FF:1352-25E3: Difference between revisions

Latest revision as of 19:01, 4 June 2020

Name:	intestine, neonate N25
Species:	Mouse (Mus musculus)
Library ID:	CNhs11121
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	intestine
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		SAMD00004971

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11121		CAGE		DRX009002		DRR009876

Accession ID Mm9

Library id		BAM		CTSS
CNhs11121		DRZ001301		DRZ002684

Accession ID Mm10

Library id		BAM		CTSS
CNhs11121		DRZ012651		DRZ014034

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

CNhs11121

0	0
1	0
10	0
100	0
1000	0.114
1001	0.0979
1002	0.125
1003	-0.0856
1004	0
1005	0.215
1006	0
1007	-0.0276
1008	2.076
1009	0.027
101	-0.109
1010	0
1011	-0.118
1012	0.0582
1013	0.266
1014	-0.00956
1015	-0.256
1016	-0.323
1017	0
1018	0.4
1019	0
102	0
1020	0
1021	-0.0487
1022	0.0156
1023	0
1024	-0.00489
1025	0.619
1026	0
1027	-0.00439
1028	0
1029	0.612
103	0.085
1030	0.085
1031	-0.12
1032	0.612
1033	-0.0752
1034	0.223
1035	0
1036	-0.0979
1037	0
1038	0.0291
1039	0.0997
104	0.361
1040	-0.222
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: CNhs11121

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0622
MA0003.1	MA0003.1	0.284
MA0004.1	MA0004.1	0.587
MA0006.1	MA0006.1	0.0566
MA0007.1	MA0007.1	0.823
MA0009.1	MA0009.1	0.316
MA0014.1	MA0014.1	0.311
MA0017.1	MA0017.1	4.25992e-20
MA0018.2	MA0018.2	0.0187
MA0019.1	MA0019.1	0.374
MA0024.1	MA0024.1	0.0361
MA0025.1	MA0025.1	0.243
MA0027.1	MA0027.1	0.989
MA0028.1	MA0028.1	0.758
MA0029.1	MA0029.1	0.886
MA0030.1	MA0030.1	0.84
MA0031.1	MA0031.1	0.5
MA0035.2	MA0035.2	0.00171
MA0038.1	MA0038.1	0.589
MA0039.2	MA0039.2	0.00362
MA0040.1	MA0040.1	0.176
MA0041.1	MA0041.1	0.249
MA0042.1	MA0042.1	0.774
MA0043.1	MA0043.1	0.084
MA0046.1	MA0046.1	4.67169e-32
MA0047.2	MA0047.2	0.0018
MA0048.1	MA0048.1	0.473
MA0050.1	MA0050.1	2.28517e-7
MA0051.1	MA0051.1	3.30636e-5
MA0052.1	MA0052.1	5.76546e-5
MA0055.1	MA0055.1	0.304
MA0057.1	MA0057.1	0.162
MA0058.1	MA0058.1	0.416
MA0059.1	MA0059.1	0.943
MA0060.1	MA0060.1	0.0083
MA0061.1	MA0061.1	0.294
MA0062.2	MA0062.2	0.711
MA0065.2	MA0065.2	2.63168e-12
MA0066.1	MA0066.1	0.131
MA0067.1	MA0067.1	0.192
MA0068.1	MA0068.1	0.0948
MA0069.1	MA0069.1	0.182
MA0070.1	MA0070.1	0.0449
MA0071.1	MA0071.1	0.297
MA0072.1	MA0072.1	0.63
MA0073.1	MA0073.1	0.824
MA0074.1	MA0074.1	0.274
MA0076.1	MA0076.1	0.302
MA0077.1	MA0077.1	0.297
MA0078.1	MA0078.1	0.31
MA0079.2	MA0079.2	0.142
MA0080.2	MA0080.2	0.00117
MA0081.1	MA0081.1	0.331
MA0083.1	MA0083.1	0.787
MA0084.1	MA0084.1	0.675
MA0087.1	MA0087.1	0.935
MA0088.1	MA0088.1	0.747
MA0090.1	MA0090.1	0.974
MA0091.1	MA0091.1	0.773
MA0092.1	MA0092.1	0.477
MA0093.1	MA0093.1	0.535
MA0099.2	MA0099.2	0.00766
MA0100.1	MA0100.1	0.175
MA0101.1	MA0101.1	0.901
MA0102.2	MA0102.2	0.18
MA0103.1	MA0103.1	3.02485e-5
MA0104.2	MA0104.2	0.0813
MA0105.1	MA0105.1	0.0639
MA0106.1	MA0106.1	0.201
MA0107.1	MA0107.1	0.982
MA0108.2	MA0108.2	0.626
MA0111.1	MA0111.1	0.877
MA0112.2	MA0112.2	9.72318e-6
MA0113.1	MA0113.1	0.937
MA0114.1	MA0114.1	1.48986e-26
MA0115.1	MA0115.1	1.11528e-10
MA0116.1	MA0116.1	0.173
MA0117.1	MA0117.1	0.865
MA0119.1	MA0119.1	0.0219
MA0122.1	MA0122.1	0.606
MA0124.1	MA0124.1	0.45
MA0125.1	MA0125.1	0.153
MA0131.1	MA0131.1	0.476
MA0135.1	MA0135.1	0.374
MA0136.1	MA0136.1	0.00307
MA0137.2	MA0137.2	0.988
MA0138.2	MA0138.2	0.428
MA0139.1	MA0139.1	0.0661
MA0140.1	MA0140.1	0.163
MA0141.1	MA0141.1	6.8322e-5
MA0142.1	MA0142.1	0.173
MA0143.1	MA0143.1	0.167
MA0144.1	MA0144.1	0.147
MA0145.1	MA0145.1	0.0039
MA0146.1	MA0146.1	0.308
MA0147.1	MA0147.1	0.141
MA0148.1	MA0148.1	3.92859e-4
MA0149.1	MA0149.1	0.0369
MA0150.1	MA0150.1	0.52
MA0152.1	MA0152.1	0.171
MA0153.1	MA0153.1	5.05642e-29
MA0154.1	MA0154.1	0.0316
MA0155.1	MA0155.1	0.542
MA0156.1	MA0156.1	0.0723
MA0157.1	MA0157.1	0.993
MA0159.1	MA0159.1	0.0049
MA0160.1	MA0160.1	0.00934
MA0162.1	MA0162.1	0.272
MA0163.1	MA0163.1	0.0831
MA0164.1	MA0164.1	0.997
MA0258.1	MA0258.1	0.0097
MA0259.1	MA0259.1	0.241

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: CNhs11121

Novel motif	Logo	P-value
1	1	0.1
10	10	0.131
100	100	0.846
101	101	0.934
102	102	0.893
103	103	0.16
104	104	0.858
105	105	0.459
106	106	0.0111
107	107	0.0246
108	108	0.923
109	109	0.0611
11	11	0.179
110	110	0.199
111	111	0.0565
112	112	0.0202
113	113	0.415
114	114	0.0495
115	115	0.62
116	116	0.361
117	117	0.267
118	118	0.516
119	119	0.175
12	12	0.941
120	120	0.515
121	121	0.789
122	122	0.879
123	123	0.245
124	124	0.934
125	125	0.484
126	126	0.0871
127	127	0.455
128	128	0.0399
129	129	0.337
13	13	9.72606e-4
130	130	0.932
131	131	0.0692
132	132	0.695
133	133	0.881
134	134	0.833
135	135	0.303
136	136	0.37
137	137	0.794
138	138	0.612
139	139	0.0459
14	14	0.725
140	140	0.112
141	141	0.22
142	142	0.734
143	143	0.205
144	144	0.649
145	145	0.153
146	146	0.376
147	147	0.237
148	148	0.179
149	149	0.626
15	15	0.167
150	150	0.348
151	151	0.364
152	152	0.0578
153	153	0.61
154	154	0.304
155	155	0.541
156	156	0.491
157	157	0.85
158	158	0.563
159	159	0.164
160	160	0.187
161	161	0.624
162	162	0.783
163	163	0.451
164	164	0.106
165	165	0.476
166	166	0.995
167	167	0.734
168	168	0.77
169	169	0.00378
17	17	0.0476
18	18	0.113
19	19	0.048
2	2	0.37
20	20	0.851
21	21	0.886
22	22	0.328
23	23	0.285
24	24	0.758
25	25	0.735
26	26	0.00271
27	27	0.712
28	28	0.45
29	29	0.245
3	3	0.206
30	30	0.531
31	31	0.732
32	32	0.0283
33	33	0.233
34	34	0.821
35	35	0.683
36	36	0.78
37	37	0.0234
38	38	0.362
39	39	0.129
4	4	0.635
40	40	0.436
41	41	0.502
42	42	0.481
43	43	0.222
44	44	0.226
45	45	0.43
46	46	0.168
47	47	0.321
48	48	0.294
49	49	0.138
5	5	0.409
50	50	0.48
51	51	0.615
52	52	0.0792
53	53	0.89
54	54	0.525
55	55	0.583
56	56	0.384
57	57	0.768
58	58	0.293
59	59	0.275
6	6	0.659
60	60	0.0459
61	61	0.157
62	62	0.277
63	63	0.168
64	64	0.725
65	65	0.213
66	66	0.374
67	67	0.459
68	68	0.158
69	69	0.628
7	7	0.0622
70	70	0.0781
71	71	0.0857
72	72	0.596
73	73	0.109
74	74	0.934
75	75	0.106
76	76	0.914
77	77	0.169
78	78	0.0467
79	79	0.919
8	8	0.181
80	80	0.782
81	81	0.663
82	82	0.124
83	83	0.266
84	84	0.494
85	85	0.0309
86	86	0.226
87	87	0.878
88	88	0.592
89	89	0.352
9	9	0.725
90	90	0.159
91	91	0.28
92	92	0.355
93	93	0.671
94	94	0.872
95	95	0.144
96	96	0.772
97	97	0.875
98	98	0.854
99	99	0.0829

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: CNhs11121

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011480 mouse intestine- 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)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
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)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

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)
0011480 (mouse intestine- 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
+|DRA_sample_Accession=CAGE@SAMD00004971
+|accession_numbers=CAGE;DRX009002;DRR009876;DRZ001301;DRZ002684;DRZ012651;DRZ014034
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001555,UBERON:0005409
 |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=chr3:3634145..3634161,+!p1@Hnf4g!2.72!528.03!Hnf4g;;chr10:80555320..80555378,-!p1@Creb3l3!2.13!154.54!Creb3l3;;chr5:148118639..148118715,-!p1@Cdx2!2.13!133.36!Cdx2;;chr1:137155026..137155042,-!p1@Elf3!1.98!515.71!Elf3;;chr10:88969376..88969395,-!p1@Nr1h4!1.94!85.81!Nr1h4;;chr2:163372884..163372904,+!p1@Hnf4a!1.93!83.65!Hnf4a;;chr16:38294860..38294924,-!p1@Nr1i2!1.89!76.08!Nr1i2;;chr2:163332558..163332596,+!p2@Hnf4a!1.79!61.17!Hnf4a;;chr6:86619104..86619119,-!p1@Mxd1!1.70!380.40!Mxd1;;chr15:97738692..97738747,-!p1@Vdr!1.67!236.67!Vdr;;chr8:77396591..77396639,+!p1@Isx!1.65!43.88!Isx;;chr3:3508024..3508069,+!p2@Hnf4g!1.64!42.80!Hnf4g;;chr18:61195843..61195864,-!p2@Cdx1!1.60!38.90!Cdx1;;chr6:64679112..64679126,+!p1@Atoh1!1.58!37.18!Atoh1;;chr18:61195865..61195880,-!p1@Cdx1!1.55!34.37!Cdx1;;chr2:180069370..180069409,-!p1@Gata5!1.54!38.90!Gata5;;chr1:173144100..173144138,+!p2@Nr1i3!1.51!31.12!Nr1i3;;chr2:103143336..103143367,-!p1@Ehf!1.49!47.77!Ehf;;chr2:103123925..103123959,-!p3@Ehf!1.49!30.26!Ehf;;chr17:27865882..27865901,-!p1@Spdef!1.46!27.67!Spdef;;chr8:77397095..77397127,+!p2@Isx!1.43!26.15!Isx;;chr14:63864056..63864102,-!p1@Gata4!1.42!43.66!Gata4;;chr5:135582751..135582788,+!p1@Mlxipl!1.40!94.02!Mlxipl;;chr14:99697871..99697934,+!p1@Klf5!1.35!405.26!Klf5;;chr17:28408632..28408682,+!p1@1810013A23Rik,p4@Ppard!1.35!21.18!Ppard;;chr10:22539932..22539956,-!p1@Tcf21!1.26!45.61!Tcf21;;chr7:19608891..19608895,-!p1@Foxa3!1.26!22.48!Foxa3;;chr8:79426176..79426275,+!p1@Nr3c2!1.25!82.13!Nr3c2;;chr2:103143315..103143328,-!p2@Ehf!1.25!16.64!Ehf;;chr19:43686789..43686811,+!p1@Nkx2-3!1.25!16.64!Nkx2-3;;chr7:148452314..148452329,-!p1@Irf7!1.22!105.69!Irf7;;chr19:5560600..5560617,-!p1@Ovol1!1.22!19.02!Ovol1;;chr5:148118840..148118857,-!p2@Cdx2!1.19!14.48!Cdx2;;chr8:77397492..77397514,+!p3@Isx!1.19!14.48!Isx;;chr8:77396650..77396662,+!p4@Isx!1.18!14.27!Isx;;chr17:28409136..28409150,+!p3@Ppard!1.18!14.27!Ppard;;chr5:115421065..115421088,-!p1@Hnf1a!1.17!13.83!Hnf1a;;chr15:35225845..35225867,+!p1@Osr2!1.16!33.72!Osr2;;chr3:3508005..3508021,+!p3@Hnf4g!1.16!13.62!Hnf4g;;chr8:77397190..77397202,+!p5@Isx!1.16!13.40!Isx;;chr3:90046995..90047031,-!p2@Creb3l4!1.14!15.99!Creb3l4;;chr8:123608252..123608268,+!p1@Foxf1a!1.09!16.86!Foxf1a;;chr5:148118792..148118806,-!p3@Cdx2!1.08!11.02!Cdx2;;chr4:55545337..55545357,-!p1@Klf4!1.07!160.81!Klf4;;chr1:138857048..138857071,-!p2@Nr5a2!1.06!10.37!Nr5a2;;chr1:194979315..194979359,+!p1@Irf6!1.05!62.90!Irf6;;chr10:80555398..80555409,-!p2@Creb3l3!1.05!10.16!Creb3l3;;chr2:173044380..173044432,-!p1@Zbp1!1.04!23.99!Zbp1;;chr1:39250584..39250643,+!p1@Npas2!1.03!49.50!Npas2;;chr18:64499674..64499696,+!p1@Onecut2!1.02!16.43!Onecut2;;chr1:165219345..165219366,-!p7@Prrx1!1.02!9.51!Prrx1;;chr1:173144144..173144176,+!p1@Nr1i3!1.02!9.51!Nr1i3;;chr1:57029281..57029326,-!p1@Satb2!1.01!14.70!Satb2;;chr2:163372869..163372882,+!p3@Hnf4a!1.00!9.08!Hnf4a;;chr11:70500401..70500460,-!p3@Camta2!1.00!9.08!Camta2;;chr8:118231678..118231692,-!p2@Maf!0.98!78.24!Maf;;chr3:89197057..89197114,-!p1@Zbtb7b!0.98!29.39!Zbtb7b;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.98!25.07!Tfcp2l1;;chr6:39068163..39068176,-!p2@Parp12!0.98!16.21!Parp12;;chr18:64499706..64499721,+!p2@Onecut2!0.98!12.32!Onecut2;;chr3:30039329..30039355,-!p5@Mecom!0.98!8.65!Mecom;;chr2:166888058..166888105,-!p2@Znfx1!0.97!27.45!Znfx1;;chr4:148178559..148178603,+!p1@Casz1!0.94!22.69!Casz1;;chr5:120121020..120121049,+!p1@Tbx3!0.93!47.98!Tbx3;;chr10:88996336..88996380,-!p2@Nr1h4!0.93!9.29!Nr1h4;;chr5:120121446..120121461,+!p2@Tbx3!0.92!24.86!Tbx3;;chr11:96055613..96055628,+!p1@Hoxb13!0.92!7.35!Hoxb13;;chr1:194979361..194979373,+!p2@Irf6!0.91!9.73!Irf6;;chr12:58646974..58647003,-!p1@Foxa1!0.91!9.73!Foxa1;;chr11:98614335..98614349,+!p8@Thra!0.91!7.13!Thra;;chr11:53583544..53583559,+!p1@Irf1!0.89!119.09!Irf1;;chr18:36441119..36441158,+!p2@Pura!0.88!16.64!Pura;;chr2:79296783..79296801,-!p1@Neurod1!0.87!6.48!Neurod1;;chr8:123260252..123260264,+!p1@Irf8!0.86!46.69!Irf8;;chr10:20880629..20880683,-!p1@Myb!0.86!19.02!Myb;;chr18:11052485..11052508,+!p2@Gata6!0.86!18.37!Gata6;;chr13:31717548..31717596,+!p1@Foxf2!0.86!12.75!Foxf2;;chr11:96153767..96153822,+!p1@Hoxb6!0.86!9.94!Hoxb6;;chr10:127095407..127095440,+!p3@Stat6!0.86!7.78!Stat6;;chr7:20213752..20213778,-!p2@Relb!0.86!6.27!Relb;;chr2:180069640..180069660,-!p4@Gata5!0.86!6.27!Gata5;;chr19:6996243..6996293,-!p1@Esrra!0.85!71.97!Esrra;;chr11:98636531..98636559,-!p1@Nr1d1!0.85!36.96!Nr1d1;;chr10:30375579..30375616,-!p3@Ncoa7!0.85!15.13!Ncoa7;;chr11:57645506..57645523,-!p1@Hand1!0.85!6.05!Hand1;;chr12:78063146..78063159,-!p2@Max!0.84!16.21!Max;;chr12:86814833..86814846,+!p1@Fos!0.83!145.24!Fos;;chr5:148118809..148118832,-!p5@Cdx2!0.83!5.84!Cdx2;;chr4:133109285..133109308,+!p1@Nr0b2!0.83!5.84!Nr0b2;;chr4:148178529..148178548,+!p3@Casz1!0.82!14.05!Casz1;;chr19:53384910..53384937,+!p3@Mxi1!0.81!16.21!Mxi1;;chr19:5560570..5560582,-!p2@Ovol1!0.81!5.40!Ovol1;;chr14:63890519..63890539,-!p3@Gata4!0.81!5.40!Gata4;;chr11:98822047..98822072,+!p9@Rara!0.81!5.40!Rara;;chr5:148118614..148118625,-!p4@Cdx2!0.81!5.40!Cdx2;;chr1:138857076..138857105,-!p1@Nr5a2!0.81!5.40!Nr5a2;;chr8:118231705..118231722,-!p3@Maf!0.80!45.82!Maf;;chr6:52190467..52190500,-!p1@Hoxa10!0.79!5.19!Hoxa10;;chr5:115421126..115421137,-!p4@Hnf1a!0.79!5.19!Hnf1a;;chr14:76887526..76887555,+!p10@Tsc22d1!0.78!4.97!Tsc22d1;;chr8:77397169..77397182,+!p7@Isx!0.78!4.97!Isx;;chr11:96055681..96055693,+!p2@Hoxb13!0.78!4.97!Hoxb13;;chr3:94176733..94176794,+!p1@Rorc!0.77!41.07!Rorc;;chr8:59799772..59799789,+!p1@Hand2!0.76!14.70!Hand2;;chr4:87452180..87452196,-!p3@Mllt3!0.76!9.94!Mllt3;;chr3:89197216..89197258,-!p3@Zbtb7b!0.75!10.37!Zbtb7b;;chr6:39068181..39068206,-!p3@Parp12!0.75!10.16!Parp12;;chr10:88996295..88996335,-!p3@Nr1h4!0.75!5.62!Nr1h4;;chr13:44825008..44825066,+!p5@Jarid2!0.74!9.51!Jarid2;;chr14:63890545..63890560,-!p5@Gata4!0.74!4.54!Gata4;;chr2:24278519..24278530,-!p3@Pax8!0.74!4.54!Pax8;;chr6:37391910..37391928,-!p3@Creb3l2!0.73!4.97!Creb3l2;;chr6:52190668..52190682,-!p3@Hoxa10!0.73!4.32!Hoxa10;;chr2:180069410..180069421,-!p3@Gata5!0.73!4.32!Gata5;;chr4:148178459..148178482,+!p4@Casz1!0.73!4.32!Casz1;;chr1:193007123..193007139,-!p1@Atf3!0.72!26.58!Atf3;;chr2:91035254..91035271,-!p3@Nr1h3!0.72!5.40!Nr1h3;;chr2:173044357..173044377,-!p2@Zbp1!0.71!6.27!Zbp1;;chr2:180069423..180069434,-!p2@Gata5!0.71!4.11!Gata5;;chr4:114581497..114581519,-!p2@Foxd2!0.71!4.11!Foxd2;;chr6:52168685..52168715,-!p9@Hoxa7!0.71!4.11!Hoxa7;;chr10:80555285..80555291,-!p4@Creb3l3!0.71!4.11!Creb3l3;;chr11:83664365..83664383,+!p1@Hnf1b!0.71!4.11!Hnf1b;;chr10:61595830..61595846,+!p1@Neurog3!0.71!4.11!Neurog3;;chr7:20408047..20408125,-!p1@Bcl3!0.70!51.22!Bcl3;;chr17:28409059..28409076,+!p6@Ppard!0.69!3.89!Ppard;;chr3:89197551..89197606,-!p2@Zbtb7b!0.68!14.48!Zbtb7b;;chr4:124805061..124805087,-!p1@Zc3h12a!0.68!12.97!Zc3h12a;;chr5:120121169..120121171,+!p4@Tbx3!0.68!7.35!Tbx3;;chr1:135557526..135557551,-!p1@Zbed6!0.68!6.48!Zbed6;;chr6:39068210..39068251,-!p1@Parp12!0.67!19.24!Parp12;;chr4:87452200..87452229,-!p2@Mllt3!0.67!8.65!Mllt3;;chr11:53583960..53584007,+!p2@Irf1!0.67!8.65!Irf1;;chr6:52176164..52176195,-!p1@Hoxa9!0.67!4.76!Hoxa9;;chr1:194979383..194979393,+!p3@Irf6!0.67!3.67!Irf6;;chr3:128918394..128918413,+!p5@Pitx2!0.67!3.67!Pitx2;;chr2:75543089..75543122,-!p3@Nfe2l2!0.67!3.67!Nfe2l2;;chr1:133904946..133904974,+!p7@Elk4!0.66!5.84!Elk4;;chr8:79423144..79423178,+!p3@Nr3c2!0.66!5.19!Nr3c2;;chr15:85566051..85566080,+!p4@Ppara!0.66!4.32!Ppara;;chr19:55816770..55816793,+!p2@Tcf7l2!0.65!34.80!Tcf7l2;;chr10:80555299..80555306,-!p3@Creb3l3!0.65!3.46!Creb3l3;;chr11:100948597..100948637,+!p1@Mlx!0.64!94.67!Mlx;;chr2:91864661..91864686,-!p1@Creb3l1!0.64!86.46!Creb3l1;;chr5:138187583..138187602,+!p6@Tsc22d4!0.64!6.70!Tsc22d4;;chr2:75542527..75542590,-!p1@Nfe2l2!0.63!342.79!Nfe2l2;;chr16:55822241..55822258,-!p1@Nfkbiz!0.63!121.25!Nfkbiz;;chr11:98636400..98636418,-!p4@Nr1d1!0.63!4.54!Nr1d1;;chr11:96055650..96055665,+!p3@Hoxb13!0.63!3.24!Hoxb13;;chr6:99216375..99216395,-!p5@Foxp1!0.63!3.24!Foxp1;;chr1:138846079..138846103,-!p6@Nr5a2!0.63!3.24!Nr5a2;;chr9:31720903..31720918,-!p2@Barx2!0.63!3.24!Barx2;;chr13:5860776..5860796,+!p1@Klf6!0.62!90.99!Klf6;;chr18:11052642..11052659,+!p1@Gata6!0.62!18.59!Gata6;;chrX:103070960..103070973,-!p7@Atrx!0.62!4.54!Atrx;;chr4:55545051..55545110,-!p2@Klf4!0.62!4.11!Klf4;;chr4:148275237..148275311,+!p2@Casz1!0.61!14.91!Casz1;;chr15:37162796..37162828,+!p1@Grhl2!0.61!5.62!Grhl2;;chr13:55932591..55932622,-!p1@Pitx1!0.60!3.67!Pitx1;;chr11:83664334..83664353,+!p2@Hnf1b!0.60!3.03!Hnf1b;;chr5:65194752..65194769,+!p1@Klf3!0.59!118.01!Klf3;;chr17:32506357..32506377,-!p3@Wiz!0.58!6.70!Wiz;;chr4:135700687..135700719,+!p2@Id3!0.58!4.76!Id3;;chr5:120121091..120121100,+!p7@Tbx3!0.58!3.46!Tbx3;;chr1:138846009..138846038,-!p3@Nr5a2!0.58!3.24!Nr5a2;;chr2:147871627..147871641,-!p1@Foxa2!0.58!2.81!Foxa2;;chr13:31717597..31717613,+!p2@Foxf2!0.58!2.81!Foxf2;;chr14:63890491..63890516,-!p2@Gata4!0.58!2.81!Gata4;;chr9:59797503..59797513,-!p3@Nr2e3!0.58!2.81!Nr2e3;;chr18:11052606..11052633,+!p4@Gata6!0.57!8.00!Gata6;;chr7:134519473..134519502,-!p3@Zfp747!0.57!3.89!Zfp747;;chr1:138846047..138846074,-!p5@Nr5a2!0.57!3.03!Nr5a2;;chr14:79915425..79915501,+!p1@Elf1!0.56!28.96!Elf1;;chr14:18493386..18493464,+!p1@Thrb!0.56!12.10!Thrb;;chr10:80598209..80598236,+!p4@Zbtb7a!0.56!4.97!Zbtb7a;;chr8:47825166..47825178,+!p2@Irf2!0.56!4.54!Irf2;;chr14:76887566..76887579,+!p18@Tsc22d1!0.56!2.59!Tsc22d1;;chr6:99216360..99216372,-!p8@Foxp1!0.56!2.59!Foxp1;;chr1:194982959..194983007,+!p5@Irf6!0.56!2.59!Irf6;;chr1:135320989..135321043,-!p1@Sox13!0.55!35.23!Sox13;;chr5:65213356..65213412,+!p6@Klf3!0.55!6.27!Klf3;;chr5:76733981..76734018,-!p3@Clock!0.55!6.27!Clock;;chr5:120120981..120120992,+!p5@Tbx3!0.55!3.67!Tbx3;;chr8:87502608..87502623,-!p1@Junb!0.54!50.58!Junb;;chr1:52176315..52176343,+!p1@Stat1!0.54!45.61!Stat1;;chr1:135320962..135320981,-!p2@Sox13!0.54!9.94!Sox13;;chr2:91035197..91035237,-!p1@Nr1h3!0.5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30..52253070,+!p1@Irf3!0.10!24.86!Irf3;;chr11:106134020..106134128,-!p1@Smarcd2!0.10!21.61!Smarcd2;;chrX:20639107..20639188,-!p1@Zfp182!0.10!13.83!Zfp182;;chr2:73730596..73730612,-!p3@Atf2,p3@LOC100047997!0.10!13.83!Atf2;;chr7:134565516..134565573,-!p1@Zfp688!0.10!12.54!Zfp688;;chr12:36219645..36219730,-!p1@Ahr!0.10!10.37!Ahr;;chr3:94819338..94819384,-!p1@Zfp687!0.10!9.94!Zfp687;;chr14:56223010..56223067,+!p1@Irf9!0.10!8.21!Irf9;;chr7:56136362..56136400,-!p1@E2f8!0.10!6.70!E2f8;;chr13:67209482..67209545,-!p1@Zfp708!0.10!4.54!Zfp708;;chr17:48061605..48061629,-!p6@Foxp4!0.10!3.89!Foxp4;;chr17:25152743..25152766,-!p2@Cramp1l!0.10!3.89!Cramp1l;;chr3:88753953..88754004,+!p1@Ash1l!0.10!3.03!Ash1l;;chr10:127984472..127984504,-!p2@Zc3h10!0.10!2.81!Zc3h10;;chr18:84255771..84255795,-!p3@Tshz1!0.10!2.59!Tshz1;;chr7:4990015..4990028,-!p2@Zfp784!0.10!2.38!Zfp784;;chr17:44872561..44872615,-!p1@Runx2!0.10!1.73!Runx2;;chr10:20880731..20880775,-!p2@Myb!0.10!1.51!Myb;;chr5:67698263..67698272,+!p3@Slc30a9!0.10!0.86!Slc30a9;;chr6:99471147..99471161,-!p9@Foxp1!0.10!0.65!Foxp1;;chr17:44873258..44873281,-!p5@Runx2!0.10!0.65!Runx2;;chr8:81923375..81923380,-!p6@Smad1!0.10!0.65!Smad1;;chr1:64168228..64168250,-!p7@Klf7!0.10!0.65!Klf7;;chr1:64168030..64168037,-!p9@Klf7!0.10!0.65!Klf7;;chr11:98821917..98821934,+!p11@Rara!0.10!0.43!Rara;;chr3:30993641..30993651,+!p7@Skil!0.10!0.43!Skil;;chr13:44829403..44829438,+!p11@Jarid2!0.10!0.43!Jarid2;;chr8:73222830..73222844,+!p1@Jund!0.09!281.84!Jund;;chr12:56593574..56593592,-!p1@Nfkbia!0.09!57.28!Nfkbia;;chr10:127896346..127896384,+!p1@Smarcc2!0.09!42.58!Smarcc2;;chr12:112277544..112277610,+!p1@Rcor1!0.09!41.50!Rcor1;;chr12:41172341..41172385,-!p1@Zfp277!0.09!37.61!Zfp277;;chr2:165818125..165818167,+!p1@Ncoa3!0.09!28.75!Ncoa3;;chr18:74427905..74427991,+!p1@Mbd1!0.09!20.53!Mbd1;;chr15:10400285..10400360,-!p1@Dnajc21!0.09!13.83!Dnajc21;;chr14:31832345..31832364,+!p2@Pbrm1!0.09!9.08!Pbrm1;;chr12:80397253..80397297,-!p1@Zfyve26!0.09!9.08!Zfyve26;;chr1:135557964..135557976,-!p2@Zc3h11a!0.09!8.86!Zc3h11a;;chr10:75495343..75495405,+!p1@Zfp280b!0.09!8.65!Zfp280b;;chr11:65620712..65620729,+!p1@Zkscan6!0.09!8.43!Zkscan6;;chr14:76904356..76904367,+!p3@Tsc22d1!0.09!7.35!Tsc22d1;;chr4:120488308..120488366,-!p1@Nfyc!0.09!5.62!Nfyc;;chr13:67585161..67585205,-!p1@Zfp874b!0.09!4.97!Zfp874b;;chr15:76709732..76709764,+!p1@Zfp7!0.09!4.54!Zfp7;;chr5:147760305..147760324,+!p2@Gtf3a!0.09!4.54!Gtf3a;;chr19:5610038..5610066,-!p1@Kat5!0.09!4.54!Kat5;;chr18:84758852..84758878,-!p2@Zfp407!0.09!3.46!Zfp407;;chr18:69505414..69505465,+!p6@Tcf4!0.09!3.24!Tcf4;;chr7:4866778..4866801,+!p3@Zfp628!0.09!3.24!Zfp628;;chr1:13362515..13362538,-!p2@Ncoa2!0.09!3.03!Ncoa2;;chr7:134519542..134519569,-!p1@Zfp747!0.09!2.59!Zfp747;;chr11:49016816..49016846,+!p2@Zfp62!0.09!2.38!Zfp62;;chr6:124959016..124959061,+!p3@Zfp384!0.09!2.16!Zfp384;;chr9:96653072..96653154,-!p1@Zbtb38!0.09!2.16!Zbtb38;;chr11:120494669..120494688,-!p2@Mafg!0.09!1.95!Mafg;;chr3:135354452..135354475,-!p5@Nfkb1!0.09!1.95!Nfkb1;;chr13:37870307..37870337,+!p5@Rreb1!0.09!1.73!Rreb1;;chr12:87027598..87027652,+!p1@Batf!0.09!1.73!Batf;;chr11:100683839..100683890,-!p2@Stat5b!0.09!1.73!Stat5b;;chr16:55973899..55973913,+!p7@Rpl24,p7@Zbtb11!0.09!1.73!Zbtb11;;chr7:56137011..56137041,-!p2@E2f8!0.09!1.30!E2f8;;chr9:122775033..122775044,-!p2@Zfp445!0.09!1.08!Zfp445;;chr18:83079981..83080037,+!p6@Zfp516!0.09!1.08!Zfp516;;chr18:39648811..39648818,-!p4@Nr3c1!0.09!1.08!Nr3c1;;chr6:98978868..98978918,-!p6@Foxp1!0.09!1.08!Foxp1;;chr16:92697354..92697362,-!p3@Runx1!0.09!0.86!Runx1;;chr1:9690474..9690493,-!p3@Mybl1!0.09!0.86!Mybl1;;chr1:135551736..135551746,-!p3@Zc3h11a!0.09!0.86!Zc3h11a;;chr11:98602203..98602266,+!p4@Thra!0.09!0.86!Thra;;chr10:41996451..41996462,-!p5@Foxo3!0.09!0.65!Foxo3;;chr19:55817629..55817652,+!p14@Tcf7l2!0.09!0.65!Tcf7l2;;chr9:19426719..19426729,+!p4@Zfp317!0.09!0.65!Zfp317;;chr8:73905892..73905903,-!p5@Nr2f6!0.09!0.43!Nr2f6;;chr17:48025139..48025166,-!p8@Foxp4!0.09!0.43!Foxp4;;
@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011480
 |is_obsolete=
+|library_id=CNhs11121
+|library_id_phase_based=2:CNhs11121
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1352
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1352
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N25.CNhs11121.1352-25E3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N25.CNhs11121.1352-25E3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N25.CNhs11121.1352-25E3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N25.CNhs11121.1352-25E3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N25.CNhs11121.1352-25E3.mm9.nobarcode.rdna.fa.gz
 |name=intestine, neonate N25
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11121,LSID734,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.284797978430444,0,0,0,0.156026744954718,0.109795596601252,0.417763981006746,0,0.0424914383301275,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.0358666059278566,0,0,0,0,0,0.0849828766602549,0,0,0,0,0,0,0,0.328083699488927,0,0,0,0,0,0.19026341901062,-0.0661618130246221,0.0535590558982972,-0.177797259137615,-0.113841893055633,0,0,0,0,0,0,0,0,0,0,0.0849828766602549,0,0.0900211973912776,0,0,0,0,0.294315448867765,0,0.0442170682186428,0,0,0.0237951068154987,0.11646511611472,0.217947085415202,-0.0731081661108277,0.0561912162868101,0,0.217066333756752,-0.0294970106911897,-0.147340100553513,0,0,0,0.059374068042059,0.210499226599642,0.0771951501148106,0,0,0,0,0,0,0.121239955477947,0.290272542311705,0.00830370676506865,0.00460193394932117,0,0,0,0
 |rna_box=25
 |rna_catalog_number=
@@ Line 58: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=25E3
+|rna_tube_id=2.50E+04
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1352-25E3;search_select_hide=table117:1352-25E3
 }}

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FF:1352-25E3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:01, 4 June 2020

CNhs11121

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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