FF:12229-129F6: Difference between revisions

Latest revision as of 18:35, 4 June 2020

Name:	Lgr5 positive intestinal stem cells, pool2
Species:	Mouse (Mus musculus)
Library ID:	CNhs12556
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	female
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		SAMD00005032

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12556		CAGE		DRX008770		DRR009642

Accession ID Mm9

Library id		BAM		CTSS
CNhs12556		DRZ001067		DRZ002452

Accession ID Mm10

Library id		BAM		CTSS
CNhs12556		DRZ012417		DRZ013802

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

CNhs12556

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0668
1002	-0.116
1003	-0.123
1004	0
1005	0.108
1006	-0.2
1007	-0.204
1008	1.787
1009	-0.19
101	0.128
1010	0
1011	-0.255
1012	0
1013	0.0769
1014	-0.0874
1015	-0.236
1016	-0.465
1017	0
1018	0.5
1019	0
102	0
1020	0
1021	0
1022	0.125
1023	0
1024	-0.14
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.176
103	-0.0887
1030	0
1031	-0.93
1032	0.415
1033	0.26
1034	0
1035	0
1036	0.387
1037	0
1038	-0.158
1039	0.193
104	0
1040	-0.936
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: CNhs12556

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.176
MA0003.1	MA0003.1	0.739
MA0004.1	MA0004.1	0.0466
MA0006.1	MA0006.1	0.906
MA0007.1	MA0007.1	0.106
MA0009.1	MA0009.1	0.266
MA0014.1	MA0014.1	0.123
MA0017.1	MA0017.1	1.2258e-14
MA0018.2	MA0018.2	0.0243
MA0019.1	MA0019.1	0.647
MA0024.1	MA0024.1	1.45434e-4
MA0025.1	MA0025.1	0.126
MA0027.1	MA0027.1	0.262
MA0028.1	MA0028.1	3.36025e-7
MA0029.1	MA0029.1	0.123
MA0030.1	MA0030.1	0.923
MA0031.1	MA0031.1	0.547
MA0035.2	MA0035.2	5.7974e-4
MA0038.1	MA0038.1	0.483
MA0039.2	MA0039.2	0.00477
MA0040.1	MA0040.1	0.0352
MA0041.1	MA0041.1	0.179
MA0042.1	MA0042.1	0.364
MA0043.1	MA0043.1	0.0122
MA0046.1	MA0046.1	6.47713e-38
MA0047.2	MA0047.2	0.00318
MA0048.1	MA0048.1	0.0238
MA0050.1	MA0050.1	0.0319
MA0051.1	MA0051.1	0.0233
MA0052.1	MA0052.1	0.00304
MA0055.1	MA0055.1	4.85488e-4
MA0057.1	MA0057.1	0.207
MA0058.1	MA0058.1	0.0422
MA0059.1	MA0059.1	7.03105e-4
MA0060.1	MA0060.1	2.08378e-4
MA0061.1	MA0061.1	0.32
MA0062.2	MA0062.2	4.0465e-9
MA0065.2	MA0065.2	2.38691e-7
MA0066.1	MA0066.1	0.499
MA0067.1	MA0067.1	0.791
MA0068.1	MA0068.1	0.641
MA0069.1	MA0069.1	0.349
MA0070.1	MA0070.1	0.425
MA0071.1	MA0071.1	0.0154
MA0072.1	MA0072.1	0.626
MA0073.1	MA0073.1	0.958
MA0074.1	MA0074.1	0.514
MA0076.1	MA0076.1	2.22101e-6
MA0077.1	MA0077.1	0.359
MA0078.1	MA0078.1	0.173
MA0079.2	MA0079.2	0.105
MA0080.2	MA0080.2	0.00282
MA0081.1	MA0081.1	0.962
MA0083.1	MA0083.1	0.00464
MA0084.1	MA0084.1	0.0702
MA0087.1	MA0087.1	0.0927
MA0088.1	MA0088.1	0.00983
MA0090.1	MA0090.1	0.845
MA0091.1	MA0091.1	0.704
MA0092.1	MA0092.1	0.556
MA0093.1	MA0093.1	0.0526
MA0099.2	MA0099.2	0.0896
MA0100.1	MA0100.1	0.116
MA0101.1	MA0101.1	0.0736
MA0102.2	MA0102.2	0.521
MA0103.1	MA0103.1	4.44e-6
MA0104.2	MA0104.2	0.0138
MA0105.1	MA0105.1	0.0718
MA0106.1	MA0106.1	0.294
MA0107.1	MA0107.1	0.248
MA0108.2	MA0108.2	0.818
MA0111.1	MA0111.1	0.832
MA0112.2	MA0112.2	0.0178
MA0113.1	MA0113.1	0.09
MA0114.1	MA0114.1	7.01781e-16
MA0115.1	MA0115.1	2.28165e-9
MA0116.1	MA0116.1	0.0589
MA0117.1	MA0117.1	0.954
MA0119.1	MA0119.1	0.224
MA0122.1	MA0122.1	0.399
MA0124.1	MA0124.1	0.685
MA0125.1	MA0125.1	0.186
MA0131.1	MA0131.1	0.167
MA0135.1	MA0135.1	0.725
MA0136.1	MA0136.1	1.1514e-9
MA0137.2	MA0137.2	2.29938e-5
MA0138.2	MA0138.2	0.25
MA0139.1	MA0139.1	0.0776
MA0140.1	MA0140.1	0.208
MA0141.1	MA0141.1	1.51017e-5
MA0142.1	MA0142.1	0.151
MA0143.1	MA0143.1	0.457
MA0144.1	MA0144.1	0.00436
MA0145.1	MA0145.1	0.558
MA0146.1	MA0146.1	0.33
MA0147.1	MA0147.1	0.00257
MA0148.1	MA0148.1	0.00193
MA0149.1	MA0149.1	0.00401
MA0150.1	MA0150.1	0.323
MA0152.1	MA0152.1	0.262
MA0153.1	MA0153.1	8.25846e-29
MA0154.1	MA0154.1	0.52
MA0155.1	MA0155.1	0.71
MA0156.1	MA0156.1	3.15287e-6
MA0157.1	MA0157.1	0.93
MA0159.1	MA0159.1	5.253e-4
MA0160.1	MA0160.1	1.47013e-4
MA0162.1	MA0162.1	0.652
MA0163.1	MA0163.1	0.00542
MA0164.1	MA0164.1	0.981
MA0258.1	MA0258.1	0.0796
MA0259.1	MA0259.1	0.115

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: CNhs12556

Novel motif	Logo	P-value
1	1	0.195
10	10	0.0393
100	100	0.34
101	101	0.426
102	102	0.816
103	103	0.127
104	104	0.897
105	105	0.435
106	106	0.306
107	107	0.742
108	108	0.617
109	109	0.0164
11	11	0.155
110	110	0.105
111	111	0.113
112	112	0.0688
113	113	0.0915
114	114	0.932
115	115	0.615
116	116	0.523
117	117	0.017
118	118	0.397
119	119	0.61
12	12	1
120	120	0.842
121	121	0.527
122	122	0.572
123	123	0.0149
124	124	0.0264
125	125	0.0379
126	126	0.00424
127	127	0.429
128	128	0.815
129	129	0.593
13	13	2.22926e-6
130	130	0.408
131	131	0.678
132	132	0.658
133	133	0.751
134	134	0.468
135	135	0.085
136	136	0.015
137	137	0.707
138	138	0.277
139	139	0.711
14	14	0.842
140	140	0.414
141	141	0.849
142	142	0.755
143	143	0.105
144	144	0.0322
145	145	0.0149
146	146	0.314
147	147	0.824
148	148	0.719
149	149	0.382
15	15	0.179
150	150	0.469
151	151	0.861
152	152	0.519
153	153	0.798
154	154	0.73
155	155	0.756
156	156	0.177
157	157	0.467
158	158	0.443
159	159	0.748
160	160	0.565
161	161	0.268
162	162	0.377
163	163	0.727
164	164	0.036
165	165	0.115
166	166	0.512
167	167	0.206
168	168	0.814
169	169	0.0843
17	17	0.128
18	18	0.38
19	19	0.851
2	2	0.362
20	20	0.119
21	21	0.895
22	22	0.877
23	23	0.311
24	24	0.0725
25	25	0.166
26	26	6.30996e-4
27	27	0.912
28	28	0.995
29	29	0.00184
3	3	0.255
30	30	0.831
31	31	0.54
32	32	0.699
33	33	0.042
34	34	0.662
35	35	0.625
36	36	0.117
37	37	0.185
38	38	0.493
39	39	0.367
4	4	0.366
40	40	0.069
41	41	0.181
42	42	0.693
43	43	0.792
44	44	0.437
45	45	0.918
46	46	0.201
47	47	0.371
48	48	0.187
49	49	0.614
5	5	0.817
50	50	0.982
51	51	0.805
52	52	0.677
53	53	0.491
54	54	0.96
55	55	0.393
56	56	0.888
57	57	0.696
58	58	0.238
59	59	0.944
6	6	0.422
60	60	0.169
61	61	0.246
62	62	0.204
63	63	0.293
64	64	0.473
65	65	0.5
66	66	0.446
67	67	0.977
68	68	0.975
69	69	0.347
7	7	0.02
70	70	0.0561
71	71	0.0168
72	72	0.335
73	73	0.0925
74	74	0.933
75	75	0.0102
76	76	0.362
77	77	0.496
78	78	0.032
79	79	0.442
8	8	0.0725
80	80	0.757
81	81	0.814
82	82	0.77
83	83	0.268
84	84	0.767
85	85	0.574
86	86	0.425
87	87	0.014
88	88	0.502
89	89	0.681
9	9	0.675
90	90	0.0197
91	91	0.264
92	92	0.642
93	93	0.154
94	94	0.878
95	95	0.0021
96	96	0.332
97	97	0.914
98	98	0.305
99	99	0.421

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: CNhs12556

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
-|DRA_sample_Accession=CAGE@DRS008660
+|DRA_sample_Accession=CAGE@SAMD00005032
-|accession_numbers=CAGE;DRX008770;DRR009642;DRZ001067;DRZ002452
+|accession_numbers=CAGE;DRX008770;DRR009642;DRZ001067;DRZ002452;DRZ012417;DRZ013802
 |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
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:163332558..163332596,+!p2@Hnf4a!2.17!145.95!Hnf4a;;chr1:137155026..137155042,-!p1@Elf3!2.00!546.58!Elf3;;chr2:103123925..103123959,-!p3@Ehf!1.99!96.08!Ehf;;chr5:148118639..148118715,-!p1@Cdx2!1.89!76.97!Cdx2;;chr18:61195865..61195880,-!p1@Cdx1!1.77!57.35!Cdx1;;chr2:163372884..163372904,+!p1@Hnf4a!1.71!49.70!Hnf4a;;chr18:61195843..61195864,-!p2@Cdx1!1.61!39.56!Cdx1;;chr8:77396591..77396639,+!p1@Isx!1.55!34.08!Isx;;chr5:148118840..148118857,-!p2@Cdx2!1.53!32.58!Cdx2;;chr15:97738692..97738747,-!p1@Vdr!1.52!167.90!Vdr;;chr10:127095407..127095440,+!p3@Stat6!1.51!38.90!Stat6;;chr7:19608891..19608895,-!p1@Foxa3!1.50!39.40!Foxa3;;chr2:103143336..103143367,-!p1@Ehf!1.49!47.38!Ehf;;chr10:20880629..20880683,-!p1@Myb!1.48!82.78!Myb;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.44!33.75!Zbtb11;;chr3:3508024..3508069,+!p2@Hnf4g!1.42!25.27!Hnf4g;;chr7:150155143..150155156,-!p1@Ascl2!1.37!22.28!Ascl2;;chr16:38294860..38294924,-!p1@Nr1i2!1.35!21.61!Nr1i2;;chr3:3634145..3634161,+!p1@Hnf4g!1.33!20.61!Hnf4g;;chr14:63864056..63864102,-!p1@Gata4!1.31!33.08!Gata4;;chr3:30039329..30039355,-!p5@Mecom!1.27!17.79!Mecom;;chr5:135582751..135582788,+!p1@Mlxipl!1.24!65.50!Mlxipl;;chr10:61595830..61595846,+!p1@Neurog3!1.21!15.29!Neurog3;;chr5:148118792..148118806,-!p3@Cdx2!1.18!13.96!Cdx2;;chr7:19895354..19895369,-!p1@Fosb!1.17!18.95!Fosb;;chr5:148118809..148118832,-!p5@Cdx2!1.17!13.63!Cdx2;;chr2:103143315..103143328,-!p2@Ehf!1.16!13.47!Ehf;;chr19:5560600..5560617,-!p1@Ovol1!1.15!15.96!Ovol1;;chr10:88969376..88969395,-!p1@Nr1h4!1.12!12.14!Nr1h4;;chr8:77397095..77397127,+!p2@Isx!1.11!11.97!Isx;;chr2:180069370..180069409,-!p1@Gata5!1.10!13.63!Gata5;;chr1:138857048..138857071,-!p2@Nr5a2!1.10!11.64!Nr5a2;;chr14:76887526..76887555,+!p10@Tsc22d1!1.07!10.81!Tsc22d1;;chr11:106128936..106128955,-!p4@Smarcd2!1.05!11.80!Smarcd2;;chr18:64499706..64499721,+!p2@Onecut2!1.04!13.96!Onecut2;;chr14:99697871..99697934,+!p1@Klf5!1.03!196.66!Klf5;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!1.03!24.27!Hmga1;;chr12:86814833..86814846,+!p1@Fos!1.02!221.59!Fos;;chr5:77524250..77524300,-!p1@Hopx!1.01!190.34!Hopx;;chr17:27865882..27865901,-!p1@Spdef!1.01!9.31!Spdef;;chr9:59797503..59797513,-!p3@Nr2e3!1.01!9.14!Nr2e3;;chr1:193007123..193007139,-!p1@Atf3!0.99!50.04!Atf3;;chr17:28409136..28409150,+!p3@Ppard!0.99!8.81!Ppard;;chr10:20880698..20880717,-!p3@Myb!0.98!13.63!Myb;;chr7:19895384..19895399,-!p2@Fosb!0.98!12.30!Fosb;;chr8:77397492..77397514,+!p3@Isx!0.98!8.48!Isx;;chr9:59797525..59797538,-!p2@Nr2e3!0.98!8.48!Nr2e3;;chr5:29805118..29805137,-!p1@Mnx1!0.96!8.15!Mnx1;;chr1:194979315..194979359,+!p1@Irf6!0.95!49.37!Irf6;;chr14:63890545..63890560,-!p5@Gata4!0.95!7.98!Gata4;;chr18:64499674..64499696,+!p1@Onecut2!0.94!13.47!Onecut2;;chr4:94718861..94718872,-!p2@Jun!0.92!57.18!Jun;;chr2:70313168..70313184,+!p1@Sp5!0.92!11.30!Sp5;;chr10:80555320..80555378,-!p1@Creb3l3!0.91!8.31!Creb3l3;;chr8:123260252..123260264,+!p1@Irf8!0.90!51.03!Irf8;;chr17:27693746..27693759,+!p6@Hmga1-rs1,p7@Hmga1!0.89!13.80!Hmga1;;chr12:58646974..58647003,-!p1@Foxa1!0.89!9.31!Foxa1;;chr3:128918394..128918413,+!p5@Pitx2!0.89!6.82!Pitx2;;chr18:11052642..11052659,+!p1@Gata6!0.88!34.91!Gata6;;chr4:124805061..124805087,-!p1@Zc3h12a!0.87!20.78!Zc3h12a;;chr17:27693788..27693803,+!p3@Hmga1,p4@Hmga1-rs1!0.86!29.76!Hmga1;;chr3:90046995..90047031,-!p2@Creb3l4!0.85!7.65!Creb3l4;;chr18:11052606..11052633,+!p4@Gata6!0.84!15.79!Gata6;;chr6:64679112..64679126,+!p1@Atoh1!0.84!5.98!Atoh1;;chr1:194979361..194979373,+!p2@Irf6!0.82!7.81!Irf6;;chr8:77396650..77396662,+!p4@Isx!0.82!5.65!Isx;;chr4:122673187..122673201,+!p2@Mycl1!0.80!9.81!Mycl1;;chr15:37162796..37162828,+!p1@Grhl2!0.80!9.14!Grhl2;;chr8:124806048..124806094,+!p1@Zfpm1!0.79!51.70!Zfpm1;;chr3:94176733..94176794,+!p1@Rorc!0.79!43.55!Rorc;;chr3:3508005..3508021,+!p3@Hnf4g!0.79!5.15!Hnf4g;;chr1:173144100..173144138,+!p2@Nr1i3!0.79!5.15!Nr1i3;;chr2:163372869..163372882,+!p3@Hnf4a!0.78!4.99!Hnf4a;;chr11:83664365..83664383,+!p1@Hnf1b!0.78!4.99!Hnf1b;;chr5:77543897..77543911,-!p2@Hopx!0.77!9.97!Hopx;;chr2:152561980..152561997,+!p1@Id1!0.76!154.10!Id1;;chr14:63890491..63890516,-!p2@Gata4!0.76!4.82!Gata4;;chr17:28409059..28409076,+!p6@Ppard!0.76!4.82!Ppard;;chr5:115421065..115421088,-!p1@Hnf1a!0.75!4.65!Hnf1a;;chr14:63890519..63890539,-!p3@Gata4!0.75!4.65!Gata4;;chr2:147871627..147871641,-!p1@Foxa2!0.75!4.65!Foxa2;;chr8:77397190..77397202,+!p5@Isx!0.74!4.49!Isx;;chr11:53583544..53583559,+!p1@Irf1!0.73!81.29!Irf1;;chr13:44825008..44825066,+!p5@Jarid2!0.73!9.14!Jarid2;;chr14:76887566..76887579,+!p18@Tsc22d1!0.73!4.32!Tsc22d1;;chr1:138857076..138857105,-!p1@Nr5a2!0.73!4.32!Nr5a2;;chr1:189432881..189432903,+!p2@Esrrg!0.71!4.16!Esrrg;;chr11:106128919..106128933,-!p8@Smarcd2!0.71!4.16!Smarcd2;;chr8:73905344..73905381,-!p2@Nr2f6!0.69!10.31!Nr2f6;;chr5:77524231..77524245,-!p3@Hopx!0.67!10.14!Hopx;;chr13:55932739..55932756,-!p5@Pitx1!0.65!3.49!Pitx1;;chr2:180069640..180069660,-!p4@Gata5!0.65!3.49!Gata5;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.64!4.99!Carhsp1;;chr1:194982959..194983007,+!p5@Irf6!0.64!3.32!Irf6;;chr5:148081686..148081715,+!p1@Pdx1!0.64!3.32!Pdx1;;chr4:122673278..122673336,+!p1@Mycl1!0.63!11.80!Mycl1;;chr3:96002383..96002407,-!p4@Bola1!0.63!4.49!Bola1;;chr1:93309740..93309811,-!p1@Hes6!0.62!75.64!Hes6;;chr12:109242266..109242295,-!p1@Bcl11b!0.62!31.42!Bcl11b;;chr13:55932591..55932622,-!p1@Pitx1!0.62!3.99!Pitx1;;chr4:133109285..133109308,+!p1@Nr0b2!0.62!3.16!Nr0b2;;chr5:29805170..29805178,-!p2@Mnx1!0.62!3.16!Mnx1;;chr19:5560570..5560582,-!p2@Ovol1!0.62!3.16!Ovol1;;chr19:6996243..6996293,-!p1@Esrra!0.61!40.23!Esrra;;chr4:154010918..154010931,-!p1@Prdm16!0.61!10.31!Prdm16;;chr11:98636508..98636524,-!p3@Nr1d1!0.60!3.82!Nr1d1;;chr5:148081667..148081678,+!p3@Pdx1!0.60!2.99!Pdx1;;chr3:128918433..128918448,+!p8@Pitx2!0.60!2.99!Pitx2;;chr2:91077082..91077122,-!p1@Ddb2!0.59!21.78!Ddb2;;chr1:189821714..189821761,+!p1@Esrrg!0.59!5.98!Esrrg;;chr9:31720843..31720888,-!p1@Barx2!0.59!3.32!Barx2;;chr10:70700755..70700772,-!p2@Tfam!0.58!16.12!Tfam;;chr18:11052485..11052508,+!p2@Gata6!0.57!8.98!Gata6;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.56!151.77!Hmga1;;chr9:59796270..59796294,-!p4@Nr2e3!0.56!2.66!Nr2e3;;chr5:77544170..77544181,-!p6@Hopx!0.56!2.66!Hopx;;chr5:77524304..77524315,-!p5@Hopx!0.55!6.15!Hopx;;chr18:35020854..35020869,+!p1@Egr1!0.54!122.02!Egr1;;chr13:64254457..64254497,-!p1@Zfp367!0.54!13.63!Zfp367;;chr18:35020615..35020641,+!p2@Egr1!0.53!2.99!Egr1;;chr14:79915425..79915501,+!p1@Elf1!0.52!26.60!Elf1;;chr15:35225845..35225867,+!p1@Osr2!0.52!6.98!Osr2;;chr11:53583960..53584007,+!p2@Irf1!0.52!5.82!Irf1;;chr3:128916868..128916890,+!p1@Pitx2!0.52!3.49!Pitx2;;chr13:55932624..55932641,-!p2@Pitx1!0.52!2.33!Pitx1;;chr15:85566014..85566045,+!p3@Ppara!0.51!3.32!Ppara;;chr7:31206743..31206761,+!p1@Nfkbid!0.51!3.32!Nfkbid;;chr2:91035254..91035271,-!p3@Nr1h3!0.51!2.99!Nr1h3;;chr4:133801453..133801492,-!p1@Zfp593!0.50!23.11!Zfp593;;chr16:4559721..4559747,-!p3@Tfap4!0.50!5.65!Tfap4;;chr5:148118614..148118625,-!p4@Cdx2!0.50!2.16!Cdx2;;chr2:79296783..79296801,-!p1@Neurod1!0.50!2.16!Neurod1;;chr1:189432907..189432926,+!p3@Esrrg!0.50!2.16!Esrrg;;chr7:35904304..35904320,+!p1@Cebpa!0.48!55.36!Cebpa;;chr8:124806017..124806040,+!p2@Zfpm1!0.48!29.42!Zfpm1;;chr14:63890459..63890484,-!p4@Gata4!0.48!1.99!Gata4;;chr11:83664334..83664353,+!p2@Hnf1b!0.48!1.99!Hnf1b;;chr14:98568971..98569025,-!p1@Dach1!0.47!20.28!Dach1;;chr10:70700783..70700832,-!p1@Tfam!0.46!98.58!Tfam;;chr5:140267510..140267555,+!p2@Mafk!0.46!5.49!Mafk;;chr7:134519473..134519502,-!p3@Zfp747!0.46!2.83!Zfp747;;chr7:133839456..133839523,+!p1@Bola2!0.45!128.33!Bola2;;chr4:148178559..148178603,+!p1@Casz1!0.45!6.65!Casz1;;chrX:48559079..48559108,-!p2@Mbnl3!0.45!5.15!Mbnl3;;chr4:154010940..154010962,-!p3@Prdm16!0.45!4.99!Prdm16;;chr5:76733981..76734018,-!p3@Clock!0.45!4.82!Clock;;chr17:71200415..71200427,-!p5@Tgif1!0.45!3.49!Tgif1;;chr15:37162834..37162849,+!p2@Grhl2!0.45!2.33!Grhl2;;chr11:98614335..98614349,+!p8@Thra!0.45!1.83!Thra;;chr1:194979383..194979393,+!p3@Irf6!0.45!1.83!Irf6;;chr2:147871948..147871977,-!p3@Foxa2!0.45!1.83!Foxa2;;chr1:189821700..189821713,+!p4@Esrrg!0.45!1.83!Esrrg;;chr17:48061381..48061399,-!p1@Foxp4!0.44!27.93!Foxp4;;chr7:20408047..20408125,-!p1@Bcl3!0.44!27.93!Bcl3;;chr10:107769168..107769215,+!p1@Pawr!0.44!25.27!Pawr;;chr8:79426176..79426275,+!p1@Nr3c2!0.44!11.80!Nr3c2;;chr8:124984566..124984595,-!p1@Snai3!0.44!3.16!Snai3;;chr11:102178005..102178022,-!p8@Ubtf!0.43!3.32!Ubtf;;chr11:98822047..98822072,+!p9@Rara!0.43!1.66!Rara;;chr9:31720903..31720918,-!p2@Barx2!0.43!1.66!Barx2;;chr9:43013917..43013968,-!p1@Pou2f3!0.43!1.66!Pou2f3;;chr4:94718879..94718898,-!p1@Jun!0.42!171.89!Jun;;chr15:61817095..61817111,+!p1@Myc!0.42!142.13!Myc;;chr15:81702313..81702346,-!p1@Phf5a!0.42!71.81!Phf5a;;chr16:4559608..4559681,-!p1@Tfap4!0.42!19.12!Tfap4;;chr2:91077034..91077078,-!p2@Ddb2!0.41!4.49!Ddb2;;chr17:32506357..32506377,-!p3@Wiz!0.41!4.16!Wiz;;chr15:85566051..85566080,+!p4@Ppara!0.41!1.99!Ppara;;chr6:83299445..83299490,+!p1@Bola3!0.40!96.58!Bola3;;chr5:120121020..120121049,+!p1@Tbx3!0.40!13.47!Tbx3;;chr16:55966451..55966484,+!p3@Rpl24,p3@Zbtb11!0.40!12.80!Zbtb11;;chr4:6917921..6917970,-!p2@Tox!0.40!5.65!Tox;;chr13:64254502..64254515,-!p3@Zfp367!0.40!2.66!Zfp367;;chr15:37163124..37163153,+!p3@Grhl2!0.40!1.50!Grhl2;;chr5:77543935..77543947,-!p4@Hopx!0.40!1.50!Hopx;;chr1:138857112..138857130,-!p7@Nr5a2!0.40!1.50!Nr5a2;;chr19:5447692..5447711,+!p2@Fosl1!0.40!1.50!Fosl1;;chr7:20213752..20213778,-!p2@Relb!0.40!1.50!Relb;;chr13:30077847..30077906,-!p1@E2f3!0.39!16.79!E2f3;;chr6:124662297..124662371,+!p1@Phb2!0.38!435.37!Phb2;;chr3:96001503..96001557,-!p1@Bola1!0.38!45.55!Bola1;;chr2:162880387..162880413,+!p1@Mybl2!0.38!12.97!Mybl2;;chr5:147760305..147760324,+!p2@Gtf3a!0.38!9.97!Gtf3a;;chr10:20880731..20880775,-!p2@Myb!0.38!3.82!Myb;;chr2:146047829..146047847,+!p1@Insm1!0.38!3.16!Insm1;;chr3:89197057..89197114,-!p1@Zbtb7b!0.37!6.48!Zbtb7b;;chr2:180069410..180069421,-!p3@Gata5!0.37!1.33!Gata5;;chr11:106134020..106134128,-!p1@Smarcd2!0.36!40.56!Smarcd2;;chr8:87502608..87502623,-!p1@Junb!0.36!33.25!Junb;;chr1:39250584..39250643,+!p1@Npas2!0.36!9.81!Npas2;;chr5:147760297..147760304,+!p4@Gtf3a!0.36!2.99!Gtf3a;;chr12:113916993..113917009,+!p2@Zbtb42!0.36!2.83!Zbtb42;;chr8:124806111..124806122,+!p3@Zfpm1!0.36!1.83!Zfpm1;;chr16:55822241..55822258,-!p1@Nfkbiz!0.35!62.50!Nfkbiz;;chr2:154395581..154395610,-!p1@E2f1!0.35!20.11!E2f1;;chr5:34163023..34163090,+!p2@Whsc1!0.35!12.47!Whsc1;;chr15:25914114..25914128,+!p2@Zfp622!0.35!7.65!Zfp622;;chr1:133904946..133904974,+!p7@Elk4!0.35!2.33!Elk4;;chr5:144951153..144951203,+!p1@Bhlha15!0.35!2.16!Bhlha15;;chr2:162880418..162880429,+!p4@Mybl2!0.35!1.83!Mybl2;;chr2:75542527..75542590,-!p1@Nfe2l2!0.34!176.54!Nfe2l2;;chr10:119913310..119913366,-!p1@Hmga2!0.34!14.79!Hmga2;;chr17:48061584..48061601,-!p2@Foxp4!0.34!12.30!Foxp4;;chr6:115310872..115310899,+!p2@Pparg!0.34!2.66!Pparg;;chr14:52634651..52634678,-!p7@Zfp219!0.34!2.33!Zfp219;;chrX:48559029..48559051,-!p7@Mbnl3!0.34!1.83!Mbnl3;;chr1:138845748..138845766,-!p4@Nr5a2!0.34!1.83!Nr5a2;;chr14:99698164..99698208,+!p2@Klf5!0.34!1.50!Klf5;;chr1:173144144..173144176,+!p1@Nr1i3!0.34!1.16!Nr1i3;;chr5:148081722..148081744,+!p2@Pdx1!0.34!1.16!Pdx1;;chr6:99216375..99216395,-!p5@Foxp1!0.34!1.16!Foxp1;;chr5:115420882..115420896,-!p3@Hnf1a!0.34!1.16!Hnf1a;;chr16:38294929..38294940,-!p2@Nr1i2!0.34!1.16!Nr1i2;;chr8:73222425..73222444,+!p2@Jund!0.34!1.16!Jund;;chr15:38230448..38230470,-!p1@Klf10!0.33!39.90!Klf10;;chr14:47896467..47896523,-!p1@Wdhd1!0.33!23.11!Wdhd1;;chr18:55152206..55152251,-!p1@Zfp608!0.33!18.12!Zfp608;;chr15:79177964..79177986,+!p1@Maff!0.33!5.98!Maff;;chr7:56137011..56137041,-!p2@E2f8!0.33!2.99!E2f8;;chr11:3189171..3189197,+!p4@Patz1!0.33!2.99!Patz1;;chr8:28087609..28087634,+!p1@Zfp703!0.32!42.72!Zfp703;;chr17:71200529..71200556,-!p1@Tgif1!0.32!29.76!Tgif1;;chr11:69393868..69393884,+!p2@Trp53!0.32!25.77!Trp53;;chr8:72663098..72663160,-!p2@LOC100048268,p2@Rfxank!0.32!8.81!Rfxank;;chr17:48061605..48061629,-!p6@Foxp4!0.32!6.98!Foxp4;;chr11:52096750..52096772,-!p4@Tcf7!0.32!2.16!Tcf7;;chr13:67476665..67476693,-!p2@Zfp456!0.32!2.16!Zfp456;;chr19:10315179..10315241,-!p1@Gm98!0.31!18.78!Gm98;;chr4:133801494..133801519,-!p2@Zfp593!0.31!12.47!Zfp593;;chr7:133838869..133838945,+!p2@Bola2!0.31!7.15!Bola2;;chr11:106134144..106134174,-!p3@Smarcd2!0.31!4.82!Smarcd2;;chr8:92872242..92872285,-!p1@Tox3!0.31!3.99!Tox3;;chr1:95651388..95651434,-!p2@Thap4!0.31!3.66!Thap4;;chr11:112643496..112643562,+!p1@Sox9!0.30!66.66!Sox9;;chr17:71199121..71199165,-!p2@Tgif1!0.30!12.47!Tgif1;;chr2:162880327..162880385,+!p2@Mybl2!0.30!11.47!Mybl2;;chr18:36441119..36441158,+!p2@Pura!0.30!3.66!Pura;;chr4:6917971..6918000,-!p3@Tox!0.30!2.83!Tox;;chr19:10315252..10315266,-!p2@Gm98!0.30!1.99!Gm98;;chr12:109241852..109241873,-!p4@Bcl11b!0.30!1.33!Bcl11b;;chr12:109241897..109241915,-!p6@Bcl11b!0.30!1.00!Bcl11b;;chr9:31721051..31721068,-!p3@Barx2!0.30!1.00!Barx2;;chr9:59796330..59796350,-!p6@Nr2e3!0.30!1.00!Nr2e3;;chr9:59797133..59797145,-!p7@Nr2e3!0.30!1.00!Nr2e3;;chr14:63864337..63864381,-!p6@Gata4!0.30!1.00!Gata4;;chr1:138846079..138846103,-!p6@Nr5a2!0.30!1.00!Nr5a2;;chr2:180069423..180069434,-!p2@Gata5!0.30!1.00!Gata5;;chr2:84877326..84877362,+!p2@Ssrp1!0.29!37.40!Ssrp1;;chr14:98568761..98568814,-!p2@Dach1!0.29!11.47!Dach1;;chr13:67461490..67461531,-!p1@Zfp595,p1@Zfp953!0.29!6.48!Zfp953;;chr16:55966407..55966447,+!p6@Rpl24,p6@Zbtb11!0.29!3.49!Zbtb11;;chr14:52639709..52639753,-!p5@Zfp219!0.29!3.16!Zfp219;;chr1:95651267..95651284,-!p4@Thap4!0.29!2.49!Thap4;;chr15:79178060..79178074,+!p2@Maff!0.29!1.50!Maff;;chr17:84587279..84587294,-!p1@Zfp36l2!0.28!183.52!Zfp36l2;;chr6:131338435..131338482,-!p1@Csda!0.28!163.74!Csda;;chr16:95924055..95924077,+!p1@Ets2!0.28!93.42!Ets2;;chr11:100948597..100948637,+!p1@Mlx!0.28!40.73!Mlx;;chr8:28087578..28087599,+!p2@Zfp703!0.28!16.29!Zfp703;;chr7:56136362..56136400,-!p1@E2f8!0.28!10.47!E2f8;;chr17:28314341..28314394,+!p2@Zfp523!0.28!9.31!Zfp523;;chr10:82226833..82226864,-!p3@Nfyb!0.28!8.15!Nfyb;;chr6:131338363..131338383,-!p4@Csda!0.28!6.98!Csda;;chr2:38781916..38781974,-!p1@Nr6a1!0.28!4.49!Nr6a1;;chr18:55152179..55152194,-!p5@Zfp608!0.28!4.16!Zfp608;;chr7:97591412..97591431,+!p2@Crebzf!0.28!3.82!Crebzf;;chr1:95651346..95651383,-!p3@Thap4!0.28!3.32!Thap4;;chr1:13364477..13364492,-!p6@Ncoa2!0.28!1.33!Ncoa2;;chr5:21290933..21291050,-!p1@Dnajc2!0.27!63.50!Dnajc2;;chr10:127080031..127080090,+!p1@Stat6!0.27!36.41!Stat6;;chr17:35653725..35653780,-!p1@Tcf19!0.27!27.76!Tcf19;;chr11:95528303..95528319,+!p1@1700071K01Rik,p1@Phb!0.27!22.11!Phb;;chr7:105851601..105851647,+!p2@Prkrir!0.27!14.96!Prkrir;;chr1:194979301..194979310,+!p4@Irf6!0.27!1.16!Irf6;;chr4:135728581..135728668,+!p1@E2f2!0.26!7.15!E2f2;;chr6:115803317..115803361,-!p2@Mbd4!0.26!3.32!Mbd4;;chr11:23977565..23977612,+!p5@Bcl11a!0.26!2.83!Bcl11a;;chr7:134376558..134376587,+!p2@Zfp553!0.26!1.99!Zfp553;;chr16:55822638..55822669,-!p3@Nfkbiz!0.26!1.66!Nfkb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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs12556
-|library_id_phase_based=1:CNhs12556
+|library_id_phase_based=2:CNhs12556
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12229
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12229
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/Lgr5%2520positive%2520intestinal%2520stem%2520cells%252c%2520pool2.CNhs12556.12229-129F6.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%2520pool2.CNhs12556.12229-129F6.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%2520pool2.CNhs12556.12229-129F6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Lgr5%2520positive%2520intestinal%2520stem%2520cells%252c%2520pool2.CNhs12556.12229-129F6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Lgr5%2520positive%2520intestinal%2520stem%2520cells%252c%2520pool2.CNhs12556.12229-129F6.mm9.nobarcode.rdna.fa.gz
 |name=Lgr5 positive intestinal stem cells, pool2
 |namespace=FANTOM5
@@ Line 51: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12556,LSID921,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.132120113106938,0,0,0,0,0,-0.54574872134261,0,0,0,0,-0.0843392403965415,0,0,0,0,0.062328604336794,0,-0.125107412010099,0,0,0,0,0,0,0,0,0,0,0,0,0.0550871510082505,-0.161158757544321,0,0,0,0,-0.0419832096074401,-0.113601151722794,-0.155840949826514,-0.116314427158887,-0.984211366477826,-0.269868638010351,0.0667859388724756,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.0239389837896008,0,0,0,0,-0.0182038793878014,-0.112274844064713,-0.0101839001614549,-0.158091042771083,-0.0710217064336806,0,-0.0780086007519514,-0.119580349178297,0,0,0,-0.082741796264546,-0.264304937600917,-0.42019903283428,0.183897835142603,0,0,0,0,0,0.0667859388724756,-0.201406801177529,-0.638786293821845,-0.236410032795162,0,0,0,0,0
@@ Line 70: / Line 79: @@
 |sample_cell_catalog=
 |sample_cell_line=
-|sample_cell_lot=09122010
+|sample_cell_lot=9122010
 |sample_cell_type=stem cell
 |sample_collaboration=Marc van de Wetering
@@ Line 88: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12229-129F6;search_select_hide=table117:12229-129F6
 }}

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FF:12229-129F6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:35, 4 June 2020

CNhs12556

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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