FF:1251-16I5: Difference between revisions

Latest revision as of 18:39, 4 June 2020

Name:	intestine, embryo E12
Species:	Mouse (Mus musculus)
Library ID:	CNhs11019
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	intestine
dev stage	12 days embryo
sex	mixture
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004885

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11019		CAGE		DRX008990		DRR009864

Accession ID Mm9

Library id		BAM		CTSS
CNhs11019		DRZ001289		DRZ002672

Accession ID Mm10

Library id		BAM		CTSS
CNhs11019		DRZ012639		DRZ014022

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

CNhs11019

0	0
1	0
10	0
100	0.0477
1000	0
1001	-0.0275
1002	0.75
1003	-0.156
1004	0
1005	-0.0389
1006	-0.11
1007	0.15
1008	0
1009	0.00821
101	0.159
1010	0.084
1011	0.0175
1012	0
1013	-0.217
1014	0.551
1015	0.32
1016	0.324
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0
1023	0
1024	0.0081
1025	0.843
1026	0
1027	0.0933
1028	0
1029	0.175
103	0.0672
1030	0
1031	0.342
1032	-0.0536
1033	0.0867
1034	0
1035	0.084
1036	0.212
1037	0
1038	-0.0714
1039	-0.145
104	0
1040	0.125
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: CNhs11019

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	2.26863e-4
MA0003.1	MA0003.1	0.134
MA0004.1	MA0004.1	0.777
MA0006.1	MA0006.1	0.277
MA0007.1	MA0007.1	0.384
MA0009.1	MA0009.1	0.384
MA0014.1	MA0014.1	0.351
MA0017.1	MA0017.1	2.65087e-4
MA0018.2	MA0018.2	0.73
MA0019.1	MA0019.1	0.719
MA0024.1	MA0024.1	1.51362e-6
MA0025.1	MA0025.1	5.80579e-5
MA0027.1	MA0027.1	0.0516
MA0028.1	MA0028.1	0.0534
MA0029.1	MA0029.1	0.368
MA0030.1	MA0030.1	0.241
MA0031.1	MA0031.1	0.051
MA0035.2	MA0035.2	0.106
MA0038.1	MA0038.1	0.0711
MA0039.2	MA0039.2	0.00767
MA0040.1	MA0040.1	0.374
MA0041.1	MA0041.1	0.114
MA0042.1	MA0042.1	0.346
MA0043.1	MA0043.1	0.489
MA0046.1	MA0046.1	0.107
MA0047.2	MA0047.2	0.12
MA0048.1	MA0048.1	0.00931
MA0050.1	MA0050.1	1.26772e-5
MA0051.1	MA0051.1	5.44563e-6
MA0052.1	MA0052.1	1.28283e-9
MA0055.1	MA0055.1	0.0149
MA0057.1	MA0057.1	0.0616
MA0058.1	MA0058.1	0.563
MA0059.1	MA0059.1	0.329
MA0060.1	MA0060.1	7.41325e-11
MA0061.1	MA0061.1	0.119
MA0062.2	MA0062.2	0.326
MA0065.2	MA0065.2	1.09072e-4
MA0066.1	MA0066.1	0.054
MA0067.1	MA0067.1	0.376
MA0068.1	MA0068.1	0.771
MA0069.1	MA0069.1	0.726
MA0070.1	MA0070.1	0.881
MA0071.1	MA0071.1	0.0571
MA0072.1	MA0072.1	0.0164
MA0073.1	MA0073.1	0.325
MA0074.1	MA0074.1	0.81
MA0076.1	MA0076.1	0.0492
MA0077.1	MA0077.1	0.284
MA0078.1	MA0078.1	0.592
MA0079.2	MA0079.2	0.0564
MA0080.2	MA0080.2	9.63726e-9
MA0081.1	MA0081.1	0.219
MA0083.1	MA0083.1	0.0359
MA0084.1	MA0084.1	0.554
MA0087.1	MA0087.1	0.538
MA0088.1	MA0088.1	0.911
MA0090.1	MA0090.1	0.895
MA0091.1	MA0091.1	0.922
MA0092.1	MA0092.1	0.702
MA0093.1	MA0093.1	0.762
MA0099.2	MA0099.2	5.96972e-7
MA0100.1	MA0100.1	0.591
MA0101.1	MA0101.1	0.569
MA0102.2	MA0102.2	0.621
MA0103.1	MA0103.1	0.00184
MA0104.2	MA0104.2	0.259
MA0105.1	MA0105.1	0.387
MA0106.1	MA0106.1	0.253
MA0107.1	MA0107.1	0.209
MA0108.2	MA0108.2	0.0379
MA0111.1	MA0111.1	0.658
MA0112.2	MA0112.2	4.79069e-4
MA0113.1	MA0113.1	0.79
MA0114.1	MA0114.1	0.00155
MA0115.1	MA0115.1	0.0846
MA0116.1	MA0116.1	0.247
MA0117.1	MA0117.1	0.0409
MA0119.1	MA0119.1	0.0296
MA0122.1	MA0122.1	0.446
MA0124.1	MA0124.1	0.217
MA0125.1	MA0125.1	0.564
MA0131.1	MA0131.1	0.122
MA0135.1	MA0135.1	0.297
MA0136.1	MA0136.1	3.10422e-4
MA0137.2	MA0137.2	0.264
MA0138.2	MA0138.2	8.01999e-4
MA0139.1	MA0139.1	0.343
MA0140.1	MA0140.1	0.555
MA0141.1	MA0141.1	0.00637
MA0142.1	MA0142.1	0.45
MA0143.1	MA0143.1	0.0161
MA0144.1	MA0144.1	0.258
MA0145.1	MA0145.1	0.0177
MA0146.1	MA0146.1	0.389
MA0147.1	MA0147.1	0.294
MA0148.1	MA0148.1	0.0234
MA0149.1	MA0149.1	0.0771
MA0150.1	MA0150.1	6.25113e-4
MA0152.1	MA0152.1	0.255
MA0153.1	MA0153.1	0.167
MA0154.1	MA0154.1	0.0272
MA0155.1	MA0155.1	0.97
MA0156.1	MA0156.1	0.0999
MA0157.1	MA0157.1	0.0394
MA0159.1	MA0159.1	0.0408
MA0160.1	MA0160.1	0.0136
MA0162.1	MA0162.1	0.95
MA0163.1	MA0163.1	0.888
MA0164.1	MA0164.1	0.685
MA0258.1	MA0258.1	6.84469e-4
MA0259.1	MA0259.1	0.502

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: CNhs11019

Novel motif	Logo	P-value
1	1	0.149
10	10	0.853
100	100	0.762
101	101	0.639
102	102	0.617
103	103	0.177
104	104	0.882
105	105	0.161
106	106	0.0101
107	107	0.0724
108	108	0.871
109	109	0.14
11	11	0.191
110	110	0.575
111	111	0.265
112	112	0.0841
113	113	0.375
114	114	0.0106
115	115	0.404
116	116	0.461
117	117	0.969
118	118	0.845
119	119	0.031
12	12	0.695
120	120	0.83
121	121	0.449
122	122	0.668
123	123	0.0827
124	124	0.291
125	125	0.939
126	126	0.753
127	127	0.0937
128	128	0.0335
129	129	0.0782
13	13	0.738
130	130	0.379
131	131	0.144
132	132	0.615
133	133	0.823
134	134	0.447
135	135	0.965
136	136	0.659
137	137	0.946
138	138	0.423
139	139	0.0142
14	14	0.321
140	140	0.00305
141	141	0.399
142	142	0.842
143	143	0.846
144	144	0.934
145	145	0.92
146	146	0.216
147	147	0.584
148	148	0.467
149	149	0.186
15	15	0.068
150	150	0.616
151	151	0.0793
152	152	0.0349
153	153	0.202
154	154	0.839
155	155	0.935
156	156	0.0134
157	157	0.932
158	158	0.623
159	159	0.322
160	160	0.856
161	161	0.617
162	162	0.767
163	163	0.0887
164	164	0.818
165	165	0.341
166	166	0.0899
167	167	0.321
168	168	0.501
169	169	0.0429
17	17	0.12
18	18	0.397
19	19	0.578
2	2	0.444
20	20	0.431
21	21	0.912
22	22	0.295
23	23	0.0492
24	24	0.393
25	25	0.312
26	26	0.632
27	27	0.259
28	28	0.251
29	29	0.967
3	3	0.477
30	30	0.6
31	31	0.328
32	32	0.327
33	33	0.734
34	34	0.692
35	35	0.458
36	36	0.658
37	37	0.163
38	38	0.317
39	39	0.724
4	4	0.45
40	40	0.383
41	41	0.0869
42	42	0.824
43	43	0.248
44	44	0.0619
45	45	0.286
46	46	0.386
47	47	0.197
48	48	0.195
49	49	0.18
5	5	0.126
50	50	0.898
51	51	0.596
52	52	0.321
53	53	0.556
54	54	0.389
55	55	0.774
56	56	0.366
57	57	0.846
58	58	0.304
59	59	0.0615
6	6	0.754
60	60	0.126
61	61	0.511
62	62	0.0905
63	63	0.172
64	64	0.498
65	65	0.143
66	66	0.789
67	67	0.703
68	68	0.114
69	69	0.545
7	7	0.31
70	70	4.19463e-4
71	71	0.672
72	72	0.511
73	73	0.083
74	74	0.888
75	75	0.248
76	76	0.295
77	77	0.162
78	78	0.182
79	79	0.479
8	8	0.282
80	80	0.0654
81	81	0.338
82	82	0.0629
83	83	0.537
84	84	0.27
85	85	0.0062
86	86	0.516
87	87	0.0507
88	88	0.843
89	89	0.128
9	9	0.424
90	90	0.446
91	91	0.191
92	92	0.188
93	93	0.999
94	94	0.815
95	95	0.0954
96	96	0.604
97	97	0.769
98	98	0.0688
99	99	0.984

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: CNhs11019

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011524 mouse natural helper cells- IL2 treated, day15 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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0002679 (natural helper lymphocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000350 (experimentally modified sample)
0000391 (15 days sample)
0000636 (IL-2 treatment sample)
0000295 (mouse embryonic day 12 sample)
0011524 (mouse natural helper cells- IL2 treated, day15 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:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008853
+|DRA_sample_Accession=CAGE@SAMD00004885
-|accession_numbers=CAGE;DRX008990;DRR009864;DRZ001289;DRZ002672
+|accession_numbers=CAGE;DRX008990;DRR009864;DRZ001289;DRZ002672;DRZ012639;DRZ014022
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000160,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001555,UBERON:0005409
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002371,CL:0000542,CL:0000219,CL:0000738,CL:0002087,CL:0002242,CL:0000255,CL:0002679
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:59799772..59799789,+!p1@Hand2!1.98!262.34!Hand2;;chr10:22539932..22539956,-!p1@Tcf21!1.95!226.73!Tcf21;;chr10:119913278..119913298,-!p2@Hmga2!1.88!160.39!Hmga2;;chr10:119914001..119914078,-!p4@Hmga2!1.87!98.54!Hmga2;;chr10:119913546..119913583,-!p3@Hmga2!1.86!145.25!Hmga2;;chr11:57645506..57645523,-!p1@Hand1!1.86!71.02!Hand1;;chr8:123608252..123608268,+!p1@Foxf1a!1.84!98.97!Foxf1a;;chr10:119913310..119913366,-!p1@Hmga2!1.74!395.22!Hmga2;;chr13:31717548..31717596,+!p1@Foxf2!1.49!57.80!Foxf2;;chr2:74549968..74549996,+!p1@Hoxd3!1.40!30.07!Hoxd3;;chr19:43686789..43686811,+!p1@Nkx2-3!1.36!21.76!Nkx2-3;;chr12:3891810..3891829,+!p2@Dnmt3a!1.34!32.21!Dnmt3a;;chr10:119913792..119913820,-!p5@Hmga2!1.31!33.27!Hmga2;;chr13:55932591..55932622,-!p1@Pitx1!1.30!22.61!Pitx1;;chr13:48758276..48758291,+!p1@Barx1!1.30!18.98!Barx1;;chr11:96153767..96153822,+!p1@Hoxb6!1.29!28.58!Hoxb6;;chr5:67490284..67490302,-!p1@Phox2b!1.29!18.56!Phox2b;;chr15:102828658..102828678,+!p1@Hoxc6!1.25!16.64!Hoxc6;;chr5:148118639..148118715,-!p1@Cdx2!1.23!16.00!Cdx2;;chr12:28027561..28027591,-!p1@Sox11!1.19!94.49!Sox11;;chr10:86956396..86956411,-!p1@Ascl1!1.18!21.54!Ascl1;;chr6:83020355..83020371,-!p1@Tlx2!1.18!14.29!Tlx2;;chr6:52190467..52190500,-!p1@Hoxa10!1.13!12.37!Hoxa10;;chr6:52163319..52163342,-!p1@Hoxa3!1.11!17.28!Hoxa3;;chr10:12810631..12810649,+!p1@Plagl1!1.09!293.70!Plagl1;;chr10:119913266..119913277,-!p6@Hmga2!1.09!11.30!Hmga2;;chr11:18918434..18918489,-!p3@Meis1!1.06!16.64!Meis1;;chr2:74529970..74529997,+!p1@Hoxd10!1.06!10.45!Hoxd10;;chr2:115891534..115891589,-!p1@Meis2!1.05!146.53!Meis2;;chr15:102820964..102821006,+!p1@Hoxc8!1.05!10.24!Hoxc8;;chr6:52154414..52154462,-!p1@Hoxa5!1.04!13.86!Hoxa5;;chr6:52176164..52176195,-!p1@Hoxa9!1.04!12.58!Hoxa9;;chr10:119913974..119913992,-!p9@Hmga2!1.04!10.02!Hmga2;;chr11:96164821..96164865,+!p1@Hoxb5!1.03!9.60!Hoxb5;;chr7:108966820..108966835,+!p1@Phox2a!1.03!9.60!Phox2a;;chr8:77396591..77396639,+!p1@Isx!1.03!9.60!Isx;;chr12:34642510..34642530,+!p1@Twist1!1.02!30.93!Twist1;;chr15:102865088..102865107,+!p1@Hoxc4!1.02!12.80!Hoxc4;;chr3:128916868..128916890,+!p1@Pitx2!1.01!12.80!Pitx2;;chr11:23978291..23978323,+!p7@Bcl11a!1.00!8.96!Bcl11a;;chr2:74550015..74550057,+!p2@Hoxd3!0.99!8.74!Hoxd3;;chr2:104966766..104966786,+!p1@Wt1!0.97!13.44!Wt1;;chr11:96143666..96143725,+!p1@Hoxb8!0.97!9.60!Hoxb8;;chr9:55388997..55389016,+!p1@Isl2!0.97!8.32!Isl2;;chr13:117099847..117099907,-!p1@Isl1!0.96!15.14!Isl1;;chr1:186556323..186556370,-!p2@Hlx!0.95!22.18!Hlx;;chr14:63864056..63864102,-!p1@Gata4!0.95!14.08!Gata4;;chr10:119913954..119913972,-!p8@Hmga2!0.95!7.89!Hmga2;;chr15:102865131..102865151,+!p2@Hoxc4!0.94!8.74!Hoxc4;;chr15:102839948..102839975,+!p3@Hoxc6!0.94!7.68!Hoxc6;;chr6:52184901..52184959,-!p2@Hoxa10!0.93!7.47!Hoxa10;;chr10:126778916..126778974,-!p1@Gli1!0.91!16.42!Gli1;;chr2:74583776..74583815,+!p3@Hoxd3!0.91!7.04!Hoxd3;;chr6:14851440..14851497,+!p2@Foxp2!0.90!17.70!Foxp2;;chr12:3891753..3891801,+!p4@Dnmt3a!0.90!11.52!Dnmt3a;;chr12:58646974..58647003,-!p1@Foxa1!0.90!9.38!Foxa1;;chr10:119913839..119913869,-!p7@Hmga2!0.90!8.96!Hmga2;;chr19:10315179..10315241,-!p1@Gm98!0.89!74.65!Gm98;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.89!11.94!Hoxb2;;chr11:96147952..96147967,+!p1@Hoxb7!0.89!8.53!Hoxb7;;chr2:180069370..180069409,-!p1@Gata5!0.89!8.10!Gata5;;chr5:148118840..148118857,-!p2@Cdx2!0.89!6.83!Cdx2;;chr6:14851287..14851342,+!p1@Foxp2!0.88!22.40!Foxp2;;chr6:52154386..52154407,-!p2@Hoxa5!0.88!8.53!Hoxa5;;chr2:115891381..115891392,-!p5@Meis2!0.87!13.22!Meis2;;chr15:102820946..102820961,+!p3@Hoxc8!0.87!6.40!Hoxc8;;chr15:102844431..102844445,+!p1@Hoxc5!0.87!6.40!Hoxc5;;chr13:31717597..31717613,+!p2@Foxf2!0.87!6.40!Foxf2;;chr13:15555670..15555771,+!p2@Gli3!0.86!16.42!Gli3;;chr2:115890469..115890485,-!p7@Meis2!0.86!10.24!Meis2;;chr6:14851250..14851277,+!p4@Foxp2!0.86!8.10!Foxp2;;chr5:42155788..42155800,-!p1@Nkx3-2!0.86!6.19!Nkx3-2;;chr11:57645586..57645597,-!p2@Hand1!0.86!6.19!Hand1;;chr16:14705925..14705951,+!p1@Snai2!0.85!45.00!Snai2;;chr11:96180045..96180059,+!p1@Hoxb4!0.85!8.74!Hoxb4;;chr4:99322820..99322845,+!p1@Foxd3!0.85!7.89!Foxd3;;chr1:140739014..140739032,-!p1@Lhx9!0.85!7.89!Lhx9;;chr2:71384802..71384815,-!p1@Dlx2!0.85!7.68!Dlx2;;chr7:6649134..6649167,-!p1@Zim1!0.84!34.13!Zim1;;chr4:84320893..84320910,-!p1@Bnc2!0.84!13.86!Bnc2;;chr15:102821007..102821021,+!p2@Hoxc8!0.84!5.97!Hoxc8;;chr11:18918917..18918944,-!p1@Meis1!0.83!78.70!Meis1;;chr17:48061584..48061601,-!p2@Foxp4!0.83!40.31!Foxp4;;chr1:186556375..186556404,-!p3@Hlx!0.83!10.66!Hlx;;chr2:163332558..163332596,+!p2@Hnf4a!0.83!5.76!Hnf4a;;chr2:104966933..104966966,+!p3@Wt1!0.83!5.76!Wt1;;chr2:104966874..104966907,+!p2@Wt1!0.83!5.76!Wt1;;chr15:102797288..102797302,+!p1@Hoxc10!0.83!5.76!Hoxc10;;chr7:52471143..52471186,+!p1@Tead2!0.82!64.63!Tead2;;chr1:186556410..186556424,-!p1@Hlx!0.82!18.77!Hlx;;chr3:3508024..3508069,+!p2@Hnf4g!0.82!5.55!Hnf4g;;chr16:14705961..14705978,+!p2@Snai2!0.80!26.45!Snai2;;chrX:45245679..45245702,-!p1@Smarca1!0.80!25.59!Smarca1;;chr1:170361678..170361689,-!p13@Pbx1!0.80!6.61!Pbx1;;chr11:96213183..96213188,+!p@chr11:96213183..96213188,+!0.80!5.33!Hoxb2;;chr2:74520048..74520064,+!p1@Hoxd11!0.80!5.33!Hoxd11;;chr11:96143962..96144035,+!p2@Hoxb8!0.79!5.12!Hoxb8;;chr6:52195795..52195825,-!p1@Hoxa11!0.79!5.12!Hoxa11;;chr17:28487603..28487626,-!p2@Tead3!0.78!11.30!Tead3;;chr11:18918820..18918831,-!p4@Meis1!0.78!10.02!Meis1;;chr6:52167459..52167492,-!p1@Hoxa7!0.78!6.19!Hoxa7;;chr2:115891427..115891441,-!p4@Meis2!0.77!11.09!Meis2;;chr2:65683890..65683907,+!p1@Csrnp3!0.77!9.81!Csrnp3;;chr6:14851212..14851226,+!p12@Foxp2!0.77!4.91!Foxp2;;chr11:96180069..96180089,+!p3@Hoxb4!0.77!4.91!Hoxb4;;chr11:96160360..96160397,+!p3@Hoxb6!0.76!4.69!Hoxb6;;chr2:74517742..74517758,+!p2@Hoxd11!0.76!4.69!Hoxd11;;chr11:96145450..96145517,+!p2@Hoxb7!0.75!7.25!Hoxb7;;chr11:96213264..96213282,+!p@chr11:96213264..96213282,+!0.75!5.97!Hoxb2;;chr2:115891409..115891425,-!p2@Meis2!0.74!14.29!Meis2;;chr7:89137163..89137200,-!p1@Bnc1!0.74!5.55!Bnc1;;chr6:52190668..52190682,-!p3@Hoxa10!0.74!4.48!Hoxa10;;chr2:74529998..74530020,+!p2@Hoxd10!0.74!4.48!Hoxd10;;chr17:86087592..86087615,-!p1@Six2!0.74!4.48!Six2;;chr19:43686882..43686906,+!p2@Nkx2-3!0.74!4.48!Nkx2-3;;chr13:99124189..99124205,+!p1@Foxd1!0.73!7.04!Foxd1;;chr11:18918959..18918976,-!p2@Meis1!0.72!64.84!Meis1;;chr7:17647736..17647772,-!p1@Hif3a!0.72!16.64!Hif3a;;chr4:13670571..13670625,+!p1@Runx1t1!0.72!12.80!Runx1t1;;chr1:120950098..120950132,-!p2@Gli2!0.72!10.45!Gli2;;chr8:90483433..90483457,-!p2@Zfp423!0.72!5.97!Zfp423;;chr15:102865048..102865073,+!p3@Hoxc4!0.72!5.55!Hoxc4;;chr6:52195763..52195792,-!p2@Hoxa11!0.72!4.27!Hoxa11;;chr11:83664365..83664383,+!p1@Hnf1b!0.72!4.27!Hnf1b;;chr2:169458192..169458247,+!p1@Tshz2!0.71!41.38!Tshz2;;chr17:35031460..35031518,+!p1@Zbtb12!0.71!23.46!Zbtb12;;chr4:54957910..54957954,+!p2@Zfp462!0.71!13.65!Zfp462;;chr15:75447162..75447217,+!p2@Zfp41!0.71!13.22!Zfp41;;chr18:64499706..64499721,+!p2@Onecut2!0.70!5.97!Onecut2;;chr13:48758358..48758415,+!p2@Barx1!0.70!4.05!Barx1;;chr1:186556307..186556318,-!p7@Hlx!0.70!4.05!Hlx;;chr10:119913766..119913779,-!p10@Hmga2!0.70!4.05!Hmga2;;chr10:119913301..119913302,-!p11@Hmga2!0.70!4.05!Hmga2;;chr2:74520343..74520383,+!p4@Hoxd11!0.70!4.05!Hoxd11;;chr11:18918406..18918431,-!p6@Meis1!0.68!5.33!Meis1;;chr13:55932624..55932641,-!p2@Pitx1!0.68!3.84!Pitx1;;chr5:148118792..148118806,-!p3@Cdx2!0.68!3.84!Cdx2;;chr17:37139472..37139514,+!p1@Zfp57!0.67!28.58!Zfp57;;chr13:22036953..22037009,+!p1@Zfp184!0.67!10.88!Zfp184;;chr1:93698068..93698085,+!p2@Twist2!0.67!4.48!Twist2;;chr2:115890864..115890869,-!p14@Meis2!0.67!3.63!Meis2;;chr3:128902837..128902861,+!p3@Pitx2!0.67!3.63!Pitx2;;chr14:22807083..22807104,-!p1@Zfp503!0.66!73.16!Zfp503;;chr12:12948633..12948651,-!p1@Mycn!0.66!39.46!Mycn;;chr15:78994907..78994926,-!p1@Sox10!0.66!10.24!Sox10;;chr6:14851344..14851364,+!p6@Foxp2!0.66!4.48!Foxp2;;chr2:152223441..152223465,-!p2@Sox12!0.65!16.42!Sox12;;chr2:169458799..169458832,+!p5@Tshz2!0.65!6.19!Tshz2;;chr3:5218546..5218561,+!p4@Zfhx4!0.65!5.76!Zfhx4;;chr7:77505617..77505632,-!p1@Nr2f2!0.64!185.56!Nr2f2;;chr7:77511234..77511302,-!p2@Nr2f2!0.64!25.81!Nr2f2;;chr13:15555079..15555136,+!p3@Gli3!0.64!12.16!Gli3;;chr2:146047829..146047847,+!p1@Insm1!0.64!6.61!Insm1;;chr2:156666727..156666753,+!p2@Tgif2!0.64!5.33!Tgif2;;chrX:110411840..110411860,+!p1@Dach2!0.64!4.27!Dach2;;chr7:52472041..52472065,+!p2@Tead2!0.64!4.05!Tead2;;chr15:102839976..102839989,+!p4@Hoxc6!0.64!3.41!Hoxc6;;chr4:3865501..3865548,-!p1@Plag1!0.63!19.62!Plag1;;chr14:22807107..22807119,-!p2@Zfp503!0.63!16.64!Zfp503;;chr2:115891454..115891471,-!p3@Meis2!0.63!11.30!Meis2;;chr2:169458838..169458859,+!p4@Tshz2!0.63!7.25!Tshz2;;chr11:85646303..85646329,+!p1@Tbx2!0.62!24.74!Tbx2;;chr4:54957886..54957907,+!p3@Zfp462!0.62!5.97!Zfp462;;chr6:52141694..52141715,-!p1@Hoxa4!0.62!4.27!Hoxa4;;chr5:148118809..148118832,-!p5@Cdx2!0.62!3.20!Cdx2;;chr5:67490474..67490494,-!p2@Phox2b!0.62!3.20!Phox2b;;chr11:96143843..96143868,+!p3@Hoxb8!0.62!3.20!Hoxb8;;chr2:147871627..147871641,-!p1@Foxa2!0.62!3.20!Foxa2;;chr13:31717614..31717628,+!p3@Foxf2!0.62!3.20!Foxf2;;chrX:98449898..98449913,+!p2@Foxo4!0.61!11.52!Foxo4;;chr11:3189683..3189744,+!p2@Patz1!0.61!7.04!Patz1;;chr1:93698030..93698064,+!p1@Twist2!0.61!6.83!Twist2;;chr3:5218590..5218614,+!p3@Zfhx4!0.61!5.76!Zfhx4;;chr13:15555555..15555574,+!p5@Gli3!0.61!4.27!Gli3;;chr17:25707623..25707639,-!p1@Sox8!0.60!14.93!Sox8;;chr2:152223783..152223812,-!p4@Sox12!0.60!7.68!Sox12;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.60!5.76!Zfhx3;;chr1:170361695..170361722,-!p12@Pbx1!0.60!4.05!Pbx1;;chr17:37139519..37139531,+!p5@Zfp57!0.60!3.63!Zfp57;;chr6:14851377..14851396,+!p10@Foxp2!0.60!2.99!Foxp2;;chr3:102768047..102768060,-!p1@Nr1h5!0.60!2.99!Nr1h5;;chr2:84877369..84877459,+!p1@Ssrp1!0.59!73.58!Ssrp1;;chr9:106356211..106356242,+!p1@Pcbp4!0.59!68.47!Pcbp4;;chr1:170362040..170362113,-!p2@Pbx1!0.59!27.30!Pbx1;;chrX:45245644..45245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ead1;;chr19:10315252..10315266,-!p2@Gm98!0.32!2.13!Gm98;;chr10:127176667..127176679,+!p2@Zbtb39!0.32!2.13!Zbtb39;;chr12:9581317..9581333,+!p3@Osr1!0.32!2.13!Osr1;;chr2:30700788..30700824,+!p2@Prrx2!0.32!2.13!Prrx2;;chr13:40826150..40826167,-!p3@Tfap2a!0.32!1.28!Tfap2a;;chr12:39510290..39510309,+!p5@Etv1!0.32!1.07!Etv1;;chr15:102797170..102797182,+!p3@Hoxc10!0.32!1.07!Hoxc10;;chr15:102797225..102797243,+!p2@Hoxc10!0.32!1.07!Hoxc10;;chr14:17407671..17407684,-!p7@Rarb!0.32!1.07!Rarb;;chr12:58647114..58647128,-!p2@Foxa1!0.32!1.07!Foxa1;;chr12:87702062..87702081,+!p4@Esrrb!0.32!1.07!Esrrb;;chr13:78339241..78339273,-!p9@Nr2f1!0.32!1.07!Nr2f1;;chr14:34791987..34791998,-!p2@Zfp488!0.32!1.07!Zfp488;;chr17:37139555..37139562,+!p6@Zfp57!0.32!1.07!Zfp57;;chr5:29805118..29805137,-!p1@Mnx1!0.32!1.07!Mnx1;;chr6:52210774..52210787,-!p1@Hoxa13!0.32!1.07!Hoxa13;;chr7:147129712..147129774,+!p1@Utf1!0.32!1.07!Utf1;;chr5:42155277..42155281,-!p2@Nkx3-2!0.32!1.07!Nkx3-2;;chr5:120285144..120285160,+!p1@Tbx5!0.32!1.07!Tbx5;;chr2:74583741..74583750,+!p10@Hoxd3!0.32!1.07!Hoxd3;;chr4:13678723..13678739,+!p10@Runx1t1!0.32!1.07!Runx1t1;;chr2:168592636..168592651,-!p1@Sall4!0.32!1.07!Sall4;;chr2:38570011..38570034,-!p1@Nr5a1!0.32!1.07!Nr5a1;;chr1:140743964..140743976,-!p3@Lhx9!0.32!1.07!Lhx9;;chr19:59533139..59533152,+!p2@Emx2!0.32!1.07!Emx2;;chr1:138857112..138857130,-!p7@Nr5a2!0.32!1.07!Nr5a2;;chr2:115874845..115874865,-!p20@Meis2!0.32!1.07!Meis2;;chr8:77396650..77396662,+!p4@Isx!0.32!1.07!Isx;;chr11:96144050..96144065,+!p5@Hoxb8!0.32!1.07!Hoxb8;;chr11:120624106..120624107,+!p13@Hmga1-rs1,p14@Hmga1!0.32!1.07!Hmga1;;chr11:98826216..98826227,+!p10@Rara!0.32!1.07!Rara;;chr11:33103563..33103583,-!p1@Tlx3!0.32!1.07!Tlx3;;chr11:96145362..96145389,+!p4@Hoxb7!0.32!1.07!Hoxb7;;chr6:64992569..64992656,+!p1@Smarcad1!0.31!54.18!Smarcad1;;chr5:108494715..108494757,+!p1@Mtf2!0.31!27.73!Mtf2;;chr6:64992801..64992894,+!p2@Smarcad1!0.31!26.66!Smarcad1;;chr8:109620410..109620462,-!p1@Terf2!0.31!17.28!Terf2;;chr7:88005795..88005858,+!p1@Zscan2!0.31!12.58!Zscan2;;chr18:69504157..69504184,+!p3@Tcf4!0.31!11.09!Tcf4;;chr19:28086045..28086080,-!p4@Rfx3!0.31!8.10!Rfx3;;chr7:26067242..26067273,+!p3@Cic!0.31!7.25!Cic;;chrX:132420525..132420558,+!p3@Bhlhb9!0.31!7.25!Bhlhb9;;chrX:108810678..108810736,-!p1@Hdx!0.31!5.55!Hdx;;chr5:120121446..120121461,+!p2@Tbx3!0.31!5.33!Tbx3;;chr7:134169741..134169760,-!p10@Maz!0.31!4.91!Maz;;chr8:13338745..13338756,+!p2@Tfdp1!0.31!3.41!Tfdp1;;chr7:4946900..4946921,-!p5@Zfp579!0.31!2.35!Zfp579;;chr1:57029281..57029326,-!p1@Satb2!0.31!2.13!Satb2;;chr3:30993859..30993870,+!p5@Skil!0.31!1.92!Skil;;chr5:108494765..108494786,+!p2@Mtf2!0.31!1.71!Mtf2;;chr2:77654815..77654872,-!p2@Zfp385b!0.31!1.49!Zfp385b;;chr3:29912058..29912071,-!p6@Mecom!0.31!1.28!Mecom;;chr13:78338288..78338309,-!p7@Nr2f1!0.31!1.28!Nr2f1;;chr7:4947786..4947797,-!p9@Zfp579!0.31!1.28!Zfp579;;chr4:135699731..135699747,+!p1@Id3!0.30!205.40!Id3;;chr11:69393894..69393921,+!p1@Trp53!0.30!166.36!Trp53;;chr11:87881569..87881633,+!p2@Vezf1!0.30!13.44!Vezf1;;chr15:76709732..76709764,+!p1@Zfp7!0.30!8.10!Zfp7;;chr10:92773818..92773906,-!p2@Elk3!0.30!7.89!Elk3;;chr6:115803364..115803407,-!p1@Mbd4!0.30!7.25!Mbd4;;chr4:133310175..133310212,-!p5@Arid1a!0.30!5.12!Arid1a;;chr18:76401074..76401118,+!p3@Smad2!0.30!3.41!Smad2;;chr2:34227446..34227511,-!p1@Pbx3!0.30!3.41!Pbx3;;chr4:114732112..114732158,+!p1@Tal1!0.30!3.20!Tal1;;chr14:52639709..52639753,-!p5@Zfp219!0.30!3.20!Zfp219;;chr14:76903992..76904056,+!p6@Tsc22d1!0.30!2.99!Tsc22d1;;chr4:13712228..13712267,+!p3@Runx1t1!0.30!2.35!Runx1t1;;chr2:70313168..70313184,+!p1@Sp5!0.30!1.92!Sp5;;chr14:65568567..65568588,-!p3@Hmbox1!0.30!1.92!Hmbox1;;chr7:77511622..77511657,-!p5@Nr2f2!0.30!1.49!Nr2f2;;chr18:53623836..53623839,+!p1@Prdm6!0.30!1.28!Prdm6;;chr11:23978229..23978268,+!p8@Bcl11a!0.30!1.28!Bcl11a;;chr3:151873433..151873498,+!p1@Fubp1!0.29!234.19!Fubp1;;chr11:99091744..99091778,-!p1@Smarce1!0.29!74.44!Smarce1;;chr16:20141134..20141213,+!p1@Yeats2!0.29!46.07!Yeats2;;chr8:28087609..28087634,+!p1@Zfp703!0.29!39.67!Zfp703;;chr9:19426523..19426584,+!p1@Zfp317!0.29!25.38!Zfp317;;chr10:22451142..22451191,-!p2@Tbpl1!0.29!16.85!Tbpl1;;chr18:55152206..55152251,-!p1@Zfp608!0.29!16.42!Zfp608;;chr17:48061692..48061723,-!p5@Foxp4!0.29!7.68!Foxp4;;chr7:28764153..28764173,-!p2@Zfp780b!0.29!5.33!Zfp780b;;chr5:108494686..108494701,+!p3@Mtf2!0.29!1.71!Mtf2;;chr10:126723307..126723319,-!p6@Mbd6!0.29!1.49!Mbd6;;chr13:78339382..78339420,-!p3@Nr2f1!0.29!1.28!Nr2f1;;chr1:170362273..170362317,-!p1@Pbx1!0.28!48.84!Pbx1;;chr9:20757282..20757325,-!p2@Dnmt1!0.28!40.31!Dnmt1;;chr10:110182489..110182589,+!p1@E2f7!0.28!20.05!E2f7;;chr18:69505797..69505852,+!p2@Tcf4!0.28!19.41!Tcf4;;chr17:23723181..23723236,-!p1@Zfp13!0.28!15.78!Zfp13;;chr4:136604692..136604722,-!p1@Zbtb40!0.28!15.78!Zbtb40;;chr10:26095768..26095808,-!p1@L3mbtl3!0.28!14.50!L3mbtl3;;chr7:17200307..17200370,-!p2@Grlf1!0.28!11.94!Grlf1;;chr7:13063668..13063721,+!p1@Zfp606!0.28!11.52!Zfp606;;chr10:82226649.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@@ Line 44: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11019
-|library_ids=CNhs11019
+|library_id_phase_based=2:CNhs11019
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1251
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1251
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E12.CNhs11019.1251-16I5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E12.CNhs11019.1251-16I5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E12.CNhs11019.1251-16I5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E12.CNhs11019.1251-16I5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E12.CNhs11019.1251-16I5.mm9.nobarcode.rdna.fa.gz
 |name=intestine, embryo E12
 |namespace=FANTOM5
@@ Line 50: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11019,LSID731,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0398159352284091,0,0,0,0,0.0563766168868881,0.088106202067755,0,0.074297172617198,0,0,0.940883497623527,0,0,0,0,0,0,0.304050756659847,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0862729502268075,0,0,0,0.0839639919176933,0,0.00178044623044955,0.0376121267649224,-0.0227489779156667,0.651584654514109,0.330672525054497,0,0,0,0,0,0,0,0,0,0,0,0,0.291877772142372,0,0,0,0,0,0,0,0,0,0.000783675069602391,0.25198632585554,0.121726243738716,-0.158091042771083,0.289673046580859,0,0,0,-0.00276795069954106,0.0839639919176933,0,0.066403097270208,-0.0443877679710551,-0.238031561034758,0.0754634710949467,0,0,0,0,0,0,-0.0608798593163665,0.10189598575663,-0.0852514537930093,0.00735659648855311,0,0,0,0
@@ Line 87: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1251-16I5;search_select_hide=table117:1251-16I5
 }}

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FF:1251-16I5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:39, 4 June 2020

CNhs11019

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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