FF:1340-24B8: Difference between revisions

Latest revision as of 18:58, 4 June 2020

Name:	stomach, neonate N03
Species:	Mouse (Mus musculus)
Library ID:	CNhs11193
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	stomach
dev stage	3 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		SAMD00005673

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11193		CAGE		DRX009096		DRR009970

Accession ID Mm9

Library id		BAM		CTSS
CNhs11193		DRZ001395		DRZ002778

Accession ID Mm10

Library id		BAM		CTSS
CNhs11193		DRZ012745		DRZ014128

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

CNhs11193

0	0
1	0
10	0
100	0
1000	0.234
1001	0.14
1002	0.444
1003	0.174
1004	0
1005	0.0549
1006	0.00158
1007	-0.00206
1008	0
1009	0.267
101	-0.0069
1010	0
1011	0
1012	0
1013	0.16
1014	0.432
1015	-0.00299
1016	0.0354
1017	0.371
1018	0.289
1019	0.104
102	0
1020	0
1021	0.00626
1022	0.148
1023	0
1024	0.0577
1025	0.797
1026	0
1027	0.0427
1028	0
1029	0.401
103	0.318
1030	0
1031	0.338
1032	0.169
1033	0.0238
1034	0.296
1035	0.0285
1036	0.0214
1037	0
1038	0.0588
1039	0.0124
104	0
1040	0.162
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: CNhs11193

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.13
MA0003.1	MA0003.1	0.266
MA0004.1	MA0004.1	0.158
MA0006.1	MA0006.1	0.0422
MA0007.1	MA0007.1	0.682
MA0009.1	MA0009.1	0.158
MA0014.1	MA0014.1	0.967
MA0017.1	MA0017.1	0.339
MA0018.2	MA0018.2	9.35163e-6
MA0019.1	MA0019.1	0.301
MA0024.1	MA0024.1	0.449
MA0025.1	MA0025.1	0.00658
MA0027.1	MA0027.1	0.0592
MA0028.1	MA0028.1	1.83924e-4
MA0029.1	MA0029.1	0.781
MA0030.1	MA0030.1	0.197
MA0031.1	MA0031.1	0.935
MA0035.2	MA0035.2	0.86
MA0038.1	MA0038.1	0.863
MA0039.2	MA0039.2	0.00219
MA0040.1	MA0040.1	0.604
MA0041.1	MA0041.1	0.191
MA0042.1	MA0042.1	0.287
MA0043.1	MA0043.1	2.68106e-4
MA0046.1	MA0046.1	1.17261e-16
MA0047.2	MA0047.2	1.07733e-6
MA0048.1	MA0048.1	0.747
MA0050.1	MA0050.1	0.212
MA0051.1	MA0051.1	0.0227
MA0052.1	MA0052.1	0.00912
MA0055.1	MA0055.1	0.409
MA0057.1	MA0057.1	0.0433
MA0058.1	MA0058.1	0.0121
MA0059.1	MA0059.1	0.142
MA0060.1	MA0060.1	0.0263
MA0061.1	MA0061.1	0.727
MA0062.2	MA0062.2	4.93369e-11
MA0065.2	MA0065.2	0.0821
MA0066.1	MA0066.1	0.171
MA0067.1	MA0067.1	0.157
MA0068.1	MA0068.1	0.0398
MA0069.1	MA0069.1	0.0234
MA0070.1	MA0070.1	0.872
MA0071.1	MA0071.1	0.0482
MA0072.1	MA0072.1	0.25
MA0073.1	MA0073.1	0.653
MA0074.1	MA0074.1	0.779
MA0076.1	MA0076.1	9.41325e-6
MA0077.1	MA0077.1	0.182
MA0078.1	MA0078.1	0.284
MA0079.2	MA0079.2	0.146
MA0080.2	MA0080.2	7.40013e-4
MA0081.1	MA0081.1	6.50169e-5
MA0083.1	MA0083.1	7.38539e-8
MA0084.1	MA0084.1	0.91
MA0087.1	MA0087.1	0.104
MA0088.1	MA0088.1	0.391
MA0090.1	MA0090.1	0.0125
MA0091.1	MA0091.1	0.439
MA0092.1	MA0092.1	0.0555
MA0093.1	MA0093.1	0.0894
MA0099.2	MA0099.2	7.86986e-6
MA0100.1	MA0100.1	0.00385
MA0101.1	MA0101.1	0.157
MA0102.2	MA0102.2	0.812
MA0103.1	MA0103.1	2.06468e-4
MA0104.2	MA0104.2	0.0513
MA0105.1	MA0105.1	0.426
MA0106.1	MA0106.1	0.0165
MA0107.1	MA0107.1	0.336
MA0108.2	MA0108.2	9.1602e-7
MA0111.1	MA0111.1	0.857
MA0112.2	MA0112.2	0.0053
MA0113.1	MA0113.1	0.525
MA0114.1	MA0114.1	0.0184
MA0115.1	MA0115.1	0.413
MA0116.1	MA0116.1	0.227
MA0117.1	MA0117.1	0.252
MA0119.1	MA0119.1	0.0744
MA0122.1	MA0122.1	0.0407
MA0124.1	MA0124.1	0.745
MA0125.1	MA0125.1	0.47
MA0131.1	MA0131.1	0.288
MA0135.1	MA0135.1	0.554
MA0136.1	MA0136.1	1.74657e-7
MA0137.2	MA0137.2	0.82
MA0138.2	MA0138.2	0.502
MA0139.1	MA0139.1	0.376
MA0140.1	MA0140.1	0.712
MA0141.1	MA0141.1	0.195
MA0142.1	MA0142.1	0.125
MA0143.1	MA0143.1	0.69
MA0144.1	MA0144.1	0.242
MA0145.1	MA0145.1	0.00513
MA0146.1	MA0146.1	0.389
MA0147.1	MA0147.1	0.0313
MA0148.1	MA0148.1	7.88988e-8
MA0149.1	MA0149.1	0.767
MA0150.1	MA0150.1	0.687
MA0152.1	MA0152.1	0.155
MA0153.1	MA0153.1	2.97328e-11
MA0154.1	MA0154.1	0.0427
MA0155.1	MA0155.1	0.384
MA0156.1	MA0156.1	6.96984e-6
MA0157.1	MA0157.1	0.742
MA0159.1	MA0159.1	0.892
MA0160.1	MA0160.1	0.0407
MA0162.1	MA0162.1	0.276
MA0163.1	MA0163.1	0.075
MA0164.1	MA0164.1	0.978
MA0258.1	MA0258.1	0.423
MA0259.1	MA0259.1	0.0861

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: CNhs11193

Novel motif	Logo	P-value
1	1	0.478
10	10	0.539
100	100	0.768
101	101	0.907
102	102	0.692
103	103	0.0568
104	104	0.929
105	105	0.867
106	106	0.00269
107	107	0.0074
108	108	0.674
109	109	0.202
11	11	0.876
110	110	0.513
111	111	0.596
112	112	0.278
113	113	0.473
114	114	0.448
115	115	0.891
116	116	0.449
117	117	0.519
118	118	0.233
119	119	0.156
12	12	0.614
120	120	0.739
121	121	0.543
122	122	0.207
123	123	0.429
124	124	0.745
125	125	0.819
126	126	0.114
127	127	0.737
128	128	0.00861
129	129	0.906
13	13	0.027
130	130	0.329
131	131	0.813
132	132	0.343
133	133	0.0555
134	134	0.788
135	135	0.894
136	136	0.783
137	137	0.292
138	138	0.00724
139	139	0.372
14	14	0.756
140	140	0.0354
141	141	0.823
142	142	0.32
143	143	0.0944
144	144	0.247
145	145	0.118
146	146	0.135
147	147	0.488
148	148	0.892
149	149	0.221
15	15	0.875
150	150	0.427
151	151	0.71
152	152	0.031
153	153	0.607
154	154	0.856
155	155	0.89
156	156	5.72562e-8
157	157	0.311
158	158	0.464
159	159	0.0806
160	160	0.0825
161	161	0.492
162	162	0.268
163	163	0.8
164	164	0.481
165	165	0.605
166	166	0.11
167	167	0.448
168	168	0.266
169	169	0.00854
17	17	0.0336
18	18	0.88
19	19	0.0255
2	2	0.174
20	20	0.266
21	21	0.924
22	22	0.241
23	23	0.283
24	24	0.475
25	25	0.373
26	26	0.00647
27	27	0.763
28	28	0.863
29	29	0.912
3	3	0.616
30	30	0.149
31	31	0.683
32	32	0.0357
33	33	0.989
34	34	0.97
35	35	0.445
36	36	0.309
37	37	0.142
38	38	0.787
39	39	0.0959
4	4	0.0683
40	40	0.869
41	41	0.213
42	42	0.58
43	43	0.169
44	44	0.777
45	45	0.355
46	46	0.315
47	47	0.562
48	48	0.885
49	49	0.342
5	5	0.288
50	50	0.574
51	51	0.411
52	52	0.0199
53	53	0.326
54	54	0.223
55	55	0.694
56	56	0.369
57	57	0.503
58	58	0.718
59	59	0.441
6	6	0.193
60	60	0.036
61	61	0.303
62	62	0.949
63	63	0.277
64	64	0.982
65	65	0.668
66	66	0.624
67	67	0.843
68	68	0.146
69	69	0.428
7	7	0.219
70	70	0.628
71	71	0.0742
72	72	0.928
73	73	0.203
74	74	0.297
75	75	0.87
76	76	0.102
77	77	0.00446
78	78	0.279
79	79	0.877
8	8	0.586
80	80	0.0592
81	81	0.874
82	82	0.353
83	83	0.527
84	84	0.941
85	85	0.23
86	86	0.583
87	87	0.354
88	88	0.151
89	89	0.381
9	9	0.181
90	90	0.909
91	91	0.528
92	92	0.19
93	93	0.399
94	94	0.533
95	95	0.673
96	96	0.7
97	97	0.243
98	98	0.934
99	99	0.0507

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: CNhs11193

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011498 mouse stomach, neonate N03 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)
0000311 (mouse neonate N3 sample)
0011498 (mouse stomach, neonate N03 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@SAMD00005673
+|accession_numbers=CAGE;DRX009096;DRR009970;DRZ001395;DRZ002778;DRZ012745;DRZ014128
+|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:0000311,FF:0011498
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr13:55932591..55932622,-!p1@Pitx1!1.93!101.15!Pitx1;;chr5:77543897..77543911,-!p2@Hopx!1.86!132.44!Hopx;;chr4:135129538..135129558,-!p1@Grhl3!1.81!94.41!Grhl3;;chr2:103143336..103143367,-!p1@Ehf!1.70!77.55!Ehf;;chr13:48758276..48758291,+!p1@Barx1!1.65!43.83!Barx1;;chr8:59799772..59799789,+!p1@Hand2!1.58!103.98!Hand2;;chr13:31650185..31650201,+!p1@Foxq1!1.57!121.11!Foxq1;;chr1:137155026..137155042,-!p1@Elf3!1.54!188.81!Elf3;;chr11:121380640..121380655,-!p1@Zfp750!1.50!50.03!Zfp750;;chr5:77543935..77543947,-!p4@Hopx!1.49!29.94!Hopx;;chr10:22539932..22539956,-!p1@Tcf21!1.48!75.25!Tcf21;;chr16:25801993..25802014,+!p1@Trp63!1.47!28.73!Trp63;;chr12:58646974..58647003,-!p1@Foxa1!1.44!35.06!Foxa1;;chr2:103143315..103143328,-!p2@Ehf!1.43!25.89!Ehf;;chr17:27865882..27865901,-!p1@Spdef!1.40!23.87!Spdef;;chr2:163332558..163332596,+!p2@Hnf4a!1.39!23.60!Hnf4a;;chr8:123608252..123608268,+!p1@Foxf1a!1.37!32.64!Foxf1a;;chr13:48758358..48758415,+!p2@Barx1!1.36!21.71!Barx1;;chr14:118636214..118636235,-!p1@Sox21!1.35!25.62!Sox21;;chr13:55937467..55937516,-!p3@Pitx1!1.34!20.90!Pitx1;;chr16:38294860..38294924,-!p1@Nr1i2!1.34!20.90!Nr1i2;;chr10:88969376..88969395,-!p1@Nr1h4!1.30!19.02!Nr1h4;;chr4:87452180..87452196,-!p3@Mllt3!1.29!36.01!Mllt3;;chr2:164228702..164228719,+!p1@Rbpjl!1.27!17.80!Rbpjl;;chr13:55932624..55932641,-!p2@Pitx1!1.27!17.67!Pitx1;;chr1:189821714..189821761,+!p1@Esrrg!1.26!31.42!Esrrg;;chr7:19608891..19608895,-!p1@Foxa3!1.26!22.12!Foxa3;;chr13:55937432..55937460,-!p4@Pitx1!1.26!16.99!Pitx1;;chr3:34548909..34548927,+!p1@Sox2!1.25!28.05!Sox2;;chr19:5560600..5560617,-!p1@Ovol1!1.22!18.75!Ovol1;;chr11:121380594..121380609,-!p2@Zfp750!1.18!24.14!Zfp750;;chr3:90046995..90047031,-!p2@Creb3l4!1.18!17.80!Creb3l4;;chr13:31717548..31717596,+!p1@Foxf2!1.11!23.87!Foxf2;;chr2:103264245..103264268,+!p2@Elf5!1.11!11.87!Elf5;;chr4:87452200..87452229,-!p2@Mllt3!1.09!24.01!Mllt3;;chr11:121380611..121380625,-!p3@Zfp750!1.08!13.49!Zfp750;;chr13:72766250..72766273,+!p1@Irx2!1.07!16.59!Irx2;;chr14:63864056..63864102,-!p1@Gata4!1.06!18.34!Gata4;;chr5:144951153..144951203,+!p1@Bhlha15!1.06!15.24!Bhlha15;;chr2:180069370..180069409,-!p1@Gata5!1.05!12.00!Gata5;;chr13:117099847..117099907,-!p1@Isl1!1.02!17.53!Isl1;;chr14:99697871..99697934,+!p1@Klf5!0.99!176.40!Klf5;;chr4:55545337..55545357,-!p1@Klf4!0.99!133.11!Klf4;;chr9:31720843..31720888,-!p1@Barx2!0.98!9.44!Barx2;;chr13:40829137..40829205,-!p1@Tfap2a!0.97!9.44!Tfap2a;;chr3:29911808..29911833,-!p8@Mecom!0.96!8.09!Mecom;;chr10:80555320..80555378,-!p1@Creb3l3!0.94!9.04!Creb3l3;;chr2:103252231..103252256,+!p4@Elf5!0.93!7.42!Elf5;;chr10:12810631..12810649,+!p1@Plagl1!0.92!198.66!Plagl1;;chr6:51382677..51382783,+!p1@Nfe2l3!0.92!19.29!Nfe2l3;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.91!21.04!Tfcp2l1;;chr3:30408603..30408668,-!p1@Mecom!0.91!16.86!Mecom;;chr12:57796615..57796687,+!p1@Pax9!0.90!6.88!Pax9;;chr7:123182248..123182264,-!p3@Sox6!0.88!8.09!Sox6;;chr11:96880072..96880079,+!p1@Sp6!0.88!6.61!Sp6;;chr2:77357622..77357704,-!p1@Zfp385b!0.87!18.07!Zfp385b;;chr15:102865131..102865151,+!p2@Hoxc4!0.87!7.42!Hoxc4;;chr11:94981424..94981439,+!p1@Dlx3!0.87!7.28!Dlx3;;chr12:25257265..25257294,+!p2@Grhl1!0.87!6.47!Grhl1;;chr3:34548946..34548972,+!p2@Sox2!0.86!7.01!Sox2;;chr2:172375081..172375105,+!p1@Tfap2c!0.86!6.20!Tfap2c;;chr15:102865088..102865107,+!p1@Hoxc4!0.85!8.23!Hoxc4;;chr4:46356509..46356527,+!p1@Foxe1!0.84!5.93!Foxe1;;chr2:147871627..147871641,-!p1@Foxa2!0.84!5.93!Foxa2;;chr8:26958093..26958148,-!p2@Ash2l!0.82!5.66!Ash2l;;chr13:31650026..31650045,+!p2@Foxq1!0.81!9.58!Foxq1;;chr2:103264213..103264233,+!p1@Elf5!0.81!5.53!Elf5;;chr7:123182318..123182332,-!p11@Sox6!0.81!5.53!Sox6;;chr14:118636238..118636257,-!p2@Sox21!0.81!5.39!Sox21;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.79!21.85!Ppp1r13l;;chr13:72766279..72766296,+!p2@Irx2!0.79!7.96!Irx2;;chr1:189821700..189821713,+!p4@Esrrg!0.78!4.99!Esrrg;;chr17:28409136..28409150,+!p3@Ppard!0.77!4.86!Ppard;;chr6:14851287..14851342,+!p1@Foxp2!0.75!16.72!Foxp2;;chr2:133377954..133377973,+!p1@Bmp2!0.75!16.05!Bmp2;;chr11:121381087..121381108,-!p4@Zfp750!0.75!4.59!Zfp750;;chr14:63890491..63890516,-!p2@Gata4!0.75!4.59!Gata4;;chr4:148178559..148178603,+!p1@Casz1!0.74!13.89!Casz1;;chr6:14851440..14851497,+!p2@Foxp2!0.74!11.87!Foxp2;;chr6:52163319..52163342,-!p1@Hoxa3!0.73!6.61!Hoxa3;;chr12:25257176..25257190,+!p3@Grhl1!0.73!4.99!Grhl1;;chr18:76219118..76219155,+!p1@Zbtb7c!0.72!7.96!Zbtb7c;;chr11:69468531..69468557,+!p1@Sox15!0.71!4.18!Sox15;;chr18:11052642..11052659,+!p1@Gata6!0.70!22.93!Gata6;;chr17:86087592..86087615,-!p1@Six2!0.70!4.05!Six2;;chr4:87452167..87452178,-!p8@Mllt3!0.70!4.05!Mllt3;;chr9:31720746..31720762,-!p4@Barx2!0.70!4.05!Barx2;;chr3:30408384..30408431,-!p4@Mecom!0.69!5.12!Mecom;;chr11:96143666..96143725,+!p1@Hoxb8!0.69!4.59!Hoxb8;;chr14:63890519..63890539,-!p3@Gata4!0.69!3.91!Gata4;;chr15:81977802..81977828,+!p2@Srebf2!0.68!37.22!Srebf2;;chr7:6649134..6649167,-!p1@Zim1!0.68!23.06!Zim1;;chr4:148275237..1482753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Mecom;;chr5:102094214..102094230,-!p1@Nkx6-1!0.15!0.40!Nkx6-1;;chr5:102094266..102094273,-!p3@Nkx6-1!0.15!0.40!Nkx6-1;;chr4:53792566..53792578,+!p1@Tal2!0.15!0.40!Tal2;;chr3:128918394..128918413,+!p5@Pitx2!0.15!0.40!Pitx2;;chr2:75543089..75543122,-!p3@Nfe2l2!0.15!0.40!Nfe2l2;;chr13:40826100..40826108,-!p10@Tfap2a!0.15!0.40!Tfap2a;;chr15:37163041..37163061,+!p5@Grhl2!0.15!0.40!Grhl2;;chr14:70477113..70477173,+!p1@Egr3!0.15!0.40!Egr3;;chr15:102839912..102839938,+!p5@Hoxc6!0.15!0.40!Hoxc6;;chr13:40829337..40829360,-!p5@Tfap2a!0.15!0.40!Tfap2a;;chr12:39510260..39510271,+!p10@Etv1!0.15!0.40!Etv1;;chr13:78339096..78339116,-!p12@Nr2f1!0.15!0.40!Nr2f1;;chr12:87702062..87702081,+!p4@Esrrb!0.15!0.40!Esrrb;;chr12:57792498..57792515,+!p2@Pax9!0.15!0.40!Pax9;;chr7:138697803..138697813,+!p1@Hmx2!0.15!0.40!Hmx2;;chr19:55972767..55972779,+!p20@Tcf7l2!0.15!0.40!Tcf7l2;;chr1:138857048..138857071,-!p2@Nr5a2!0.15!0.40!Nr5a2;;chr1:138857076..138857105,-!p1@Nr5a2!0.15!0.40!Nr5a2;;chr1:138857112..138857130,-!p7@Nr5a2!0.15!0.40!Nr5a2;;chr2:115890864..115890869,-!p14@Meis2!0.15!0.40!Meis2;;chr2:17976830..17976848,+!p12@Mllt10!0.15!0.40!Mllt10;;chr1:6720216..6720232,+!p1@St18!0.15!0.40!St18;;chr2:133378740..133378753,+!p2@Bmp2!0.15!0.40!Bmp2;;chr1:135557400..135557421,-!p4@Zbed6!0.15!0.40!Zbed6;;chr2:147872074..147872079,-!p4@Foxa2!0.15!0.40!Foxa2;;chr2:104966874..104966907,+!p2@Wt1!0.15!0.40!Wt1;;chr2:163372869..163372882,+!p3@Hnf4a!0.15!0.40!Hnf4a;;chr7:38557887..38557910,-!p5@Zfp536!0.15!0.40!Zfp536;;chr9:119893782..119893802,-!p1@Csrnp1!0.15!0.40!Csrnp1;;chr8:81551868..81551877,+!p13@Zfp827!0.15!0.40!Zfp827;;chr9:74709682..74709691,+!p3@Onecut1!0.15!0.40!Onecut1;;chr7:52960663..52960677,+!p6@Dbp!0.15!0.40!Dbp;;chr11:96213183..96213188,+!p@chr11:96213183..96213188,+!0.15!0.40!Hoxb2;;chr11:96143843..96143868,+!p3@Hoxb8!0.15!0.40!Hoxb8;;chr11:90249521..90249551,-!p3@Hlf!0.15!0.40!Hlf;;chr11:96145393..96145407,+!p3@Hoxb7!0.15!0.40!Hoxb7;;chr11:96143728..96143745,+!p4@Hoxb8!0.15!0.40!Hoxb8;;chr11:96976641..96976646,-!p1@Tbx21!0.15!0.40!Tbx21;;chr11:69468501..69468515,+!p2@Sox15!0.15!0.40!Sox15;;chr11:96160360..96160397,+!p3@Hoxb6!0.15!0.40!Hoxb6;;chr17:26978409..26978442,-!p1@Nkx2-5!0.15!0.40!Nkx2-5;;chr17:28409059..28409076,+!p6@Ppard!0.15!0.40!Ppard;;chr17:26978449..26978458,-!p3@Nkx2-5!0.15!0.40!Nkx2-5;;chr17:37139555..37139562,+!p6@Zfp57!0.15!0.40!Zfp57;;chr18:3281015..3281028,-!p18@Crem!0.15!0.40!Crem;;chr16:25802129..25802142,+!p3@Trp63!0.15!0.40!Trp63;;chrX:70656436..70656464,+!p1@Zfp92!0.15!0.40!Zfp92;;chr4:87679232..87679277,-!p1@Mllt3!0.14!14.03!Mllt3;;chr6:140572167..140572236,+!p2@Aebp2!0.14!12.00!Aebp2;;chr13:5860749..5860772,+!p2@Klf6!0.14!11.46!Klf6;;chr11:87881569..87881633,+!p2@Vezf1!0.14!9.04!Vezf1;;chr14:98568761..98568814,-!p2@Dach1!0.14!7.82!Dach1;;chr10:30522690..30522752,-!p2@Ncoa7!0.14!6.74!Ncoa7;;chr4:43575544..43575565,+!p2@Creb3!0.14!6.61!Creb3;;chr10:79389784..79389833,+!p1@Arid3a!0.14!5.80!Arid3a;;chr8:72498134..72498156,-!p7@Gatad2a!0.14!4.05!Gatad2a;;chr14:22319053..22319105,+!p2@Myst4!0.14!3.37!Myst4;;chrX:45807489..45807502,-!p2@Elf4!0.14!3.10!Elf4;;chr18:83080305..83080335,+!p2@Zfp516!0.14!3.10!Zfp516;;chr4:6917921..6917970,-!p2@Tox!0.14!2.70!Tox;;chr3:30993883..30993898,+!p2@Skil!0.14!2.56!Skil;;chr16:44173384..44173407,+!p2@Gm608!0.14!2.43!Gm608;;chr5:139060915..139060929,-!p3@Zfp68!0.14!2.29!Zfp68;;chr2:169458352..169458397,+!p3@Tshz2!0.14!2.29!Tshz2;;chr10:30375579..30375616,-!p3@Ncoa7!0.14!2.16!Ncoa7;;chr1:170361730..170361769,-!p7@Pbx1!0.14!2.02!Pbx1;;chr8:87324292..87324303,-!p4@Nfix!0.14!2.02!Nfix;;chr2:27532479..27532509,+!p3@Rxra!0.14!1.75!Rxra;;chr2:48805633..48805648,+!p5@Mbd5!0.14!1.62!Mbd5;;chrX:137135036..137135064,-!p4@Tsc22d3!0.14!1.62!Tsc22d3;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!0.14!1.48!Zbtb38;;chr13:37949830..37949861,+!p7@Rreb1!0.14!1.48!Rreb1;;chr12:85534720..85534751,-!p4@C130039O16Rik!0.14!1.48!C130039O16Rik;;chr15:40486754..40486771,+!p2@Zfpm2!0.14!1.35!Zfpm2;;chr11:98821858..98821907,+!p6@Rara!0.14!1.21!Rara;;chr11:52096750..52096772,-!p4@Tcf7!0.14!1.08!Tcf7;;chr10:80600725..80600737,+!p9@Zbtb7a!0.14!1.08!Zbtb7a;;chr3:5218546..5218561,+!p4@Zfhx4!0.14!1.08!Zfhx4;;chr4:135840552..135840567,+!p4@Zfp46!0.14!1.08!Zfp46;;chr5:122499831..122499891,-!p1@Cux2!0.14!1.08!Cux2;;chr1:135551736..135551746,-!p3@Zc3h11a!0.14!1.08!Zc3h11a;;chr2:151969288..151969294,+!p1@Tcf15!0.14!1.08!Tcf15;;chr2:173044357..173044377,-!p2@Zbp1!0.14!0.94!Zbp1;;chr3:94668075..94668087,+!p6@Pogz!0.14!0.94!Pogz;;chr11:87881881..87881887,+!p5@Vezf1!0.14!0.94!Vezf1;;chr4:135840623..135840632,+!p5@Zfp46!0.14!0.81!Zfp46;;chr8:87237711..87237727,-!p11@Nfix!0.14!0.81!Nfix;;chr9:63869890..63869908,-!p6@Smad6!0.14!0.81!Smad6;;chr18:65741911..65741929,+!p3@Zfp532!0.14!0.81!Zfp532;;chr15:81633224..81633235,+!p5@Tef!0.14!0.67!Tef;;chr4:128483422..128483430,-!p6@Zfp362!0.14!0.67!Zfp362;;chr3:133207214..133207228,-!p2@Tet2!0.14!0.67!Tet2;;chr11:98636508..98636524,-!p3@Nr1d1!0.14!0.67!Nr1d1;;chr2:115888250.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+|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:1340-24B8
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011498
+|is_a=EFO:0002091;;FF:0011498
+|is_obsolete=
+|library_id=CNhs11193
+|library_id_phase_based=2:CNhs11193
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1340
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1340
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N03.CNhs11193.1340-24B8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N03.CNhs11193.1340-24B8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N03.CNhs11193.1340-24B8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N03.CNhs11193.1340-24B8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N03.CNhs11193.1340-24B8.mm9.nobarcode.rdna.fa.gz
 |name=stomach, neonate N03
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11193,LSID746,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.166145981296717,0.0381647760831268,0,0,0.054943952156948,0.0739251985302683,0.289095742804311,0,0.145539302593421,0,0,0.748116461241074,0,0,0,0,0,0,0.178923742763653,0,0,0,0.103710933695783,0,0.054943952156948,0.223838914215041,0,0,0,0,0,0,0.178015418603739,0,0.054943952156948,0,0.103710933695783,0.0317325262880084,0.0279412881751789,0,-0.0253313185287924,0.678968202875331,0.487546532988642,0,0,0,0,0,0,0,0,0,0,0.103710933695783,0.103710933695783,0.304811546082787,0,0,0,0,0,0,0.11564583367827,0.103710933695783,0.187367671491058,0.0631505843538842,0.263113873595051,0.2878132532101,0.508552093188752,0.140991755988501,0.054943952156948,0.109359070739107,0.00378328378108539,0,0.223838914215041,0,0.0522700783117905,-0.0206659302949228,-0.177883506639338,-0.0238876426829594,0.027471976078474,0,0,0,0,0,-0.0642809461339438,0.148294624832039,0.0536665953466779,0.054943952156948,0,0,0,0
 |rna_box=24
 |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:2.75791368134;ZNF148:2.50765824203;CDC5L:1.98721053622;HMX1:1.88520358952;SRF:1.68515392161;MYBL2:1.63499706629;TBP:1.5860773489;FOXA2:1.57163942277;FOS_FOS{B,L1}_JUN{B,D}:1.53806527377;TFCP2:1.53658881891;RXRA_VDR{dimer}:1.49289924751;NKX3-1:1.44202740725;SNAI1..3:1.367480718;TP53:1.35976846302;PAX1,9:1.33548138611;TOPORS:1.31888266437;NKX3-2:1.30966595228;FOX{F1,F2,J1}:1.30422463973;PPARG:1.2616319153;EBF1:1.25745315168;IKZF2:1.20857297994;DBP:1.10629296588;FOX{I1,J2}:1.09292633478;TBX4,5:1.02132939787;ZIC1..3:1.01082450805;FOXP1:0.986083090283;NKX2-2,8:0.919483824454;NKX2-1,4:0.91900817206;TEAD1:0.9167554147;HNF1A:0.869509095657;FOX{D1,D2}:0.845600241823;XCPE1{core}:0.804379082917;SP1:0.738422233654;NFE2L2:0.737683862213;GCM1,2:0.718417516888;HAND1,2:0.682536452513;NR3C1:0.654180641995;FOSL2:0.652174568297;AR:0.651725190221;TLX1..3_NFIC{dimer}:0.645795226756;RBPJ:0.624045484042;ZNF238:0.620270399868;GTF2I:0.612583227027;TEF:0.602702813235;NFIX:0.60246788801;ZEB1:0.575790364508;BACH2:0.575130399155;NFE2:0.565458320182;HMGA1,2:0.562386085112;FOXL1:0.540655982153;MYOD1:0.540006392526;ZNF423:0.494523830765;HOX{A5,B5}:0.492187209805;TFAP4:0.482786526991;PAX5:0.481749306115;MAZ:0.480893917784;EN1,2:0.469753389445;HNF4A_NR2F1,2:0.463662808109;LEF1_TCF7_TCF7L1,2:0.443182399924;ADNP_IRX_SIX_ZHX:0.437851626899;POU5F1:0.433271277551;ZNF384:0.421745716447;GATA6:0.414032962338;GFI1B:0.405668127557;IKZF1:0.404386333699;GATA4:0.393708908673;ONECUT1,2:0.373755356174;CEBPA,B_DDIT3:0.361567539742;FOXM1:0.35479567228;TLX2:0.345949741085;STAT1,3:0.34036343497;POU6F1:0.330162020853;PITX1..3:0.320483353128;IRF7:0.299575945776;GZF1:0.297039037151;CRX:0.267866351916;GFI1:0.262754449066;NKX6-1,2:0.262635825313;E2F1..5:0.253365100694;TAL1_TCF{3,4,12}:0.23580321941;CDX1,2,4:0.235576916018;STAT2,4,6:0.216071633918;KLF4:0.212740345855;SMAD1..7,9:0.204668120657;EVI1:0.194647875469;BPTF:0.173141521988;NANOG:0.156261716187;HLF:0.122121122647;GTF2A1,2:0.120581345394;RREB1:0.0976634517931;GLI1..3:0.0964984752789;PAX8:0.0809249136472;TFAP2{A,C}:0.0674765205322;LMO2:0.054703360314;PAX4:0.0379653126934;FOXN1:0.0016346557002;TFAP2B:-0.030825720207;NKX2-3_NKX2-5:-0.0372349172053;MYFfamily:-0.0431048773643;ATF6:-0.0432956749747;PATZ1:-0.0453933421739;HOX{A4,D4}:-0.0489680173757;ESRRA:-0.0492081056561;HIC1:-0.0561301429339;NR6A1:-0.0624899373465;REST:-0.0681187565564;UFEwm:-0.0729674114244;PRDM1:-0.0770971083675;NFATC1..3:-0.0933686029511;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.11207603683;MAFB:-0.132690846013;IRF1,2:-0.152389576566;TFDP1:-0.161386057108;AIRE:-0.168700866744;BREu{core}:-0.186790675368;ESR1:-0.188668776374;NFY{A,B,C}:-0.205470147887;ETS1,2:-0.239300705159;SOX5:-0.243866612636;HIF1A:-0.24731997541;ATF2:-0.248521756116;STAT5{A,B}:-0.250439909777;TGIF1:-0.251877069449;EGR1..3:-0.273565003264;HSF1,2:-0.284137849787;ELF1,2,4:-0.298258741627;MED-1{core}:-0.307546383108;VSX1,2:-0.310162329361;DMAP1_NCOR{1,2}_SMARC:-0.310353420229;MZF1:-0.334350268727;POU3F1..4:-0.340875141638;ALX4:-0.351077896891;SPZ1:-0.37859384697;NFIL3:-0.401512880355;MTE{core}:-0.401588173394;LHX3,4:-0.402265938158;EP300:-0.434352338804;HOXA9_MEIS1:-0.451745517952;MTF1:-0.452369920183;FOXD3:-0.456770023518;CUX2:-0.456970473256;RFX2..5_RFXANK_RFXAP:-0.479067003605;NR5A1,2:-0.482524791829;POU1F1:-0.485211281337;ZBTB16:-0.490321958787;MEF2{A,B,C,D}:-0.499016096888;FOXO1,3,4:-0.513632913835;CREB1:-0.544476516274;SOX17:-0.559811070928;PBX1:-0.608321820124;PRRX1,2:-0.608817001494;ARID5B:-0.615521093231;HBP1_HMGB_SSRP1_UBTF:-0.630882881395;RFX1:-0.636188388788;ZNF143:-0.644691008184;NFKB1_REL_RELA:-0.671436513385;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.689446348528;MYB:-0.694276506612;POU2F1..3:-0.706052839106;ZFP161:-0.72315025725;PAX6:-0.725930692772;SOX2:-0.729922373755;SPI1:-0.733639753124;ZBTB6:-0.73975939663;AHR_ARNT_ARNT2:-0.740723538465;SOX{8,9,10}:-0.741501701959;SPIB:-0.77975668963;RUNX1..3:-0.782482155989;OCT4_SOX2{dimer}:-0.788992100524;NR1H4:-0.807281150583;JUN:-0.81919593595;ELK1,4_GABP{A,B1}:-0.823745401805;NHLH1,2:-0.826426301923;PDX1:-0.836197252057;NRF1:-0.894415546823;bHLH_family:-0.918752673198;ATF5_CREB3:-0.927181806196;SREBF1,2:-0.932555114677;FOXQ1:-1.10113119794;ATF4:-1.10585991264;RXR{A,B,G}:-1.13302249201;NANOG{mouse}:-1.14422401099;YY1:-1.34858455241;NFE2L1:-1.35050403053;RORA:-1.40099201871;PAX2:-1.47300158392;FOXP3:-1.47412128211;HES1:-1.49755150554;ALX1:-1.57400369274
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1340-24B8;search_select_hide=table117:1340-24B8
 }}

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FF:1340-24B8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:58, 4 June 2020

CNhs11193

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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