	0.00684
27	27	0.787
28	28	0.95
29	29	0.00903
3	3	0.351
30	30	0.875
31	31	0.326
32	32	0.237
33	33	0.053
34	34	0.367
35	35	0.827
36	36	0.107
37	37	0.235
38	38	0.678
39	39	0.628
4	4	0.61
40	40	0.0615
41	41	0.239
42	42	0.767
43	43	0.802
44	44	0.979
45	45	0.851
46	46	0.437
47	47	0.598
48	48	0.276
49	49	0.897
5	5	0.849
50	50	0.985
51	51	0.856
52	52	0.782
53	53	0.495
54	54	0.978
55	55	0.705
56	56	0.936
57	57	0.742
58	58	0.285
59	59	0.732
6	6	0.572
60	60	0.198
61	61	0.305
62	62	0.261
63	63	0.5
64	64	0.645
65	65	0.909
66	66	0.337
67	67	0.694
68	68	0.661
69	69	0.176
7	7	0.0168
70	70	0.234
71	71	0.0382
72	72	0.408
73	73	0.0721
74	74	0.525
75	75	0.0132
76	76	0.618
77	77	0.665
78	78	0.0285
79	79	0.746
8	8	0.333
80	80	0.589
81	81	0.483
82	82	0.791
83	83	0.498
84	84	0.755
85	85	0.743
86	86	0.369
87	87	0.00428
88	88	0.52
89	89	0.975
9	9	0.693
90	90	0.104
91	91	0.0323
92	92	0.121
93	93	0.142
94	94	0.401
95	95	0.00292
96	96	0.597
97	97	0.994
98	98	0.557
99	99	0.753

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: CNhs12555

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000079 mouse Lgr5-positive intestinal epithelial stem 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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0002250 (intestinal crypt stem cell)

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)
0000079 (mouse Lgr5-positive intestinal epithelial stem 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
CL:0000223 (endodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000060,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000119,UBERON:0000160,UBERON:0000344,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000485,UBERON:0000490,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001242,UBERON:0001262,UBERON:0001277,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0003350,UBERON:0003929,UBERON:0004119,UBERON:0004185,UBERON:0004786,UBERON:0004808,UBERON:0004921,UBERON:0004923,UBERON:0005409,UBERON:0005423,UBERON:0005911,UBERON:0007026
+|DRA_sample_Accession=CAGE@SAMD00005052
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000066,CL:0000144,CL:0000220,CL:0000223,CL:0000255,CL:0000548,CL:0000723,CL:0002076,CL:0002250,CL:0002251,CL:0002321,CL:0002371,CL:0002563
+|accession_numbers=CAGE;DRX008769;DRR009641;DRZ001066;DRZ002451;DRZ012416;DRZ013801
+|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:0000723,CL:0000048,CL:0000548,CL:0000066,CL:0002371,CL:0002563,CL:0000255,CL:0000034,CL:0002076,CL:0002251,CL:0002250
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000079
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:163332558..163332596,+!p2@Hnf4a!2.15!139.23!Hnf4a;;chr1:137155026..137155042,-!p1@Elf3!2.00!541.60!Elf3;;chr5:148118639..148118715,-!p1@Cdx2!1.83!65.86!Cdx2;;chr2:103123925..103123959,-!p3@Ehf!1.78!58.93!Ehf;;chr15:97738692..97738747,-!p1@Vdr!1.64!221.55!Vdr;;chr2:103143336..103143367,-!p1@Ehf!1.64!68.46!Ehf;;chr2:163372884..163372904,+!p1@Hnf4a!1.61!39.28!Hnf4a;;chr18:61195865..61195880,-!p1@Cdx1!1.59!37.55!Cdx1;;chr10:20880629..20880683,-!p1@Myb!1.57!101.10!Myb;;chr5:135582751..135582788,+!p1@Mlxipl!1.54!129.41!Mlxipl;;chr8:77396591..77396639,+!p1@Isx!1.51!31.20!Isx;;chr3:3508024..3508069,+!p2@Hnf4g!1.49!30.04!Hnf4g;;chr16:38294860..38294924,-!p1@Nr1i2!1.48!29.17!Nr1i2;;chr5:148118840..148118857,-!p2@Cdx2!1.45!27.15!Cdx2;;chr18:61195843..61195864,-!p2@Cdx1!1.43!26.00!Cdx1;;chr7:19608891..19608895,-!p1@Foxa3!1.40!31.48!Foxa3;;chr7:19895354..19895369,-!p1@Fosb!1.39!32.06!Fosb;;chr14:63864056..63864102,-!p1@Gata4!1.38!39.57!Gata4;;chr10:88969376..88969395,-!p1@Nr1h4!1.36!21.66!Nr1h4;;chr19:5560600..5560617,-!p1@Ovol1!1.35!25.71!Ovol1;;chr18:64499706..64499721,+!p2@Onecut2!1.33!28.60!Onecut2;;chr10:127095407..127095440,+!p3@Stat6!1.31!23.97!Stat6;;chr3:30039329..30039355,-!p5@Mecom!1.31!19.64!Mecom;;chr5:148118792..148118806,-!p3@Cdx2!1.28!18.20!Cdx2;;chr12:86814833..86814846,+!p1@Fos!1.25!378.40!Fos;;chr18:64499674..64499696,+!p1@Onecut2!1.25!28.89!Onecut2;;chr2:180069370..180069409,-!p1@Gata5!1.25!19.64!Gata5;;chr2:103143315..103143328,-!p2@Ehf!1.24!16.46!Ehf;;chr1:193007123..193007139,-!p1@Atf3!1.23!87.23!Atf3;;chr11:106128936..106128955,-!p4@Smarcd2!1.18!16.46!Smarcd2;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.16!17.33!Zbtb11;;chr9:59797525..59797538,-!p2@Nr2e3!1.13!12.42!Nr2e3;;chr3:3634145..3634161,+!p1@Hnf4g!1.13!12.42!Hnf4g;;chr4:124805061..124805087,-!p1@Zc3h12a!1.12!37.55!Zc3h12a;;chr8:77397095..77397127,+!p2@Isx!1.11!11.84!Isx;;chr4:94718861..94718872,-!p2@Jun!1.10!87.23!Jun;;chr7:19895384..19895399,-!p2@Fosb!1.10!16.46!Fosb;;chr7:150155143..150155156,-!p1@Ascl2!1.08!10.98!Ascl2;;chr5:148118809..148118832,-!p5@Cdx2!1.06!10.40!Cdx2;;chr14:99697871..99697934,+!p1@Klf5!1.05!205.95!Klf5;;chr1:138857048..138857071,-!p2@Nr5a2!1.05!10.11!Nr5a2;;chr3:128918394..128918413,+!p5@Pitx2!1.02!9.53!Pitx2;;chr5:29805118..29805137,-!p1@Mnx1!1.01!9.24!Mnx1;;chr10:61595830..61595846,+!p1@Neurog3!1.00!8.95!Neurog3;;chr13:44825008..44825066,+!p5@Jarid2!0.99!17.62!Jarid2;;chr10:80555320..80555378,-!p1@Creb3l3!0.98!10.11!Creb3l3;;chr8:123260252..123260264,+!p1@Irf8!0.97!59.79!Irf8;;chr18:11052642..11052659,+!p1@Gata6!0.97!42.75!Gata6;;chr1:138857076..138857105,-!p1@Nr5a2!0.97!8.38!Nr5a2;;chr8:73222425..73222444,+!p2@Jund!0.96!8.09!Jund;;chr9:59797503..59797513,-!p3@Nr2e3!0.96!8.09!Nr2e3;;chr8:77396650..77396662,+!p4@Isx!0.96!8.09!Isx;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!0.95!20.22!Hmga1;;chr17:28409136..28409150,+!p3@Ppard!0.94!7.80!Ppard;;chr5:115421065..115421088,-!p1@Hnf1a!0.94!7.80!Hnf1a;;chr14:76887526..76887555,+!p10@Tsc22d1!0.94!7.80!Tsc22d1;;chr8:77397492..77397514,+!p3@Isx!0.93!7.51!Isx;;chr3:3508005..3508021,+!p3@Hnf4g!0.93!7.51!Hnf4g;;chr10:20880698..20880717,-!p3@Myb!0.91!11.55!Myb;;chr2:147871627..147871641,-!p1@Foxa2!0.91!7.22!Foxa2;;chr2:163372869..163372882,+!p3@Hnf4a!0.91!7.22!Hnf4a;;chr5:77524250..77524300,-!p1@Hopx!0.90!145.87!Hopx;;chr15:37162796..37162828,+!p1@Grhl2!0.90!11.84!Grhl2;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.90!11.27!Ncoa4;;chr2:70313168..70313184,+!p1@Sp5!0.90!10.69!Sp5;;chr12:58646974..58647003,-!p1@Foxa1!0.89!9.24!Foxa1;;chr1:194979315..194979359,+!p1@Irf6!0.88!42.46!Irf6;;chr17:27693746..27693759,+!p6@Hmga1-rs1,p7@Hmga1!0.87!13.29!Hmga1;;chr14:63890545..63890560,-!p5@Gata4!0.87!6.35!Gata4;;chr4:122673187..122673201,+!p2@Mycl1!0.85!11.27!Mycl1;;chr1:173144100..173144138,+!p2@Nr1i3!0.85!6.07!Nr1i3;;chr14:63890491..63890516,-!p2@Gata4!0.85!6.07!Gata4;;chr14:63890519..63890539,-!p3@Gata4!0.85!6.07!Gata4;;chr19:5560570..5560582,-!p2@Ovol1!0.85!6.07!Ovol1;;chr18:11052606..11052633,+!p4@Gata6!0.84!15.60!Gata6;;chr5:140267510..140267555,+!p2@Mafk!0.83!14.44!Mafk;;chr11:98636508..98636524,-!p3@Nr1d1!0.83!7.22!Nr1d1;;chr11:83664365..83664383,+!p1@Hnf1b!0.83!5.78!Hnf1b;;chr5:77544170..77544181,-!p6@Hopx!0.83!5.78!Hopx;;chr3:128918433..128918448,+!p8@Pitx2!0.83!5.78!Pitx2;;chr17:27693788..27693803,+!p3@Hmga1,p4@Hmga1-rs1!0.82!27.15!Hmga1;;chr17:27865882..27865901,-!p1@Spdef!0.81!5.49!Spdef;;chr15:37163124..37163153,+!p3@Grhl2!0.81!5.49!Grhl2;;chr10:67000609..67000625,+!p1@Egr2!0.80!13.00!Egr2;;chr5:77543897..77543911,-!p2@Hopx!0.80!10.69!Hopx;;chr18:35020854..35020869,+!p1@Egr1!0.79!218.08!Egr1;;chr9:59796270..59796294,-!p4@Nr2e3!0.79!5.20!Nr2e3;;chr8:124806048..124806094,+!p1@Zfpm1!0.78!49.97!Zfpm1;;chr8:87502608..87502623,-!p1@Junb!0.77!87.81!Junb;;chr12:109242266..109242295,-!p1@Bcl11b!0.77!45.06!Bcl11b;;chr1:189821714..189821761,+!p1@Esrrg!0.76!9.24!Esrrg;;chr3:128916868..128916890,+!p1@Pitx2!0.75!6.64!Pitx2;;chr1:189432881..189432903,+!p2@Esrrg!0.75!4.62!Esrrg;;chr11:106128919..106128933,-!p8@Smarcd2!0.75!4.62!Smarcd2;;chr17:28409059..28409076,+!p6@Ppard!0.75!4.62!Ppard;;chr5:148081686..148081715,+!p1@Pdx1!0.75!4.62!Pdx1;;chr6:64679112..64679126,+!p1@Atoh1!0.75!4.62!Atoh1;;chr4:154010918..154010931,-!p1@Prdm16!0.74!14.44!Prdm16;;chr3:96002383..96002407,-!p4@Bola1!0.74!6.07!Bola1;;chr13:55932739..55932756,-!p5@Pitx1!0.73!4.33!Pitx1;;chr19:5447692..5447711,+!p2@Fosl1!0.73!4.33!Fosl1;;chr2:152561980..152561997,+!p1@Id1!0.72!138.94!Id1;;chr11:53583544..53583559,+!p1@Irf1!0.72!80.01!Irf1;;chr14:98568971..98569025,-!p1@Dach1!0.70!34.66!Dach1;;chr4:154010940..154010962,-!p3@Prdm16!0.69!9.24!Prdm16;;chr1:194979361..194979373,+!p2@Irf6!0.69!5.49!Irf6;;chr4:94718879..94718898,-!p1@Jun!0.68!312.83!Jun;;chr4:6917921..6917970,-!p2@Tox!0.68!11.55!Tox;;chr7:31206743..31206761,+!p1@Nfkbid!0.68!5.49!Nfkbid;;chr3:90046995..90047031,-!p2@Creb3l4!0.68!4.91!Creb3l4;;chr5:77543935..77543947,-!p4@Hopx!0.68!3.76!Hopx;;chr8:79426176..79426275,+!p1@Nr3c2!0.66!20.51!Nr3c2;;chr8:77397190..77397202,+!p5@Isx!0.65!3.47!Isx;;chr2:180069640..180069660,-!p4@Gata5!0.65!3.47!Gata5;;chr1:194979383..194979393,+!p3@Irf6!0.65!3.47!Irf6;;chr16:55822241..55822258,-!p1@Nfkbiz!0.64!124.78!Nfkbiz;;chr13:55932591..55932622,-!p1@Pitx1!0.63!4.04!Pitx1;;chr5:76733981..76734018,-!p3@Clock!0.62!7.51!Clock;;chr5:115420882..115420896,-!p3@Hnf1a!0.62!3.18!Hnf1a;;chr4:133109285..133109308,+!p1@Nr0b2!0.62!3.18!Nr0b2;;chr11:53583960..53584007,+!p2@Irf1!0.61!7.51!Irf1;;chr2:91077082..91077122,-!p1@Ddb2!0.60!22.24!Ddb2;;chr15:35225845..35225867,+!p1@Osr2!0.60!8.67!Osr2;;chr18:55152206..55152251,-!p1@Zfp608!0.59!34.37!Zfp608;;chr10:70700755..70700772,-!p2@Tfam!0.59!16.75!Tfam;;chr5:77524304..77524315,-!p5@Hopx!0.59!6.93!Hopx;;chr11:98614335..98614349,+!p8@Thra!0.59!2.89!Thra;;chr11:83666422..83666446,+!p4@Hnf1b!0.59!2.89!Hnf1b;;chr1:138857112..138857130,-!p7@Nr5a2!0.59!2.89!Nr5a2;;chr15:37162834..37162849,+!p2@Grhl2!0.58!3.47!Grhl2;;chr18:35020615..35020641,+!p2@Egr1!0.58!3.47!Egr1;;chr19:6996243..6996293,-!p1@Esrra!0.57!36.97!Esrra;;chr14:79915425..79915501,+!p1@Elf1!0.56!28.89!Elf1;;chr10:119913310..119913366,-!p1@Hmga2!0.56!25.42!Hmga2;;chr17:32506357..32506377,-!p3@Wiz!0.56!6.35!Wiz;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.56!4.04!Carhsp1;;chr5:29805170..29805178,-!p2@Mnx1!0.56!2.60!Mnx1;;chr14:76887566..76887579,+!p18@Tsc22d1!0.56!2.60!Tsc22d1;;chr9:59796330..59796350,-!p6@Nr2e3!0.56!2.60!Nr2e3;;chr15:25914114..25914128,+!p2@Zfp622!0.55!12.71!Zfp622;;chr4:6917971..6918000,-!p3@Tox!0.55!5.78!Tox;;chr7:35904304..35904320,+!p1@Cebpa!0.54!64.13!Cebpa;;chr1:93309740..93309811,-!p1@Hes6!0.54!62.97!Hes6;;chr15:79177964..79177986,+!p1@Maff!0.54!10.40!Maff;;chr5:77524231..77524245,-!p3@Hopx!0.54!7.22!Hopx;;chr2:91077034..91077078,-!p2@Ddb2!0.54!6.35!Ddb2;;chr7:135381498..135381509,-!p2@9130023H24Rik!0.53!4.62!9130023H24Rik;;chr2:91035254..91035271,-!p3@Nr1h3!0.53!3.18!Nr1h3;;chr4:122673278..122673336,+!p1@Mycl1!0.52!8.95!Mycl1;;chr16:4559721..4559747,-!p3@Tfap4!0.52!6.07!Tfap4;;chr11:83664334..83664353,+!p2@Hnf1b!0.52!2.31!Hnf1b;;chr13:55932624..55932641,-!p2@Pitx1!0.52!2.31!Pitx1;;chr2:75543089..75543122,-!p3@Nfe2l2!0.52!2.31!Nfe2l2;;chr9:31720903..31720918,-!p2@Barx2!0.52!2.31!Barx2;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.51!136.34!Hmga1;;chr10:107769168..107769215,+!p1@Pawr!0.51!29.17!Pawr;;chr2:146047829..146047847,+!p1@Insm1!0.51!4.62!Insm1;;chr7:20162663..20162678,+!p1@Zfp296!0.51!3.18!Zfp296;;chr19:10315179..10315241,-!p1@Gm98!0.49!29.17!Gm98;;chr1:64579555..64579570,+!p3@Creb1!0.49!12.71!Creb1;;chr8:73905344..73905381,-!p2@Nr2f6!0.49!6.07!Nr2f6;;chr11:23977565..23977612,+!p5@Bcl11a!0.49!5.49!Bcl11a;;chr13:64254437..64254453,-!p4@Zfp367!0.49!3.18!Zfp367;;chr17:48061381..48061399,-!p1@Foxp4!0.48!30.91!Foxp4;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.48!7.22!Tfcp2l1;;chr10:30375579..30375616,-!p3@Ncoa7!0.48!5.78!Ncoa7;;chr11:102178005..102178022,-!p8@Ubtf!0.48!3.76!Ubtf;;chr15:79178060..79178074,+!p2@Maff!0.48!2.89!Maff;;chr1:138845748..138845766,-!p4@Nr5a2!0.48!2.89!Nr5a2;;chr9:31720843..31720888,-!p1@Barx2!0.48!2.31!Barx2;;chr9:43013917..43013968,-!p1@Pou2f3!0.48!2.02!Pou2f3;;chr1:189432634..189432643,+!p8@Esrrg!0.48!2.02!Esrrg;;chr1:189432857..189432870,+!p7@Esrrg!0.48!2.02!Esrrg;;chr1:189432907..189432926,+!p3@Esrrg!0.48!2.02!Esrrg;;chr2:147872074..147872079,-!p4@Foxa2!0.48!2.02!Foxa2;;chr1:194982959..194983007,+!p5@Irf6!0.48!2.02!Irf6;;chr16:38294929..38294940,-!p2@Nr1i2!0.48!2.02!Nr1i2;;chr17:28408632..28408682,+!p1@1810013A23Rik,p4@Ppard!0.48!2.02!Ppard;;chr5:148081667..148081678,+!p3@Pdx1!0.48!2.02!Pdx1;;chr8:124806017..124806040,+!p2@Zfpm1!0.47!28.60!Zfpm1;;chr13:30077847..30077906,-!p1@E2f3!0.47!20.22!E2f3;;chr17:71199121..71199165,-!p2@Tgif1!0.47!18.78!Tgif1;;chr13:64254457..64254497,-!p1@Zfp367!0.47!11.27!Zfp367;;chr5:65203599..65203617,+!p8@Klf3!0.47!3.76!Klf3;;chr8:124806111..124806122,+!p3@Zfpm1!0.47!2.60!Zfpm1;;chr10:70700783..70700832,-!p1@Tfam!0.46!10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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:12228-129F5
-|is_a=EFO:0002091;;FF:0000002;;FF:0000079;;FF:0000103
+|is_a=EFO:0002091;;FF:0000079
+|is_obsolete=
+|library_id=CNhs12555
+|library_id_phase_based=2:CNhs12555
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12228
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12228
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/Lgr5%2520positive%2520intestinal%2520stem%2520cells%252c%2520pool1.CNhs12555.12228-129F5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/Lgr5%2520positive%2520intestinal%2520stem%2520cells%252c%2520pool1.CNhs12555.12228-129F5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Lgr5%2520positive%2520intestinal%2520stem%2520cells%252c%2520pool1.CNhs12555.12228-129F5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Lgr5%2520positive%2520intestinal%2520stem%2520cells%252c%2520pool1.CNhs12555.12228-129F5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Lgr5%2520positive%2520intestinal%2520stem%2520cells%252c%2520pool1.CNhs12555.12228-129F5.mm9.nobarcode.rdna.fa.gz
 |name=Lgr5 positive intestinal stem cells, pool1
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12555,LSID921,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.122348855585641,0,0,0,0,0,-0.375404552499205,0,0,0,0,-0.0843392403965415,0,0,0,0,0.0551014608363205,0,-0.191893350882575,0,0,0,0.436657066447869,0,0,0,0,0,0,0,0,0.0551014608363205,-0.558422792324031,0,0,0,0,-0.0357396457000611,-0.015249194074845,-0.199560385736905,-0.171792890934346,-0.984211366477826,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.0673559665897667,0,0,0,0,-0.00634332011581207,-0.157354263504885,-0.0396098986939413,-0.158091042771083,-0.103373762788871,0,-0.0780086007519514,-0.120128438895423,-0.0703089438245028,0,0,-0.0877598160830127,-0.0837910309749567,-0.59591488074057,0.119193722432223,0,0,0,0,0,0.19802531727213,-0.147656715672568,-0.528412653622489,-0.159600080558758,0,0,0,0,0
 |rna_box=129
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=1.77795
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
-|sample_cell_lot=08122010
+|sample_cell_lot=8122010
 |sample_cell_type=stem cell
 |sample_collaboration=Marc van de Wetering
@@ Line 76: / Line 96: @@
 |sample_tissue=small intestine
 |top_motifs=bHLH_family:2.87047087162;ZEB1:2.16728755001;PAX8:1.88035306166;YY1:1.75189575529;NFY{A,B,C}:1.59961898955;ELK1,4_GABP{A,B1}:1.58251366338;NFIX:1.57400290279;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.37765414116;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.37421586123;SNAI1..3:1.35843154748;E2F1..5:1.29664151864;FOXN1:1.22453640917;ZNF143:1.21554404902;STAT1,3:1.14893654383;HNF4A_NR2F1,2:1.14611324233;NR6A1:1.12471875797;HNF1A:1.0623923795;ARID5B:1.02906633854;ATF4:0.979722202371;CREB1:0.96277466112;ADNP_IRX_SIX_ZHX:0.929463248338;LMO2:0.927757013238;ATF5_CREB3:0.882032375914;NFKB1_REL_RELA:0.878774640337;STAT5{A,B}:0.826573929409;HSF1,2:0.824679877427;MYB:0.756383902849;PDX1:0.648850420975;LEF1_TCF7_TCF7L1,2:0.639279528158;NANOG:0.589564004615;CRX:0.542607472574;HES1:0.541447872819;ONECUT1,2:0.535809913461;GFI1:0.521967270368;OCT4_SOX2{dimer}:0.461014428384;FOX{D1,D2}:0.44054828969;ESRRA:0.428023482111;PAX2:0.424720004676;SOX17:0.401002551709;CDX1,2,4:0.351979954577;NR5A1,2:0.323151989113;NKX6-1,2:0.31833855197;FOX{I1,J2}:0.279090422077;POU2F1..3:0.258286684022;GATA6:0.24976597279;PPARG:0.24728446185;IRF1,2:0.246472638294;ELF1,2,4:0.238037331204;STAT2,4,6:0.233073675898;TP53:0.213608122953;TLX2:0.19883759471;FOSL2:0.196849583476;MYOD1:0.181730717584;JUN:0.174722112666;NRF1:0.171405243077;GTF2A1,2:0.151157093857;T:0.144040692971;SOX{8,9,10}:0.126158024906;ATF6:0.125661819717;FOXM1:0.119720779871;DMAP1_NCOR{1,2}_SMARC:0.0873387953924;FOXL1:0.0866273140074;PBX1:0.0499924198632;NFIL3:0.0404626083043;ETS1,2:0.0226478258021;TBX4,5:0.000437899709267;NFE2L1:-0.0202618937351;AR:-0.0405680641319;VSX1,2:-0.0509270659483;PAX6:-0.0671573723844;RBPJ:-0.0678876377172;AHR_ARNT_ARNT2:-0.0722544759896;FOS_FOS{B,L1}_JUN{B,D}:-0.0879672114552;POU5F1:-0.0915334679955;ALX4:-0.0968910912993;BACH2:-0.103440569469;IRF7:-0.115388346328;FOXA2:-0.126604015848;FOXO1,3,4:-0.153743281168;ZBTB16:-0.177038964996;SP1:-0.178604313287;FOXQ1:-0.186170110314;POU3F1..4:-0.18856908929;RXRA_VDR{dimer}:-0.189157063665;RFX2..5_RFXANK_RFXAP:-0.201736992207;CDC5L:-0.206334408081;RORA:-0.221195189205;NKX2-2,8:-0.224934571741;POU6F1:-0.235812467845;TEF:-0.27809440758;HOX{A4,D4}:-0.280455682304;HBP1_HMGB_SSRP1_UBTF:-0.297059544031;SOX2:-0.301744657546;HLF:-0.307472110393;BREu{core}:-0.310797674563;FOX{F1,F2,J1}:-0.316759451264;AIRE:-0.331104154616;SRF:-0.338443149181;TBP:-0.350837733286;PAX5:-0.372058621292;RFX1:-0.374491743942;RUNX1..3:-0.382021996976;NR1H4:-0.383065374504;LHX3,4:-0.489985524151;MEF2{A,B,C,D}:-0.490109537318;BPTF:-0.539830878016;HOX{A5,B5}:-0.541499589221;GZF1:-0.548001945212;SPI1:-0.564212674494;XCPE1{core}:-0.650195856142;TEAD1:-0.677576284402;TFDP1:-0.684903899553;CEBPA,B_DDIT3:-0.687720144268;SPIB:-0.690896399796;NANOG{mouse}:-0.700944333235;NR3C1:-0.705823174564;TLX1..3_NFIC{dimer}:-0.706797491117;EN1,2:-0.718018847176;CUX2:-0.73189668275;NFE2L2:-0.748314552419;MED-1{core}:-0.748761235973;ZFP161:-0.749183116011;NKX2-3_NKX2-5:-0.781658865803;TOPORS:-0.784919797262;ZBTB6:-0.804798460429;REST:-0.805752268688;NFE2:-0.805953478653;ATF2:-0.810991471331;ZNF423:-0.817453741196;NKX3-1:-0.822179224537;FOXD3:-0.824006054736;HIF1A:-0.82969234482;RXR{A,B,G}:-0.830822308563;GFI1B:-0.839445575807;SREBF1,2:-0.854069721983;PRRX1,2:-0.859406568923;PAX1,9:-0.890089858919;HMX1:-0.919792480076;HOXA9_MEIS1:-0.931149483792;MTF1:-0.974421064574;ZNF384:-0.982455619783;DBP:-1.00377761848;PITX1..3:-1.00745707101;POU1F1:-1.04137532961;EP300:-1.06880894454;KLF4:-1.07212001895;GCM1,2:-1.08621878123;NKX2-1,4:-1.12518735646;HIC1:-1.13483911493;GLI1..3:-1.14492560094;ZNF238:-1.17118418049;FOXP3:-1.20847878363;MYBL2:-1.20915305897;HMGA1,2:-1.21392039396;FOXP1:-1.2139850457;GTF2I:-1.23305903667;UFEwm:-1.2781467389;MAFB:-1.32069868167;EGR1..3:-1.35396953339;EBF1:-1.3830511913;TFAP2B:-1.40556867898;MAZ:-1.40879457578;IKZF1:-1.41324490802;MZF1:-1.48143249964;SOX5:-1.49013733968;PRDM1:-1.49805892054;MYFfamily:-1.51466737153;ZIC1..3:-1.52537594504;TFAP2{A,C}:-1.5296178259;NHLH1,2:-1.54886377389;TGIF1:-1.57279314844;ALX1:-1.6190780221;PAX4:-1.64787881334;SPZ1:-1.67229038318;MTE{core}:-1.67742954085;PATZ1:-1.69670798442;EVI1:-1.7267284791;RREB1:-1.74337898268;TFCP2:-1.74372547037;NFATC1..3:-1.77913252142;TFAP4:-1.79549389105;NKX3-2:-1.81168068083;IKZF2:-1.83160643805;ESR1:-1.86693093338;TAL1_TCF{3,4,12}:-1.90384652533;ZNF148:-1.90952850117;HAND1,2:-1.97639976796;GATA4:-2.09989590101;SMAD1..7,9:-2.11027945693
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12228-129F5;search_select_hide=table117:12228-129F5
 }}

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FF:12228-129F5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:35, 4 June 2020

CNhs12555

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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