FF:33-1H6: Difference between revisions

Latest revision as of 19:09, 4 June 2020

Name:	stomach, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10503
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	stomach
dev stage	adult
sex	male
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		SAMD00005432

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10503		CAGE		DRX009090		DRR009964

Accession ID Mm9

Library id		BAM		CTSS
CNhs10503		DRZ001389		DRZ002772

Accession ID Mm10

Library id		BAM		CTSS
CNhs10503		DRZ012739		DRZ014122

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

CNhs10503

0	0
1	0
10	0
100	0
1000	0.749
1001	0.0714
1002	0.535
1003	0.275
1004	0
1005	0.0941
1006	-0.0864
1007	-0.115
1008	0
1009	0.101
101	-0.105
1010	0
1011	0
1012	0
1013	0.407
1014	0
1015	-0.187
1016	-0.2
1017	0.761
1018	0.683
1019	0
102	0
1020	0
1021	-0.0487
1022	0.549
1023	0
1024	0.0265
1025	0.587
1026	0
1027	0
1028	0
1029	0.316
103	0
1030	0
1031	-0.256
1032	0.285
1033	-0.0665
1034	0.291
1035	0
1036	-0.2
1037	0
1038	0.0249
1039	0.256
104	0
1040	0.035
1041	0.464

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: CNhs10503

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.114
MA0003.1	MA0003.1	0.194
MA0004.1	MA0004.1	0.961
MA0006.1	MA0006.1	0.242
MA0007.1	MA0007.1	0.233
MA0009.1	MA0009.1	0.116
MA0014.1	MA0014.1	0.78
MA0017.1	MA0017.1	0.00795
MA0018.2	MA0018.2	0.00343
MA0019.1	MA0019.1	0.981
MA0024.1	MA0024.1	0.0011
MA0025.1	MA0025.1	0.0778
MA0027.1	MA0027.1	0.643
MA0028.1	MA0028.1	0.224
MA0029.1	MA0029.1	0.556
MA0030.1	MA0030.1	0.971
MA0031.1	MA0031.1	0.56
MA0035.2	MA0035.2	0.39
MA0038.1	MA0038.1	0.15
MA0039.2	MA0039.2	0.146
MA0040.1	MA0040.1	0.176
MA0041.1	MA0041.1	0.233
MA0042.1	MA0042.1	0.374
MA0043.1	MA0043.1	6.3758e-5
MA0046.1	MA0046.1	2.335e-7
MA0047.2	MA0047.2	2.07395e-4
MA0048.1	MA0048.1	0.913
MA0050.1	MA0050.1	0.516
MA0051.1	MA0051.1	0.94
MA0052.1	MA0052.1	0.899
MA0055.1	MA0055.1	0.304
MA0057.1	MA0057.1	0.0389
MA0058.1	MA0058.1	0.822
MA0059.1	MA0059.1	0.488
MA0060.1	MA0060.1	8.98166e-9
MA0061.1	MA0061.1	0.55
MA0062.2	MA0062.2	0.0394
MA0065.2	MA0065.2	0.00208
MA0066.1	MA0066.1	0.117
MA0067.1	MA0067.1	0.515
MA0068.1	MA0068.1	0.0538
MA0069.1	MA0069.1	0.176
MA0070.1	MA0070.1	0.281
MA0071.1	MA0071.1	0.97
MA0072.1	MA0072.1	0.677
MA0073.1	MA0073.1	0.714
MA0074.1	MA0074.1	0.148
MA0076.1	MA0076.1	0.0729
MA0077.1	MA0077.1	0.537
MA0078.1	MA0078.1	0.947
MA0079.2	MA0079.2	0.378
MA0080.2	MA0080.2	0.697
MA0081.1	MA0081.1	0.0465
MA0083.1	MA0083.1	0.0324
MA0084.1	MA0084.1	0.548
MA0087.1	MA0087.1	0.628
MA0088.1	MA0088.1	0.246
MA0090.1	MA0090.1	0.288
MA0091.1	MA0091.1	0.347
MA0092.1	MA0092.1	0.207
MA0093.1	MA0093.1	0.88
MA0099.2	MA0099.2	5.95523e-5
MA0100.1	MA0100.1	0.301
MA0101.1	MA0101.1	0.547
MA0102.2	MA0102.2	0.188
MA0103.1	MA0103.1	1.14931e-4
MA0104.2	MA0104.2	0.825
MA0105.1	MA0105.1	0.0246
MA0106.1	MA0106.1	0.074
MA0107.1	MA0107.1	0.588
MA0108.2	MA0108.2	0.0167
MA0111.1	MA0111.1	0.255
MA0112.2	MA0112.2	5.02786e-6
MA0113.1	MA0113.1	0.662
MA0114.1	MA0114.1	0.014
MA0115.1	MA0115.1	0.201
MA0116.1	MA0116.1	0.0138
MA0117.1	MA0117.1	0.831
MA0119.1	MA0119.1	0.0667
MA0122.1	MA0122.1	0.681
MA0124.1	MA0124.1	0.214
MA0125.1	MA0125.1	0.0546
MA0131.1	MA0131.1	0.172
MA0135.1	MA0135.1	0.139
MA0136.1	MA0136.1	0.0406
MA0137.2	MA0137.2	0.652
MA0138.2	MA0138.2	0.076
MA0139.1	MA0139.1	0.0412
MA0140.1	MA0140.1	0.884
MA0141.1	MA0141.1	0.0762
MA0142.1	MA0142.1	0.873
MA0143.1	MA0143.1	0.479
MA0144.1	MA0144.1	0.516
MA0145.1	MA0145.1	0.00529
MA0146.1	MA0146.1	0.237
MA0147.1	MA0147.1	0.977
MA0148.1	MA0148.1	1.92768e-6
MA0149.1	MA0149.1	0.0145
MA0150.1	MA0150.1	0.262
MA0152.1	MA0152.1	0.249
MA0153.1	MA0153.1	4.29083e-6
MA0154.1	MA0154.1	0.00675
MA0155.1	MA0155.1	0.384
MA0156.1	MA0156.1	0.144
MA0157.1	MA0157.1	0.495
MA0159.1	MA0159.1	0.0147
MA0160.1	MA0160.1	0.492
MA0162.1	MA0162.1	0.21
MA0163.1	MA0163.1	0.00809
MA0164.1	MA0164.1	0.783
MA0258.1	MA0258.1	0.00122
MA0259.1	MA0259.1	0.668

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: CNhs10503

Novel motif	Logo	P-value
1	1	0.12
10	10	0.215
100	100	0.63
101	101	0.632
102	102	0.373
103	103	0.0369
104	104	0.703
105	105	0.425
106	106	0.0158
107	107	0.119
108	108	0.678
109	109	0.0796
11	11	0.191
110	110	0.214
111	111	0.0202
112	112	0.0726
113	113	0.966
114	114	0.112
115	115	0.499
116	116	0.497
117	117	0.31
118	118	0.898
119	119	0.0322
12	12	0.753
120	120	0.441
121	121	0.678
122	122	0.957
123	123	0.888
124	124	0.884
125	125	0.844
126	126	0.266
127	127	0.951
128	128	0.0333
129	129	0.382
13	13	0.0532
130	130	0.651
131	131	0.862
132	132	0.698
133	133	0.754
134	134	0.667
135	135	0.521
136	136	0.646
137	137	0.357
138	138	0.531
139	139	0.00513
14	14	0.653
140	140	0.00623
141	141	0.108
142	142	0.586
143	143	0.395
144	144	0.144
145	145	0.131
146	146	0.2
147	147	0.987
148	148	0.229
149	149	0.0952
15	15	0.139
150	150	0.398
151	151	0.339
152	152	0.0674
153	153	0.983
154	154	0.947
155	155	0.443
156	156	2.18241e-39
157	157	0.812
158	158	0.626
159	159	0.723
160	160	0.264
161	161	0.424
162	162	0.736
163	163	0.896
164	164	0.362
165	165	0.0796
166	166	0.882
167	167	0.761
168	168	0.301
169	169	0.00137
17	17	0.0263
18	18	0.812
19	19	0.105
2	2	0.477
20	20	0.669
21	21	0.902
22	22	0.227
23	23	0.437
24	24	0.416
25	25	0.87
26	26	0.103
27	27	0.38
28	28	0.583
29	29	0.409
3	3	0.207
30	30	0.408
31	31	0.28
32	32	0.0188
33	33	0.655
34	34	0.777
35	35	0.321
36	36	0.123
37	37	0.0415
38	38	0.745
39	39	0.278
4	4	0.0553
40	40	0.218
41	41	0.832
42	42	0.494
43	43	0.178
44	44	0.275
45	45	0.384
46	46	0.153
47	47	0.191
48	48	0.318
49	49	0.169
5	5	0.0596
50	50	0.767
51	51	0.58
52	52	0.103
53	53	0.684
54	54	0.481
55	55	0.424
56	56	0.299
57	57	0.509
58	58	0.278
59	59	0.12
6	6	0.786
60	60	0.0399
61	61	0.244
62	62	0.188
63	63	0.132
64	64	0.45
65	65	0.311
66	66	0.813
67	67	0.445
68	68	0.797
69	69	0.587
7	7	0.167
70	70	0.0103
71	71	0.0934
72	72	0.601
73	73	0.0931
74	74	0.588
75	75	0.141
76	76	0.609
77	77	0.0209
78	78	0.127
79	79	0.0987
8	8	0.0626
80	80	0.824
81	81	0.481
82	82	0.0144
83	83	0.306
84	84	0.465
85	85	0.0152
86	86	0.356
87	87	0.736
88	88	0.378
89	89	0.0271
9	9	0.465
90	90	0.532
91	91	0.149
92	92	0.133
93	93	0.366
94	94	0.969
95	95	0.383
96	96	0.0607
97	97	0.00327
98	98	0.26
99	99	0.162

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: CNhs10503

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011312 mouse stomach- adult 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)
0007023 (adult 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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011312 (mouse stomach- adult 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)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,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@SAMD00005432
+|accession_numbers=CAGE;DRX009090;DRR009964;DRZ001389;DRZ002772;DRZ012739;DRZ014122
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,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:0000998,FF:0000004,FF:0011312
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr1:137155026..137155042,-!p1@Elf3!2.28!1046.32!Elf3;;chr4:87452180..87452196,-!p3@Mllt3!2.07!221.48!Mllt3;;chr2:164228702..164228719,+!p1@Rbpjl!2.03!105.01!Rbpjl;;chr2:163332558..163332596,+!p2@Hnf4a!1.95!87.83!Hnf4a;;chr4:87452200..87452229,-!p2@Mllt3!1.90!162.29!Mllt3;;chr17:27865882..27865901,-!p1@Spdef!1.89!77.33!Spdef;;chr13:31650185..31650201,+!p1@Foxq1!1.85!231.98!Foxq1;;chr7:19608891..19608895,-!p1@Foxa3!1.82!83.06!Foxa3;;chr5:77543897..77543911,-!p2@Hopx!1.79!113.61!Hopx;;chr13:55932591..55932622,-!p1@Pitx1!1.77!69.69!Pitx1;;chr12:58646974..58647003,-!p1@Foxa1!1.74!70.65!Foxa1;;chr2:180069370..180069409,-!p1@Gata5!1.71!58.23!Gata5;;chr5:144951153..144951203,+!p1@Bhlha15!1.64!61.10!Bhlha15;;chr2:103143336..103143367,-!p1@Ehf!1.61!63.01!Ehf;;chr4:87452167..87452178,-!p8@Mllt3!1.58!37.23!Mllt3;;chr1:189821714..189821761,+!p1@Esrrg!1.57!65.87!Esrrg;;chr14:63864056..63864102,-!p1@Gata4!1.55!58.23!Gata4;;chr2:147871627..147871641,-!p1@Foxa2!1.55!34.37!Foxa2;;chr4:135129538..135129558,-!p1@Grhl3!1.53!49.64!Grhl3;;chr4:55545337..55545357,-!p1@Klf4!1.52!452.51!Klf4;;chr11:121380640..121380655,-!p1@Zfp750!1.51!51.55!Zfp750;;chr3:90046995..90047031,-!p2@Creb3l4!1.47!35.32!Creb3l4;;chr14:63890491..63890516,-!p2@Gata4!1.47!28.64!Gata4;;chr6:86619104..86619119,-!p1@Mxd1!1.45!210.98!Mxd1;;chr11:121380594..121380609,-!p2@Zfp750!1.41!42.01!Zfp750;;chr19:5560600..5560617,-!p1@Ovol1!1.41!29.59!Ovol1;;chr13:55937432..55937460,-!p4@Pitx1!1.41!24.82!Pitx1;;chr14:118636214..118636235,-!p1@Sox21!1.40!28.64!Sox21;;chr5:77543935..77543947,-!p4@Hopx!1.40!23.87!Hopx;;chr8:59799772..59799789,+!p1@Hand2!1.39!66.83!Hand2;;chr14:63864337..63864381,-!p6@Gata4!1.32!20.05!Gata4;;chr13:48758276..48758291,+!p1@Barx1!1.32!20.05!Barx1;;chr14:63890519..63890539,-!p3@Gata4!1.30!19.09!Gata4;;chr2:19367259..19367278,+!p1@Ptf1a!1.30!19.09!Ptf1a;;chr11:98636531..98636559,-!p1@Nr1d1!1.29!104.06!Nr1d1;;chr2:77357622..77357704,-!p1@Zfp385b!1.29!48.69!Zfp385b;;chr8:123608252..123608268,+!p1@Foxf1a!1.28!26.73!Foxf1a;;chr10:22539932..22539956,-!p1@Tcf21!1.26!44.87!Tcf21;;chr10:88969376..88969395,-!p1@Nr1h4!1.26!17.18!Nr1h4;;chr3:29911808..29911833,-!p8@Mecom!1.26!17.18!Mecom;;chr4:55545051..55545110,-!p2@Klf4!1.25!21.00!Klf4;;chr18:76219118..76219155,+!p1@Zbtb7c!1.24!28.64!Zbtb7c;;chr14:63890459..63890484,-!p4@Gata4!1.24!16.23!Gata4;;chr18:11052606..11052633,+!p4@Gata6!1.22!39.14!Gata6;;chr13:55932624..55932641,-!p2@Pitx1!1.21!15.27!Pitx1;;chr9:31720843..31720888,-!p1@Barx2!1.19!16.23!Barx2;;chr2:103143315..103143328,-!p2@Ehf!1.19!14.32!Ehf;;chr13:48758358..48758415,+!p2@Barx1!1.16!13.37!Barx1;;chr19:5447692..5447711,+!p2@Fosl1!1.16!13.37!Fosl1;;chr16:25801993..25802014,+!p1@Trp63!1.13!12.41!Trp63;;chr18:11052642..11052659,+!p1@Gata6!1.10!58.23!Gata6;;chr7:146768691..146768707,-!p1@Nkx6-2!1.10!11.46!Nkx6-2;;chr19:10315179..10315241,-!p1@Gm98!1.09!117.42!Gm98;;chr11:94981424..94981439,+!p1@Dlx3!1.08!12.41!Dlx3;;chr16:38294860..38294924,-!p1@Nr1i2!1.06!10.50!Nr1i2;;chr2:75542527..75542590,-!p1@Nfe2l2!1.04!897.39!Nfe2l2;;chr2:133377954..133377973,+!p1@Bmp2!1.04!32.46!Bmp2;;chr13:31717548..31717596,+!p1@Foxf2!1.04!20.05!Foxf2;;chr11:98636508..98636524,-!p3@Nr1d1!1.04!12.41!Nr1d1;;chr14:99697871..99697934,+!p1@Klf5!1.03!196.66!Klf5;;chr13:72766250..72766273,+!p1@Irx2!1.03!15.27!Irx2;;chr13:55937467..55937516,-!p3@Pitx1!1.02!9.55!Pitx1;;chr11:83664334..83664353,+!p2@Hnf1b!1.02!9.55!Hnf1b;;chr2:147872074..147872079,-!p4@Foxa2!1.02!9.55!Foxa2;;chr11:121380611..121380625,-!p3@Zfp750!1.01!11.46!Zfp750;;chr7:52960555..52960662,+!p1@Dbp!0.99!76.37!Dbp;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.99!25.78!Tfcp2l1;;chr13:117099847..117099907,-!p1@Isl1!0.98!16.23!Isl1;;chr14:63890545..63890560,-!p5@Gata4!0.98!8.59!Gata4;;chr4:87452236..87452249,-!p9@Mllt3!0.98!8.59!Mllt3;;chr4:133109285..133109308,+!p1@Nr0b2!0.98!8.59!Nr0b2;;chr17:28409136..28409150,+!p3@Ppard!0.98!8.59!Ppard;;chr6:15135215..15135244,+!p11@Foxp2!0.98!8.59!Foxp2;;chr4:148275237..148275311,+!p2@Casz1!0.95!33.41!Casz1;;chr2:147871948..147871977,-!p3@Foxa2!0.94!7.64!Foxa2;;chr2:152561980..152561997,+!p1@Id1!0.93!229.12!Id1;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.93!30.55!Ppp1r13l;;chr15:102865131..102865151,+!p2@Hoxc4!0.93!8.59!Hoxc4;;chr3:30408674..30408716,-!p2@Mecom!0.92!12.41!Mecom;;chr2:91864661..91864686,-!p1@Creb3l1!0.91!161.34!Creb3l1;;chr4:124805061..124805087,-!p1@Zc3h12a!0.89!21.96!Zc3h12a;;chr13:40829137..40829205,-!p1@Tfap2a!0.89!7.64!Tfap2a;;chr14:118635860..118635885,-!p3@Sox21!0.89!6.68!Sox21;;chr5:148081686..148081715,+!p1@Pdx1!0.89!6.68!Pdx1;;chr7:86956107..86956152,+!p@chr7:86956107..86956152,+!0.88!10.50!Mesp2;;chr6:115311030..115311065,+!p4@Pparg!0.87!9.55!Pparg;;chr14:22808697..22808715,-!p4@Zfp503!0.87!7.64!Zfp503;;chr17:15701286..15701323,-!p1@Prdm9!0.86!25.78!Prdm9;;chr3:34548946..34548972,+!p2@Sox2!0.84!6.68!Sox2;;chr3:3508024..3508069,+!p2@Hnf4g!0.83!5.73!Hnf4g;;chr2:172375081..172375105,+!p1@Tfap2c!0.83!5.73!Tfap2c;;chr6:97879817..97879857,+!p2@Mitf!0.83!5.73!Mitf;;chr18:76219161..76219176,+!p4@Zbtb7c!0.82!7.64!Zbtb7c;;chr15:81977802..81977828,+!p2@Srebf2!0.80!49.64!Srebf2;;chr7:148452314..148452329,-!p1@Irf7!0.80!40.10!Irf7;;chr2:115890469..115890485,-!p7@Meis2!0.79!8.59!Meis2;;chr15:81977766..81977789,+!p3@Srebf2!0.78!34.37!Srebf2;;chr2:173044380..173044432,-!p1@Zbp1!0.77!12.41!Zbp1;;chr3:34548909..34548927,+!p1@Sox2!0.77!8.59!Sox2;;chr13:31650026..31650045,+!p2@Foxq1!0.77!8.59!Foxq1;;chr15:102865088..102865107,+!p1@Hoxc4!0.77!6.68!Hoxc4;;chr18:36441119..36441158,+!p2@Pura!0.76!12.41!Pura;;chr17:15701263..15701277,-!p2@Prdm9!0.76!12.41!Prdm9;;chr12:25257141..25257173,+!p1@Grhl1!0.76!10.50!Grhl1;;chr13:72766234..72766243,+!p3@Irx2!0.76!4.77!Irx2;;chr13:48757894..48757908,+!p5@Barx1!0.76!4.77!Barx1;;chr19:5560570..5560582,-!p2@Ovol1!0.76!4.77!Ovol1;;chr19:5447886..5447905,+!p1@Fosl1!0.76!4.77!Fosl1;;chr2:180069423..180069434,-!p2@Gata5!0.76!4.77!Gata5;;chr4:115612528..115612533,-!p1@Dmbx1!0.76!4.77!Dmbx1;;chr11:83664365..83664383,+!p1@Hnf1b!0.76!4.77!Hnf1b;;chr12:86814833..86814846,+!p1@Fos!0.75!120.29!Fos;;chr5:65194752..65194769,+!p1@Klf3!0.74!166.11!Klf3;;chr18:75528166..75528170,+!p3@Smad7!0.74!12.41!Smad7;;chr8:73905344..73905381,-!p2@Nr2f6!0.74!11.46!Nr2f6;;chr11:5420954..5420969,+!p2@Xbp1!0.73!61.10!Xbp1;;chr1:194979315..194979359,+!p1@Irf6!0.73!29.59!Irf6;;chr17:32506357..32506377,-!p3@Wiz!0.72!9.55!Wiz;;chr8:107793688..107793736,+!p1@Hsf4!0.72!5.73!Hsf4;;chr12:25257114..25257131,+!p4@Grhl1!0.72!5.73!Grhl1;;chr7:77511234..77511302,-!p2@Nr2f2!0.71!30.55!Nr2f2;;chr7:4946990..4947016,-!p4@Zfp579!0.71!7.64!Zfp579;;chr6:115310872..115310899,+!p2@Pparg!0.71!7.64!Pparg;;chr12:25257176..25257190,+!p3@Grhl1!0.71!4.77!Grhl1;;chr16:55822241..55822258,-!p1@Nfkbiz!0.70!142.25!Nfkbiz;;chr10:44178521..44178557,-!p1@Prdm1!0.70!7.64!Prdm1;;chr2:25562263..25562314,+!p2@Bmyc!0.69!17.18!Bmyc;;chr2:56976543..56976558,-!p2@Nr4a2!0.69!9.55!Nr4a2;;chr8:72663049..72663061,-!p4@LOC100048268,p4@Rfxank!0.69!7.64!Rfxank;;chr15:37162834..37162849,+!p2@Grhl2!0.69!4.77!Grhl2;;chr4:55545152..55545194,-!p3@Klf4!0.69!4.77!Klf4;;chr3:30408603..30408668,-!p1@Mecom!0.68!9.55!Mecom;;chr6:146744595..146744613,+!p2@Arntl2!0.68!6.68!Arntl2;;chr1:87546583..87546595,+!p1@Sp100!0.68!5.73!Sp100;;chr5:115421065..115421088,-!p1@Hnf1a!0.68!3.82!Hnf1a;;chr5:148081722..148081744,+!p2@Pdx1!0.68!3.82!Pdx1;;chr11:5420655..5420659,+!p3@Xbp1!0.68!3.82!Xbp1;;chr11:96880072..96880079,+!p1@Sp6!0.68!3.82!Sp6;;chr11:69468531..69468557,+!p1@Sox15!0.68!3.82!Sox15;;chr3:89191265..89191276,-!p16@Zbtb7b!0.68!3.82!Zbtb7b;;chr3:90046983..90046994,-!p6@Creb3l4!0.68!3.82!Creb3l4;;chr15:102820964..102821006,+!p1@Hoxc8!0.68!3.82!Hoxc8;;chr12:25257265..25257294,+!p2@Grhl1!0.68!3.82!Grhl1;;chr12:57796615..57796687,+!p1@Pax9!0.68!3.82!Pax9;;chr13:55932739..55932756,-!p5@Pitx1!0.68!3.82!Pitx1;;chr14:118636238..118636257,-!p2@Sox21!0.68!3.82!Sox21;;chr13:72766279..72766296,+!p2@Irx2!0.67!5.73!Irx2;;chr8:94325321..94325366,-!p1@Irx3!0.66!9.55!Irx3;;chr11:98821937..98821987,+!p4@Rara!0.65!8.59!Rara;;chr5:24108047..24108106,-!p3@Smarcd3!0.65!6.68!Smarcd3;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.65!4.77!Hoxb2;;chr3:96002383..96002407,-!p4@Bola1!0.65!4.77!Bola1;;chr15:36937137..36937157,-!p2@Gm10193,p2@Zfp706!0.64!122.20!Zfp706;;chr6:115310968..115310980,+!p8@Pparg!0.64!3.82!Pparg;;chr6:51382677..51382783,+!p1@Nfe2l3!0.63!9.55!Nfe2l3;;chr5:65213356..65213412,+!p6@Klf3!0.63!7.64!Klf3;;chr7:52071956..52071978,-!p1@Atf5!0.62!123.15!Atf5;;chr8:87502608..87502623,-!p1@Junb!0.62!62.05!Junb;;chr17:48061381..48061399,-!p1@Foxp4!0.62!42.96!Foxp4;;chr8:124806048..124806094,+!p1@Zfpm1!0.62!34.37!Zfpm1;;chr7:4946900..4946921,-!p5@Zfp579!0.62!5.73!Zfp579;;chr7:52963269..52963305,+!p4@Dbp!0.62!4.77!Dbp;;chr7:77505617..77505632,-!p1@Nr2f2!0.61!170.89!Nr2f2;;chr7:20408047..20408125,-!p1@Bcl3!0.61!42.01!Bcl3;;chr16:92697560..92697592,-!p2@Runx1!0.61!22.91!Runx1;;chr6:72849280..72849297,-!p6@Kcmf1!0.61!6.68!Kcmf1;;chr16:30065419..30065437,+!p1@Hes1!0.60!191.89!Hes1;;chr17:48061584..48061601,-!p2@Foxp4!0.60!22.91!Foxp4;;chr1:193007123..193007139,-!p1@Atf3!0.60!20.05!Atf3;;chr7:4947646..4947696,-!p1@Zfp579!0.59!96.42!Zfp579;;chr10:80600749..80600766,+!p2@Zbtb7a!0.59!18.14!Zbtb7a;;chr12:113917014..113917034,+!p1@Zbtb42!0.59!5.73!Zbtb42;;chr10:107769219..107769226,+!p5@Pawr!0.59!3.82!Pawr;;chr6:52154386..52154407,-!p2@Hoxa5!0.59!3.82!Hoxa5;;chr6:99216375..99216395,-!p5@Foxp1!0.59!2.86!Foxp1;;chr6:52133827..52133854,-!p2@Hoxa3!0.59!2.86!Hoxa3;;chr17:28408632..28408682,+!p1@1810013A23Rik,p4@Ppard!0.59!2.86!Ppard;;chr15:102828658..102828678,+!p1@Hoxc6!0.59!2.86!Hoxc6;;chr15:102820946..102820961,+!p3@Hoxc8!0.59!2.86!Hoxc8;;chr13:40826961..40827001,-!p4@Tfap2a!0.59!2.86!Tfap2a;;chr13:48758328..48758335,+!p4@Barx1!0.59!2.86!Barx1;;chr15:102839948..102839975,+!p3@Hoxc6!0.59!2.86!Hoxc6;;chr11:98631631..98631667,-!p12@Nr1d1!0.59!2.86!Nr1d1;;chr11:98822081..98822092,+!p14@Rara!0.59!2.86!Rara;;chr2:180069640..180069660,-!p4@Gata5!0.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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:33-1H6
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011312
+|is_a=EFO:0002091;;FF:0011312
+|is_obsolete=
+|library_id=CNhs10503
+|library_id_phase_based=2:CNhs10503
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;33
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;33
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520adult.CNhs10503.33-1H6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520adult.CNhs10503.33-1H6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520adult.CNhs10503.33-1H6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520adult.CNhs10503.33-1H6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520adult.CNhs10503.33-1H6.mm9.nobarcode.rdna.fa.gz
 |name=stomach, adult
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10503,LSID648,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0277411960778935,0,0,0,0,0.058590869474023,0.023547805981419,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0.291073584836546,0,0,0,0,0,0,0.124505517007808,0,0.291073584836546,0,0,0,0.022574605776315,-0.0841329673068767,-0.595192290906871,0.227302422834934,0.491559481134245,0,0,0,0,0,0,0,0,0,0,0,0,0.225068037273106,0,0,0,0,0,0,0,0.587038450077457,0.761428119144596,0,0.121067201549465,-0.310650657339386,0.428947407306375,-0.0202569200098091,0,0,-0.0798688665684492,0,0.291073584836546,0,-0.0361530356473614,-0.22174669304237,-0.59591488074057,0.212241989996639,0,0,0,0,0,0,-0.265112817523478,-1.1713845300097,-0.269803002231399,0,0,0,0,0
 |rna_box=1
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=stomach
 |top_motifs=T:3.95107121191;RXRA_VDR{dimer}:3.33232660221;SNAI1..3:2.38075136347;NFE2L2:2.25028837356;HOX{A5,B5}:2.23719961499;IRF7:2.22801202517;TFCP2:2.2165960431;ZNF148:2.1894777403;HMX1:2.12212313416;HAND1,2:2.10527968346;MYOD1:2.03154838418;FOXA2:1.90864675757;FOXL1:1.87483675489;TP53:1.84264960061;PAX8:1.82568624089;CDX1,2,4:1.80851866862;BACH2:1.7851918981;TBP:1.7748177059;ARID5B:1.7515179993;ZEB1:1.71417960182;SRF:1.63005981534;ZIC1..3:1.61204371649;STAT5{A,B}:1.60769278784;FOS_FOS{B,L1}_JUN{B,D}:1.56025992746;FOX{F1,F2,J1}:1.51728378055;NR1H4:1.38525937719;NKX3-2:1.37272894331;TBX4,5:1.3570992215;FOSL2:1.32498778036;NFE2:1.31657296256;FOXO1,3,4:1.30632210475;NKX6-1,2:1.16738300738;EBF1:1.16605390347;NR5A1,2:1.12047770308;TOPORS:1.10604305929;FOXP1:1.02963769748;TFAP4:0.90450149091;ESRRA:0.878157965619;IKZF1:0.852613722998;CDC5L:0.844086423861;LMO2:0.815245757884;NFIX:0.786754811395;TLX1..3_NFIC{dimer}:0.65112355978;HNF1A:0.62899007063;TEF:0.626880314731;AR:0.624897980332;ESR1:0.619244148742;SMAD1..7,9:0.615321047581;FOX{D1,D2}:0.567827541557;CRX:0.505801979644;PAX1,9:0.485726475638;MYBL2:0.46318589152;PPARG:0.441895644278;MAFB:0.435286464644;HNF4A_NR2F1,2:0.411767333433;NKX3-1:0.397885531144;TLX2:0.374710318925;RBPJ:0.366265017019;LHX3,4:0.365671231449;GATA6:0.335042524952;POU6F1:0.333132061193;SPZ1:0.312979389635;POU5F1:0.305327525585;EN1,2:0.296508264659;ATF6:0.26880559433;FOXN1:0.249944129303;HLF:0.241103735376;XCPE1{core}:0.240171978172;FOX{I1,J2}:0.230731311897;IKZF2:0.227353604699;MYFfamily:0.222060906527;FOXM1:0.199594236123;UFEwm:0.17701086291;GCM1,2:0.147690026608;DBP:0.13518168812;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0931237617143;ZBTB6:0.0771414683617;bHLH_family:-0.0167510771623;CEBPA,B_DDIT3:-0.0187073044073;GTF2I:-0.0454090061678;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0554776889284;NR3C1:-0.0598529144263;ADNP_IRX_SIX_ZHX:-0.0699419394456;HOX{A4,D4}:-0.071313236457;NKX2-3_NKX2-5:-0.100029138681;ETS1,2:-0.126293537501;ZNF423:-0.13859068996;NKX2-2,8:-0.141013469096;TEAD1:-0.144590866651;SP1:-0.178461421728;PBX1:-0.180881741125;MEF2{A,B,C,D}:-0.19804888784;BPTF:-0.200101774278;IRF1,2:-0.233124687038;REST:-0.258066084499;KLF4:-0.29765935127;PITX1..3:-0.318264660738;NKX2-1,4:-0.345653092087;GTF2A1,2:-0.361743599103;STAT2,4,6:-0.378215990107;RUNX1..3:-0.385674281399;RFX2..5_RFXANK_RFXAP:-0.39420562335;PAX4:-0.400098219713;HMGA1,2:-0.401659068024;DMAP1_NCOR{1,2}_SMARC:-0.407232076685;PAX5:-0.411836139993;NANOG:-0.416597590873;STAT1,3:-0.439845929578;ELF1,2,4:-0.457603970332;NFKB1_REL_RELA:-0.459478936313;PRRX1,2:-0.469707145636;TFAP2{A,C}:-0.476664096622;HIC1:-0.517673458359;ZNF238:-0.530609243532;LEF1_TCF7_TCF7L1,2:-0.542555657238;POU1F1:-0.600425229473;EP300:-0.61702473628;RREB1:-0.637554828592;AIRE:-0.645397829562;PATZ1:-0.65416055826;ONECUT1,2:-0.684993354723;GZF1:-0.690478537246;ALX4:-0.695198966297;POU2F1..3:-0.712906353562;NR6A1:-0.715742909922;YY1:-0.717117173819;TAL1_TCF{3,4,12}:-0.721773244665;NFATC1..3:-0.745185711174;PRDM1:-0.76817765712;RFX1:-0.774834139372;TGIF1:-0.775236836512;MAZ:-0.780714333697;HIF1A:-0.781431605138;MTF1:-0.786888260754;ZBTB16:-0.801805156064;OCT4_SOX2{dimer}:-0.820202924458;FOXQ1:-0.823361582986;SPI1:-0.827443615954;MYB:-0.87339806376;VSX1,2:-0.908760819368;HOXA9_MEIS1:-0.915857076415;ATF5_CREB3:-0.94358746501;GFI1B:-0.950762659004;ELK1,4_GABP{A,B1}:-0.953111408052;NANOG{mouse}:-0.954868430335;GLI1..3:-0.95978701868;MED-1{core}:-0.970936923751;SREBF1,2:-0.974145578161;ALX1:-0.980562486276;NHLH1,2:-0.998917940313;ATF4:-1.0129586373;SPIB:-1.01440863082;PAX6:-1.0198808067;NFIL3:-1.03481970868;TFAP2B:-1.03925731863;SOX17:-1.03931595484;HBP1_HMGB_SSRP1_UBTF:-1.05415722198;ATF2:-1.07513090584;JUN:-1.08083908202;NFE2L1:-1.08371031419;BREu{core}:-1.14488722717;CREB1:-1.15783775534;EGR1..3:-1.24272896712;GATA4:-1.25511194619;SOX2:-1.27635903891;HSF1,2:-1.27868009296;EVI1:-1.29872379171;E2F1..5:-1.32856253419;PDX1:-1.35838394473;AHR_ARNT_ARNT2:-1.37480733266;HES1:-1.39657127764;CUX2:-1.48861951313;SOX5:-1.48889690099;GFI1:-1.54355243561;FOXD3:-1.56386868416;MZF1:-1.56553285252;RORA:-1.6060720145;ZNF143:-1.65587363755;ZFP161:-1.6649733068;POU3F1..4:-1.71081599513;NRF1:-1.84819259199;ZNF384:-1.91281202902;NFY{A,B,C}:-1.96432986565;PAX2:-2.01174996146;SOX{8,9,10}:-2.09124708055;FOXP3:-2.09627893747;MTE{core}:-2.20268273019;RXR{A,B,G}:-2.26758961046;TFDP1:-2.42990252583
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:33-1H6;search_select_hide=table117:33-1H6
 }}

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FF:33-1H6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:09, 4 June 2020

CNhs10503

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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