FF:1355-25E4: Difference between revisions

Latest revision as of 19:02, 4 June 2020

Name:	stomach, neonate N25
Species:	Mouse (Mus musculus)
Library ID:	CNhs11104
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	stomach
dev stage	25 days neonate
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		SAMD00005716

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11104		CAGE		DRX009098		DRR009972

Accession ID Mm9

Library id		BAM		CTSS
CNhs11104		DRZ001397		DRZ002780

Accession ID Mm10

Library id		BAM		CTSS
CNhs11104		DRZ012747		DRZ014130

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

CNhs11104

0	0
1	0
10	0
100	0
1000	0.3
1001	0.0966
1002	0.322
1003	0.0426
1004	0
1005	0.0328
1006	0.0351
1007	-0.0222
1008	0
1009	0.243
101	-0.0783
1010	0
1011	-0.0339
1012	0
1013	0.33
1014	0
1015	-0.237
1016	-0.154
1017	0.252
1018	0.617
1019	0
102	0
1020	0
1021	0
1022	0.363
1023	0
1024	0.145
1025	0.72
1026	0
1027	7.687337e-4
1028	0
1029	0.135
103	0.216
1030	0
1031	0.0211
1032	0.271
1033	-0.0665
1034	0.41
1035	0
1036	-0.0983
1037	0
1038	0.121
1039	0.388
104	0
1040	0.0928
1041	0.101

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: CNhs11104

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.356
MA0003.1	MA0003.1	0.226
MA0004.1	MA0004.1	0.481
MA0006.1	MA0006.1	0.0616
MA0007.1	MA0007.1	0.149
MA0009.1	MA0009.1	0.0279
MA0014.1	MA0014.1	0.362
MA0017.1	MA0017.1	0.755
MA0018.2	MA0018.2	0.00343
MA0019.1	MA0019.1	0.556
MA0024.1	MA0024.1	9.45939e-5
MA0025.1	MA0025.1	0.301
MA0027.1	MA0027.1	0.41
MA0028.1	MA0028.1	0.0392
MA0029.1	MA0029.1	0.856
MA0030.1	MA0030.1	0.0345
MA0031.1	MA0031.1	0.0124
MA0035.2	MA0035.2	0.251
MA0038.1	MA0038.1	0.671
MA0039.2	MA0039.2	3.39725e-4
MA0040.1	MA0040.1	0.512
MA0041.1	MA0041.1	0.374
MA0042.1	MA0042.1	0.255
MA0043.1	MA0043.1	2.49607e-4
MA0046.1	MA0046.1	2.00532e-9
MA0047.2	MA0047.2	6.16337e-11
MA0048.1	MA0048.1	0.442
MA0050.1	MA0050.1	0.116
MA0051.1	MA0051.1	0.457
MA0052.1	MA0052.1	0.032
MA0055.1	MA0055.1	0.148
MA0057.1	MA0057.1	0.0398
MA0058.1	MA0058.1	0.251
MA0059.1	MA0059.1	0.505
MA0060.1	MA0060.1	0.00125
MA0061.1	MA0061.1	0.997
MA0062.2	MA0062.2	0.00127
MA0065.2	MA0065.2	0.0902
MA0066.1	MA0066.1	0.314
MA0067.1	MA0067.1	0.921
MA0068.1	MA0068.1	0.0814
MA0069.1	MA0069.1	0.106
MA0070.1	MA0070.1	0.834
MA0071.1	MA0071.1	0.304
MA0072.1	MA0072.1	0.791
MA0073.1	MA0073.1	0.961
MA0074.1	MA0074.1	0.528
MA0076.1	MA0076.1	0.0121
MA0077.1	MA0077.1	0.161
MA0078.1	MA0078.1	0.0644
MA0079.2	MA0079.2	0.0541
MA0080.2	MA0080.2	0.766
MA0081.1	MA0081.1	0.0475
MA0083.1	MA0083.1	3.28332e-7
MA0084.1	MA0084.1	0.998
MA0087.1	MA0087.1	0.514
MA0088.1	MA0088.1	0.713
MA0090.1	MA0090.1	6.15806e-4
MA0091.1	MA0091.1	0.926
MA0092.1	MA0092.1	0.174
MA0093.1	MA0093.1	0.405
MA0099.2	MA0099.2	7.34574e-13
MA0100.1	MA0100.1	0.0225
MA0101.1	MA0101.1	0.563
MA0102.2	MA0102.2	0.337
MA0103.1	MA0103.1	1.83476e-5
MA0104.2	MA0104.2	0.101
MA0105.1	MA0105.1	0.908
MA0106.1	MA0106.1	0.0243
MA0107.1	MA0107.1	0.65
MA0108.2	MA0108.2	1.72586e-8
MA0111.1	MA0111.1	0.492
MA0112.2	MA0112.2	2.9478e-4
MA0113.1	MA0113.1	0.468
MA0114.1	MA0114.1	0.733
MA0115.1	MA0115.1	0.0937
MA0116.1	MA0116.1	0.526
MA0117.1	MA0117.1	0.873
MA0119.1	MA0119.1	0.147
MA0122.1	MA0122.1	0.964
MA0124.1	MA0124.1	0.663
MA0125.1	MA0125.1	0.0955
MA0131.1	MA0131.1	0.185
MA0135.1	MA0135.1	0.324
MA0136.1	MA0136.1	0.0978
MA0137.2	MA0137.2	0.933
MA0138.2	MA0138.2	0.0278
MA0139.1	MA0139.1	0.172
MA0140.1	MA0140.1	0.797
MA0141.1	MA0141.1	0.524
MA0142.1	MA0142.1	0.107
MA0143.1	MA0143.1	0.0339
MA0144.1	MA0144.1	0.463
MA0145.1	MA0145.1	0.00116
MA0146.1	MA0146.1	0.169
MA0147.1	MA0147.1	0.0975
MA0148.1	MA0148.1	1.51974e-11
MA0149.1	MA0149.1	0.371
MA0150.1	MA0150.1	0.256
MA0152.1	MA0152.1	0.299
MA0153.1	MA0153.1	1.30667e-7
MA0154.1	MA0154.1	0.0413
MA0155.1	MA0155.1	0.868
MA0156.1	MA0156.1	0.232
MA0157.1	MA0157.1	0.0257
MA0159.1	MA0159.1	0.104
MA0160.1	MA0160.1	0.966
MA0162.1	MA0162.1	0.404
MA0163.1	MA0163.1	0.72
MA0164.1	MA0164.1	0.57
MA0258.1	MA0258.1	0.0178
MA0259.1	MA0259.1	0.0948

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: CNhs11104

Novel motif	Logo	P-value
1	1	0.337
10	10	0.903
100	100	0.548
101	101	0.847
102	102	0.367
103	103	0.177
104	104	0.6
105	105	0.26
106	106	0.00239
107	107	0.0205
108	108	0.785
109	109	0.123
11	11	0.579
110	110	0.528
111	111	0.267
112	112	0.328
113	113	0.815
114	114	0.999
115	115	0.797
116	116	0.37
117	117	0.716
118	118	0.272
119	119	0.0123
12	12	0.967
120	120	0.951
121	121	0.741
122	122	0.556
123	123	0.493
124	124	0.739
125	125	0.781
126	126	0.109
127	127	0.715
128	128	0.011
129	129	0.868
13	13	0.0192
130	130	0.978
131	131	0.731
132	132	0.775
133	133	0.52
134	134	0.724
135	135	0.399
136	136	0.503
137	137	0.45
138	138	0.294
139	139	0.0892
14	14	0.44
140	140	0.0781
141	141	0.264
142	142	0.979
143	143	0.0609
144	144	0.261
145	145	0.18
146	146	0.101
147	147	0.805
148	148	0.764
149	149	0.0199
15	15	0.328
150	150	0.351
151	151	0.407
152	152	0.00796
153	153	0.774
154	154	0.856
155	155	0.889
156	156	0.00331
157	157	0.135
158	158	0.772
159	159	0.934
160	160	0.32
161	161	0.486
162	162	0.335
163	163	0.939
164	164	0.887
165	165	0.394
166	166	0.137
167	167	0.37
168	168	0.0662
169	169	0.0049
17	17	0.028
18	18	0.49
19	19	0.1
2	2	0.175
20	20	0.286
21	21	0.847
22	22	0.243
23	23	0.187
24	24	0.119
25	25	0.835
26	26	0.0779
27	27	0.574
28	28	0.673
29	29	0.909
3	3	0.598
30	30	0.167
31	31	0.492
32	32	0.0159
33	33	0.804
34	34	0.537
35	35	0.623
36	36	0.548
37	37	0.0443
38	38	0.61
39	39	0.258
4	4	0.00481
40	40	0.587
41	41	0.318
42	42	0.859
43	43	0.258
44	44	0.592
45	45	0.206
46	46	0.316
47	47	0.471
48	48	0.606
49	49	0.309
5	5	0.527
50	50	0.578
51	51	0.543
52	52	0.0348
53	53	0.428
54	54	0.276
55	55	0.242
56	56	0.356
57	57	0.663
58	58	0.465
59	59	0.201
6	6	0.312
60	60	0.03
61	61	0.365
62	62	0.4
63	63	0.125
64	64	0.981
65	65	0.329
66	66	0.927
67	67	0.689
68	68	0.584
69	69	0.943
7	7	0.176
70	70	0.0455
71	71	0.22
72	72	0.73
73	73	0.0306
74	74	0.838
75	75	0.639
76	76	0.111
77	77	0.0164
78	78	0.112
79	79	0.635
8	8	0.474
80	80	0.506
81	81	0.373
82	82	0.159
83	83	0.931
84	84	0.517
85	85	0.0246
86	86	0.36
87	87	0.222
88	88	0.446
89	89	0.137
9	9	0.345
90	90	0.872
91	91	0.891
92	92	0.146
93	93	0.9
94	94	0.405
95	95	0.183
96	96	0.066
97	97	0.0198
98	98	0.674
99	99	0.0618

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: CNhs11104

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011493 mouse stomach- neonate N25 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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000309 (mouse neonate N25 sample)
0011493 (mouse stomach- neonate N25 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:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000945,UBERON:0001007,UBERON:0001041,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0003104,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0009142
+|DRA_sample_Accession=CAGE@SAMD00005716
+|accession_numbers=CAGE;DRX009098;DRR009972;DRZ001397;DRZ002780;DRZ012747;DRZ014130
+|ancestors_in_anatomy_facet=UBERON:0000468,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:0000004,FF:0000303,FF:0000309,FF:0011493
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr1:137155026..137155042,-!p1@Elf3!1.89!422.21!Elf3;;chr5:77543897..77543911,-!p2@Hopx!1.80!116.22!Hopx;;chr1:189821714..189821761,+!p1@Esrrg!1.77!104.70!Esrrg;;chr13:55932591..55932622,-!p1@Pitx1!1.76!67.01!Pitx1;;chr13:31650185..31650201,+!p1@Foxq1!1.70!166.74!Foxq1;;chr7:19608891..19608895,-!p1@Foxa3!1.69!61.77!Foxa3;;chr2:163332558..163332596,+!p2@Hnf4a!1.68!46.33!Hnf4a;;chr4:135129538..135129558,-!p1@Grhl3!1.64!64.13!Grhl3;;chr4:87452180..87452196,-!p3@Mllt3!1.61!76.96!Mllt3;;chr2:103143336..103143367,-!p1@Ehf!1.57!57.59!Ehf;;chr17:27865882..27865901,-!p1@Spdef!1.57!35.86!Spdef;;chr12:58646974..58647003,-!p1@Foxa1!1.56!46.33!Foxa1;;chr13:48758276..48758291,+!p1@Barx1!1.47!28.27!Barx1;;chr5:77543935..77543947,-!p4@Hopx!1.46!27.75!Hopx;;chr4:87452200..87452229,-!p2@Mllt3!1.42!52.61!Mllt3;;chr2:103143315..103143328,-!p2@Ehf!1.38!22.77!Ehf;;chr14:63864056..63864102,-!p1@Gata4!1.36!37.95!Gata4;;chr14:118636214..118636235,-!p1@Sox21!1.35!25.65!Sox21;;chr11:121380640..121380655,-!p1@Zfp750!1.33!33.77!Zfp750;;chr19:5560600..5560617,-!p1@Ovol1!1.32!24.08!Ovol1;;chr3:90046995..90047031,-!p2@Creb3l4!1.31!24.34!Creb3l4;;chr9:31720843..31720888,-!p1@Barx2!1.31!21.73!Barx2;;chr16:25801993..25802014,+!p1@Trp63!1.31!19.63!Trp63;;chr13:48758358..48758415,+!p2@Barx1!1.31!19.37!Barx1;;chr13:55937432..55937460,-!p4@Pitx1!1.30!19.11!Pitx1;;chr2:180069370..180069409,-!p1@Gata5!1.28!21.20!Gata5;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.23!45.55!Tfcp2l1;;chr10:22539932..22539956,-!p1@Tcf21!1.22!40.83!Tcf21;;chr6:86619104..86619119,-!p1@Mxd1!1.21!121.19!Mxd1;;chr8:59799772..59799789,+!p1@Hand2!1.21!42.93!Hand2;;chr8:123608252..123608268,+!p1@Foxf1a!1.21!22.51!Foxf1a;;chr4:55545337..55545357,-!p1@Klf4!1.20!216.21!Klf4;;chr3:29911808..29911833,-!p8@Mecom!1.17!13.87!Mecom;;chr4:133109285..133109308,+!p1@Nr0b2!1.14!12.83!Nr0b2;;chr13:55937467..55937516,-!p3@Pitx1!1.13!12.56!Pitx1;;chr10:88969376..88969395,-!p1@Nr1h4!1.12!12.04!Nr1h4;;chr14:63890491..63890516,-!p2@Gata4!1.11!11.78!Gata4;;chr5:144951153..144951203,+!p1@Bhlha15!1.10!16.75!Bhlha15;;chr12:57796615..57796687,+!p1@Pax9!1.06!10.47!Pax9;;chr18:76219118..76219155,+!p1@Zbtb7c!1.04!17.80!Zbtb7c;;chr1:189821700..189821713,+!p4@Esrrg!1.04!9.95!Esrrg;;chr2:77357622..77357704,-!p1@Zfp385b!1.03!26.70!Zfp385b;;chr13:31717548..31717596,+!p1@Foxf2!1.03!19.37!Foxf2;;chr6:97879817..97879857,+!p2@Mitf!1.03!9.68!Mitf;;chr4:87452167..87452178,-!p8@Mllt3!1.02!9.42!Mllt3;;chr16:38294860..38294924,-!p1@Nr1i2!1.02!9.42!Nr1i2;;chr11:121380594..121380609,-!p2@Zfp750!1.01!16.23!Zfp750;;chr14:63864337..63864381,-!p6@Gata4!1.01!9.16!Gata4;;chr14:118636238..118636257,-!p2@Sox21!1.01!9.16!Sox21;;chr3:30408674..30408716,-!p2@Mecom!0.99!14.66!Mecom;;chr14:63890545..63890560,-!p5@Gata4!0.98!8.64!Gata4;;chr14:63890519..63890539,-!p3@Gata4!0.98!8.64!Gata4;;chr13:55932624..55932641,-!p2@Pitx1!0.98!8.64!Pitx1;;chr13:117099847..117099907,-!p1@Isl1!0.97!15.71!Isl1;;chr14:63890459..63890484,-!p4@Gata4!0.95!7.85!Gata4;;chr12:25257265..25257294,+!p2@Grhl1!0.93!7.59!Grhl1;;chr2:133377954..133377973,+!p1@Bmp2!0.92!24.61!Bmp2;;chr2:147871627..147871641,-!p1@Foxa2!0.91!7.07!Foxa2;;chr11:69468531..69468557,+!p1@Sox15!0.91!7.07!Sox15;;chr13:40829137..40829205,-!p1@Tfap2a!0.90!7.85!Tfap2a;;chr14:99697871..99697934,+!p1@Klf5!0.89!141.87!Klf5;;chr1:194979315..194979359,+!p1@Irf6!0.89!42.93!Irf6;;chr11:96880072..96880079,+!p1@Sp6!0.89!6.81!Sp6;;chr4:148178559..148178603,+!p1@Casz1!0.87!19.11!Casz1;;chr3:34548909..34548927,+!p1@Sox2!0.87!11.26!Sox2;;chr13:72766250..72766273,+!p1@Irx2!0.87!10.21!Irx2;;chr11:121380611..121380625,-!p3@Zfp750!0.87!7.85!Zfp750;;chr11:94981424..94981439,+!p1@Dlx3!0.87!7.33!Dlx3;;chr19:5560570..5560582,-!p2@Ovol1!0.85!6.02!Ovol1;;chr14:118635860..118635885,-!p3@Sox21!0.85!6.02!Sox21;;chr18:11052642..11052659,+!p1@Gata6!0.83!31.41!Gata6;;chr4:148275237..148275311,+!p2@Casz1!0.82!24.87!Casz1;;chr4:154010918..154010931,-!p1@Prdm16!0.81!17.01!Prdm16;;chr3:30408603..30408668,-!p1@Mecom!0.81!13.35!Mecom;;chr12:25257141..25257173,+!p1@Grhl1!0.81!11.78!Grhl1;;chr6:115311030..115311065,+!p4@Pparg!0.81!8.11!Pparg;;chr4:124805061..124805087,-!p1@Zc3h12a!0.80!17.54!Zc3h12a;;chr3:30408384..30408431,-!p4@Mecom!0.80!6.81!Mecom;;chr13:31650026..31650045,+!p2@Foxq1!0.79!9.16!Foxq1;;chr2:103264245..103264268,+!p2@Elf5!0.79!5.24!Elf5;;chr18:76219161..76219176,+!p4@Zbtb7c!0.78!6.81!Zbtb7c;;chr18:11052606..11052633,+!p4@Gata6!0.77!13.09!Gata6;;chr15:81977802..81977828,+!p2@Srebf2!0.76!44.76!Srebf2;;chr15:102087880..102087927,-!p2@Rarg!0.76!11.78!Rarg;;chr10:44178521..44178557,-!p1@Prdm1!0.76!8.90!Prdm1;;chr7:146768691..146768707,-!p1@Nkx6-2!0.76!4.71!Nkx6-2;;chr19:10315179..10315241,-!p1@Gm98!0.75!53.14!Gm98;;chr2:172375081..172375105,+!p1@Tfap2c!0.74!4.45!Tfap2c;;chr3:34548946..34548972,+!p2@Sox2!0.73!4.97!Sox2;;chr2:75542527..75542590,-!p1@Nfe2l2!0.72!429.54!Nfe2l2;;chr6:51382677..51382783,+!p1@Nfe2l3!0.72!11.78!Nfe2l3;;chr15:37162796..37162828,+!p1@Grhl2!0.72!7.59!Grhl2;;chr7:201626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2af1!0.18!0.79!Pou2af1;;chr10:88996295..88996335,-!p3@Nr1h4!0.18!0.79!Nr1h4;;chr10:12844757..12844771,+!p2@Plagl1!0.18!0.52!Plagl1;;chr11:98822081..98822092,+!p14@Rara!0.18!0.52!Rara;;chr11:53164494..53164501,+!p10@Aff4!0.18!0.52!Aff4;;chr11:96880133..96880141,+!p2@Sp6!0.18!0.52!Sp6;;chr11:100553754..100553787,-!p1@Zfp385c!0.18!0.52!Zfp385c;;chr10:51397572..51397595,+!p1@Rfx6!0.18!0.52!Rfx6;;chr11:23978291..23978323,+!p7@Bcl11a!0.18!0.52!Bcl11a;;chr11:98822093..98822104,+!p16@Rara!0.18!0.52!Rara;;chr11:69749491..69749502,+!p6@Ybx2!0.18!0.52!Ybx2;;chr11:121381115..121381124,-!p5@Zfp750!0.18!0.52!Zfp750;;chr11:96180069..96180089,+!p3@Hoxb4!0.18!0.52!Hoxb4;;chr11:23671230..23671264,-!p6@Rel!0.18!0.52!Rel;;chr8:73222425..73222444,+!p2@Jund!0.18!0.52!Jund;;chr8:91568074..91568094,-!p1@Sall1!0.18!0.52!Sall1;;chr9:8900409..8900425,+!p2@Pgr!0.18!0.52!Pgr;;chr9:63869918..63869936,-!p9@Smad6!0.18!0.52!Smad6;;chr7:50817698..50817710,+!p4@Zfp658!0.18!0.52!Zfp658;;chr14:70477113..70477173,+!p1@Egr3!0.18!0.52!Egr3;;chr12:87702380..87702394,+!p6@Esrrb!0.18!0.52!Esrrb;;chr12:87702062..87702081,+!p4@Esrrb!0.18!0.52!Esrrb;;chr13:40824310..40824314,-!p6@Tfap2a!0.18!0.52!Tfap2a;;chr13:83643136..83643158,+!p7@Mef2c!0.18!0.52!Mef2c;;chr12:39510290..39510309,+!p5@Etv1!0.18!0.52!Etv1;;chr12:39510260..39510271,+!p10@Etv1!0.18!0.52!Etv1;;chr19:12871064..12871095,-!p2@Zfp91!0.18!0.52!Zfp91;;chr16:25684232..25684285,+!p2@Trp63!0.18!0.52!Trp63;;chr18:69681413..69681424,+!p24@Tcf4!0.18!0.52!Tcf4;;chr16:43364258..43364270,+!p27@Zbtb20!0.18!0.52!Zbtb20;;chr17:71201050..71201078,-!p9@Tgif1!0.18!0.52!Tgif1;;chr18:11052516..11052525,+!p5@Gata6!0.18!0.52!Gata6;;chr16:30064437..30064449,+!p11@Hes1!0.18!0.52!Hes1;;chr2:104966874..104966907,+!p2@Wt1!0.18!0.52!Wt1;;chr2:181501745..181501778,+!p1@Myt1!0.18!0.52!Myt1;;chr1:169528433..169528456,+!p10@Rxrg!0.18!0.52!Rxrg;;chr1:189433521..189433548,+!p5@Esrrg!0.18!0.52!Esrrg;;chr2:115890864..115890869,-!p14@Meis2!0.18!0.52!Meis2;;chr2:147872074..147872079,-!p4@Foxa2!0.18!0.52!Foxa2;;chr4:139388835..139388867,-!p1@Pax7!0.18!0.52!Pax7;;chr5:102094214..102094230,-!p1@Nkx6-1!0.18!0.52!Nkx6-1;;chr4:97444557..97444558,+!p23@Nfia!0.18!0.52!Nfia;;chr4:107107224..107107259,+!p2@Glis1!0.18!0.52!Glis1;;chr4:119487109..119487131,+!p4@Hivep3!0.18!0.52!Hivep3;;chr4:154010313..154010324,-!p9@Prdm16!0.18!0.52!Prdm16;;chr2:74543397..74543435,+!p2@Hoxd8!0.18!0.52!Hoxd8;;chr3:58219238..58219246,+!p3@Tsc22d2!0.18!0.52!Tsc22d2;;chr2:74542974..74542986,+!p5@Hoxd8!0.18!0.52!Hoxd8;;chr4:84321280..84321298,-!p5@Bnc2!0.18!0.52!Bnc2;;chr2:74550015..74550057,+!p2@Hoxd3!0.18!0.52!Hoxd3;;chr2:74583776..74583815,+!p3@Hoxd3!0.18!0.52!Hoxd3;;chr3:66785201..66785226,-!p3@Shox2!0.18!0.52!Shox2;;chr6:99216360..99216372,-!p8@Foxp1!0.18!0.52!Foxp1;;chr5:144951136..144951139,+!p2@Bhlha15!0.18!0.52!Bhlha15;;chr5:29805118..29805137,-!p1@Mnx1!0.18!0.52!Mnx1;;chr5:77544170..77544181,-!p6@Hopx!0.18!0.52!Hopx;;chr5:67490447..67490458,-!p7@Phox2b!0.18!0.52!Phox2b;;chr6:52167434..52167450,-!p3@Hoxa7!0.18!0.52!Hoxa7;;chr5:148118639..148118715,-!p1@Cdx2!0.18!0.52!Cdx2;;chr6:72185396..72185413,-!p6@Atoh8!0.18!0.52!Atoh8;;chr5:76733756..76733815,-!p1@Clock!0.17!20.42!Clock;;chr2:115891534..115891589,-!p1@Meis2!0.17!18.32!Meis2;;chr11:18918959..18918976,-!p2@Meis1!0.17!17.54!Meis1;;chr4:87679232..87679277,-!p1@Mllt3!0.17!15.18!Mllt3;;chr5:20387850..20387869,-!p1@Phtf2!0.17!13.09!Phtf2;;chr13:37917887..37917913,+!p1@Rreb1!0.17!8.11!Rreb1;;chr18:69504157..69504184,+!p3@Tcf4!0.17!7.59!Tcf4;;chr4:129055091..129055168,-!p1@Zbtb8a!0.17!7.07!Zbtb8a;;chr5:145962698..145962742,-!p1@Zkscan14!0.17!5.50!Zkscan14;;chr9:96620228..96620308,-!p3@Zbtb38!0.17!5.50!Zbtb38;;chr2:152758901..152758925,-!p1@Foxs1!0.17!5.24!Foxs1;;chr9:69137672..69137702,+!p2@Rora!0.17!4.97!Rora;;chr15:25914114..25914128,+!p2@Zfp622!0.17!4.71!Zfp622;;chr7:25101609..25101678,-!p1@Zfp94!0.17!4.19!Zfp94;;chr14:52898807..52898863,+!p2@Tox4!0.17!3.14!Tox4;;chr14:75684121..75684132,+!p2@Zc3h13!0.17!2.88!Zc3h13;;chr1:64167550..64167618,-!p4@Klf7!0.17!2.88!Klf7;;chr19:5637489..5637500,+!p5@Rela!0.17!2.62!Rela;;chr18:69681439..69681456,+!p7@Tcf4!0.17!2.62!Tcf4;;chr11:85646263..85646278,+!p2@Tbx2!0.17!2.62!Tbx2;;chr10:26093876..26093894,-!p2@L3mbtl3!0.17!2.36!L3mbtl3;;chr15:103170516..103170531,-!p2@Zfp385a!0.17!2.36!Zfp385a;;chr8:87297280..87297326,-!p2@Nfix!0.17!2.36!Nfix;;chr9:63869729..63869749,-!p4@Smad6!0.17!1.83!Smad6;;chr10:92773736..92773761,-!p4@Elk3!0.17!1.31!Elk3;;chr7:52963269..52963305,+!p4@Dbp!0.17!1.05!Dbp;;chr7:19895384..19895399,-!p2@Fosb!0.17!1.05!Fosb;;chr13:37870253..37870272,+!p13@Rreb1!0.17!1.05!Rreb1;;chr12:77470718..77470752,-!p4@Zbtb25!0.17!1.05!Zbtb25;;chr16:18587076..18587106,-!p1@Tbx1!0.17!1.05!Tbx1;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.17!1.05!Carhsp1;;chr11:98636508..98636524,-!p3@Nr1d1!0.17!0.79!Nr1d1;;chr3:99057269..99057306,+!p1@Tbx15!0.17!0.79!Tbx15;;chr4:84321300..84321315,-!p2@Bnc2!0.17!0.79!Bnc2;;chr14:79915521..79915539,+!p5@Elf1!0.17!0.79!Elf1;;chr1:17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chr8:13339656..13339661,+!p3@Tfdp1!0.11!1.83!Tfdp1;;chr16:43363152..43363186,+!p3@Zbtb20!0.11!1.83!Zbtb20;;chr5:145962744..145962760,-!p2@Zkscan14!0.11!1.57!Zkscan14;;chr16:43363837..43363842,+!p11@Zbtb20!0.11!1.31!Zbtb20;;chr9:19426687..19426708,+!p3@Zfp317!0.11!1.31!Zfp317;;chr5:65203599..65203617,+!p8@Klf3!0.11!1.05!Klf3;;chr15:50721211..50721234,-!p6@Trps1!0.11!1.05!Trps1;;chr14:67853457..67853482,+!p2@Ebf2!0.11!0.79!Ebf2;;chr4:63071717..63071736,-!p4@Akna!0.11!0.79!Akna;;chr6:52167513..52167549,-!p2@Hoxa7!0.11!0.79!Hoxa7;;chr6:53523346..53523353,+!p3@Creb5!0.11!0.79!Creb5;;chr6:92041506..92041517,+!p5@Nr2c2!0.11!0.79!Nr2c2;;chr18:64499706..64499721,+!p2@Onecut2!0.11!0.79!Onecut2;;chr16:30065394..30065398,+!p3@Hes1!0.11!0.79!Hes1;;chr19:23215446..23215457,+!p8@Klf9!0.11!0.52!Klf9;;chr15:61819047..61819076,+!p5@Myc!0.11!0.52!Myc;;chr9:96159427..96159432,+!p11@Tfdp2!0.11!0.52!Tfdp2;;chr11:98636321..98636332,-!p8@Nr1d1!0.11!0.52!Nr1d1;;chr10:62328027..62328038,-!p6@Tet1!0.11!0.52!Tet1;;chr1:92950099..92950109,+!p3@Lrrfip1!0.11!0.52!Lrrfip1;;chr2:56976467..56976482,-!p4@Nr4a2!0.11!0.52!Nr4a2;;chr6:52664406..52664434,+!p3@Tax1bp1!0.11!0.52!Tax1bp1;;chr6:29490887..29490891,+!p5@Irf5!0.11!0.52!Irf5;;chr5:65203575..65203589,+!p11@Klf3!0.11!0.52!Klf3;;chr4:107107175..107107204,+!p1@Glis1!0.11!0.52!Glis1;;chr8:73222830..73222844,+!p1@Jund!0.10!286.36!Jund;;chr16:15887371..15887385,+!p1@Cebpd!0.10!38.48!Cebpd;;chr8:73905806..73905876,-!p1@Nr2f6!0.10!23.30!Nr2f6;;chr1:179372411..179372509,+!p1@Zfp238!0.10!13.61!Zfp238;;chr17:84105551..84105600,+!p1@Mta3!0.10!12.04!Mta3;;chr7:4967068..4967111,+!p1@Zfp524!0.10!11.78!Zfp524;;chr18:3281034..3281104,-!p1@Crem!0.10!7.33!Crem;;chr17:28314341..28314394,+!p2@Zfp523!0.10!5.76!Zfp523;;chr5:38611639..38611698,-!p1@Zbtb49!0.10!4.97!Zbtb49;;chr13:67552527..67552574,-!p1@Zfp874a!0.10!4.19!Zfp874a;;chr9:32443818..32443854,+!p2@Ets1!0.10!4.19!Ets1;;chr17:45570455..45570479,-!p2@Cdc5l!0.10!3.40!Cdc5l;;chr15:79177964..79177986,+!p1@Maff!0.10!3.14!Maff;;chr10:126726021..126726053,-!p4@Mbd6!0.10!3.14!Mbd6;;chr13:15555496..15555544,+!p1@Gli3!0.10!3.14!Gli3;;chr5:138187181..138187192,+!p5@Tsc22d4!0.10!2.09!Tsc22d4;;chr17:13897299..13897342,+!p3@Mllt4!0.10!1.83!Mllt4;;chr5:65213356..65213412,+!p6@Klf3!0.10!1.57!Klf3;;chr6:99471044..99471066,-!p4@Foxp1!0.10!1.57!Foxp1;;chr5:104182963..104182982,+!p5@Aff1!0.10!1.57!Aff1;;chr4:48058129..48058179,+!p2@Nr4a3!0.10!1.31!Nr4a3;;chr14:56443698..56443726,+!p2@Nfatc4!0.10!1.31!Nfatc4;;chr2:127347067..127347093,-!p1@Kcnip3!0.10!1.05!Kcnip3;;chr5:3648045..3648074,-!p2@Gatad1!0.10!1.05!Gatad1;;chr8:72498017..72498059,-!p13@Gatad2a!0.10!1.05!Gatad2a;;chr19:53385060..53385069,+!p6@Mxi1!0.10!0.79!Mxi1;;chr12:32635051..32635062,-!p2@Hbp1!0.10!0.79!Hbp1;;chr13:29045274..29045293,-!p6@Sox4!0.10!0.52!Sox4;;chr1:14746065..14746079,-!p1@Msc!0.10!0.52!Msc;;chr7:52960700..52960719,+!p2@Dbp!0.10!0.52!Dbp;;chr11:90251852..90251855,-!p4@Hlf!0.10!0.52!Hlf;;chr11:69749396..69749433,+!p1@Ybx2!0.10!0.26!Ybx2;;chr11:96145537..96145556,+!p6@Hoxb7!0.10!0.26!Hoxb7;;chr11:100683794..100683805,-!p4@Stat5b!0.10!0.26!Stat5b;;chr11:70500401..70500460,-!p3@Camta2!0.10!0.26!Camta2;;chr11:69749437..69749467,+!p3@Ybx2!0.10!0.26!Ybx2;;chr11:44431115..44431132,+!p9@Ebf1!0.10!0.26!Ebf1;;chr11:96145393..96145407,+!p3@Hoxb7!0.10!0.26!Hoxb7;;chr11:23978206..23978219,+!p12@Bcl11a!0.10!0.26!Bcl11a;;chr11:78200195..78200211,-!p2@Foxn1!0.10!0.26!Foxn1;;chr10:67375342..67375365,-!p3@Zfp365!0.10!0.26!Zfp365;;chr11:23978270..23978290,+!p9@Bcl11a!0.10!0.26!Bcl11a;;chr11:96160426..96160443,+!p2@Hoxb6!0.10!0.26!Hoxb6;;
+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:1355-25E4
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011493
+|is_a=EFO:0002091;;FF:0011493
+|is_obsolete=
+|library_id=CNhs11104
+|library_id_phase_based=2:CNhs11104
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1355
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1355
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N25.CNhs11104.1355-25E4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N25.CNhs11104.1355-25E4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N25.CNhs11104.1355-25E4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N25.CNhs11104.1355-25E4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N25.CNhs11104.1355-25E4.mm9.nobarcode.rdna.fa.gz
 |name=stomach, neonate N25
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11104,LSID733,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.114383331519716,0,0,0,0,0,0.195878422527787,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0.100975358632432,0,0,0,0,0,0,0,0,0,0.0853088530103566,0,0,0,0,0,0.0720904062465054,0,-0.0253923670759784,-0.425795693170007,0.288547035297468,0,0,0,0,0,0,0,0,0,0,0,0.182845846232878,0.185697830648274,0,0,0,0,0,0,0.101482362409309,0,0,0.0128495370594577,-0.004166848749449,0.0527318397483745,0.367705477031102,-0.0102322697916078,0,0.00515803474089704,0,-0.00789101514333651,0.311122885272949,0,0,-0.0834118688814169,0.26634429881404,0.0221437637925246,0,0,0,0,0,0.100975358632432,0.270665269210061,0.577173715781788,0.25466832530464,0,0,0,0,0
 |rna_box=25
 |rna_catalog_number=
@@ Line 54: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=25E4
+|rna_tube_id=2.50E+05
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=stomach
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+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1355-25E4;search_select_hide=table117:1355-25E4
 }}

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FF:1355-25E4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:02, 4 June 2020

CNhs11104

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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