FF:459-17D4: Difference between revisions

Latest revision as of 19:16, 4 June 2020

Name:	stomach, embryo E16
Species:	Mouse (Mus musculus)
Library ID:	CNhs11022
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	stomach
dev stage	16 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		SAMD00005650

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11022		CAGE		DRX009093		DRR009967

Accession ID Mm9

Library id		BAM		CTSS
CNhs11022		DRZ001392		DRZ002775

Accession ID Mm10

Library id		BAM		CTSS
CNhs11022		DRZ012742		DRZ014125

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

CNhs11022

0	0
1	0.00282
10	0
100	0
1000	0.0479
1001	0.00312
1002	0.47
1003	0.086
1004	0
1005	0.0849
1006	-0.114
1007	0.0605
1008	0
1009	0.15
101	0.074
1010	0.122
1011	-0.063
1012	0.0445
1013	-0.0608
1014	0.649
1015	0.125
1016	0.149
1017	0.799
1018	0.418
1019	0
102	0
1020	0
1021	-0.00415
1022	-0.0704
1023	0
1024	-0.0177
1025	0.821
1026	0.0151
1027	0.0666
1028	0
1029	0.285
103	0.257
1030	0
1031	0.367
1032	0.0745
1033	0.0232
1034	0.101
1035	0
1036	0.135
1037	0
1038	0.0166
1039	-0.074
104	0
1040	0.0604
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: CNhs11022

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00757
MA0003.1	MA0003.1	0.69
MA0004.1	MA0004.1	0.233
MA0006.1	MA0006.1	0.285
MA0007.1	MA0007.1	0.84
MA0009.1	MA0009.1	0.245
MA0014.1	MA0014.1	0.912
MA0017.1	MA0017.1	0.715
MA0018.2	MA0018.2	1.91569e-4
MA0019.1	MA0019.1	0.443
MA0024.1	MA0024.1	9.8003e-7
MA0025.1	MA0025.1	1.85249e-4
MA0027.1	MA0027.1	0.015
MA0028.1	MA0028.1	0.00957
MA0029.1	MA0029.1	0.855
MA0030.1	MA0030.1	0.899
MA0031.1	MA0031.1	0.227
MA0035.2	MA0035.2	0.876
MA0038.1	MA0038.1	0.45
MA0039.2	MA0039.2	0.0889
MA0040.1	MA0040.1	0.741
MA0041.1	MA0041.1	0.154
MA0042.1	MA0042.1	0.273
MA0043.1	MA0043.1	5.35077e-4
MA0046.1	MA0046.1	1.80805e-20
MA0047.2	MA0047.2	0.00782
MA0048.1	MA0048.1	0.015
MA0050.1	MA0050.1	0.0154
MA0051.1	MA0051.1	4.36365e-4
MA0052.1	MA0052.1	1.28973e-6
MA0055.1	MA0055.1	0.239
MA0057.1	MA0057.1	0.343
MA0058.1	MA0058.1	0.0239
MA0059.1	MA0059.1	0.338
MA0060.1	MA0060.1	0.00334
MA0061.1	MA0061.1	0.287
MA0062.2	MA0062.2	1.37405e-6
MA0065.2	MA0065.2	0.0308
MA0066.1	MA0066.1	0.511
MA0067.1	MA0067.1	0.016
MA0068.1	MA0068.1	0.279
MA0069.1	MA0069.1	0.0703
MA0070.1	MA0070.1	0.424
MA0071.1	MA0071.1	0.00176
MA0072.1	MA0072.1	0.0218
MA0073.1	MA0073.1	0.432
MA0074.1	MA0074.1	0.89
MA0076.1	MA0076.1	0.00137
MA0077.1	MA0077.1	0.748
MA0078.1	MA0078.1	0.259
MA0079.2	MA0079.2	0.886
MA0080.2	MA0080.2	1.74044e-4
MA0081.1	MA0081.1	0.00844
MA0083.1	MA0083.1	6.81589e-7
MA0084.1	MA0084.1	0.557
MA0087.1	MA0087.1	0.502
MA0088.1	MA0088.1	0.405
MA0090.1	MA0090.1	0.36
MA0091.1	MA0091.1	0.968
MA0092.1	MA0092.1	0.442
MA0093.1	MA0093.1	0.176
MA0099.2	MA0099.2	0.461
MA0100.1	MA0100.1	0.00575
MA0101.1	MA0101.1	0.077
MA0102.2	MA0102.2	0.825
MA0103.1	MA0103.1	0.0164
MA0104.2	MA0104.2	0.166
MA0105.1	MA0105.1	0.535
MA0106.1	MA0106.1	0.489
MA0107.1	MA0107.1	0.0348
MA0108.2	MA0108.2	0.253
MA0111.1	MA0111.1	0.685
MA0112.2	MA0112.2	0.949
MA0113.1	MA0113.1	0.621
MA0114.1	MA0114.1	0.77
MA0115.1	MA0115.1	0.365
MA0116.1	MA0116.1	0.362
MA0117.1	MA0117.1	0.00281
MA0119.1	MA0119.1	0.842
MA0122.1	MA0122.1	0.103
MA0124.1	MA0124.1	0.734
MA0125.1	MA0125.1	0.983
MA0131.1	MA0131.1	0.771
MA0135.1	MA0135.1	0.714
MA0136.1	MA0136.1	3.38478e-6
MA0137.2	MA0137.2	0.105
MA0138.2	MA0138.2	0.0417
MA0139.1	MA0139.1	0.29
MA0140.1	MA0140.1	0.79
MA0141.1	MA0141.1	1.32523e-4
MA0142.1	MA0142.1	0.233
MA0143.1	MA0143.1	0.658
MA0144.1	MA0144.1	0.485
MA0145.1	MA0145.1	0.288
MA0146.1	MA0146.1	0.527
MA0147.1	MA0147.1	0.11
MA0148.1	MA0148.1	0.00623
MA0149.1	MA0149.1	0.88
MA0150.1	MA0150.1	0.00176
MA0152.1	MA0152.1	0.31
MA0153.1	MA0153.1	2.10491e-14
MA0154.1	MA0154.1	0.228
MA0155.1	MA0155.1	0.159
MA0156.1	MA0156.1	0.00149
MA0157.1	MA0157.1	0.368
MA0159.1	MA0159.1	0.163
MA0160.1	MA0160.1	5.57235e-4
MA0162.1	MA0162.1	0.222
MA0163.1	MA0163.1	0.0777
MA0164.1	MA0164.1	0.971
MA0258.1	MA0258.1	0.0597
MA0259.1	MA0259.1	0.401

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: CNhs11022

Novel motif	Logo	P-value
1	1	0.423
10	10	0.877
100	100	0.637
101	101	0.49
102	102	0.504
103	103	0.696
104	104	0.725
105	105	0.891
106	106	0.183
107	107	0.0903
108	108	0.931
109	109	0.582
11	11	0.173
110	110	0.932
111	111	0.141
112	112	0.929
113	113	0.119
114	114	0.0124
115	115	0.619
116	116	0.441
117	117	0.19
118	118	0.174
119	119	0.459
12	12	0.443
120	120	0.423
121	121	0.138
122	122	0.798
123	123	0.247
124	124	0.429
125	125	0.419
126	126	0.31
127	127	0.613
128	128	0.883
129	129	0.487
13	13	0.0235
130	130	0.211
131	131	0.326
132	132	0.687
133	133	0.644
134	134	0.428
135	135	0.927
136	136	0.922
137	137	0.72
138	138	0.00316
139	139	0.379
14	14	0.465
140	140	0.2
141	141	0.955
142	142	0.909
143	143	0.206
144	144	0.472
145	145	0.388
146	146	0.567
147	147	0.411
148	148	0.597
149	149	0.86
15	15	0.0398
150	150	0.414
151	151	0.0992
152	152	0.358
153	153	0.216
154	154	0.982
155	155	0.541
156	156	0.017
157	157	0.434
158	158	0.432
159	159	0.0834
160	160	0.0168
161	161	0.387
162	162	0.924
163	163	0.638
164	164	0.513
165	165	0.735
166	166	0.0613
167	167	0.772
168	168	0.271
169	169	0.565
17	17	0.626
18	18	0.0681
19	19	0.103
2	2	0.936
20	20	0.292
21	21	0.605
22	22	0.594
23	23	0.619
24	24	0.585
25	25	0.0437
26	26	0.0525
27	27	0.68
28	28	0.235
29	29	0.711
3	3	0.608
30	30	0.37
31	31	0.488
32	32	0.691
33	33	0.861
34	34	0.991
35	35	0.0662
36	36	0.682
37	37	0.858
38	38	0.572
39	39	0.248
4	4	0.275
40	40	0.945
41	41	0.0575
42	42	0.968
43	43	0.498
44	44	0.296
45	45	0.77
46	46	0.795
47	47	0.653
48	48	0.322
49	49	0.17
5	5	0.515
50	50	0.361
51	51	0.945
52	52	0.0792
53	53	0.506
54	54	0.999
55	55	0.485
56	56	0.577
57	57	0.591
58	58	0.44
59	59	0.541
6	6	0.39
60	60	0.383
61	61	0.612
62	62	0.0531
63	63	0.5
64	64	0.507
65	65	0.496
66	66	0.508
67	67	0.385
68	68	0.0923
69	69	0.0499
7	7	0.721
70	70	0.0192
71	71	0.574
72	72	0.948
73	73	0.501
74	74	0.483
75	75	0.375
76	76	0.413
77	77	0.149
78	78	0.987
79	79	0.813
8	8	0.225
80	80	0.184
81	81	0.544
82	82	0.134
83	83	0.402
84	84	0.393
85	85	0.142
86	86	0.997
87	87	0.00533
88	88	0.181
89	89	0.672
9	9	0.499
90	90	0.25
91	91	0.566
92	92	0.881
93	93	0.696
94	94	0.229
95	95	0.335
96	96	0.736
97	97	0.662
98	98	0.082
99	99	0.128

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: CNhs11022

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011358 mouse stomach- embryo E16 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)
0000299 (mouse embryonic day 16 sample)
0011358 (mouse stomach- embryo E16 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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000945,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000077,UBERON:0000062,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004921,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0010039,UBERON:0003104,UBERON:0000925,UBERON:0006598,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0005409,UBERON:0007026,UBERON:0001041,UBERON:0009142,UBERON:0006595,UBERON:0006603
+|DRA_sample_Accession=CAGE@SAMD00005650
+|accession_numbers=CAGE;DRX009093;DRR009967;DRZ001392;DRZ002775;DRZ012742;DRZ014125
+|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=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000299,FF:0011358
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr13:55932591..55932622,-!p1@Pitx1!1.92!97.96!Pitx1;;chr10:22539932..22539956,-!p1@Tcf21!1.68!121.40!Tcf21;;chr5:77543897..77543911,-!p2@Hopx!1.67!85.54!Hopx;;chr8:59799772..59799789,+!p1@Hand2!1.64!119.56!Hand2;;chr4:135129538..135129558,-!p1@Grhl3!1.63!62.64!Grhl3;;chr13:48758276..48758291,+!p1@Barx1!1.62!41.04!Barx1;;chr1:137155026..137155042,-!p1@Elf3!1.52!179.72!Elf3;;chr16:25801993..25802014,+!p1@Trp63!1.49!29.81!Trp63;;chr8:123608252..123608268,+!p1@Foxf1a!1.48!42.45!Foxf1a;;chr12:58646974..58647003,-!p1@Foxa1!1.35!28.51!Foxa1;;chr2:164228702..164228719,+!p1@Rbpjl!1.35!21.17!Rbpjl;;chr13:48758358..48758415,+!p2@Barx1!1.34!20.85!Barx1;;chr2:103143336..103143367,-!p1@Ehf!1.33!32.51!Ehf;;chr11:121380640..121380655,-!p1@Zfp750!1.30!30.78!Zfp750;;chr3:34548909..34548927,+!p1@Sox2!1.29!31.21!Sox2;;chr17:27865882..27865901,-!p1@Spdef!1.29!18.68!Spdef;;chr5:77543935..77543947,-!p4@Hopx!1.29!18.36!Hopx;;chr3:3634145..3634161,+!p1@Hnf4g!1.27!17.71!Hnf4g;;chr13:31650185..31650201,+!p1@Foxq1!1.26!59.08!Foxq1;;chr13:55937467..55937516,-!p3@Pitx1!1.25!16.96!Pitx1;;chr2:163332558..163332596,+!p2@Hnf4a!1.25!16.85!Hnf4a;;chr13:55932624..55932641,-!p2@Pitx1!1.23!15.98!Pitx1;;chr14:118636214..118636235,-!p1@Sox21!1.22!18.68!Sox21;;chr13:31717548..31717596,+!p1@Foxf2!1.18!28.19!Foxf2;;chr7:17647736..17647772,-!p1@Hif3a!1.17!49.14!Hif3a;;chr10:88969376..88969395,-!p1@Nr1h4!1.17!13.72!Nr1h4;;chr7:108966820..108966835,+!p1@Phox2a!1.16!13.39!Phox2a;;chr10:12810631..12810649,+!p1@Plagl1!1.13!320.88!Plagl1;;chr19:5560600..5560617,-!p1@Ovol1!1.12!14.80!Ovol1;;chr2:19367259..19367278,+!p1@Ptf1a!1.12!12.31!Ptf1a;;chr5:148118639..148118715,-!p1@Cdx2!1.12!12.20!Cdx2;;chr14:63864056..63864102,-!p1@Gata4!1.09!19.55!Gata4;;chr15:102865088..102865107,+!p1@Hoxc4!1.07!14.26!Hoxc4;;chr16:38294860..38294924,-!p1@Nr1i2!1.06!10.48!Nr1i2;;chr14:99697871..99697934,+!p1@Klf5!1.04!200.57!Klf5;;chr7:19608891..19608895,-!p1@Foxa3!1.03!12.74!Foxa3;;chr13:117099847..117099907,-!p1@Isl1!1.01!17.50!Isl1;;chr1:189821714..189821761,+!p1@Esrrg!1.01!17.28!Esrrg;;chr10:86956396..86956411,-!p1@Ascl1!0.98!13.39!Ascl1;;chr15:102865131..102865151,+!p2@Hoxc4!0.97!9.40!Hoxc4;;chr3:3508024..3508069,+!p2@Hnf4g!0.97!8.42!Hnf4g;;chr2:103143315..103143328,-!p2@Ehf!0.96!8.21!Ehf;;chr10:126778916..126778974,-!p1@Gli1!0.95!18.25!Gli1;;chr3:90046995..90047031,-!p2@Creb3l4!0.95!9.94!Creb3l4;;chr2:103264245..103264268,+!p2@Elf5!0.95!7.88!Elf5;;chr12:39510206..39510249,+!p3@Etv1!0.94!7.78!Etv1;;chr3:30408603..30408668,-!p1@Mecom!0.93!17.71!Mecom;;chr6:14851440..14851497,+!p2@Foxp2!0.92!18.58!Foxp2;;chr5:67490284..67490302,-!p1@Phox2b!0.92!7.24!Phox2b;;chr19:43686789..43686811,+!p1@Nkx2-3!0.92!7.24!Nkx2-3;;chr17:86087592..86087615,-!p1@Six2!0.91!7.13!Six2;;chr12:57796615..57796687,+!p1@Pax9!0.91!7.13!Pax9;;chr13:55937432..55937460,-!p4@Pitx1!0.91!7.13!Pitx1;;chr11:121380594..121380609,-!p2@Zfp750!0.89!12.10!Zfp750;;chr5:144951153..144951203,+!p1@Bhlha15!0.89!10.04!Bhlha15;;chr10:119913310..119913366,-!p1@Hmga2!0.88!54.54!Hmga2;;chr18:64499674..64499696,+!p1@Onecut2!0.87!11.34!Onecut2;;chr2:103264213..103264233,+!p1@Elf5!0.85!6.05!Elf5;;chr18:64499706..64499721,+!p2@Onecut2!0.84!8.64!Onecut2;;chr3:34548946..34548972,+!p2@Sox2!0.84!6.70!Sox2;;chr6:52163319..52163342,-!p1@Hoxa3!0.83!8.53!Hoxa3;;chr3:29911808..29911833,-!p8@Mecom!0.83!5.83!Mecom;;chr11:121380611..121380625,-!p3@Zfp750!0.82!7.02!Zfp750;;chr1:170361991..170362015,-!p6@Pbx1!0.81!12.85!Pbx1;;chr10:119913546..119913583,-!p3@Hmga2!0.81!11.88!Hmga2;;chr6:52154414..52154462,-!p1@Hoxa5!0.81!7.78!Hoxa5;;chr10:80555320..80555378,-!p1@Creb3l3!0.81!6.37!Creb3l3;;chr6:14851287..14851342,+!p1@Foxp2!0.80!18.79!Foxp2;;chr14:118636238..118636257,-!p2@Sox21!0.80!5.29!Sox21;;chr16:14705961..14705978,+!p2@Snai2!0.79!26.25!Snai2;;chr10:61595830..61595846,+!p1@Neurog3!0.79!5.18!Neurog3;;chr7:6649134..6649167,-!p1@Zim1!0.78!29.59!Zim1;;chr2:71367871..71367898,+!p1@Dlx1!0.78!5.08!Dlx1;;chr11:69468531..69468557,+!p1@Sox15!0.77!4.86!Sox15;;chr2:180069370..180069409,-!p1@Gata5!0.76!5.72!Gata5;;chr9:31720843..31720888,-!p1@Barx2!0.76!5.29!Barx2;;chr16:14705925..14705951,+!p1@Snai2!0.75!35.75!Snai2;;chr4:135129447..135129467,-!p2@Grhl3!0.75!5.72!Grhl3;;chr3:30408674..30408716,-!p2@Mecom!0.74!7.78!Mecom;;chr2:163372884..163372904,+!p1@Hnf4a!0.73!4.32!Hnf4a;;chr8:77396591..77396639,+!p1@Isx!0.73!4.32!Isx;;chr4:46356509..46356527,+!p1@Foxe1!0.72!4.21!Foxe1;;chr5:29805118..29805137,-!p1@Mnx1!0.72!4.21!Mnx1;;chr2:115891534..115891589,-!p1@Meis2!0.71!65.78!Meis2;;chr6:52167459..52167492,-!p1@Hoxa7!0.71!5.08!Hoxa7;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.69!7.13!Hoxb2;;chr1:194979361..194979373,+!p2@Irf6!0.69!5.51!Irf6;;chr3:30408384..30408431,-!p4@Mecom!0.69!5.08!Mecom;;chr9:55388997..55389016,+!p1@Isl2!0.69!3.89!Isl2;;chr15:102839948..102839975,+!p3@Hoxc6!0.68!3.78!Hoxc6;;chr1:194979315..194979359,+!p1@Irf6!0.67!25.49!Irf6;;chr6:52114821..52114828,-!p1@Hoxa2!0.67!5.83!Hoxa2;;chr6:52154386..5215440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krir!0.16!3.78!Prkrir;;chrX:108810678..108810736,-!p1@Hdx!0.16!3.67!Hdx;;chr7:30638630..30638702,-!p1@Zfp940!0.16!3.67!Zfp940;;chrX:98449898..98449913,+!p2@Foxo4!0.16!3.46!Foxo4;;chr4:54957910..54957954,+!p2@Zfp462!0.16!3.13!Zfp462;;chr11:106134144..106134174,-!p3@Smarcd2!0.16!3.13!Smarcd2;;chr10:30562571..30562597,-!p1@Hey2!0.16!2.27!Hey2;;chr3:152058408..152058453,+!p5@Gm8261,p5@Zzz3!0.16!2.05!Zzz3;;chr15:75799598..75799619,+!p3@Zfp707!0.16!1.94!Zfp707;;chr8:87225702..87225726,+!p3@Lyl1!0.16!1.84!Lyl1;;chr9:63869729..63869749,-!p4@Smad6!0.16!1.73!Smad6;;chr11:102179350..102179375,-!p7@Ubtf!0.16!1.73!Ubtf;;chr4:126700683..126700704,+!p6@Sfpq!0.16!1.73!Sfpq;;chr11:101755669..101755686,-!p1@Meox1!0.16!1.51!Meox1;;chr12:113916993..113917009,+!p2@Zbtb42!0.16!1.40!Zbtb42;;chr7:13404215..13404220,-!p2@Zfp329!0.16!1.40!Zfp329;;chr2:153067138..153067147,-!p3@Plagl2!0.16!1.30!Plagl2;;chr4:135840552..135840567,+!p4@Zfp46!0.16!1.19!Zfp46;;chr11:99092312..99092333,-!p4@Smarce1!0.16!1.08!Smarce1;;chr2:154395552..154395561,-!p3@E2f1!0.16!0.97!E2f1;;chr4:61869573..61869595,-!p2@Zfp37!0.16!0.86!Zfp37;;chr4:6918396..6918411,-!p4@Tox!0.16!0.86!Tox;;chr18:14131020..14131033,-!p4@Zfp521!0.16!0.86!Zfp521;;chr7:123177120..123177138,-!p10@Sox6!0.16!0.76!Sox6;;chr2:153067233..153067236,-!p4@Plagl2!0.16!0.76!Plagl2;;chr11:52096066..52096081,-!p2@Tcf7!0.16!0.76!Tcf7;;chr15:50721942..50721987,-!p13@Trps1!0.16!0.65!Trps1;;chr13:44936126..44936164,+!p6@Jarid2!0.16!0.65!Jarid2;;chr15:102820964..102821006,+!p1@Hoxc8!0.16!0.43!Hoxc8;;chr15:102196790..102196799,-!p3@Sp7!0.16!0.43!Sp7;;chr14:17407857..17407875,-!p4@Rarb!0.16!0.43!Rarb;;chr12:30219426..30219506,+!p2@Myt1l!0.16!0.43!Myt1l;;chr13:72766234..72766243,+!p3@Irx2!0.16!0.43!Irx2;;chr15:76352832..76352900,-!p1@Scrt1!0.16!0.43!Scrt1;;chr14:63890691..63890718,-!p8@Gata4!0.16!0.43!Gata4;;chr14:17408022..17408043,-!p6@Rarb!0.16!0.43!Rarb;;chr13:48757894..48757908,+!p5@Barx1!0.16!0.43!Barx1;;chr14:34791937..34791977,-!p1@Zfp488!0.16!0.43!Zfp488;;chr13:40829337..40829360,-!p5@Tfap2a!0.16!0.43!Tfap2a;;chr5:148118809..148118832,-!p5@Cdx2!0.16!0.43!Cdx2;;chr6:144157968..144157989,-!p7@Sox5!0.16!0.43!Sox5;;chr5:115421126..115421137,-!p4@Hnf1a!0.16!0.43!Hnf1a;;chr6:115311132..115311147,+!p9@Pparg!0.16!0.43!Pparg;;chr6:52134126..52134150,-!p3@Hoxa3!0.16!0.43!Hoxa3;;chr4:87452167..87452178,-!p8@Mllt3!0.16!0.43!Mllt3;;chr3:29912249..29912262,-!p26@Mecom!0.16!0.43!Mecom;;chr4:13678723..13678739,+!p10@Runx1t1!0.16!0.43!Runx1t1;;chr2:71384401..71384424,-!p3@Dlx2!0.16!0.43!Dlx2;;chr4:13669922..13669957,+!p13@Runx1t1!0.16!0.43!Runx1t1;;chr2:81893447..81893468,+!p2@Zfp804a!0.16!0.43!Zfp804a;;chr3:128902878..128902893,+!p6@Pitx2!0.16!0.43!Pitx2;;chr3:29912169..29912182,-!p12@Mecom!0.16!0.43!Mecom;;chr2:71368815..71368836,+!p4@Dlx1!0.16!0.43!Dlx1;;chr18:11052516..11052525,+!p5@Gata6!0.16!0.43!Gata6;;chr19:55967419..55967424,+!p19@Tcf7l2!0.16!0.43!Tcf7l2;;chr18:76400957..76400968,+!p12@Smad2!0.16!0.43!Smad2;;chr16:38294929..38294940,-!p2@Nr1i2!0.16!0.43!Nr1i2;;chr19:12871064..12871095,-!p2@Zfp91!0.16!0.43!Zfp91;;chr11:23978270..23978290,+!p9@Bcl11a!0.16!0.43!Bcl11a;;chr11:96976641..96976646,-!p1@Tbx21!0.16!0.43!Tbx21;;chr10:119913766..119913779,-!p10@Hmga2!0.16!0.43!Hmga2;;chr10:119913301..119913302,-!p11@Hmga2!0.16!0.43!Hmga2;;chr11:96164887..96164894,+!p4@Hoxb5!0.16!0.43!Hoxb5;;chr11:96160403..96160416,+!p4@Hoxb6!0.16!0.43!Hoxb6;;chr11:70043718..70043743,-!p3@Bcl6b!0.16!0.43!Bcl6b;;chr2:169458593..169458603,+!p13@Tshz2!0.16!0.43!Tshz2;;chr1:120524563..120524591,+!p2@Tfcp2l1!0.16!0.43!Tfcp2l1;;chr2:181501988..181502026,+!p3@Myt1!0.16!0.43!Myt1;;chr2:168780729..168780740,-!p3@LOC100502777,p3@Zfp64!0.16!0.43!Zfp64;;chr2:65683842..65683856,+!p3@Csrnp3!0.16!0.43!Csrnp3;;chr1:6720216..6720232,+!p1@St18!0.16!0.43!St18;;chr19:55972767..55972779,+!p20@Tcf7l2!0.16!0.43!Tcf7l2;;chr9:24578720..24578735,-!p1@Tbx20!0.16!0.43!Tbx20;;chr9:59796330..59796350,-!p6@Nr2e3!0.16!0.43!Nr2e3;;chr9:96159210..96159221,+!p10@Tfdp2!0.16!0.43!Tfdp2;;chr9:74714303..74714318,+!p2@Onecut1!0.16!0.43!Onecut1;;chr9:43013917..43013968,-!p1@Pou2f3!0.16!0.43!Pou2f3;;chr7:89137554..89137565,-!p2@Bnc1!0.16!0.43!Bnc1;;chr5:46248712..46248750,-!p1@Lcorl!0.15!18.90!Lcorl;;chr2:17986272..17986332,+!p2@Mllt10!0.15!12.85!Mllt10;;chr7:28645585..28645659,+!p1@Zfp607!0.15!11.45!Zfp607;;chr13:67784412..67784499,-!p1@Zfp738!0.15!11.02!Zfp738;;chr1:135557964..135557976,-!p2@Zc3h11a!0.15!10.48!Zc3h11a;;chr4:133801453..133801492,-!p1@Zfp593!0.15!9.83!Zfp593;;chr10:79862134..79862173,-!p3@Mbd3!0.15!9.50!Mbd3;;chr11:72990738..72990763,+!p2@LOC100047518,p2@Tax1bp3!0.15!6.37!Tax1bp3;;chr1:39250584..39250643,+!p1@Npas2!0.15!5.72!Npas2;;chr13:67825201..67825277,-!p1@Zfp71-rs1!0.15!5.62!Zfp71-rs1;;chr6:29476690..29476724,+!p1@Irf5!0.15!5.18!Irf5;;chr7:148513409..148513455,-!p2@Deaf1!0.15!5.18!Deaf1;;chr6:131338363..131338383,-!p4@Csda!0.15!4.86!Csda;;chrX:66613481..66613562,+!p1@Aff2!0.15!4.75!Aff2;;chrX:53599567..53599592,+!p1@Zfp449!0.15!4.54!Zfp449;;chr18:69505414..69505465,+!p6@Tcf4!0.15!3.89!Tcf4;;chr10:114821532..114821565,-!p4@Thap2!0.15!3.78!Thap2;;chr17:45570488..45570510,-!p3@Cdc5l!0.15!3.67!Cdc5l;;chr17:21520689..21520730,+!p1@Zfp677!0.15!3.67!Zfp677;;chr3:89197551..89197606,-!p2@Zbtb7b!0.15!3.56!Zbtb7b;;chr6:48552000..48552042,+!p@chr6:48552000..48552042,+!0.15!3.02!Zfp775;;chr9:18278055..18278126,-!p1@Zfp558!0.15!2.81!Zfp558;;chr2:153475210..153475252,+!p2@Dnmt3b!0.15!2.70!Dnmt3b;;chr1:9690424..9690467,-!p1@Mybl1!0.15!1.84!Mybl1;;chr9:63869802..63869815,-!p3@Smad6!0.15!1.73!Smad6;;chr7:130644017..130644092,-!p1@Zkscan2!0.15!1.62!Zkscan2;;chr5:120120667..120120685,+!p3@Tbx3!0.15!1.62!Tbx3;;chr12:113917014..113917034,+!p1@Zbtb42!0.15!1.40!Zbtb42;;chr13:96095097..96095114,+!p5@Zbed3!0.15!1.40!Zbed3;;chr18:14131045..14131062,-!p3@Zfp521!0.15!1.19!Zfp521;;chr16:50429979..50429997,-!p4@Bbx!0.15!1.19!Bbx;;chr7:19946535..19946550,+!p3@Ppp1r13l!0.15!1.08!Ppp1r13l;;chr4:87679181..87679192,-!p10@Mllt3!0.15!0.97!Mllt3;;chr9:122812411..122812426,+!p@chr9:122812411..122812426,+!0.15!0.86!Gm8008;;chr17:71200967..71200983,-!p8@Tgif1!0.15!0.76!Tgif1;;chr6:144157924..144157955,-!p2@Sox5!0.15!0.76!Sox5;;chr6:15135439..15135452,+!p13@Foxp2!0.15!0.65!Foxp2;;chr15:85566051..85566080,+!p4@Ppara!0.15!0.65!Ppara;;chr12:109241852..109241873,-!p4@Bcl11b!0.15!0.65!Bcl11b;;chr2:17977331..17977360,+!p11@Mllt10!0.15!0.54!Mllt10;;chr14:76904313..76904328,+!p1@Tsc22d1!0.14!239.02!Tsc22d1;;chr10:20032267..20032298,+!p1@Bclaf1!0.14!62.10!Bclaf1;;chr8:26951227..26951266,-!p1@Ash2l!0.14!49.79!Ash2l;;chr1:182499044..182499091,+!p1@Parp1!0.14!40.50!Parp1;;chr4:82151653..82151706,-!p2@Nfib!0.14!34.67!Nfib;;chr7:26035739..26035757,-!p1@Erf!0.14!30.13!Erf;;chr9:20757282..20757325,-!p2@Dnmt1!0.14!28.73!Dnmt1;;chr8:77517558..77517597,+!p1@Hmgxb4!0.14!26.68!Hmgxb4;;chr8:124806017..124806040,+!p2@Zfpm1!0.14!12.85!Zfpm1;;chr17:31701694..31701799,+!p1@Pknox1!0.14!12.85!Pknox1;;chr13:96095150..96095184,+!p2@Zbed3!0.14!7.99!Zbed3;;chr2:83484634..83484647,+!p4@Zc3h15!0.14!7.88!Zc3h15;;chr5:24107779..24107825,-!p1@Smarcd3!0.14!7.67!Smarcd3;;chr5:34163023..34163090,+!p2@Whsc1!0.14!7.34!Whsc1;;chrX:132420399..132420436,+!p1@Bhlhb9!0.14!6.70!Bhlhb9;;chr4:120488308..120488366,-!p1@Nfyc!0.14!6.37!Nfyc;;chr2:152223469..152223512,-!p1@Sox12!0.14!5.72!Sox12;;chr17:4994697..4994730,+!p4@Arid1b!0.14!5.08!Arid1b;;chr10:114821572..114821618,-!p3@Thap2!0.14!4.64!Thap2;;chr17:46693078..46693097,-!p3@Srf!0.14!4.32!Srf;;chr8:4613182..4613207,+!p2@Zfp958!0.14!4.21!Zfp958;;chr11:59285934..59285962,-!p1@Zfp867!0.14!3.89!Zfp867;;chr6:117813087..117813121,+!p1@Zfp239!0.14!3.89!Zfp239;;chr18:69504123..69504155,+!p5@Tcf4!0.14!3.78!Tcf4;;chr5:110539087..110539133,+!p1@Zfp605!0.14!2.92!Zfp605;;chr4:6917921..6917970,-!p2@Tox!0.14!2.70!Tox;;chr1:170362322..170362333,-!p8@Pbx1!0.14!2.48!Pbx1;;chr1:15795704..15795713,+!p2@Terf1!0.14!2.27!Terf1;;chr18:83080255..83080277,+!p4@Zfp516!0.14!2.27!Zfp516;;chr4:87678743..87678767,-!p7@Mllt3!0.14!2.16!Mllt3;;chr7:30954700..30954715,-!p2@LOC677248,p2@Zfp146!0.14!2.16!Zfp146;;chr11:98821937..98821987,+!p4@Rara!0.14!1.94!Rara;;chr6:72739034..72739055,-!p3@Tcf7l1!0.14!1.84!Tcf7l1;;chr5:34163132..34163158,+!p3@Whsc1!0.14!1.73!Whsc1;;chr14:76814784..76814803,+!p7@Tsc22d1!0.14!1.51!Tsc22d1;;chr14:100683884..100683908,-!p4@Klf12!0.14!1.51!Klf12;;chr15:100382267..100382287,-!p3@Tfcp2!0.14!1.19!Tfcp2;;chr3:5218563..5218587,+!p5@Zfhx4!0.14!1.19!Zfhx4;;chr18:69505476..69505494,+!p15@Tcf4!0.14!1.19!Tcf4;;chr3:9610033..9610040,-!p3@Zfp704!0.14!1.08!Zfp704;;chr13:72101178..72101203,-!p1@Irx1!0.14!1.08!Irx1;;chr14:52634651..52634678,-!p7@Zfp219!0.14!1.08!Zfp219;;chr13:67476665..67476693,-!p2@Zfp456!0.14!1.08!Zfp456;;
+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011358
 |is_obsolete=
+|library_id=CNhs11022
+|library_id_phase_based=2:CNhs11022
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;459
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;459
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E16.CNhs11022.459-17D4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E16.CNhs11022.459-17D4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E16.CNhs11022.459-17D4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E16.CNhs11022.459-17D4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E16.CNhs11022.459-17D4.mm9.nobarcode.rdna.fa.gz
 |name=stomach, embryo E16
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11022,LSID731,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.16868410697775,0.0157264469861144,0,0,0.0849373898696927,0.0736735985312235,0.224020267352476,0,0.070308472437381,0,0,1.01453183245832,0,0,0,0,0,0,0.103024145498743,0,0,0,0.0445418537893845,0,0,0,0,0,0,0,0,0,0.121022087665277,0,0,0,0.0445418537893845,0.0229421373163961,0.00387995437339481,0.0208986985097768,0.00429363593656684,0.583588490327602,0.357513629754171,0,0,0,0.0445418537893845,0,0,0,0,0,0,0.155949496944283,0,0.228911948817878,0,0,0,0,-0.0198114598826162,0,-0.0369324396602712,0,0.0849373898696927,0.0445418537893845,0.0962209394943651,0.050333348984451,0.0588746092510091,0.100535190713882,0,0.0779408961923312,0.0148748863599584,0,0.155949496944283,0,0.0388335172431082,-0.0665900728179426,-0.0816179282160692,0.0430616458726918,0,0,0,0,0.0222709268946923,0.0445418537893845,0,0.145252419838412,-0.0528373502093075,0.0415122980016656,0,0.0445418537893845,0,0
 |rna_box=17
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:459-17D4;search_select_hide=table117:459-17D4
 }}

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FF:459-17D4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:16, 4 June 2020

CNhs11022

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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