FF:718-18A9: Difference between revisions

Latest revision as of 19:19, 4 June 2020

Name:	stomach, neonate N07
Species:	Mouse (Mus musculus)
Library ID:	CNhs11210
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	stomach
dev stage	7 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		SAMD00005361

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11210		CAGE		DRX009097		DRR009971

Accession ID Mm9

Library id		BAM		CTSS
CNhs11210		DRZ001396		DRZ002779

Accession ID Mm10

Library id		BAM		CTSS
CNhs11210		DRZ012746		DRZ014129

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

CNhs11210

0	0
1	0.0345
10	0
100	0
1000	0.161
1001	0.0957
1002	0.323
1003	0.11
1004	0
1005	0.132
1006	0.0962
1007	0.0315
1008	0
1009	0.191
101	-0.0161
1010	0.0664
1011	0.0655
1012	0.0159
1013	0.179
1014	0.175
1015	-0.0407
1016	0.0762
1017	0.0962
1018	0.334
1019	0.0664
102	0
1020	0
1021	0
1022	0.281
1023	0
1024	0.138
1025	0.826
1026	0
1027	0.0352
1028	0.0345
1029	0.235
103	0.355
1030	0
1031	0.312
1032	0.188
1033	-0.0396
1034	0.284
1035	0.0664
1036	-0.0588
1037	0
1038	0.179
1039	0.112
104	0
1040	0.147
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: CNhs11210

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.858
MA0003.1	MA0003.1	0.133
MA0004.1	MA0004.1	0.255
MA0006.1	MA0006.1	0.0543
MA0007.1	MA0007.1	0.924
MA0009.1	MA0009.1	0.412
MA0014.1	MA0014.1	0.963
MA0017.1	MA0017.1	0.00145
MA0018.2	MA0018.2	1.05774e-4
MA0019.1	MA0019.1	0.601
MA0024.1	MA0024.1	0.0431
MA0025.1	MA0025.1	0.398
MA0027.1	MA0027.1	0.0632
MA0028.1	MA0028.1	8.95519e-6
MA0029.1	MA0029.1	0.887
MA0030.1	MA0030.1	5.05533e-4
MA0031.1	MA0031.1	0.0207
MA0035.2	MA0035.2	0.0995
MA0038.1	MA0038.1	0.989
MA0039.2	MA0039.2	0.00317
MA0040.1	MA0040.1	0.597
MA0041.1	MA0041.1	0.461
MA0042.1	MA0042.1	0.267
MA0043.1	MA0043.1	0.00189
MA0046.1	MA0046.1	1.3569e-56
MA0047.2	MA0047.2	1.59747e-12
MA0048.1	MA0048.1	0.47
MA0050.1	MA0050.1	0.0959
MA0051.1	MA0051.1	0.538
MA0052.1	MA0052.1	0.426
MA0055.1	MA0055.1	0.0432
MA0057.1	MA0057.1	0.0843
MA0058.1	MA0058.1	0.0381
MA0059.1	MA0059.1	0.049
MA0060.1	MA0060.1	0.0267
MA0061.1	MA0061.1	0.883
MA0062.2	MA0062.2	8.04541e-11
MA0065.2	MA0065.2	8.90416e-4
MA0066.1	MA0066.1	0.397
MA0067.1	MA0067.1	0.259
MA0068.1	MA0068.1	0.362
MA0069.1	MA0069.1	0.0421
MA0070.1	MA0070.1	0.657
MA0071.1	MA0071.1	0.32
MA0072.1	MA0072.1	0.703
MA0073.1	MA0073.1	0.847
MA0074.1	MA0074.1	0.899
MA0076.1	MA0076.1	2.0303e-6
MA0077.1	MA0077.1	0.27
MA0078.1	MA0078.1	0.153
MA0079.2	MA0079.2	0.021
MA0080.2	MA0080.2	0.107
MA0081.1	MA0081.1	0.00169
MA0083.1	MA0083.1	1.56913e-9
MA0084.1	MA0084.1	0.897
MA0087.1	MA0087.1	0.0756
MA0088.1	MA0088.1	0.479
MA0090.1	MA0090.1	0.011
MA0091.1	MA0091.1	0.209
MA0092.1	MA0092.1	0.0706
MA0093.1	MA0093.1	0.178
MA0099.2	MA0099.2	1.66115e-6
MA0100.1	MA0100.1	0.00319
MA0101.1	MA0101.1	0.375
MA0102.2	MA0102.2	0.613
MA0103.1	MA0103.1	0.00383
MA0104.2	MA0104.2	0.0288
MA0105.1	MA0105.1	0.857
MA0106.1	MA0106.1	0.187
MA0107.1	MA0107.1	0.787
MA0108.2	MA0108.2	2.39243e-9
MA0111.1	MA0111.1	0.929
MA0112.2	MA0112.2	0.0184
MA0113.1	MA0113.1	0.466
MA0114.1	MA0114.1	9.3969e-6
MA0115.1	MA0115.1	0.666
MA0116.1	MA0116.1	0.843
MA0117.1	MA0117.1	0.262
MA0119.1	MA0119.1	0.059
MA0122.1	MA0122.1	0.205
MA0124.1	MA0124.1	0.941
MA0125.1	MA0125.1	0.808
MA0131.1	MA0131.1	0.161
MA0135.1	MA0135.1	0.369
MA0136.1	MA0136.1	9.66533e-5
MA0137.2	MA0137.2	0.879
MA0138.2	MA0138.2	0.0714
MA0139.1	MA0139.1	0.452
MA0140.1	MA0140.1	0.891
MA0141.1	MA0141.1	0.302
MA0142.1	MA0142.1	0.0201
MA0143.1	MA0143.1	0.977
MA0144.1	MA0144.1	0.404
MA0145.1	MA0145.1	0.00107
MA0146.1	MA0146.1	0.421
MA0147.1	MA0147.1	0.0124
MA0148.1	MA0148.1	2.10633e-15
MA0149.1	MA0149.1	0.529
MA0150.1	MA0150.1	0.788
MA0152.1	MA0152.1	0.989
MA0153.1	MA0153.1	4.35342e-31
MA0154.1	MA0154.1	0.0854
MA0155.1	MA0155.1	0.338
MA0156.1	MA0156.1	4.24954e-4
MA0157.1	MA0157.1	0.0136
MA0159.1	MA0159.1	0.925
MA0160.1	MA0160.1	0.343
MA0162.1	MA0162.1	0.615
MA0163.1	MA0163.1	0.69
MA0164.1	MA0164.1	0.847
MA0258.1	MA0258.1	0.32
MA0259.1	MA0259.1	0.0351

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: CNhs11210

Novel motif	Logo	P-value
1	1	0.963
10	10	0.395
100	100	0.465
101	101	0.709
102	102	0.327
103	103	0.196
104	104	0.966
105	105	0.381
106	106	0.00101
107	107	0.00124
108	108	0.888
109	109	0.477
11	11	0.938
110	110	0.771
111	111	0.947
112	112	0.344
113	113	0.894
114	114	0.555
115	115	0.903
116	116	0.403
117	117	0.102
118	118	0.221
119	119	0.116
12	12	0.753
120	120	0.384
121	121	0.962
122	122	0.273
123	123	0.468
124	124	0.617
125	125	0.3
126	126	0.222
127	127	0.991
128	128	0.00419
129	129	0.823
13	13	0.0641
130	130	0.223
131	131	0.418
132	132	0.435
133	133	0.335
134	134	0.818
135	135	0.306
136	136	0.456
137	137	0.617
138	138	0.0195
139	139	0.415
14	14	0.427
140	140	0.152
141	141	0.69
142	142	0.692
143	143	0.015
144	144	0.221
145	145	0.305
146	146	0.0433
147	147	0.855
148	148	0.742
149	149	0.0974
15	15	0.977
150	150	0.379
151	151	0.59
152	152	0.00708
153	153	0.854
154	154	0.865
155	155	0.479
156	156	0.0116
157	157	0.048
158	158	0.227
159	159	0.498
160	160	0.146
161	161	0.838
162	162	0.174
163	163	0.399
164	164	0.799
165	165	0.778
166	166	0.0796
167	167	0.146
168	168	0.0931
169	169	0.00754
17	17	0.091
18	18	0.546
19	19	0.0278
2	2	0.0108
20	20	0.111
21	21	0.396
22	22	0.168
23	23	0.144
24	24	0.283
25	25	0.357
26	26	0.0386
27	27	0.554
28	28	0.854
29	29	0.326
3	3	0.846
30	30	0.112
31	31	0.548
32	32	0.035
33	33	0.963
34	34	0.623
35	35	0.285
36	36	0.14
37	37	0.344
38	38	0.711
39	39	0.0978
4	4	0.278
40	40	0.77
41	41	0.16
42	42	0.835
43	43	0.255
44	44	0.735
45	45	0.156
46	46	0.493
47	47	0.762
48	48	0.966
49	49	0.407
5	5	0.497
50	50	0.53
51	51	0.433
52	52	0.0139
53	53	0.237
54	54	0.247
55	55	0.995
56	56	0.442
57	57	0.837
58	58	0.684
59	59	0.376
6	6	0.53
60	60	0.0273
61	61	0.412
62	62	0.853
63	63	0.288
64	64	0.752
65	65	0.394
66	66	0.689
67	67	0.594
68	68	0.143
69	69	0.653
7	7	0.521
70	70	1
71	71	0.494
72	72	0.807
73	73	0.258
74	74	0.747
75	75	0.683
76	76	0.0273
77	77	0.0165
78	78	0.273
79	79	0.717
8	8	0.912
80	80	0.561
81	81	0.681
82	82	0.297
83	83	0.995
84	84	0.554
85	85	0.225
86	86	0.565
87	87	0.429
88	88	0.178
89	89	0.236
9	9	0.18
90	90	0.31
91	91	0.748
92	92	0.242
93	93	0.423
94	94	0.163
95	95	0.55
96	96	0.658
97	97	0.155
98	98	0.823
99	99	0.0386

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: CNhs11210

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011410 mouse stomach- neonate N07 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)
0000313 (mouse neonate N7 sample)
0011410 (mouse stomach- neonate N07 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship Analyst: Hideya Kawaji link to source data data
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005361
+|accession_numbers=CAGE;DRX009097;DRR009971;DRZ001396;DRZ002779;DRZ012746;DRZ014129
 |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=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr13:55932591..55932622,-!p1@Pitx1!1.81!75.05!Pitx1;;chr13:31650185..31650201,+!p1@Foxq1!1.72!174.40!Foxq1;;chr13:48758276..48758291,+!p1@Barx1!1.70!49.34!Barx1;;chr8:59799772..59799789,+!p1@Hand2!1.59!104.56!Hand2;;chr2:103143336..103143367,-!p1@Ehf!1.56!56.70!Ehf;;chr17:27865882..27865901,-!p1@Spdef!1.55!34.38!Spdef;;chr5:77543897..77543911,-!p2@Hopx!1.54!63.64!Hopx;;chr4:135129538..135129558,-!p1@Grhl3!1.54!50.83!Grhl3;;chr12:58646974..58647003,-!p1@Foxa1!1.54!44.22!Foxa1;;chr2:163332558..163332596,+!p2@Hnf4a!1.53!32.90!Hnf4a;;chr8:123608252..123608268,+!p1@Foxf1a!1.51!45.96!Foxf1a;;chr16:25801993..25802014,+!p1@Trp63!1.50!30.75!Trp63;;chr10:22539932..22539956,-!p1@Tcf21!1.49!78.11!Tcf21;;chr1:137155026..137155042,-!p1@Elf3!1.47!158.20!Elf3;;chr7:19608891..19608895,-!p1@Foxa3!1.44!34.55!Foxa3;;chr13:48758358..48758415,+!p2@Barx1!1.44!26.61!Barx1;;chr11:121380640..121380655,-!p1@Zfp750!1.42!41.16!Zfp750;;chr16:38294860..38294924,-!p1@Nr1i2!1.40!24.22!Nr1i2;;chr10:88969376..88969395,-!p1@Nr1h4!1.34!20.66!Nr1h4;;chr13:31717548..31717596,+!p1@Foxf2!1.31!37.86!Foxf2;;chr14:63864056..63864102,-!p1@Gata4!1.31!33.06!Gata4;;chr3:90046995..90047031,-!p2@Creb3l4!1.31!24.47!Creb3l4;;chr1:189821714..189821761,+!p1@Esrrg!1.29!34.30!Esrrg;;chr13:55937467..55937516,-!p3@Pitx1!1.29!18.35!Pitx1;;chr10:80555320..80555378,-!p1@Creb3l3!1.27!20.58!Creb3l3;;chr2:103143315..103143328,-!p2@Ehf!1.25!16.86!Ehf;;chr14:118636214..118636235,-!p1@Sox21!1.24!19.59!Sox21;;chr2:164228702..164228719,+!p1@Rbpjl!1.22!15.54!Rbpjl;;chr5:77543935..77543947,-!p4@Hopx!1.21!15.13!Hopx;;chr4:87452180..87452196,-!p3@Mllt3!1.20!29.01!Mllt3;;chr13:55932624..55932641,-!p2@Pitx1!1.15!13.22!Pitx1;;chr13:55937432..55937460,-!p4@Pitx1!1.15!13.06!Pitx1;;chr2:180069370..180069409,-!p1@Gata5!1.14!15.21!Gata5;;chr13:117099847..117099907,-!p1@Isl1!1.13!23.06!Isl1;;chr4:55545337..55545357,-!p1@Klf4!1.12!180.68!Klf4;;chr4:87452200..87452229,-!p2@Mllt3!1.11!25.29!Mllt3;;chr14:99697871..99697934,+!p1@Klf5!1.10!229.53!Klf5;;chr11:121380594..121380609,-!p2@Zfp750!1.08!19.09!Zfp750;;chr3:34548909..34548927,+!p1@Sox2!1.08!18.76!Sox2;;chr1:173144144..173144176,+!p1@Nr1i3!1.03!9.67!Nr1i3;;chr13:72766250..72766273,+!p1@Irx2!1.02!14.63!Irx2;;chr19:5560600..5560617,-!p1@Ovol1!1.02!11.74!Ovol1;;chr11:121380611..121380625,-!p3@Zfp750!1.01!11.32!Zfp750;;chr5:144951153..144951203,+!p1@Bhlha15!1.00!13.31!Bhlha15;;chr2:147871627..147871641,-!p1@Foxa2!0.99!8.68!Foxa2;;chr3:29911808..29911833,-!p8@Mecom!0.98!8.51!Mecom;;chr2:133377954..133377973,+!p1@Bmp2!0.97!27.36!Bmp2;;chr2:103264245..103264268,+!p2@Elf5!0.96!8.02!Elf5;;chr6:51382677..51382783,+!p1@Nfe2l3!0.95!20.58!Nfe2l3;;chr18:11052642..11052659,+!p1@Gata6!0.94!40.00!Gata6;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.94!23.06!Tfcp2l1;;chr2:77357622..77357704,-!p1@Zfp385b!0.93!20.91!Zfp385b;;chr2:163372884..163372904,+!p1@Hnf4a!0.93!7.60!Hnf4a;;chr13:31650026..31650045,+!p2@Foxq1!0.92!12.56!Foxq1;;chr9:31720843..31720888,-!p1@Barx2!0.91!8.02!Barx2;;chr17:86087592..86087615,-!p1@Six2!0.89!6.69!Six2;;chr18:76219118..76219155,+!p1@Zbtb7c!0.88!12.07!Zbtb7c;;chr8:26958093..26958148,-!p2@Ash2l!0.88!6.61!Ash2l;;chr14:63890491..63890516,-!p2@Gata4!0.86!6.28!Gata4;;chr15:102865131..102865151,+!p2@Hoxc4!0.83!6.61!Hoxc4;;chr3:34548946..34548972,+!p2@Sox2!0.83!6.45!Sox2;;chr11:96880072..96880079,+!p1@Sp6!0.82!5.62!Sp6;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.81!22.73!Ppp1r13l;;chr13:40829137..40829205,-!p1@Tfap2a!0.81!6.20!Tfap2a;;chr7:108966820..108966835,+!p1@Phox2a!0.81!5.46!Phox2a;;chr6:86619104..86619119,-!p1@Mxd1!0.80!47.03!Mxd1;;chr4:148178559..148178603,+!p1@Casz1!0.80!16.45!Casz1;;chr1:173144100..173144138,+!p2@Nr1i3!0.80!5.29!Nr1i3;;chr15:102865088..102865107,+!p1@Hoxc4!0.79!7.03!Hoxc4;;chr11:94981424..94981439,+!p1@Dlx3!0.79!6.03!Dlx3;;chr14:118636238..118636257,-!p2@Sox21!0.79!5.21!Sox21;;chr1:189821700..189821713,+!p4@Esrrg!0.79!5.12!Esrrg;;chr11:90249521..90249551,-!p3@Hlf!0.79!5.12!Hlf;;chr9:74709695..74709722,+!p1@Onecut1!0.78!5.04!Onecut1;;chr12:25257265..25257294,+!p2@Grhl1!0.78!4.96!Grhl1;;chr2:172375081..172375105,+!p1@Tfap2c!0.78!4.96!Tfap2c;;chr1:170361991..170362015,-!p6@Pbx1!0.76!11.41!Pbx1;;chr15:85566184..85566238,+!p1@Ppara!0.76!7.36!Ppara;;chr13:72766279..72766296,+!p2@Irx2!0.76!7.27!Irx2;;chr14:63890519..63890539,-!p3@Gata4!0.76!4.79!Gata4;;chr4:148275237..148275311,+!p2@Casz1!0.75!20.66!Casz1;;chr5:135582751..135582788,+!p1@Mlxipl!0.75!20.17!Mlxipl;;chr10:88996336..88996380,-!p2@Nr1h4!0.75!5.87!Nr1h4;;chr7:123182248..123182264,-!p3@Sox6!0.75!5.62!Sox6;;chr3:3508024..3508069,+!p2@Hnf4g!0.75!4.63!Hnf4g;;chr14:63890545..63890560,-!p5@Gata4!0.75!4.63!Gata4;;chr10:12810631..12810649,+!p1@Plagl1!0.74!130.51!Plagl1;;chr4:154010918..154010931,-!p1@Prdm16!0.74!14.38!Prdm16;;chr11:121381087..121381108,-!p4@Zfp750!0.74!4.55!Zfp750;;chr11:69468531..69468557,+!p1@Sox15!0.74!4.46!Sox15;;chr14:118635860..118635885,-!p3@Sox21!0.74!4.46!Sox21;;chr3:30408384..30408431,-!p4@Mecom!0.73!5.62!Mecom;;chr10:88996295..88996335,-!p3@Nr1h4!0.73!5.29!Nr1h4;;chr19:10315179..10315241,-!p1@Gm98!0.72!49.43!Gm98;;chr15:81977802..81977828,+!p2@Srebf2!0.72!40.83!Srebf2;;chr1:194979315..194979359,+!p1@Irf6!0.72!28.76!Irf6;;chr12:39510206..39510249,+!p3@Etv1!0.72!4.30!Etv1;;chr14:63864337..63864381,-!p6@Gata4!0.72!4.22!Gata4;;chr13:40826961..40827001,-!p4@Tfap2a!0.72!4.22!Tfap2a;;chr2:103252231..103252256,+!p4@Elf5!0.71!4.13!Elf5;;chr6:14851440..14851497,+!p2@Foxp2!0.70!10.83!Foxp2;;chr7:123182318..123182332,-!p11@Sox6!0.70!3.97!Sox6;;chr2:147871948..147871977,-!p3@Foxa2!0.70!3.97!Foxa2;;chr14:63890459..63890484,-!p4@Gata4!0.69!3.88!Gata4;;chr6:115311030..115311065,+!p4@Pparg!0.68!5.79!Pparg;;chr13:48757894..48757908,+!p5@Barx1!0.68!3.80!Barx1;;chr6:14851287..14851342,+!p1@Foxp2!0.67!13.64!Foxp2;;chr18:76219161..76219176,+!p4@Zbtb7c!0.67!5.12!Zbtb7c;;chr15:85602655..85602680,+!p5@Ppara!0.67!3.72!Ppara;;chr13:31717597..31717613,+!p2@Foxf2!0.67!3.72!Foxf2;;chr9:43013917..43013968,-!p1@Pou2f3!0.67!3.64!Pou2f3;;chr4:133109285..133109308,+!p1@Nr0b2!0.67!3.64!Nr0b2;;chr15:102865048..102865073,+!p3@Hoxc4!0.66!4.71!Hoxc4;;chr3:90046983..90046994,-!p6@Creb3l4!0.66!3.55!Creb3l4;;chr15:102087880..102087927,-!p2@Rarg!0.65!8.84!Rarg;;chr10:126778916..126778974,-!p1@Gli1!0.65!8.51!Gli1;;chr11:83664365..83664383,+!p1@Hnf1b!0.65!3.47!Hnf1b;;chr3:94176733..94176794,+!p1@Rorc!0.64!30.50!Rorc;;chr18:11052606..11052633,+!p4@Gata6!0.64!9.59!Gata6;;chr3:30408603..30408668,-!p1@Mecom!0.64!8.60!Mecom;;chr12:25257141..25257173,+!p1@Grhl1!0.64!7.69!Grhl1;;chr3:30408674..30408716,-!p2@Mecom!0.64!6.03!Mecom;;chr1:194979361..194979373,+!p2@Irf6!0.64!4.79!Irf6;;chr5:67490284..67490302,-!p1@Phox2b!0.64!3.39!Phox2b;;chr2:91864661..91864686,-!p1@Creb3l1!0.63!84.55!Creb3l1;;chr11:96143666..96143725,+!p1@Hoxb8!0.63!3.80!Hoxb8;;chr4:46356509..46356527,+!p1@Foxe1!0.63!3.31!Foxe1;;chr12:57796615..57796687,+!p1@Pax9!0.63!3.22!Pax9;;chr6:99470943..99471024,-!p3@Foxp1!0.62!35.95!Foxp1;;chr8:94881733..94881790,+!p1@Irx5!0.62!6.86!Irx5;;chr7:38554763..38554780,-!p1@Zfp536!0.62!6.28!Zfp536;;chr10:44178521..44178557,-!p1@Prdm1!0.62!6.20!Prdm1;;chr11:83664334..83664353,+!p2@Hnf1b!0.62!3.14!Hnf1b;;chr13:48758431..48758443,+!p3@Barx1!0.62!3.14!Barx1;;chr19:5560570..5560582,-!p2@Ovol1!0.62!3.14!Ovol1;;chr4:87452167..87452178,-!p8@Mllt3!0.62!3.14!Mllt3;;chr9:71743854..71743909,-!p1@Tcf12!0.61!29.26!Tcf12;;chr12:39507680..39507715,+!p2@Etv1!0.61!6.69!Etv1;;chr11:100800641..100800669,-!p3@Stat3!0.61!5.87!Stat3;;chr6:52163319..52163342,-!p1@Hoxa3!0.61!4.79!Hoxa3;;chr6:52141694..52141715,-!p1@Hoxa4!0.61!4.13!Hoxa4;;chr6:97879817..97879857,+!p2@Mitf!0.61!3.06!Mitf;;chr4:124805061..124805087,-!p1@Zc3h12a!0.60!10.66!Zc3h12a;;chr2:173044380..173044432,-!p1@Zbp1!0.60!8.18!Zbp1;;chr15:37162796..37162828,+!p1@Grhl2!0.60!5.46!Grhl2;;chr18:64499706..64499721,+!p2@Onecut2!0.60!4.55!Onecut2;;chr15:85566537..85566552,+!p2@Ppara!0.60!2.98!Ppara;;chr2:104966766..104966786,+!p1@Wt1!0.59!4.96!Wt1;;chr4:55545051..55545110,-!p2@Klf4!0.59!3.80!Klf4;;chr15:102820964..102821006,+!p1@Hoxc8!0.59!2.89!Hoxc8;;chr11:85646303..85646329,+!p1@Tbx2!0.58!22.32!Tbx2;;chr12:25257176..25257190,+!p3@Grhl1!0.58!3.22!Grhl1;;chr17:28409136..28409150,+!p3@Ppard!0.58!2.81!Ppard;;chr11:78200071..78200100,-!p1@Foxn1!0.58!2.81!Foxn1;;chr2:103264213..103264233,+!p1@Elf5!0.58!2.81!Elf5;;chr18:64499674..64499696,+!p1@Onecut2!0.57!5.29!Onecut2;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.57!5.12!Hoxb2;;chr14:22808697..22808715,-!p4@Zfp503!0.57!3.31!Zfp503;;chr13:55932739..55932756,-!p5@Pitx1!0.57!2.73!Pitx1;;chr6:15135215..15135244,+!p11@Foxp2!0.57!2.73!Foxp2;;chr5:115421065..115421088,-!p1@Hnf1a!0.57!2.73!Hnf1a;;chr9:31720746..31720762,-!p4@Barx2!0.57!2.73!Barx2;;chr7:77511234..77511302,-!p2@Nr2f2!0.56!21.41!Nr2f2;;chr15:78994907..78994926,-!p1@Sox10!0.56!7.93!Sox10;;chr6:115310872..115310899,+!p2@Pparg!0.56!5.12!Pparg;;chr6:52114821..52114828,-!p1@Hoxa2!0.56!4.38!Hoxa2;;chr10:88145766..88145770,-!p1@Spic!0.56!3.72!Spic;;chr16:92697560..92697592,-!p2@Runx1!0.55!20.00!Runx1;;chr7:6649134..6649167,-!p1@Zim1!0.55!17.11!Zim1;;chr4:55545152..55545194,-!p3@Klf4!0.55!3.14!Klf4;;chr19:43686789..43686811,+!p1@Nkx2-3!0.55!2.56!Nkx2-3;;chr11:18918917..18918944,-!p1@Meis1!0.54!40.58!Meis1;;chr15:101097270..101097290,+!p1@Nr4a1!0.54!32.15!Nr4a1;;chr7:52960555..52960662,+!p1@Dbp!0.54!26.45!Dbp;;chr18:84255841..84255883,-!p1@Tshz1!0.54!21.82!Tshz1;;chr2:9800207..9800234,-!p1@Gata3!0.54!9.01!Gata3;;chr6:52154414..52154462,-!p1@Hoxa5!0.54!3.72!Hoxa5;;chr15:81977766..81977789,+!p3@Srebf2!0.53!18.60!Srebf2;;chr17:56970339..56970428,-!p1@Rfx2!0.53!9.09!Rfx2;;chr8:87425854..87425891,+!p1@Klf1!0.53!2.40!Klf1;;chr6:52133827..52133854,-!p2@Hoxa3!0.53!2.40!Hoxa3;;chr13:48758328..48758335,+!p4@Barx1!0.53!2.40!Barx1;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.52!3.31!Hoxb2;;chr14:22807083..22807104,-!p1@Zfp503!0.51!51.08!Zfp503;;chr11:18918959..18918976,-!p2@Meis1!0.51!39.01!Meis1;;chr18:69504195..69504213,+!p4@Tcf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13!0.25!4.71!Sox13;;chr12:85534778..85534812,-!p3@C130039O16Rik!0.25!4.05!C130039O16Rik;;chr7:119822828..119822839,+!p4@Tead1!0.25!3.88!Tead1;;chr8:92872242..92872285,-!p1@Tox3!0.25!3.39!Tox3;;chr1:170361826..170361844,-!p9@Pbx1!0.25!2.81!Pbx1;;chr2:91077034..91077078,-!p2@Ddb2!0.25!2.81!Ddb2;;chr17:87153440..87153451,+!p4@Epas1!0.25!2.48!Epas1;;chr9:63869729..63869749,-!p4@Smad6!0.25!2.40!Smad6;;chr2:181327403..181327432,-!p3@Znf512b!0.25!2.31!Znf512b;;chr14:56443698..56443726,+!p2@Nfatc4!0.25!2.23!Nfatc4;;chr5:3648045..3648074,-!p2@Gatad1!0.25!1.90!Gatad1;;chr9:96619968..96619983,-!p6@Zbtb38!0.25!1.90!Zbtb38;;chr2:168032516..168032525,-!p5@Adnp!0.25!1.74!Adnp;;chr16:92697354..92697362,-!p3@Runx1!0.25!1.65!Runx1;;chr8:87237711..87237727,-!p11@Nfix!0.25!1.32!Nfix;;chr17:71200967..71200983,-!p8@Tgif1!0.25!1.24!Tgif1;;chr1:170361695..170361722,-!p12@Pbx1!0.25!1.24!Pbx1;;chr4:84321300..84321315,-!p2@Bnc2!0.25!1.16!Bnc2;;chr3:29912058..29912071,-!p6@Mecom!0.25!0.99!Mecom;;chr6:47998498..47998527,-!p1@Zfp777!0.24!25.62!Zfp777;;chr8:87502608..87502623,-!p1@Junb!0.24!25.13!Junb;;chr10:80813050..80813114,-!p2@Hmg20b!0.24!16.45!Hmg20b;;chr16:14705925..14705951,+!p1@Snai2!0.24!10.41!Snai2;;chr6:133985993..133986029,+!p2@Etv6!0.24!9.42!Etv6;;chr16:17233653..17233683,+!p1@Hic2!0.24!9.26!Hic2;;chr2:152758901..152758925,-!p1@Foxs1!0.24!6.20!Foxs1;;chr14:22807107..22807119,-!p2@Zfp503!0.24!6.12!Zfp503;;chr4:62626594..62626651,+!p1@Zfp618!0.24!5.21!Zfp618;;chr18:69504123..69504155,+!p5@Tcf4!0.24!4.96!Tcf4;;chr10:30523091..30523182,-!p4@Ncoa7!0.24!4.71!Ncoa7;;chr10:126726021..126726053,-!p4@Mbd6!0.24!4.63!Mbd6;;chr4:114732112..114732158,+!p1@Tal1!0.24!2.64!Tal1;;chr13:5860872..5860883,+!p3@Klf6!0.24!2.31!Klf6;;chr6:146744563..146744594,+!p1@Arntl2!0.24!2.07!Arntl2;;chr13:37870253..37870272,+!p13@Rreb1!0.24!1.41!Rreb1;;chr1:170361678..170361689,-!p13@Pbx1!0.24!1.07!Pbx1;;chr1:138857112..138857130,-!p7@Nr5a2!0.24!0.74!Nr5a2;;chr15:103082088..103082136,-!p2@Nfe2!0.24!0.74!Nfe2;;chr5:120120834..120120845,+!p8@Tbx3!0.24!0.74!Tbx3;;chr6:52158644..52158677,-!p2@Hoxa6!0.24!0.74!Hoxa6;;chr11:96160360..96160397,+!p3@Hoxb6!0.24!0.74!Hoxb6;;chr11:96143962..96144035,+!p2@Hoxb8!0.24!0.74!Hoxb8;;chr7:38557887..38557910,-!p5@Zfp536!0.24!0.74!Zfp536;;chr7:52960663..52960677,+!p6@Dbp!0.24!0.74!Dbp;;chr3:29912169..29912182,-!p12@Mecom!0.24!0.74!Mecom;;chr4:148178459..148178482,+!p4@Casz1!0.24!0.74!Casz1;;chr3:34549096..34549111,+!p3@Sox2!0.24!0.74!Sox2;;chr3:3508005..3508021,+!p3@Hnf4g!0.24!0.74!Hnf4g;;chr3:29912310..29912321,-!p23@Mecom!0.24!0.74!Mecom;;chr17:26978409..26978442,-!p1@Nkx2-5!0.24!0.74!Nkx2-5;;chr7:77505617..77505632,-!p1@Nr2f2!0.23!70.59!Nr2f2;;chr4:154597177..154597195,-!p1@Ski!0.23!58.35!Ski;;chr18:70727922..70728052,+!p1@Mbd2!0.23!55.38!Mbd2;;chr2:27532754..27532815,+!p1@Rxra!0.23!44.96!Rxra;;chr7:20408047..20408125,-!p1@Bcl3!0.23!16.94!Bcl3;;chr9:121669118..121669179,+!p1@Zfp651!0.23!15.95!Zfp651;;chr14:65977324..65977372,+!p2@Zfp395!0.23!8.02!Zfp395;;chr11:23980664..23980706,+!p2@Bcl11a!0.23!5.95!Bcl11a;;chr17:23004042..23004077,-!p2@Zfp945!0.23!5.21!Zfp945;;chr2:44968721..44968734,-!p6@Zeb2!0.23!5.04!Zeb2;;chr5:65194827..65194846,+!p4@Klf3!0.23!4.63!Klf3;;chr3:5218629..5218684,+!p1@Zfhx4!0.23!4.22!Zfhx4;;chr4:122673278..122673336,+!p1@Mycl1!0.23!4.05!Mycl1;;chr4:6917921..6917970,-!p2@Tox!0.23!3.55!Tox;;chr6:133985971..133985991,+!p6@Etv6!0.23!3.39!Etv6;;chr13:56804865..56804898,+!p3@Smad5!0.23!3.31!Smad5;;chr9:63605691..63605705,-!p3@Smad3!0.23!3.14!Smad3;;chr4:87678743..87678767,-!p7@Mllt3!0.23!2.89!Mllt3;;chr17:13897299..13897342,+!p3@Mllt4!0.23!2.81!Mllt4;;chr6:15135456..15135520,+!p3@Foxp2!0.23!2.56!Foxp2;;chr11:53583960..53584007,+!p2@Irf1!0.23!2.48!Irf1;;chr4:6917971..6918000,-!p3@Tox!0.23!2.23!Tox;;chrX:137135036..137135064,-!p4@Tsc22d3!0.23!2.23!Tsc22d3;;chr5:120120667..120120685,+!p3@Tbx3!0.23!2.15!Tbx3;;chr11:62602947..62602980,-!p2@Zfp286!0.23!2.15!Zfp286;;chr10:67599375..67599386,-!p3@Arid5b!0.23!1.98!Arid5b;;chr15:40486754..40486771,+!p2@Zfpm2!0.23!1.90!Zfpm2;;chr4:122673187..122673201,+!p2@Mycl1!0.23!1.90!Mycl1;;chr2:27532817..27532828,+!p6@Rxra!0.23!1.57!Rxra;;chr13:78339476..78339515,-!p1@Nr2f1!0.23!1.57!Nr2f1;;chr11:85646469..85646488,+!p5@Tbx2!0.23!1.49!Tbx2;;chr11:98605517..98605539,+!p5@Thra!0.23!1.41!Thra;;chr15:36937137..36937157,-!p2@Gm10193,p2@Zfp706!0.22!45.79!Zfp706;;chr2:152561980..152561997,+!p1@Id1!0.22!43.72!Id1;;chr4:82151653..82151706,-!p2@Nfib!0.22!41.49!Nfib;;chr2:18314363..18314465,-!p1@Dnajc1!0.22!36.53!Dnajc1;;chr9:96096707..96096772,+!p1@Tfdp2!0.22!21.99!Tfdp2;;chr3:9610090..9610124,-!p1@Zfp704!0.22!19.42!Zfp704;;chr11:5420954..5420969,+!p2@Xbp1!0.22!17.94!Xbp1;;chr17:84105551..84105600,+!p1@Mta3!0.22!16.28!Mta3;;chr10:30522690..30522752,-!p2@Ncoa7!0.22!8.43!Ncoa7;;chr19:46379199..46379301,+!p1@Nfkb2!0.22!7.85!Nfkb2;;chr2:152223469..152223512,-!p1@Sox12!0.22!7.11!Sox12;;chr1:39250584..39250643,+!p1@Npas2!0.22!6.78!Npas2;;chr4:124805092..124805135,-!p2@Zc3h12a!0.22!5.62!Zc3h12a;;chr4: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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011410
 |is_obsolete=
+|library_id=CNhs11210
+|library_id_phase_based=2:CNhs11210
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;718
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;718
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N07.CNhs11210.718-18A9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N07.CNhs11210.718-18A9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N07.CNhs11210.718-18A9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N07.CNhs11210.718-18A9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N07.CNhs11210.718-18A9.mm9.nobarcode.rdna.fa.gz
 |name=stomach, neonate N07
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11210,LSID747,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.100472641205532,0.034489466458534,0,0,0.034489466458534,0.0121865759297809,0.133544761283267,0.0145616865786523,0.017244733229267,0,0,0.311469624835978,0.034489466458534,0,0,0,0,0,0.141986668334979,0,0,0,0.066440322267935,0,0,0,0.034489466458534,0,0,0,0,0,0.123004696030679,0,0,0,0.150224303855383,0.0367811278819826,0.0636938590481253,0.034489466458534,0.0676680762234783,0.383450746204602,0.44047494036528,0,0,0,0,0,0,0,0,0,0,0.150224303855383,0.034489466458534,0.214843151379483,0,0,0,0,0.0533538381240479,0,0.0361755526920886,0,0.034489466458534,0.066440322267935,0.00921097958784065,0.0993527009018783,0.372998139347744,0.0599391335093738,0,0.103160887450942,0.0570057259526613,0.00369770583933637,0.220429149935824,0,0.0726527209030551,-0.0236607630561924,-0.10929508323341,0.119433402908155,0,0,0,0,0,0,-0.105039060210024,-0.0980166274391756,-0.20445787239867,0.00664594233839939,0,0,0,0.0220141453696853
 |rna_box=18
 |rna_catalog_number=
@@ Line 60: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 80: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:718-18A9;search_select_hide=table117:718-18A9
 }}

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FF:718-18A9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:19, 4 June 2020

CNhs11210

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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