FF:1252-16G8: Difference between revisions

Latest revision as of 18:40, 4 June 2020

Name:	stomach, embryo E15
Species:	Mouse (Mus musculus)
Library ID:	CNhs10603
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	stomach
dev stage	15 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		SAMD00004695

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10603		CAGE		DRX009092		DRR009966

Accession ID Mm9

Library id		BAM		CTSS
CNhs10603		DRZ001391		DRZ002774

Accession ID Mm10

Library id		BAM		CTSS
CNhs10603		DRZ012741		DRZ014124

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

CNhs10603

0	0
1	0
10	0
100	0
1000	0.00779
1001	0.0474
1002	0.429
1003	0.0564
1004	0
1005	0
1006	-0.0434
1007	0.076
1008	0
1009	0.091
101	0.101
1010	0.482
1011	0.00686
1012	0
1013	-0.0891
1014	0.357
1015	0.263
1016	0.256
1017	0.0804
1018	0.305
1019	0
102	0
1020	0
1021	0
1022	0.00999
1023	0
1024	0.00862
1025	0.773
1026	0
1027	0.146
1028	0
1029	0.269
103	0.157
1030	0
1031	0.435
1032	0.0163
1033	0
1034	0
1035	0
1036	0.119
1037	0
1038	0.0684
1039	-0.141
104	0
1040	0.0799
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: CNhs10603

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00111
MA0003.1	MA0003.1	0.643
MA0004.1	MA0004.1	0.572
MA0006.1	MA0006.1	0.974
MA0007.1	MA0007.1	0.287
MA0009.1	MA0009.1	0.433
MA0014.1	MA0014.1	0.467
MA0017.1	MA0017.1	6.92823e-5
MA0018.2	MA0018.2	0.511
MA0019.1	MA0019.1	0.746
MA0024.1	MA0024.1	3.77252e-7
MA0025.1	MA0025.1	0.0389
MA0027.1	MA0027.1	0.0139
MA0028.1	MA0028.1	0.496
MA0029.1	MA0029.1	0.345
MA0030.1	MA0030.1	0.248
MA0031.1	MA0031.1	0.87
MA0035.2	MA0035.2	0.612
MA0038.1	MA0038.1	0.00192
MA0039.2	MA0039.2	0.416
MA0040.1	MA0040.1	0.909
MA0041.1	MA0041.1	0.64
MA0042.1	MA0042.1	0.668
MA0043.1	MA0043.1	0.945
MA0046.1	MA0046.1	1.83716e-17
MA0047.2	MA0047.2	0.00146
MA0048.1	MA0048.1	0.732
MA0050.1	MA0050.1	2.01891e-5
MA0051.1	MA0051.1	4.26164e-4
MA0052.1	MA0052.1	0.00951
MA0055.1	MA0055.1	0.531
MA0057.1	MA0057.1	0.534
MA0058.1	MA0058.1	0.354
MA0059.1	MA0059.1	0.15
MA0060.1	MA0060.1	1.13476e-13
MA0061.1	MA0061.1	0.211
MA0062.2	MA0062.2	0.108
MA0065.2	MA0065.2	2.71669e-4
MA0066.1	MA0066.1	0.0525
MA0067.1	MA0067.1	0.127
MA0068.1	MA0068.1	0.171
MA0069.1	MA0069.1	0.526
MA0070.1	MA0070.1	0.271
MA0071.1	MA0071.1	0.00605
MA0072.1	MA0072.1	0.0236
MA0073.1	MA0073.1	0.847
MA0074.1	MA0074.1	0.834
MA0076.1	MA0076.1	0.657
MA0077.1	MA0077.1	0.206
MA0078.1	MA0078.1	0.603
MA0079.2	MA0079.2	0.119
MA0080.2	MA0080.2	1.39501e-4
MA0081.1	MA0081.1	0.152
MA0083.1	MA0083.1	1.03307e-6
MA0084.1	MA0084.1	0.99
MA0087.1	MA0087.1	0.397
MA0088.1	MA0088.1	0.889
MA0090.1	MA0090.1	0.289
MA0091.1	MA0091.1	0.853
MA0092.1	MA0092.1	0.789
MA0093.1	MA0093.1	0.592
MA0099.2	MA0099.2	0.228
MA0100.1	MA0100.1	0.204
MA0101.1	MA0101.1	0.612
MA0102.2	MA0102.2	0.905
MA0103.1	MA0103.1	0.684
MA0104.2	MA0104.2	0.573
MA0105.1	MA0105.1	0.0272
MA0106.1	MA0106.1	0.719
MA0107.1	MA0107.1	0.485
MA0108.2	MA0108.2	0.0185
MA0111.1	MA0111.1	0.313
MA0112.2	MA0112.2	8.61779e-5
MA0113.1	MA0113.1	0.66
MA0114.1	MA0114.1	8.48374e-4
MA0115.1	MA0115.1	0.00347
MA0116.1	MA0116.1	0.0186
MA0117.1	MA0117.1	0.0218
MA0119.1	MA0119.1	0.225
MA0122.1	MA0122.1	0.443
MA0124.1	MA0124.1	0.801
MA0125.1	MA0125.1	0.195
MA0131.1	MA0131.1	0.463
MA0135.1	MA0135.1	0.0235
MA0136.1	MA0136.1	1.97159e-4
MA0137.2	MA0137.2	0.34
MA0138.2	MA0138.2	0.0404
MA0139.1	MA0139.1	0.659
MA0140.1	MA0140.1	0.792
MA0141.1	MA0141.1	1.32011e-5
MA0142.1	MA0142.1	0.755
MA0143.1	MA0143.1	0.382
MA0144.1	MA0144.1	0.587
MA0145.1	MA0145.1	0.526
MA0146.1	MA0146.1	0.267
MA0147.1	MA0147.1	0.392
MA0148.1	MA0148.1	0.00914
MA0149.1	MA0149.1	0.0287
MA0150.1	MA0150.1	0.0015
MA0152.1	MA0152.1	0.393
MA0153.1	MA0153.1	1.86046e-11
MA0154.1	MA0154.1	0.0531
MA0155.1	MA0155.1	0.527
MA0156.1	MA0156.1	0.171
MA0157.1	MA0157.1	0.666
MA0159.1	MA0159.1	0.00544
MA0160.1	MA0160.1	0.00154
MA0162.1	MA0162.1	0.948
MA0163.1	MA0163.1	0.187
MA0164.1	MA0164.1	0.687
MA0258.1	MA0258.1	8.97642e-5
MA0259.1	MA0259.1	0.725

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: CNhs10603

Novel motif	Logo	P-value
1	1	0.0464
10	10	0.123
100	100	0.7
101	101	0.577
102	102	0.606
103	103	0.0858
104	104	0.93
105	105	0.829
106	106	0.248
107	107	0.715
108	108	0.913
109	109	0.171
11	11	0.0556
110	110	0.161
111	111	0.00479
112	112	0.0701
113	113	0.692
114	114	2.86038e-5
115	115	0.846
116	116	0.738
117	117	0.0335
118	118	0.202
119	119	0.0834
12	12	0.622
120	120	0.33
121	121	0.618
122	122	0.93
123	123	0.374
124	124	0.508
125	125	0.157
126	126	0.658
127	127	0.197
128	128	0.149
129	129	0.141
13	13	0.578
130	130	0.15
131	131	0.699
132	132	0.937
133	133	0.507
134	134	0.548
135	135	0.928
136	136	0.563
137	137	0.826
138	138	0.0233
139	139	0.0224
14	14	0.577
140	140	0.778
141	141	0.754
142	142	0.472
143	143	0.0143
144	144	0.524
145	145	0.734
146	146	0.685
147	147	0.408
148	148	0.139
149	149	0.68
15	15	0.0282
150	150	0.536
151	151	0.0748
152	152	0.822
153	153	0.194
154	154	0.446
155	155	0.195
156	156	0.076
157	157	0.82
158	158	0.227
159	159	0.122
160	160	0.977
161	161	0.505
162	162	0.548
163	163	0.359
164	164	0.145
165	165	0.473
166	166	0.229
167	167	0.48
168	168	0.326
169	169	0.0321
17	17	0.148
18	18	0.0987
19	19	0.67
2	2	0.855
20	20	0.351
21	21	0.726
22	22	0.555
23	23	0.174
24	24	0.885
25	25	0.115
26	26	0.788
27	27	0.658
28	28	0.266
29	29	0.27
3	3	0.0767
30	30	0.625
31	31	0.379
32	32	0.202
33	33	0.824
34	34	0.877
35	35	0.027
36	36	0.128
37	37	0.0896
38	38	0.46
39	39	0.781
4	4	0.891
40	40	0.73
41	41	0.16
42	42	0.433
43	43	0.123
44	44	0.0724
45	45	0.985
46	46	0.224
47	47	0.156
48	48	0.0884
49	49	0.0706
5	5	0.0955
50	50	0.617
51	51	0.538
52	52	0.638
53	53	0.758
54	54	0.548
55	55	0.47
56	56	0.468
57	57	0.227
58	58	0.309
59	59	0.142
6	6	0.897
60	60	0.578
61	61	0.815
62	62	0.0279
63	63	0.208
64	64	0.36
65	65	0.285
66	66	0.655
67	67	0.357
68	68	0.0373
69	69	0.0571
7	7	0.453
70	70	5.39113e-4
71	71	0.169
72	72	0.786
73	73	0.136
74	74	0.824
75	75	0.0283
76	76	0.32
77	77	0.312
78	78	0.267
79	79	0.271
8	8	0.0534
80	80	0.394
81	81	0.28
82	82	0.0535
83	83	0.176
84	84	0.901
85	85	0.00693
86	86	0.68
87	87	0.364
88	88	0.627
89	89	0.466
9	9	0.938
90	90	0.0162
91	91	0.429
92	92	0.159
93	93	0.525
94	94	0.0286
95	95	0.085
96	96	0.18
97	97	0.707
98	98	0.286
99	99	0.724

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: CNhs10603

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011523 mouse stomach- embryo E15 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)
0000945 (stomach)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
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)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

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)
0000298 (mouse embryonic day 15 sample)
0011523 (mouse stomach- embryo E15 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@SAMD00004695
+|accession_numbers=CAGE;DRX009092;DRR009966;DRZ001391;DRZ002774;DRZ012741;DRZ014124
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000945,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010039,UBERON:0010317,UBERON:0001555,UBERON:0005409,UBERON:0001041
 |ancestors_in_cell_lineage_facet=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr13:55932591..55932622,-!p1@Pitx1!1.89!90.27!Pitx1;;chr2:164228702..164228719,+!p1@Rbpjl!1.81!63.64!Rbpjl;;chr10:22539932..22539956,-!p1@Tcf21!1.75!141.71!Tcf21;;chr13:48758276..48758291,+!p1@Barx1!1.70!49.41!Barx1;;chr8:59799772..59799789,+!p1@Hand2!1.67!128.29!Hand2;;chr8:123608252..123608268,+!p1@Foxf1a!1.55!50.42!Foxf1a;;chr2:19367259..19367278,+!p1@Ptf1a!1.47!28.67!Ptf1a;;chr12:58646974..58647003,-!p1@Foxa1!1.38!30.29!Foxa1;;chr4:135129538..135129558,-!p1@Grhl3!1.35!31.92!Grhl3;;chr7:108966820..108966835,+!p1@Phox2a!1.35!21.55!Phox2a;;chr5:144951153..144951203,+!p1@Bhlha15!1.31!27.85!Bhlha15;;chr10:61595830..61595846,+!p1@Neurog3!1.31!19.32!Neurog3;;chr1:137155026..137155042,-!p1@Elf3!1.30!106.95!Elf3;;chr13:55937467..55937516,-!p3@Pitx1!1.30!19.11!Pitx1;;chr10:12810631..12810649,+!p1@Plagl1!1.28!460.72!Plagl1;;chr13:48758358..48758415,+!p2@Barx1!1.27!17.49!Barx1;;chr16:25801993..25802014,+!p1@Trp63!1.26!17.28!Trp63;;chr13:55932624..55932641,-!p2@Pitx1!1.25!16.88!Pitx1;;chr9:74709695..74709722,+!p1@Onecut1!1.22!15.66!Onecut1;;chr13:31717548..31717596,+!p1@Foxf2!1.18!27.65!Foxf2;;chr10:86956396..86956411,-!p1@Ascl1!1.18!21.76!Ascl1;;chr14:63864056..63864102,-!p1@Gata4!1.17!23.99!Gata4;;chr3:34548909..34548927,+!p1@Sox2!1.14!21.76!Sox2;;chr2:163332558..163332596,+!p2@Hnf4a!1.14!12.81!Hnf4a;;chr13:117099847..117099907,-!p1@Isl1!1.13!22.98!Isl1;;chr7:17647736..17647772,-!p1@Hif3a!1.11!42.09!Hif3a;;chr17:86087592..86087615,-!p1@Six2!1.09!11.39!Six2;;chr13:31650185..31650201,+!p1@Foxq1!1.08!38.83!Foxq1;;chr10:119913546..119913583,-!p3@Hmga2!1.08!23.38!Hmga2;;chr14:118636214..118636235,-!p1@Sox21!1.08!13.42!Sox21;;chr10:119913310..119913366,-!p1@Hmga2!1.06!82.34!Hmga2;;chr10:126778916..126778974,-!p1@Gli1!1.06!23.59!Gli1;;chr2:103143336..103143367,-!p1@Ehf!1.06!17.08!Ehf;;chr2:147871627..147871641,-!p1@Foxa2!1.06!10.37!Foxa2;;chr7:19608891..19608895,-!p1@Foxa3!1.05!13.22!Foxa3;;chr17:27865882..27865901,-!p1@Spdef!1.05!10.17!Spdef;;chr2:104966766..104966786,+!p1@Wt1!1.04!15.86!Wt1;;chr7:6649134..6649167,-!p1@Zim1!1.02!52.46!Zim1;;chr15:102865088..102865107,+!p1@Hoxc4!1.02!12.81!Hoxc4;;chr5:42155788..42155800,-!p1@Nkx3-2!1.00!8.95!Nkx3-2;;chr12:39510206..39510249,+!p3@Etv1!0.99!8.74!Etv1;;chr19:45225149..45225186,+!p1@Tlx1!0.99!8.74!Tlx1;;chr11:121380640..121380655,-!p1@Zfp750!0.98!14.23!Zfp750;;chr15:102865131..102865151,+!p2@Hoxc4!0.98!9.76!Hoxc4;;chr6:52154414..52154462,-!p1@Hoxa5!0.97!11.59!Hoxa5;;chr10:119914001..119914078,-!p4@Hmga2!0.97!11.39!Hmga2;;chr5:67490284..67490302,-!p1@Phox2b!0.97!8.34!Phox2b;;chr14:99697871..99697934,+!p1@Klf5!0.93!153.30!Klf5;;chr1:189821714..189821761,+!p1@Esrrg!0.93!14.44!Esrrg;;chr1:170361991..170362015,-!p6@Pbx1!0.92!17.08!Pbx1;;chr13:55937432..55937460,-!p4@Pitx1!0.92!7.32!Pitx1;;chr6:14851440..14851497,+!p2@Foxp2!0.91!17.89!Foxp2;;chr10:119913278..119913298,-!p2@Hmga2!0.91!16.47!Hmga2;;chr17:26978409..26978442,-!p1@Nkx2-5!0.90!6.91!Nkx2-5;;chr16:14705961..14705978,+!p2@Snai2!0.89!32.73!Snai2;;chr5:29805118..29805137,-!p1@Mnx1!0.89!6.71!Mnx1;;chr16:14705925..14705951,+!p1@Snai2!0.88!48.80!Snai2;;chr3:3508024..3508069,+!p2@Hnf4g!0.88!6.51!Hnf4g;;chr6:14851287..14851342,+!p1@Foxp2!0.86!21.76!Foxp2;;chr14:17407549..17407575,-!p3@Rarb!0.86!9.76!Rarb;;chr19:5560600..5560617,-!p1@Ovol1!0.86!7.73!Ovol1;;chr2:79296783..79296801,-!p1@Neurod1!0.86!6.30!Neurod1;;chr2:71384802..71384815,-!p1@Dlx2!0.85!7.73!Dlx2;;chr6:52167459..52167492,-!p1@Hoxa7!0.85!7.32!Hoxa7;;chr11:121380594..121380609,-!p2@Zfp750!0.84!10.57!Zfp750;;chr2:74583776..74583815,+!p3@Hoxd3!0.84!5.90!Hoxd3;;chr14:118636238..118636257,-!p2@Sox21!0.84!5.90!Sox21;;chr8:87425854..87425891,+!p1@Klf1!0.83!5.69!Klf1;;chr6:52163319..52163342,-!p1@Hoxa3!0.82!8.34!Hoxa3;;chr3:30408603..30408668,-!p1@Mecom!0.81!13.22!Mecom;;chr3:34548946..34548972,+!p2@Sox2!0.81!6.10!Sox2;;chr11:96164821..96164865,+!p1@Hoxb5!0.81!5.49!Hoxb5;;chr17:26978521..26978536,-!p2@Nkx2-5!0.80!5.29!Nkx2-5;;chr12:9581262..9581282,+!p1@Osr1!0.78!65.27!Osr1;;chr4:84320893..84320910,-!p1@Bnc2!0.78!12.00!Bnc2;;chr2:71367871..71367898,+!p1@Dlx1!0.78!5.08!Dlx1;;chr4:46356509..46356527,+!p1@Foxe1!0.78!5.08!Foxe1;;chr19:43686789..43686811,+!p1@Nkx2-3!0.78!5.08!Nkx2-3;;chr3:90046995..90047031,-!p2@Creb3l4!0.77!6.30!Creb3l4;;chr2:103264213..103264233,+!p1@Elf5!0.77!4.88!Elf5;;chr1:138857076..138857105,-!p1@Nr5a2!0.77!4.88!Nr5a2;;chr12:34642510..34642530,+!p1@Twist1!0.75!16.06!Twist1;;chr12:57796615..57796687,+!p1@Pax9!0.75!4.68!Pax9;;chr2:103143315..103143328,-!p2@Ehf!0.75!4.68!Ehf;;chr6:15135215..15135244,+!p11@Foxp2!0.75!4.68!Foxp2;;chr6:83020355..83020371,-!p1@Tlx2!0.75!4.68!Tlx2;;chr19:10315179..10315241,-!p1@Gm98!0.74!52.25!Gm98;;chr11:18918434..18918489,-!p3@Meis1!0.74!7.52!Meis1;;chr2:104966874..104966907,+!p2@Wt1!0.74!4.47!Wt1;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.73!7.93!Hoxb2;;chr6:52114821..52114828,-!p1@Hoxa2!0.73!6.91!Hoxa2;;chr7:17642018..17642045,-!p4@Hif3a!0.73!5.08!Hif3a;;chr5:77543897..77543911,-!p2@Hopx!0.72!8.74!Hopx;;chr2:146047829..146047847,+!p1@Insm1!0.72!8.13!Insm1;;chr11:96180045..96180059,+!p1@Hoxb4!0.72!6.30!Hoxb4;;chr11:83664365..83664383,+!p1@Hnf1b!0.72!4.27!Hnf1b;;chr14:63890491..63890516,-!p2@Gata4!0.72!4.27!Gata4;;chr11:96153767..96153822,+!p1@Hoxb6!0.71!6.71!Hoxb6;;chr6:14851250..14851277,+!p4@Foxp2!0.70!5.29!Foxp2;;chr11:18918917..18918944,-!p1@Meis1!0.69!57.95!Meis1;;chr17:32506357..32506377,-!p3@Wiz!0.69!8.95!Wiz;;chr11:18918820..18918831,-!p4@Meis1!0.69!7.93!Meis1;;chr2:104966933..104966966,+!p3@Wt1!0.69!3.86!Wt1;;chr12:3891753..3891801,+!p4@Dnmt3a!0.68!6.51!Dnmt3a;;chr4:135129447..135129467,-!p2@Grhl3!0.68!4.68!Grhl3;;chrX:45245679..45245702,-!p1@Smarca1!0.67!18.71!Smarca1;;chr7:17642053..17642066,-!p2@Hif3a!0.67!5.49!Hif3a;;chr15:102865048..102865073,+!p3@Hoxc4!0.67!4.88!Hoxc4;;chr2:180069370..180069409,-!p1@Gata5!0.67!4.47!Gata5;;chr14:63890519..63890539,-!p3@Gata4!0.67!3.66!Gata4;;chr3:29911808..29911833,-!p8@Mecom!0.67!3.66!Mecom;;chr2:81893535..81893548,+!p1@Zfp804a!0.67!3.66!Zfp804a;;chr5:148081686..148081715,+!p1@Pdx1!0.67!3.66!Pdx1;;chr9:55388997..55389016,+!p1@Isl2!0.67!3.66!Isl2;;chr12:28027561..28027591,-!p1@Sox11!0.66!26.84!Sox11;;chr2:91864300..91864379,-!p2@Creb3l1!0.66!11.39!Creb3l1;;chr3:30408674..30408716,-!p2@Mecom!0.66!6.30!Mecom;;chr17:48061584..48061601,-!p2@Foxp4!0.65!26.23!Foxp4;;chr18:11052642..11052659,+!p1@Gata6!0.65!20.13!Gata6;;chr14:56443806..56443848,+!p1@Nfatc4!0.65!7.73!Nfatc4;;chr1:120879128..120879183,-!p3@Gli2!0.65!7.32!Gli2;;chr10:119913792..119913820,-!p5@Hmga2!0.65!6.51!Hmga2;;chr2:115891534..115891589,-!p1@Meis2!0.64!56.52!Meis2;;chr2:91864449..91864492,-!p3@Creb3l1!0.64!5.90!Creb3l1;;chr12:3891810..3891829,+!p2@Dnmt3a!0.64!5.69!Dnmt3a;;chr12:9581317..9581333,+!p3@Osr1!0.64!5.49!Osr1;;chr1:138846009..138846038,-!p3@Nr5a2!0.64!3.86!Nr5a2;;chr11:18918959..18918976,-!p2@Meis1!0.63!52.25!Meis1;;chr1:194979315..194979359,+!p1@Irf6!0.63!23.38!Irf6;;chr15:78994907..78994926,-!p1@Sox10!0.63!9.35!Sox10;;chr2:172375081..172375105,+!p1@Tfap2c!0.63!3.25!Tfap2c;;chr5:148081722..148081744,+!p2@Pdx1!0.63!3.25!Pdx1;;chr15:102839948..102839975,+!p3@Hoxc6!0.63!3.25!Hoxc6;;chrX:45245644..45245666,-!p2@Smarca1!0.62!11.59!Smarca1;;chr3:128916868..128916890,+!p1@Pitx2!0.62!4.68!Pitx2;;chr1:140739014..140739032,-!p1@Lhx9!0.62!4.27!Lhx9;;chr4:84321300..84321315,-!p2@Bnc2!0.62!4.07!Bnc2;;chr13:31650026..31650045,+!p2@Foxq1!0.61!5.69!Foxq1;;chr12:37835120..37835133,+!p2@Meox2!0.61!4.68!Meox2;;chr3:30408384..30408431,-!p4@Mecom!0.61!4.07!Mecom;;chr5:102094214..102094230,-!p1@Nkx6-1!0.61!3.05!Nkx6-1;;chr13:31717597..31717613,+!p2@Foxf2!0.61!3.05!Foxf2;;chr15:102844431..102844445,+!p1@Hoxc5!0.61!3.05!Hoxc5;;chrX:7544943..7545001,-!p1@Gata1!0.61!3.05!Gata1;;chr16:38294860..38294924,-!p1@Nr1i2!0.61!3.05!Nr1i2;;chr2:103264245..103264268,+!p2@Elf5!0.61!3.05!Elf5;;chr1:138857112..138857130,-!p7@Nr5a2!0.61!3.05!Nr5a2;;chr11:69468531..69468557,+!p1@Sox15!0.61!3.05!Sox15;;chr17:28487603..28487626,-!p2@Tead3!0.60!7.12!Tead3;;chr4:3865501..3865548,-!p1@Plag1!0.59!17.69!Plag1;;chr12:37835141..37835194,+!p1@Meox2!0.59!10.57!Meox2;;chr17:47278081..47278103,+!p1@Trerf1!0.59!7.73!Trerf1;;chr15:103085660..103085681,-!p1@Nfe2!0.59!4.68!Nfe2;;chr10:119913839..119913869,-!p7@Hmga2!0.59!3.86!Hmga2;;chr11:96143666..96143725,+!p1@Hoxb8!0.59!3.46!Hoxb8;;chr13:48758328..48758335,+!p4@Barx1!0.59!2.85!Barx1;;chr13:48758431..48758443,+!p3@Barx1!0.59!2.85!Barx1;;chr6:14851377..14851396,+!p10@Foxp2!0.59!2.85!Foxp2;;chr13:15555670..15555771,+!p2@Gli3!0.58!8.13!Gli3;;chr14:22807107..22807119,-!p2@Zfp503!0.57!14.44!Zfp503;;chr11:96213264..96213282,+!p@chr11:96213264..96213282,+!0.57!3.66!Hoxb2;;chr6:14851344..14851364,+!p6@Foxp2!0.57!3.46!Foxp2;;chr7:52471143..52471186,+!p1@Tead2!0.56!34.56!Tead2;;chr2:28477452..28477483,-!p1@Gfi1b!0.56!3.46!Gfi1b;;chr2:147019977..147019985,-!p2@Nkx2-2!0.56!2.64!Nkx2-2;;chr2:71367142..71367167,+!p2@Dlx1!0.56!2.64!Dlx1;;chr11:23978291..23978323,+!p7@Bcl11a!0.56!2.64!Bcl11a;;chr15:102839976..102839989,+!p4@Hoxc6!0.56!2.64!Hoxc6;;chr14:118635860..118635885,-!p3@Sox21!0.56!2.64!Sox21;;chr14:22807083..22807104,-!p1@Zfp503!0.55!56.93!Zfp503;;chr11:85646303..85646329,+!p1@Tbx2!0.55!20.94!Tbx2;;chr19:7342725..7342784,+!p1@Rcor2!0.55!12.61!Rcor2;;chr4:154010918..154010931,-!p1@Prdm16!0.55!8.95!Prdm16;;chr11:85646263..85646278,+!p2@Tbx2!0.55!7.73!Tbx2;;chr14:17407878..17407926,-!p1@Rarb!0.55!6.71!Rarb;;chr18:64499674..64499696,+!p1@Onecut2!0.55!4.88!Onecut2;;chr2:115890469..115890485,-!p7@Meis2!0.55!4.47!Meis2;;chr2:115891409..115891425,-!p2@Meis2!0.54!8.54!Meis2;;chr2:152223783..152223812,-!p4@Sox12!0.54!6.71!Sox12;;chr11:96147952..96147967,+!p1@Hoxb7!0.54!3.25!Hoxb7;;chr11:96160426..96160443,+!p2@Hoxb6!0.54!2.44!Hoxb6;;chr5:148118639..148118715,-!p1@Cdx2!0.54!2.44!Cdx2;;chr19:45225276..45225304,+!p2@Tlx1!0.54!2.44!Tlx1;;chr8:111227518..111227550,+!p@chr8:111227518..111227550,+!0.53!4.68!Zfhx3;;chr11:18918406..18918431,-!p6@Meis1!0.53!3.46!Meis1;;chr6:52154386..52154407,-!p2@Ho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Ubtf;;chr7:46773162..46773172,+!p2@Zfp619!0.20!1.63!Zfp619;;chr15:50721640..50721654,-!p7@Trps1!0.20!1.42!Trps1;;chr13:96094769..96094829,+!p4@Zbed3!0.20!1.22!Zbed3;;chr14:67853425..67853454,+!p1@Ebf2!0.20!1.22!Ebf2;;chr2:162880306..162880319,+!p3@Mybl2!0.20!1.22!Mybl2;;chr15:76755821..76755835,-!p2@Zfp647!0.20!1.02!Zfp647;;chrX:109714433..109714444,+!p2@Zfp711!0.20!1.02!Zfp711;;chrX:48559055..48559077,-!p6@Mbnl3!0.20!1.02!Mbnl3;;chr8:90328310..90328362,-!p3@Zfp423!0.20!0.81!Zfp423;;chr4:126698555..126698583,+!p1@Sfpq!0.19!755.33!Sfpq;;chr1:135557922..135557963,-!p1@Zc3h11a!0.19!162.86!Zc3h11a;;chr9:21420674..21420725,+!p1@Smarca4!0.19!111.62!Smarca4;;chr11:112643496..112643562,+!p1@Sox9!0.19!52.46!Sox9;;chr15:102301149..102301221,+!p2@Pcbp2!0.19!51.24!Pcbp2;;chr2:152561980..152561997,+!p1@Id1!0.19!40.66!Id1;;chr8:87324243..87324277,-!p1@Nfix!0.19!32.94!Nfix;;chr8:109620410..109620462,-!p1@Terf2!0.19!12.61!Terf2;;chr1:167932744..167932778,-!p1@Pou2f1!0.19!11.79!Pou2f1;;chr10:26095768..26095808,-!p1@L3mbtl3!0.19!11.59!L3mbtl3;;chr14:31832345..31832364,+!p2@Pbrm1!0.19!11.59!Pbrm1;;chr6:133985993..133986029,+!p2@Etv6!0.19!8.34!Etv6;;chr5:34163023..34163090,+!p2@Whsc1!0.19!8.34!Whsc1;;chrX:132420399..132420436,+!p1@Bhlhb9!0.19!7.73!Bhlhb9;;chr13:21454695..21454752,+!p1@Zscan12!0.19!7.32!Zscan12;;chr17:46693153..46693169,-!p2@Srf!0.19!6.51!Srf;;chr11:50872733..50872809,+!p1@Zfp354a!0.19!5.69!Zfp354a;;chr19:28085586..28085622,-!p3@Rfx3!0.19!5.29!Rfx3;;chr7:46773114..46773155,+!p1@Zfp619!0.19!4.47!Zfp619;;chr9:20385740..20385777,+!p2@Zfp846!0.19!4.27!Zfp846;;chr4:120624269..120624302,-!p1@Zfp69!0.19!4.27!Zfp69;;chr18:83080231..83080254,+!p3@Zfp516!0.19!3.86!Zfp516;;chr9:19426741..19426775,+!p2@Zfp317!0.19!3.66!Zfp317;;chr18:76401074..76401118,+!p3@Smad2!0.19!2.44!Smad2;;chr3:90097275..90097302,+!p2@Gatad2b!0.19!2.44!Gatad2b;;chr2:34227446..34227511,-!p1@Pbx3!0.19!2.44!Pbx3;;chr11:23977565..23977612,+!p5@Bcl11a!0.19!2.24!Bcl11a;;chr14:52935788..52935817,-!p2@Sall2!0.19!2.24!Sall2;;chr17:4994491..4994531,+!p6@Arid1b!0.19!2.03!Arid1b;;chr12:3807076..3807086,+!p8@Dnmt3a!0.19!1.63!Dnmt3a;;chr13:37917716..37917742,+!p9@Rreb1!0.19!1.63!Rreb1;;chr13:96095097..96095114,+!p5@Zbed3!0.19!1.63!Zbed3;;chr12:113917014..113917034,+!p1@Zbtb42!0.19!1.63!Zbtb42;;chr11:70043257..70043263,-!p1@Bcl6b!0.19!1.63!Bcl6b;;chr1:170361777..170361797,-!p10@Pbx1!0.19!1.63!Pbx1;;chr17:71200415..71200427,-!p5@Tgif1!0.19!1.42!Tgif1;;chr18:14131045..14131062,-!p3@Zfp521!0.19!1.42!Zfp521;;chr3:5218563..5218587,+!p5@Zfhx4!0.19!1.42!Zfhx4;;chr8:94325847..94325869,-!p3@Irx3!0.19!1.42!Irx3;;chr7:91558631..91558652,-!p3@Arnt2!0.19!1.22!Arnt2;;chr4:135728181..135728203,+!p2@E2f2!0.19!1.02!E2f2;;chr18:76219161..76219176,+!p4@Zbtb7c!0.19!1.02!Zbtb7c;;chr5:120120981..120120992,+!p5@Tbx3!0.19!1.02!Tbx3;;chr7:38557752..38557793,-!p3@Zfp536!0.19!0.81!Zfp536;;chr2:127308277..127308313,-!p4@Kcnip3!0.19!0.81!Kcnip3;;chr13:37918684..37918701,+!p12@Rreb1!0.19!0.81!Rreb1;;chr15:40486458..40486467,+!p9@Zfpm2!0.19!0.81!Zfpm2;;chr13:56804344..56804473,+!p1@Smad5!0.18!40.66!Smad5;;chr1:15795720..15795756,+!p1@Terf1!0.18!39.24!Terf1;;chr9:56266612..56266654,+!p1@Hmg20a!0.18!38.02!Hmg20a;;chr17:57074836..57074927,-!p1@Mllt1!0.18!37.21!Mllt1;;chr7:13404186..13404214,-!p1@Zfp329!0.18!26.02!Zfp329;;chr12:16817746..16817784,+!p1@E2f6!0.18!23.18!E2f6;;chr9:63605740..63605771,-!p1@Smad3!0.18!19.11!Smad3;;chr7:134758740..134758783,-!p1@Zfp629!0.18!18.71!Zfp629;;chr16:84835146..84835186,+!p2@Gabpa!0.18!17.69!Gabpa;;chr15:102455867..102455930,-!p1@Atf7!0.18!17.08!Atf7;;chr9:22112085..22112138,-!p1@Zfp810!0.18!16.47!Zfp810;;chr11:44430812..44430838,+!p1@Ebf1!0.18!12.61!Ebf1;;chr9:20385951..20386032,+!p1@Zfp846!0.18!10.37!Zfp846;;
@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011523
 |is_obsolete=
+|library_id=CNhs10603
+|library_id_phase_based=2:CNhs10603
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1252
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1252
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E15.CNhs10603.1252-16G8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E15.CNhs10603.1252-16G8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E15.CNhs10603.1252-16G8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E15.CNhs10603.1252-16G8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E15.CNhs10603.1252-16G8.mm9.nobarcode.rdna.fa.gz
 |name=stomach, embryo E15
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10603,LSID654,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.055372752871689,0,0,0,0,0.0164614044243826,-0.116753762353797,0,0.110490955870335,0,0,0.637447377500993,0,0,0,0,0,0,0.0665710100318368,0,0,0,0,0,0,0,0,0,0,0,0,0,0.128487717484125,0,0,0,0,0.0038898248865189,0.0722190494891722,0.0677389245619926,-0.0550453303075702,0.502709697063721,0.379118542879944,0,0,0,0,0,0,0,0,0,0,0.206814654737266,0.148182634048186,0.0143753951474933,0,0,0,0,0,0,-0.09050609409532,0,0,0,-0.0330197688845073,-0.00603146828380152,-0.00990840872289675,0.0636876918361944,0,0,0.0343857243441411,0.0687252565072957,0.0803809427109337,0,0.0636074113677944,0.0039240633086596,-0.0858373722095256,0.0693510392082783,0,0,0,0,0,0,-0.135798219778432,-0.321287230144701,-0.0923043578386732,0,0,0,0,0
 |rna_box=16
 |rna_catalog_number=
@@ Line 61: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1252-16G8;search_select_hide=table117:1252-16G8
 }}

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FF:1252-16G8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:40, 4 June 2020

CNhs10603

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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