FF:381-16D5: Difference between revisions

Latest revision as of 19:14, 4 June 2020

Name:	intestine, embryo E13
Species:	Mouse (Mus musculus)
Library ID:	CNhs11010
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	intestine
dev stage	13 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		SAMD00005002

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11010		CAGE		DRX008991		DRR009865

Accession ID Mm9

Library id		BAM		CTSS
CNhs11010		DRZ001290		DRZ002673

Accession ID Mm10

Library id		BAM		CTSS
CNhs11010		DRZ012640		DRZ014023

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

CNhs11010

0	0
1	0
10	0
100	0
1000	0
1001	0.0926
1002	0.773
1003	-0.109
1004	0
1005	-0.0389
1006	-0.0304
1007	0.0992
1008	0
1009	0.0395
101	0.129
1010	0
1011	-0.0556
1012	0.0907
1013	-0.234
1014	0.627
1015	0.226
1016	0.142
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.0907
1022	-0.0333
1023	0
1024	0.0436
1025	0.833
1026	0
1027	0.00132
1028	0
1029	0.357
103	0.146
1030	0
1031	0.367
1032	-0.184
1033	0.0907
1034	0.0209
1035	0.0467
1036	0.225
1037	0
1038	0.0595
1039	-0.22
104	0
1040	0.109
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: CNhs11010

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	6.49357e-4
MA0003.1	MA0003.1	0.0437
MA0004.1	MA0004.1	0.909
MA0006.1	MA0006.1	0.256
MA0007.1	MA0007.1	0.399
MA0009.1	MA0009.1	0.592
MA0014.1	MA0014.1	0.276
MA0017.1	MA0017.1	0.00381
MA0018.2	MA0018.2	0.186
MA0019.1	MA0019.1	0.884
MA0024.1	MA0024.1	1.26653e-6
MA0025.1	MA0025.1	6.76391e-5
MA0027.1	MA0027.1	0.0182
MA0028.1	MA0028.1	0.698
MA0029.1	MA0029.1	0.439
MA0030.1	MA0030.1	0.364
MA0031.1	MA0031.1	0.0539
MA0035.2	MA0035.2	0.435
MA0038.1	MA0038.1	0.239
MA0039.2	MA0039.2	0.00227
MA0040.1	MA0040.1	0.654
MA0041.1	MA0041.1	0.186
MA0042.1	MA0042.1	0.385
MA0043.1	MA0043.1	0.709
MA0046.1	MA0046.1	0.739
MA0047.2	MA0047.2	0.251
MA0048.1	MA0048.1	0.0253
MA0050.1	MA0050.1	0.00192
MA0051.1	MA0051.1	1.42095e-4
MA0052.1	MA0052.1	8.08567e-8
MA0055.1	MA0055.1	0.027
MA0057.1	MA0057.1	0.0817
MA0058.1	MA0058.1	0.96
MA0059.1	MA0059.1	0.468
MA0060.1	MA0060.1	1.95836e-6
MA0061.1	MA0061.1	0.171
MA0062.2	MA0062.2	0.327
MA0065.2	MA0065.2	9.24534e-6
MA0066.1	MA0066.1	0.225
MA0067.1	MA0067.1	0.275
MA0068.1	MA0068.1	0.532
MA0069.1	MA0069.1	0.554
MA0070.1	MA0070.1	0.94
MA0071.1	MA0071.1	0.0447
MA0072.1	MA0072.1	0.0238
MA0073.1	MA0073.1	0.584
MA0074.1	MA0074.1	0.716
MA0076.1	MA0076.1	0.856
MA0077.1	MA0077.1	0.845
MA0078.1	MA0078.1	0.939
MA0079.2	MA0079.2	0.0198
MA0080.2	MA0080.2	2.52132e-11
MA0081.1	MA0081.1	0.118
MA0083.1	MA0083.1	0.0111
MA0084.1	MA0084.1	0.597
MA0087.1	MA0087.1	0.267
MA0088.1	MA0088.1	0.718
MA0090.1	MA0090.1	0.864
MA0091.1	MA0091.1	0.749
MA0092.1	MA0092.1	0.833
MA0093.1	MA0093.1	0.924
MA0099.2	MA0099.2	1.93002e-6
MA0100.1	MA0100.1	0.882
MA0101.1	MA0101.1	0.287
MA0102.2	MA0102.2	0.465
MA0103.1	MA0103.1	0.00524
MA0104.2	MA0104.2	0.374
MA0105.1	MA0105.1	0.703
MA0106.1	MA0106.1	0.506
MA0107.1	MA0107.1	0.0881
MA0108.2	MA0108.2	0.0535
MA0111.1	MA0111.1	0.643
MA0112.2	MA0112.2	0.00184
MA0113.1	MA0113.1	0.648
MA0114.1	MA0114.1	0.00583
MA0115.1	MA0115.1	0.304
MA0116.1	MA0116.1	0.307
MA0117.1	MA0117.1	0.0242
MA0119.1	MA0119.1	0.0408
MA0122.1	MA0122.1	0.197
MA0124.1	MA0124.1	0.405
MA0125.1	MA0125.1	0.76
MA0131.1	MA0131.1	0.305
MA0135.1	MA0135.1	0.111
MA0136.1	MA0136.1	3.26584e-8
MA0137.2	MA0137.2	0.0961
MA0138.2	MA0138.2	1.8949e-4
MA0139.1	MA0139.1	0.286
MA0140.1	MA0140.1	0.574
MA0141.1	MA0141.1	0.00153
MA0142.1	MA0142.1	0.768
MA0143.1	MA0143.1	0.12
MA0144.1	MA0144.1	0.186
MA0145.1	MA0145.1	0.00536
MA0146.1	MA0146.1	0.131
MA0147.1	MA0147.1	0.344
MA0148.1	MA0148.1	0.263
MA0149.1	MA0149.1	0.127
MA0150.1	MA0150.1	6.29089e-4
MA0152.1	MA0152.1	0.00838
MA0153.1	MA0153.1	0.628
MA0154.1	MA0154.1	0.0359
MA0155.1	MA0155.1	0.96
MA0156.1	MA0156.1	5.45826e-4
MA0157.1	MA0157.1	0.0728
MA0159.1	MA0159.1	0.0353
MA0160.1	MA0160.1	0.00213
MA0162.1	MA0162.1	0.933
MA0163.1	MA0163.1	0.849
MA0164.1	MA0164.1	0.541
MA0258.1	MA0258.1	8.36757e-4
MA0259.1	MA0259.1	0.282

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: CNhs11010

Novel motif	Logo	P-value
1	1	0.216
10	10	0.734
100	100	0.724
101	101	0.474
102	102	0.564
103	103	0.24
104	104	0.906
105	105	0.296
106	106	0.0467
107	107	0.187
108	108	0.823
109	109	0.0854
11	11	0.204
110	110	0.547
111	111	0.17
112	112	0.323
113	113	0.457
114	114	0.00723
115	115	0.683
116	116	0.425
117	117	0.858
118	118	0.939
119	119	0.0497
12	12	0.786
120	120	0.508
121	121	0.582
122	122	0.61
123	123	0.262
124	124	0.452
125	125	0.995
126	126	0.963
127	127	0.253
128	128	0.0808
129	129	0.104
13	13	0.829
130	130	0.374
131	131	0.0594
132	132	0.973
133	133	0.329
134	134	0.897
135	135	0.686
136	136	0.232
137	137	0.84
138	138	0.299
139	139	0.0807
14	14	0.259
140	140	0.166
141	141	0.539
142	142	0.911
143	143	0.669
144	144	0.554
145	145	0.898
146	146	0.312
147	147	0.385
148	148	0.66
149	149	0.344
15	15	0.0637
150	150	0.383
151	151	0.0881
152	152	0.0229
153	153	0.635
154	154	0.964
155	155	0.619
156	156	4.62317e-10
157	157	0.792
158	158	0.763
159	159	0.0681
160	160	0.487
161	161	0.961
162	162	0.692
163	163	0.14
164	164	0.526
165	165	0.0786
166	166	0.231
167	167	0.138
168	168	0.62
169	169	0.0172
17	17	0.15
18	18	0.377
19	19	0.673
2	2	0.371
20	20	0.497
21	21	0.462
22	22	0.204
23	23	0.0801
24	24	0.0799
25	25	0.168
26	26	0.922
27	27	0.218
28	28	0.204
29	29	0.961
3	3	0.497
30	30	0.464
31	31	0.282
32	32	0.451
33	33	0.796
34	34	0.594
35	35	0.497
36	36	0.789
37	37	0.0591
38	38	0.246
39	39	0.977
4	4	0.799
40	40	0.43
41	41	0.107
42	42	0.767
43	43	0.251
44	44	0.0172
45	45	0.295
46	46	0.439
47	47	0.253
48	48	0.154
49	49	0.239
5	5	0.357
50	50	0.952
51	51	0.607
52	52	0.529
53	53	0.53
54	54	0.51
55	55	0.461
56	56	0.292
57	57	0.954
58	58	0.323
59	59	0.0378
6	6	0.689
60	60	0.212
61	61	0.943
62	62	0.0602
63	63	0.126
64	64	0.577
65	65	0.0893
66	66	0.794
67	67	0.871
68	68	0.349
69	69	0.345
7	7	0.298
70	70	1.95049e-4
71	71	0.671
72	72	0.274
73	73	0.0124
74	74	0.849
75	75	0.192
76	76	0.336
77	77	0.192
78	78	0.231
79	79	0.552
8	8	0.292
80	80	0.0468
81	81	0.365
82	82	0.108
83	83	0.304
84	84	0.512
85	85	0.0195
86	86	0.218
87	87	0.00134
88	88	0.698
89	89	0.112
9	9	0.476
90	90	0.257
91	91	0.441
92	92	0.319
93	93	0.989
94	94	0.86
95	95	0.0334
96	96	0.466
97	97	0.708
98	98	0.233
99	99	0.892

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: CNhs11010

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011330 mouse intestine- embryo E13 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

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)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000293 (mouse embryonic day 13 sample)
0011330 (mouse intestine- embryo E13 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
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@DRS008854
+|DRA_sample_Accession=CAGE@SAMD00005002
+|accession_numbers=CAGE;DRX008991;DRR009865;DRZ001290;DRZ002673;DRZ012640;DRZ014023
 |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=
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:22539932..22539956,-!p1@Tcf21!1.90!198.79!Tcf21;;chr8:59799772..59799789,+!p1@Hand2!1.89!212.96!Hand2;;chr11:57645506..57645523,-!p1@Hand1!1.68!46.45!Hand1;;chr8:123608252..123608268,+!p1@Foxf1a!1.67!67.35!Foxf1a;;chr10:119913546..119913583,-!p3@Hmga2!1.65!89.88!Hmga2;;chr10:119914001..119914078,-!p4@Hmga2!1.58!49.23!Hmga2;;chr10:119913310..119913366,-!p1@Hmga2!1.48!217.37!Hmga2;;chr10:119913278..119913298,-!p2@Hmga2!1.47!62.70!Hmga2;;chr5:148118639..148118715,-!p1@Cdx2!1.40!24.15!Cdx2;;chr19:43686789..43686811,+!p1@Nkx2-3!1.40!23.92!Nkx2-3;;chr13:31717548..31717596,+!p1@Foxf2!1.38!44.36!Foxf2;;chr5:67490284..67490302,-!p1@Phox2b!1.34!20.67!Phox2b;;chr8:77396591..77396639,+!p1@Isx!1.33!20.20!Isx;;chr6:83020355..83020371,-!p1@Tlx2!1.31!19.51!Tlx2;;chr10:86956396..86956411,-!p1@Ascl1!1.29!28.57!Ascl1;;chr7:108966820..108966835,+!p1@Phox2a!1.27!17.65!Phox2a;;chr2:74549968..74549996,+!p1@Hoxd3!1.23!19.74!Hoxd3;;chr13:55932591..55932622,-!p1@Pitx1!1.22!18.81!Pitx1;;chr15:102828658..102828678,+!p1@Hoxc6!1.21!15.33!Hoxc6;;chr11:96153767..96153822,+!p1@Hoxb6!1.18!21.60!Hoxb6;;chr2:74583776..74583815,+!p3@Hoxd3!1.17!13.93!Hoxd3;;chr10:12810631..12810649,+!p1@Plagl1!1.13!325.60!Plagl1;;chr3:3508024..3508069,+!p2@Hnf4g!1.11!11.84!Hnf4g;;chr2:180069370..180069409,-!p1@Gata5!1.10!13.47!Gata5;;chr12:58646974..58647003,-!p1@Foxa1!1.09!15.33!Foxa1;;chr12:28027561..28027591,-!p1@Sox11!1.08!72.69!Sox11;;chr10:119913792..119913820,-!p5@Hmga2!1.08!19.04!Hmga2;;chr12:3891810..3891829,+!p2@Dnmt3a!1.08!17.42!Dnmt3a;;chr5:148118840..148118857,-!p2@Cdx2!1.08!10.92!Cdx2;;chr6:52190467..52190500,-!p1@Hoxa10!1.08!10.92!Hoxa10;;chr2:163332558..163332596,+!p2@Hnf4a!1.07!10.68!Hnf4a;;chr2:115891534..115891589,-!p1@Meis2!1.05!146.31!Meis2;;chr6:14851440..14851497,+!p2@Foxp2!1.05!25.08!Foxp2;;chr2:74529970..74529997,+!p1@Hoxd10!1.05!10.22!Hoxd10;;chr6:52163319..52163342,-!p1@Hoxa3!1.02!13.93!Hoxa3;;chr6:52154414..52154462,-!p1@Hoxa5!1.02!13.01!Hoxa5;;chr2:74550015..74550057,+!p2@Hoxd3!1.00!9.06!Hoxd3;;chr1:137155026..137155042,-!p1@Elf3!0.99!51.79!Elf3;;chr10:126778916..126778974,-!p1@Gli1!0.98!19.51!Gli1;;chr12:3891753..3891801,+!p4@Dnmt3a!0.98!14.17!Dnmt3a;;chr3:128916868..128916890,+!p1@Pitx2!0.98!11.84!Pitx2;;chr11:96164821..96164865,+!p1@Hoxb5!0.96!8.13!Hoxb5;;chr6:14851287..14851342,+!p1@Foxp2!0.95!26.47!Foxp2;;chr6:52154386..52154407,-!p2@Hoxa5!0.94!9.99!Hoxa5;;chr8:87425854..87425891,+!p1@Klf1!0.93!7.43!Klf1;;chr16:14705961..14705978,+!p2@Snai2!0.92!35.07!Snai2;;chr16:14705925..14705951,+!p1@Snai2!0.91!52.72!Snai2;;chr4:84320893..84320910,-!p1@Bnc2!0.91!16.49!Bnc2;;chr9:55388997..55389016,+!p1@Isl2!0.91!7.20!Isl2;;chr13:15555670..15555771,+!p2@Gli3!0.90!18.35!Gli3;;chr2:71384802..71384815,-!p1@Dlx2!0.90!8.59!Dlx2;;chrX:45245679..45245702,-!p1@Smarca1!0.89!31.82!Smarca1;;chr15:102865131..102865151,+!p2@Hoxc4!0.89!7.66!Hoxc4;;chr15:102820964..102821006,+!p1@Hoxc8!0.89!6.73!Hoxc8;;chr14:63864056..63864102,-!p1@Gata4!0.88!11.61!Gata4;;chr18:64499674..64499696,+!p1@Onecut2!0.88!11.61!Onecut2;;chr2:104966766..104966786,+!p1@Wt1!0.88!10.68!Wt1;;chr19:43686882..43686906,+!p2@Nkx2-3!0.88!6.50!Nkx2-3;;chr15:102865088..102865107,+!p1@Hoxc4!0.87!8.59!Hoxc4;;chr7:17647736..17647772,-!p1@Hif3a!0.86!23.22!Hif3a;;chr18:64499706..64499721,+!p2@Onecut2!0.86!9.06!Onecut2;;chr11:23978291..23978323,+!p7@Bcl11a!0.85!6.04!Bcl11a;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.84!10.45!Hoxb2;;chr11:18918917..18918944,-!p1@Meis1!0.83!78.73!Meis1;;chr7:6649134..6649167,-!p1@Zim1!0.83!33.67!Zim1;;chr2:115891427..115891441,-!p4@Meis2!0.83!12.77!Meis2;;chr11:96180045..96180059,+!p1@Hoxb4!0.83!8.36!Hoxb4;;chr6:52176164..52176195,-!p1@Hoxa9!0.83!7.20!Hoxa9;;chr11:96143666..96143725,+!p1@Hoxb8!0.83!6.73!Hoxb8;;chr6:52184901..52184959,-!p2@Hoxa10!0.83!5.81!Hoxa10;;chr17:48061584..48061601,-!p2@Foxp4!0.82!38.78!Foxp4;;chr2:169458799..169458832,+!p5@Tshz2!0.82!9.52!Tshz2;;chr2:115890469..115890485,-!p7@Meis2!0.82!9.29!Meis2;;chr2:71367871..71367898,+!p1@Dlx1!0.82!5.57!Dlx1;;chr15:102839948..102839975,+!p3@Hoxc6!0.82!5.57!Hoxc6;;chr12:39510206..39510249,+!p3@Etv1!0.82!5.57!Etv1;;chr5:67490391..67490404,-!p3@Phox2b!0.80!5.34!Phox2b;;chr5:148118809..148118832,-!p5@Cdx2!0.80!5.34!Cdx2;;chr15:78994907..78994926,-!p1@Sox10!0.79!14.17!Sox10;;chr2:65683890..65683907,+!p1@Csrnp3!0.79!10.45!Csrnp3;;chr11:18918406..18918431,-!p6@Meis1!0.79!7.20!Meis1;;chr15:102820946..102820961,+!p3@Hoxc8!0.79!5.11!Hoxc8;;chr5:42155788..42155800,-!p1@Nkx3-2!0.79!5.11!Nkx3-2;;chr11:18918434..18918489,-!p3@Meis1!0.78!8.36!Meis1;;chr12:34642510..34642530,+!p1@Twist1!0.77!16.95!Twist1;;chr6:14851250..14851277,+!p4@Foxp2!0.77!6.50!Foxp2;;chr6:52195795..52195825,-!p1@Hoxa11!0.77!4.88!Hoxa11;;chr10:119913266..119913277,-!p6@Hmga2!0.77!4.88!Hmga2;;chr19:10315179..10315241,-!p1@Gm98!0.76!54.34!Gm98;;chr1:186556323..186556370,-!p2@Hlx!0.76!14.17!Hlx;;chr11:96145450..96145517,+!p2@Hoxb7!0.76!7.43!Hoxb7;;chr2:169458838..169458859,+!p4@Tshz2!0.75!9.75!Tshz2;;c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rnt2!0.40!5.57!Arnt2;;chr11:85646341..85646352,+!p3@Tbx2!0.40!3.72!Tbx2;;chr1:120949925..120949947,-!p4@Gli2!0.40!3.72!Gli2;;chr4:126700576..126700598,+!p7@Sfpq!0.40!3.48!Sfpq;;chr18:83079981..83080037,+!p6@Zfp516!0.40!3.25!Zfp516;;chr19:10315252..10315266,-!p2@Gm98!0.40!2.79!Gm98;;chr11:99092280..99092302,-!p3@Smarce1!0.40!2.79!Smarce1;;chr10:79896129..79896163,-!p6@Tcf3!0.40!2.79!Tcf3;;chr5:24107676..24107722,-!p4@Smarcd3!0.40!2.32!Smarcd3;;chr2:77654815..77654872,-!p2@Zfp385b!0.40!2.09!Zfp385b;;chr13:30077917..30077928,-!p4@E2f3!0.40!2.09!E2f3;;chr7:134170081..134170122,-!p2@Maz!0.39!39.94!Maz;;chr9:122832168..122832210,+!p1@Zfp105!0.39!16.72!Zfp105;;chr9:96159665..96159680,+!p3@Tfdp2!0.39!9.52!Tfdp2;;chr4:133276698..133276743,-!p6@Arid1a!0.39!5.57!Arid1a;;chr2:34227446..34227511,-!p1@Pbx3!0.39!4.41!Pbx3;;chr1:170361633..170361644,-!p11@Pbx1!0.39!3.02!Pbx1;;chr18:14131045..14131062,-!p3@Zfp521!0.39!2.79!Zfp521;;chr14:64562503..64562524,+!p1@Sox7!0.38!12.08!Sox7;;chr4:61869460..61869521,-!p1@Zfp37!0.38!10.92!Zfp37;;chr13:56804721..56804792,+!p2@Smad5!0.38!10.68!Smad5;;chr2:92886297..92886329,-!p1@Prdm11!0.38!9.29!Prdm11;;chr11:23980664..23980706,+!p2@Bcl11a!0.38!8.82!Bcl11a;;chr10:79390075..79390115,+!p2@Arid3a!0.38!6.73!Arid3a;;chr7:30875418..30875454,-!p2@Zfp566,p2@Zfp82!0.38!5.34!Zfp566;;chr6:115803317..115803361,-!p2@Mbd4!0.38!4.64!Mbd4;;chr4:126700683..126700704,+!p6@Sfpq!0.38!3.48!Sfpq;;chr17:35031589..35031630,+!p2@Zbtb12!0.38!3.25!Zbtb12;;chr1:38684431..38684450,-!p3@Aff3!0.38!2.79!Aff3;;chr9:21420812..21420815,+!p6@Smarca4!0.38!2.55!Smarca4;;chr1:138845748..138845766,-!p4@Nr5a2!0.38!2.09!Nr5a2;;chr15:50720589..50720600,-!p12@Trps1!0.38!2.09!Trps1;;chr12:54349410..54349461,+!p1@Npas3!0.38!1.86!Npas3;;chr4:13670441..13670463,+!p8@Runx1t1!0.38!1.86!Runx1t1;;chr15:103085690..103085710,-!p3@Nfe2!0.38!1.63!Nfe2;;chr13:55937467..55937516,-!p3@Pitx1!0.38!1.39!Pitx1;;chr12:39510290..39510309,+!p5@Etv1!0.38!1.39!Etv1;;chr15:103082088..103082136,-!p2@Nfe2!0.38!1.39!Nfe2;;chr12:30213247..30213333,+!p1@Myt1l!0.38!1.39!Myt1l;;chr2:93482464..93482491,+!p1@Alx4!0.38!1.39!Alx4;;chr2:74536026..74536039,+!p1@Hoxd9!0.38!1.39!Hoxd9;;chr2:74517609..74517621,+!p3@Hoxd11!0.38!1.39!Hoxd11;;chr18:64499879..64499895,+!p3@Onecut2!0.38!1.39!Onecut2;;chr6:52158644..52158677,-!p2@Hoxa6!0.38!1.39!Hoxa6;;chr6:52184880..52184893,-!p6@Hoxa10!0.38!1.39!Hoxa10;;chr2:180069423..180069434,-!p2@Gata5!0.38!1.39!Gata5;;chr11:23978270..23978290,+!p9@Bcl11a!0.38!1.39!Bcl11a;;chr11:57645644..57645649,-!p3@Hand1!0.38!1.39!Hand1;;chr11:98826178..98826197,+!p7@Rara!0.38!1.39!Rara;;chr14:100683672..100683717,-!p1@Klf12!0.37!9.29!Klf12;;chr7:25292141..25292158,+!p2@Zfp428!0.37!6.73!Zfp428;;chr8:87225670..87225697,+!p2@Lyl1!0.37!5.57!Lyl1;;chr7:19679964..19679982,+!p1@Six5!0.37!5.34!Six5;;chr14:52634234..52634281,-!p3@Zfp219!0.37!5.11!Zfp219;;chr3:94641455..94641486,+!p4@Pogz!0.37!4.88!Pogz;;chr4:54960387..54960415,+!p4@Zfp462!0.37!3.72!Zfp462;;chr4:133276779..133276796,-!p8@Arid1a!0.37!3.48!Arid1a;;chr14:56443698..56443726,+!p2@Nfatc4!0.37!3.25!Nfatc4;;chr1:189821714..189821761,+!p1@Esrrg!0.37!3.25!Esrrg;;chr2:127347094..127347111,-!p2@Kcnip3!0.37!2.79!Kcnip3;;chr2:127347067..127347093,-!p1@Kcnip3!0.37!2.79!Kcnip3;;chr5:134741947..134741948,-!p9@Gtf2i!0.37!2.55!Gtf2i;;chr19:7342786..7342803,+!p2@Rcor2!0.37!2.09!Rcor2;;chr1:138846009..138846038,-!p3@Nr5a2!0.37!1.63!Nr5a2;;chr4:82151178..82151262,-!p1@Nfib!0.36!84.30!Nfib;;chr4:108132605..108132635,+!p1@Zcchc11!0.36!75.94!Zcchc11;;chr5:134790507..134790546,-!p1@Gtf2i!0.36!50.40!Gtf2i;;chr11:23978022..23978076,+!p1@Bcl11a!0.36!45.05!Bcl11a;;chr6:116578973..116579022,-!p1@Zfp422!0.36!34.60!Zfp422;;chr18:69505797..69505852,+!p2@Tcf4!0.36!23.92!Tcf4;;chr9:36954842..36954908,-!p1@Pknox2!0.36!23.92!Pknox2;;chr14:52935876..52935928,-!p1@Sall2!0.36!16.26!Sall2;;chr5:24107779..24107825,-!p1@Smarcd3!0.36!13.24!Smarcd3;;chr6:118405493..118405536,-!p1@Zfp248!0.36!7.20!Zfp248;;chr14:22319053..22319105,+!p2@Myst4!0.36!6.27!Myst4;;chr2:91864300..91864379,-!p2@Creb3l1!0.36!5.34!Creb3l1;;chr17:71202822..71202877,-!p3@Tgif1!0.36!5.34!Tgif1;;chr18:79306029..79306059,-!p2@Setbp1!0.36!3.72!Setbp1;;chr2:169458496..169458516,+!p6@Tshz2!0.36!3.72!Tshz2;;chr5:120121169..120121171,+!p4@Tbx3!0.36!3.02!Tbx3;;chr7:134376558..134376587,+!p2@Zfp553!0.36!2.79!Zfp553;;chr19:25746898..25746910,+!p1@Dmrt2!0.36!2.32!Dmrt2;;chr6:128250380..128250442,-!p2@Tead4!0.36!1.86!Tead4;;chrX:90531838..90531861,+!p1@Arx!0.36!1.86!Arx;;chr18:53623836..53623839,+!p1@Prdm6!0.36!1.63!Prdm6;;chr10:79862089..79862129,-!p2@Mbd3!0.35!21.60!Mbd3;;chr7:25292331..25292421,+!p1@Zfp428!0.35!13.93!Zfp428;;chr5:120121020..120121049,+!p1@Tbx3!0.35!11.84!Tbx3;;chr15:76287876..76287894,+!p1@Scx!0.35!10.45!Scx;;chr11:99092233..99092273,-!p2@Smarce1!0.35!9.06!Smarce1;;chr17:4994697..4994730,+!p4@Arid1b!0.35!8.82!Arid1b;;chr1:170361777..170361797,-!p10@Pbx1!0.35!2.79!Pbx1;;chr8:111227518..111227550,+!p@chr8:111227518..111227550,+!0.35!2.79!Zfhx3;;chr2:91864449..918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tv1!0.25!1.16!Etv1;;chr9:21420674..21420725,+!p1@Smarca4!0.24!125.18!Smarca4;;chr17:32501375..32501433,-!p1@Wiz!0.24!37.16!Wiz;;chr2:44968512..44968530,-!p1@Zeb2!0.24!34.60!Zeb2;;chr1:136456767..136456790,+!p2@Kdm5b!0.24!32.51!Kdm5b;;chr13:96095213..96095255,+!p1@Zbed3!0.24!23.22!Zbed3;;chr6:64992801..64992894,+!p2@Smarcad1!0.24!22.53!Smarcad1;;chr17:32967140..32967197,-!p1@Zfp799!0.24!21.13!Zfp799;;chr16:4594683..4594735,+!p2@Glis2!0.24!19.74!Glis2;;chr8:108939219..108939296,+!p1@Zfp90!0.24!16.02!Zfp90;;chr18:55152206..55152251,-!p1@Zfp608!0.24!14.63!Zfp608;;chrX:137077151..137077227,-!p2@Tsc22d3!0.24!10.45!Tsc22d3;;chr3:135354476..135354528,-!p2@Nfkb1!0.24!8.13!Nfkb1;;chr15:76709732..76709764,+!p1@Zfp7!0.24!6.97!Zfp7;;chr10:20032330..20032345,+!p3@Bclaf1!0.24!6.97!Bclaf1;;chr1:4483679..4483695,-!p1@Sox17!0.24!6.73!Sox17;;chrX:132420525..132420558,+!p3@Bhlhb9!0.24!6.04!Bhlhb9;;chr16:84835315..84835342,+!p3@Gabpa!0.24!4.88!Gabpa;;chr7:30638630..30638702,-!p1@Zfp940!0.24!4.64!Zfp940;;chr7:16986617..16986632,+!p2@Zc3h4!0.24!3.72!Zc3h4;;chr17:48061631..48061648,-!p7@Foxp4!0.24!3.48!Foxp4;;chr13:44825008..44825066,+!p5@Jarid2!0.24!2.32!Jarid2;;chr11:102179350..102179375,-!p7@Ubtf!0.24!2.32!Ubtf;;chr2:120365588..120365602,-!p2@Zfp106!0.24!1.86!Zfp106;;chr15:50721239..50721260,-!p9@Trps1!0.24!1.86!Trps1;;chr4:13670626..13670657,+!p5@Runx1t1!0.24!1.63!Runx1t1;;chr5:138187411..138187422,+!p8@Tsc22d4!0.24!1.63!Tsc22d4;;chr5:122499831..122499891,-!p1@Cux2!0.24!1.63!Cux2;;chr13:78338076..78338104,-!p4@Nr2f1!0.24!1.16!Nr2f1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!0.24!1.16!Pou3f3;;chr2:115890495..115890507,-!p16@Meis2!0.24!0.93!Meis2;;chr3:29912154..29912168,-!p11@Mecom!0.24!0.93!Mecom;;chr7:4947786..4947797,-!p9@Zfp579!0.24!0.93!Zfp579;;chr11:69393894..69393921,+!p1@Trp53!0.23!141.66!Trp53;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.23!71.99!Hmga1;;chr6:64992569..64992656,+!p1@Smarcad1!0.23!44.82!Smarcad1;;chr5:138558139..138558214,+!p1@Zscan21!0.23!42.27!Zscan21;;chr17:57074836..57074927,-!p1@Mllt1!0.23!41.11!Mllt1;;chr8:77517558..77517597,+!p1@Hmgxb4!0.23!32.98!Hmgxb4;;chr1:135320989..135321043,-!p1@Sox13!0.23!16.26!Sox13;;chr8:109620410..109620462,-!p1@Terf2!0.23!14.17!Terf2;;chr14:31832369..31832400,+!p3@Pbrm1!0.23!12.31!Pbrm1;;chr13:67601387..67601448,-!p2@Zfp58!0.23!12.08!Zfp58;;chr13:55431084..55431137,-!p1@Mxd3!0.23!11.38!Mxd3;;chr19:28085628..28085671,-!p1@Rfx3!0.23!9.99!Rfx3;;chr2:83484634..83484647,+!p4@Zc3h15!0.23!9.99!Zc3h15;;chr10:79017833..79017871,-!p1@Mier2!0.23!8.13!Mier2;;chr17:27693788..27693803,+!p3@Hmga1,p4@Hmga1-rs1!0.23!6.27!Hmga1;;chr5:147760339..147760350,+!p3@Gtf3a!0.23!3.72!Gtf3a;;chr6:38204087..38204108,-!p2@D630045J12Rik!0.23!3.72!D630045J12Rik;;chr5:107125807..107125835,-!p3@Zfp644!0.23!3.48!Zfp644;;chr13:56804865..56804898,+!p3@Smad5!0.23!3.25!Smad5;;chr18:76401074..76401118,+!p3@Smad2!0.23!2.79!Smad2;;chr14:52935788..52935817,-!p2@Sall2!0.23!2.55!Sall2;;chr8:24780125..24780143,+!p1@Zmat4!0.23!1.39!Zmat4;;chr7:6315994..6316007,+!p2@Zfp78!0.23!1.16!Zfp78;;chr7:77511622..77511657,-!p5@Nr2f2!0.23!1.16!Nr2f2;;chr15:10391745..10391753,-!p3@Dnajc21!0.23!1.16!Dnajc21;;chr13:78338288..78338309,-!p7@Nr2f1!0.23!0.93!Nr2f1;;chr14:63864337..63864381,-!p6@Gata4!0.23!0.70!Gata4;;chr14:33412570..33412586,+!p1@Prrxl1!0.23!0.70!Prrxl1;;chr15:37163041..37163061,+!p5@Grhl2!0.23!0.70!Grhl2;;chr14:56443742..56443756,+!p6@Nfatc4!0.23!0.70!Nfatc4;;chr12:39510090..39510114,+!p6@Etv1!0.23!0.70!Etv1;;chr12:56700411..56700416,+!p@chr12:56700411..56700416,+!0.23!0.70!Insm2;;chr17:26978521..26978536,-!p2@Nkx2-5!0.23!0.70!Nkx2-5;;chr16:14705668..14705683,+!p3@Snai2!0.23!0.70!Snai2;;chr18:61195843..61195864,-!p2@Cdx1!0.23!0.70!Cdx1;;chr17:37139555..37139562,+!p6@Zfp57!0.23!0.70!Zfp57;;chr6:52161666..52161711,-!p1@Hoxa6!0.23!0.70!Hoxa6;;chr6:52167434..52167450,-!p3@Hoxa7!0.23!0.70!Hoxa7;;chr6:52176144..52176161,-!p2@Hoxa9!0.23!0.70!Hoxa9;;chr7:150155143..150155156,-!p1@Ascl2!0.23!0.70!Ascl2;;chr5:67490447..67490458,-!p7@Phox2b!0.23!0.70!Phox2b;;chr5:122500227..122500240,-!p6@Cux2!0.23!0.70!Cux2;;chr2:74543202..74543213,+!p3@Hoxd8!0.23!0.70!Hoxd8;;chr2:74565247..74565258,+!p3@Hoxd4!0.23!0.70!Hoxd4;;chr2:79296783..79296801,-!p1@Neurod1!0.23!0.70!Neurod1;;chr4:114581497..114581519,-!p2@Foxd2!0.23!0.70!Foxd2;;chr2:71384401..71384424,-!p3@Dlx2!0.23!0.70!Dlx2;;chr2:74536071..74536083,+!p4@Hoxd9!0.23!0.70!Hoxd9;;chr2:74536050..74536065,+!p2@Hoxd9!0.23!0.70!Hoxd9;;chr4:99322855..99322867,+!p2@Foxd3!0.23!0.70!Foxd3;;chr2:30700830..30700843,+!p4@Prrx2!0.23!0.70!Prrx2;;chr1:186556307..186556318,-!p7@Hlx!0.23!0.70!Hlx;;chr1:6720216..6720232,+!p1@St18!0.23!0.70!St18;;chr1:169528720..169528749,+!p6@Rxrg!0.23!0.70!Rxrg;;chr2:181501745..181501778,+!p1@Myt1!0.23!0.70!Myt1;;chr2:180069410..180069421,-!p3@Gata5!0.23!0.70!Gata5;;chr2:103143315..103143328,-!p2@Ehf!0.23!0.70!Ehf;;chr2:103264213..103264233,+!p1@Elf5!0.23!0.70!Elf5;;chr2:38570011..38570034,-!p1@Nr5a1!0.23!0.70!Nr5a1;;chr1:138846079..138846103,-!p6@Nr5a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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011330
 |is_obsolete=
-|library_ids=CNhs11010
+|library_id=CNhs11010
+|library_id_phase_based=2:CNhs11010
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;381
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;381
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E13.CNhs11010.381-16D5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E13.CNhs11010.381-16D5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E13.CNhs11010.381-16D5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E13.CNhs11010.381-16D5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E13.CNhs11010.381-16D5.mm9.nobarcode.rdna.fa.gz
 |name=intestine, embryo E13
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11010,LSID730,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.110227414493895,0,0,0,0.0906941294286938,0,0.249632898183195,0,0.128187800254637,0,0,0.804113412649934,0,0,0,0,0,0,0.386383612142557,0,0,0,0,0,0,0,0,0,0,0,0,0,0.210730689525417,0,0,0,0.0906941294286938,0.0152699143857571,0.0759974992088061,0.0675024727503597,-0.0432016589530648,0.913588977844548,0.358654484246654,0,0,0,0,0,0,0,0,0,0,0,0,0.313013373870158,0,0,0,0,0,0,0,0.0906941294286938,0.165681471080581,0.0580653141971036,0.242390530734069,0.179326099559504,0.331885714127808,0.290770398456495,0,0.107632413212651,0.0103532945110281,0,0.165681471080581,0,0.0714469181903413,0.0256280989515318,-0.0176379177154378,0.150776028624301,0,0,0,0,0,0,0.055921146384331,0.298544952204537,-0.024814623781954,0,0,0,0,0
@@ Line 85: / Line 97: @@
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 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:381-16D5;search_select_hide=table117:381-16D5
-|DRA_sample_Accession=CAGE@DRS008854
-|accession_numbers=DRX008991;DRR009865;DRZ001290;DRZ002673;CAGE
-|library_id=CNhs11010
 }}

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FF:381-16D5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:14, 4 June 2020

CNhs11010

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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