FF:755-23A5: Difference between revisions

Latest revision as of 19:20, 4 June 2020

Name:	intestine, neonate N10
Species:	Mouse (Mus musculus)
Library ID:	CNhs11098
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	intestine
dev stage	10 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		SAMD00004753

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11098		CAGE		DRX009000		DRR009874

Accession ID Mm9

Library id		BAM		CTSS
CNhs11098		DRZ001299		DRZ002682

Accession ID Mm10

Library id		BAM		CTSS
CNhs11098		DRZ012649		DRZ014032

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

CNhs11098

0	0
1	0
10	0
100	0
1000	0.0774
1001	0.024
1002	0.149
1003	-0.025
1004	0
1005	0.2
1006	0
1007	-0.00978
1008	0.548
1009	0.18
101	-0.0687
1010	0.0774
1011	-0.0357
1012	0
1013	0.201
1014	0.107
1015	-0.146
1016	-0.0493
1017	0
1018	0.374
1019	0
102	0
1020	0
1021	-0.0487
1022	0.00697
1023	0
1024	0.156
1025	0.784
1026	0
1027	0
1028	0
1029	0.348
103	0.15
1030	0
1031	0.0506
1032	0.325
1033	-0.0665
1034	0.0156
1035	0
1036	-0.102
1037	0
1038	0.0514
1039	0.018
104	0.143
1040	-0.0438
1041	0.0774

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: CNhs11098

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0861
MA0003.1	MA0003.1	0.121
MA0004.1	MA0004.1	0.843
MA0006.1	MA0006.1	0.0266
MA0007.1	MA0007.1	0.415
MA0009.1	MA0009.1	0.463
MA0014.1	MA0014.1	0.799
MA0017.1	MA0017.1	8.48901e-28
MA0018.2	MA0018.2	0.00228
MA0019.1	MA0019.1	0.212
MA0024.1	MA0024.1	0.0187
MA0025.1	MA0025.1	0.336
MA0027.1	MA0027.1	0.193
MA0028.1	MA0028.1	0.133
MA0029.1	MA0029.1	0.789
MA0030.1	MA0030.1	0.319
MA0031.1	MA0031.1	0.218
MA0035.2	MA0035.2	2.88729e-6
MA0038.1	MA0038.1	0.814
MA0039.2	MA0039.2	1.19223e-4
MA0040.1	MA0040.1	0.0606
MA0041.1	MA0041.1	0.37
MA0042.1	MA0042.1	0.911
MA0043.1	MA0043.1	0.00215
MA0046.1	MA0046.1	3.88361e-75
MA0047.2	MA0047.2	3.47291e-5
MA0048.1	MA0048.1	0.722
MA0050.1	MA0050.1	5.69282e-8
MA0051.1	MA0051.1	7.40381e-6
MA0052.1	MA0052.1	0.00146
MA0055.1	MA0055.1	0.184
MA0057.1	MA0057.1	0.118
MA0058.1	MA0058.1	0.595
MA0059.1	MA0059.1	0.69
MA0060.1	MA0060.1	0.0222
MA0061.1	MA0061.1	0.559
MA0062.2	MA0062.2	0.0726
MA0065.2	MA0065.2	9.17153e-12
MA0066.1	MA0066.1	0.319
MA0067.1	MA0067.1	0.41
MA0068.1	MA0068.1	0.785
MA0069.1	MA0069.1	0.0303
MA0070.1	MA0070.1	0.117
MA0071.1	MA0071.1	0.736
MA0072.1	MA0072.1	0.665
MA0073.1	MA0073.1	0.739
MA0074.1	MA0074.1	0.181
MA0076.1	MA0076.1	0.0661
MA0077.1	MA0077.1	0.115
MA0078.1	MA0078.1	0.113
MA0079.2	MA0079.2	0.235
MA0080.2	MA0080.2	0.00357
MA0081.1	MA0081.1	0.14
MA0083.1	MA0083.1	0.134
MA0084.1	MA0084.1	0.646
MA0087.1	MA0087.1	0.987
MA0088.1	MA0088.1	0.948
MA0090.1	MA0090.1	0.376
MA0091.1	MA0091.1	0.561
MA0092.1	MA0092.1	0.172
MA0093.1	MA0093.1	0.745
MA0099.2	MA0099.2	0.0118
MA0100.1	MA0100.1	0.00708
MA0101.1	MA0101.1	0.584
MA0102.2	MA0102.2	0.601
MA0103.1	MA0103.1	1.55215e-5
MA0104.2	MA0104.2	0.0716
MA0105.1	MA0105.1	0.73
MA0106.1	MA0106.1	0.815
MA0107.1	MA0107.1	0.653
MA0108.2	MA0108.2	0.00599
MA0111.1	MA0111.1	0.51
MA0112.2	MA0112.2	4.64534e-4
MA0113.1	MA0113.1	0.621
MA0114.1	MA0114.1	3.83109e-33
MA0115.1	MA0115.1	3.47783e-8
MA0116.1	MA0116.1	0.691
MA0117.1	MA0117.1	0.993
MA0119.1	MA0119.1	0.0673
MA0122.1	MA0122.1	0.88
MA0124.1	MA0124.1	0.208
MA0125.1	MA0125.1	0.613
MA0131.1	MA0131.1	0.329
MA0135.1	MA0135.1	0.029
MA0136.1	MA0136.1	0.053
MA0137.2	MA0137.2	0.588
MA0138.2	MA0138.2	0.711
MA0139.1	MA0139.1	0.0268
MA0140.1	MA0140.1	0.037
MA0141.1	MA0141.1	0.0215
MA0142.1	MA0142.1	0.062
MA0143.1	MA0143.1	0.0352
MA0144.1	MA0144.1	0.0431
MA0145.1	MA0145.1	0.00596
MA0146.1	MA0146.1	0.122
MA0147.1	MA0147.1	0.0366
MA0148.1	MA0148.1	6.41801e-7
MA0149.1	MA0149.1	0.124
MA0150.1	MA0150.1	0.773
MA0152.1	MA0152.1	0.593
MA0153.1	MA0153.1	8.24325e-48
MA0154.1	MA0154.1	0.0244
MA0155.1	MA0155.1	0.0561
MA0156.1	MA0156.1	0.0789
MA0157.1	MA0157.1	0.32
MA0159.1	MA0159.1	0.00971
MA0160.1	MA0160.1	0.132
MA0162.1	MA0162.1	0.316
MA0163.1	MA0163.1	0.0634
MA0164.1	MA0164.1	0.895
MA0258.1	MA0258.1	0.102
MA0259.1	MA0259.1	0.0594

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: CNhs11098

Novel motif	Logo	P-value
1	1	0.448
10	10	0.455
100	100	0.389
101	101	0.948
102	102	0.571
103	103	0.209
104	104	0.676
105	105	0.645
106	106	0.0127
107	107	0.00777
108	108	0.754
109	109	0.0802
11	11	0.409
110	110	0.615
111	111	0.273
112	112	0.0257
113	113	0.403
114	114	0.488
115	115	0.473
116	116	0.212
117	117	0.91
118	118	0.725
119	119	0.274
12	12	0.9
120	120	0.997
121	121	0.5
122	122	0.662
123	123	0.0804
124	124	0.623
125	125	0.832
126	126	0.133
127	127	0.903
128	128	0.0603
129	129	0.436
13	13	0.00109
130	130	0.518
131	131	0.0948
132	132	0.165
133	133	0.405
134	134	0.337
135	135	0.978
136	136	0.0866
137	137	0.766
138	138	0.0265
139	139	0.0663
14	14	0.567
140	140	0.805
141	141	0.319
142	142	0.374
143	143	0.106
144	144	0.427
145	145	0.212
146	146	0.095
147	147	0.855
148	148	0.101
149	149	0.0574
15	15	0.247
150	150	0.27
151	151	0.576
152	152	0.0159
153	153	0.429
154	154	0.737
155	155	0.719
156	156	0.107
157	157	0.556
158	158	0.663
159	159	0.134
160	160	0.13
161	161	0.244
162	162	0.57
163	163	0.0325
164	164	0.233
165	165	0.242
166	166	0.933
167	167	0.286
168	168	0.242
169	169	0.0193
17	17	0.126
18	18	0.757
19	19	0.0525
2	2	0.0562
20	20	0.342
21	21	0.833
22	22	0.209
23	23	0.314
24	24	0.712
25	25	0.921
26	26	0.00754
27	27	0.498
28	28	0.777
29	29	0.839
3	3	0.487
30	30	0.18
31	31	0.62
32	32	0.0179
33	33	0.263
34	34	0.351
35	35	0.913
36	36	0.477
37	37	0.0729
38	38	0.36
39	39	0.161
4	4	0.417
40	40	0.427
41	41	0.348
42	42	0.96
43	43	0.24
44	44	0.936
45	45	0.173
46	46	0.463
47	47	0.596
48	48	0.424
49	49	0.373
5	5	0.686
50	50	0.449
51	51	0.622
52	52	0.0284
53	53	0.607
54	54	0.595
55	55	0.417
56	56	0.383
57	57	0.346
58	58	0.541
59	59	0.094
6	6	0.638
60	60	0.034
61	61	0.391
62	62	0.868
63	63	0.287
64	64	0.878
65	65	0.25
66	66	0.382
67	67	0.251
68	68	0.564
69	69	0.89
7	7	0.126
70	70	0.291
71	71	0.224
72	72	0.714
73	73	0.149
74	74	0.804
75	75	0.425
76	76	0.286
77	77	0.0326
78	78	0.0553
79	79	0.817
8	8	0.733
80	80	0.742
81	81	0.52
82	82	0.171
83	83	0.91
84	84	0.565
85	85	0.12
86	86	0.337
87	87	0.19
88	88	0.996
89	89	0.151
9	9	0.536
90	90	0.697
91	91	0.854
92	92	0.399
93	93	0.99
94	94	0.113
95	95	0.241
96	96	0.5
97	97	0.378
98	98	0.805
99	99	0.0576

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: CNhs11098

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011418 mouse intestine- neonate N10 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)
0000305 (mouse neonate N10 sample)
0011418 (mouse intestine- neonate N10 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:0000160,UBERON:0000479,UBERON:0001007,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:0000925,UBERON:0006598,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0005409,UBERON:0007026,UBERON:0006595
+|DRA_sample_Accession=CAGE@SAMD00004753
+|accession_numbers=CAGE;DRX009000;DRR009874;DRZ001299;DRZ002682;DRZ012649;DRZ014032
+|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=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000004,FF:0000303,FF:0000305,FF:0011418
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:80555320..80555378,-!p1@Creb3l3!2.17!170.59!Creb3l3;;chr5:148118639..148118715,-!p1@Cdx2!2.15!140.76!Cdx2;;chr10:88969376..88969395,-!p1@Nr1h4!2.13!134.92!Nr1h4;;chr3:3634145..3634161,+!p1@Hnf4g!1.97!91.83!Hnf4g;;chr16:38294860..38294924,-!p1@Nr1i2!1.85!69.99!Nr1i2;;chr2:163372884..163372904,+!p1@Hnf4a!1.83!65.90!Hnf4a;;chr1:137155026..137155042,-!p1@Elf3!1.73!293.81!Elf3;;chr2:164228702..164228719,+!p1@Rbpjl!1.67!45.62!Rbpjl;;chr10:22539932..22539956,-!p1@Tcf21!1.56!91.24!Tcf21;;chr2:163332558..163332596,+!p2@Hnf4a!1.52!31.78!Hnf4a;;chr8:77396591..77396639,+!p1@Isx!1.45!26.91!Isx;;chr2:180069370..180069409,-!p1@Gata5!1.41!29.05!Gata5;;chr18:61195843..61195864,-!p2@Cdx1!1.41!24.57!Cdx1;;chr19:43686789..43686811,+!p1@Nkx2-3!1.40!24.18!Nkx2-3;;chr14:63864056..63864102,-!p1@Gata4!1.37!38.21!Gata4;;chr8:77397095..77397127,+!p2@Isx!1.37!22.23!Isx;;chr17:27865882..27865901,-!p1@Spdef!1.32!19.89!Spdef;;chr7:148452314..148452329,-!p1@Irf7!1.29!125.56!Irf7;;chr10:80555398..80555409,-!p2@Creb3l3!1.29!18.52!Creb3l3;;chr4:133109285..133109308,+!p1@Nr0b2!1.29!18.52!Nr0b2;;chr18:64499674..64499696,+!p1@Onecut2!1.28!30.61!Onecut2;;chr9:59797525..59797538,-!p2@Nr2e3!1.28!18.13!Nr2e3;;chr9:59796270..59796294,-!p4@Nr2e3!1.28!17.94!Nr2e3;;chr2:173044380..173044432,-!p1@Zbp1!1.27!41.92!Zbp1;;chr8:123608252..123608268,+!p1@Foxf1a!1.26!25.35!Foxf1a;;chr2:103123925..103123959,-!p3@Ehf!1.26!17.35!Ehf;;chr18:61195865..61195880,-!p1@Cdx1!1.26!17.35!Cdx1;;chr2:103143336..103143367,-!p1@Ehf!1.25!26.91!Ehf;;chr1:173144100..173144138,+!p2@Nr1i3!1.24!16.18!Nr1i3;;chr5:148118840..148118857,-!p2@Cdx2!1.23!15.99!Cdx2;;chr1:173144144..173144176,+!p1@Nr1i3!1.21!15.21!Nr1i3;;chr9:59796330..59796350,-!p6@Nr2e3!1.21!15.21!Nr2e3;;chr3:94176733..94176794,+!p1@Rorc!1.20!113.08!Rorc;;chr7:19608891..19608895,-!p1@Foxa3!1.20!19.30!Foxa3;;chr6:64679112..64679126,+!p1@Atoh1!1.20!15.01!Atoh1;;chr9:59797503..59797513,-!p3@Nr2e3!1.18!14.23!Nr2e3;;chr3:3508024..3508069,+!p2@Hnf4g!1.17!13.84!Hnf4g;;chr19:53384910..53384937,+!p3@Mxi1!1.16!37.43!Mxi1;;chr10:44178521..44178557,-!p1@Prdm1!1.15!23.59!Prdm1;;chr18:11052485..11052508,+!p2@Gata6!1.13!35.09!Gata6;;chr13:31717548..31717596,+!p1@Foxf2!1.13!24.76!Foxf2;;chr14:99697871..99697934,+!p1@Klf5!1.11!236.10!Klf5;;chr5:135582751..135582788,+!p1@Mlxipl!1.11!47.57!Mlxipl;;chr8:59799772..59799789,+!p1@Hand2!1.11!33.92!Hand2;;chr18:64499706..64499721,+!p2@Onecut2!1.10!16.38!Onecut2;;chr8:77396650..77396662,+!p4@Isx!1.10!11.50!Isx;;chr6:86619104..86619119,-!p1@Mxd1!1.09!93.00!Mxd1;;chr5:148118792..148118806,-!p3@Cdx2!1.09!11.31!Cdx2;;chr11:57645506..57645523,-!p1@Hand1!1.08!10.92!Hand1;;chr3:30039329..30039355,-!p5@Mecom!1.07!10.72!Mecom;;chr5:115421065..115421088,-!p1@Hnf1a!1.06!10.53!Hnf1a;;chr10:44178375..44178390,-!p2@Prdm1!1.03!13.26!Prdm1;;chr8:77397492..77397514,+!p3@Isx!1.03!9.75!Isx;;chr10:88996336..88996380,-!p2@Nr1h4!1.02!11.89!Nr1h4;;chr2:160192793..160192809,-!p1@Mafb!0.99!134.72!Mafb;;chr1:165219345..165219366,-!p7@Prrx1!0.97!8.38!Prrx1;;chr8:118231678..118231692,-!p2@Maf!0.96!75.26!Maf;;chr2:163372869..163372882,+!p3@Hnf4a!0.96!8.19!Hnf4a;;chr14:63890545..63890560,-!p5@Gata4!0.96!8.19!Gata4;;chr2:77357622..77357704,-!p1@Zfp385b!0.95!22.03!Zfp385b;;chr5:144951153..144951203,+!p1@Bhlha15!0.95!11.70!Bhlha15;;chr3:90046995..90047031,-!p2@Creb3l4!0.95!9.94!Creb3l4;;chr11:98614335..98614349,+!p8@Thra!0.95!7.99!Thra;;chr1:194979315..194979359,+!p1@Irf6!0.93!47.38!Irf6;;chr10:44178474..44178487,-!p4@Prdm1!0.93!10.92!Prdm1;;chr7:17642177..17642223,-!p3@Hif3a!0.92!7.41!Hif3a;;chr1:194982959..194983007,+!p5@Irf6!0.92!7.41!Irf6;;chr13:55932591..55932622,-!p1@Pitx1!0.91!8.58!Pitx1;;chr3:3508005..3508021,+!p3@Hnf4g!0.91!7.21!Hnf4g;;chr9:59797133..59797145,-!p7@Nr2e3!0.91!7.21!Nr2e3;;chr10:44178493..44178520,-!p3@Prdm1!0.90!9.94!Prdm1;;chr11:83664365..83664383,+!p1@Hnf1b!0.90!7.02!Hnf1b;;chr18:11052642..11052659,+!p1@Gata6!0.89!35.68!Gata6;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.89!20.28!Tfcp2l1;;chr9:59796372..59796383,-!p8@Nr2e3!0.89!6.82!Nr2e3;;chr2:19367259..19367278,+!p1@Ptf1a!0.87!6.43!Ptf1a;;chr8:123260252..123260264,+!p1@Irf8!0.86!46.40!Irf8;;chr1:138857048..138857071,-!p2@Nr5a2!0.86!6.24!Nr5a2;;chr6:52190467..52190500,-!p1@Hoxa10!0.86!6.24!Hoxa10;;chr13:31650026..31650045,+!p2@Foxq1!0.84!10.33!Foxq1;;chr6:99216375..99216395,-!p5@Foxp1!0.84!5.85!Foxp1;;chr5:148118614..148118625,-!p4@Cdx2!0.84!5.85!Cdx2;;chr5:148118809..148118832,-!p5@Cdx2!0.82!5.65!Cdx2;;chr6:16848443..16848459,-!p3@Tfec!0.82!5.65!Tfec;;chr11:53583544..53583559,+!p1@Irf1!0.81!99.43!Irf1;;chr2:180069410..180069421,-!p3@Gata5!0.81!5.46!Gata5;;chr2:103143315..103143328,-!p2@Ehf!0.81!5.46!Ehf;;chr10:79389784..79389833,+!p1@Arid3a!0.80!30.22!Arid3a;;chr1:57029281..57029326,-!p1@Satb2!0.80!8.58!Satb2;;chr10:127095407..127095440,+!p3@Stat6!0.80!6.63!Stat6;;chr14:63890519..63890539,-!p3@Gata4!0.80!5.26!Gata4;;chr13:31717597..31717613,+!p2@Foxf2!0.80!5.26!Foxf2;;chr8:77397190..77397202,+!p5@Isx!0.80!5.26!Isx;;chr15:97738692..97738747,-!p1@Vdr!0.78!29.83!Vdr;;chr13:31650185..31650201,+!p1@Foxq1!0.78!19.11!Foxq1;;chr2:166888058..166888105,-!p2@Znfx1!0.78!17.55!Znfx1;;chr18:11052456..11052477,+!p3@Gata6!0.78!16.57!Gata6;;chr7:17642018..17642045,-!p4@Hif3a!0.78!5.85!Hif3a;;chr2:180069640..180069660,-!p4@Gata5!0.78!5.07!Gata5;;chr14:63890491..63890516,-!p2@Gata4!0.78!5.07!Gata4;;chr6:39068163..39068176,-!p2@Parp12!0.77!9.75!Parp12;;chr2:153067233..153067236,-!p4@Plagl2!0.77!6.04!Plagl2;;chr5:67490284..67490302,-!p1@Phox2b!0.77!4.87!Phox2b;;chr12:58646974..58647003,-!p1@Foxa1!0.76!6.63!Foxa1;;chr6:16848395..16848416,-!p2@Tfec!0.76!5.65!Tfec;;chr5:120121446..120121461,+!p2@Tbx3!0.75!16.77!Tbx3;;chr2:153067079..153067090,-!p2@Plagl2!0.75!10.33!Plagl2;;chr2:173044357..173044377,-!p2@Zbp1!0.75!6.82!Zbp1;;chr1:194979361..194979373,+!p2@Irf6!0.75!6.43!Irf6;;chr6:99216360..99216372,-!p8@Foxp1!0.75!4.68!Foxp1;;chr2:153067094..153067130,-!p1@Plagl2!0.74!125.17!Plagl2;;chr11:96153767..96153822,+!p1@Hoxb6!0.74!7.21!Hoxb6;;chr19:5560600..5560617,-!p1@Ovol1!0.74!5.65!Ovol1;;chr2:79296783..79296801,-!p1@Neurod1!0.74!4.48!Neurod1;;chr19:6996243..6996293,-!p1@Esrra!0.72!52.84!Esrra;;chr3:128916868..128916890,+!p1@Pitx2!0.72!6.04!Pitx2;;chr10:44178575..44178590,-!p5@Prdm1!0.71!5.26!Prdm1;;chr11:83664334..83664353,+!p2@Hnf1b!0.71!4.09!Hnf1b;;chr2:153067445..153067460,-!p6@Plagl2!0.71!4.09!Plagl2;;chr6:83020355..83020371,-!p1@Tlx2!0.71!4.09!Tlx2;;chr5:120121020..120121049,+!p1@Tbx3!0.70!27.49!Tbx3;;chr2:133377954..133377973,+!p1@Bmp2!0.70!14.43!Bmp2;;chr10:126778916..126778974,-!p1@Gli1!0.70!9.75!Gli1;;chr6:115311030..115311065,+!p4@Pparg!0.70!6.04!Pparg;;chr10:30375579..30375616,-!p3@Ncoa7!0.69!10.14!Ncoa7;;chr1:138846079..138846103,-!p6@Nr5a2!0.69!3.90!Nr5a2;;chr17:28409136..28409150,+!p3@Ppard!0.69!3.90!Ppard;;chr19:43686882..43686906,+!p2@Nkx2-3!0.67!3.70!Nkx2-3;;chr9:59797088..59797101,-!p9@Nr2e3!0.67!3.70!Nr2e3;;chr8:77397026..77397036,+!p6@Isx!0.67!3.70!Isx;;chr6:108610610..108610676,+!p1@Bhlhe40!0.66!202.18!Bhlhe40;;chr4:55545337..55545357,-!p1@Klf4!0.66!61.41!Klf4;;chr15:102865131..102865151,+!p2@Hoxc4!0.66!4.09!Hoxc4;;chr10:88996295..88996335,-!p3@Nr1h4!0.65!4.29!Nr1h4;;chr1:138857076..138857105,-!p1@Nr5a2!0.65!3.51!Nr5a2;;chr5:115420882..115420896,-!p3@Hnf1a!0.65!3.51!Hnf1a;;chr9:74709695..74709722,+!p1@Onecut1!0.65!3.51!Onecut1;;chr8:118231705..118231722,-!p3@Maf!0.64!31.19!Maf;;chr1:39250584..39250643,+!p1@Npas2!0.64!19.50!Npas2;;chr3:89197057..89197114,-!p1@Zbtb7b!0.64!13.06!Zbtb7b;;chr7:17642053..17642066,-!p2@Hif3a!0.64!5.07!Hif3a;;chr8:79426176..79426275,+!p1@Nr3c2!0.63!18.91!Nr3c2;;chr5:115421126..115421137,-!p4@Hnf1a!0.63!3.31!Hnf1a;;chr1:138846009..138846038,-!p3@Nr5a2!0.62!3.70!Nr5a2;;chr16:87699237..87699279,+!p1@Bach1!0.61!38.02!Bach1;;chr10:20880629..20880683,-!p1@Myb!0.61!10.14!Myb;;chr18:36441119..36441158,+!p2@Pura!0.61!8.58!Pura;;chr11:53583960..53584007,+!p2@Irf1!0.61!7.41!Irf1;;chr11:96055613..96055628,+!p1@Hoxb13!0.61!3.12!Hoxb13;;chr10:80555299..80555306,-!p3@Creb3l3!0.61!3.12!Creb3l3;;chr12:39510206..39510249,+!p3@Etv1!0.61!3.12!Etv1;;chr19:53384985..53385042,+!p1@Mxi1!0.59!108.98!Mxi1;;chr19:6996294..6996324,-!p2@Esrra!0.59!23.01!Esrra;;chr7:51787434..51787448,-!p1@Spib!0.59!4.48!Spib;;chr6:52190668..52190682,-!p3@Hoxa10!0.59!2.92!Hoxa10;;chr5:148081686..148081715,+!p1@Pdx1!0.59!2.92!Pdx1;;chr10:80555285..80555291,-!p4@Creb3l3!0.59!2.92!Creb3l3;;chr4:154010918..154010931,-!p1@Prdm16!0.58!9.55!Prdm16;;chr12:78063146..78063159,-!p2@Max!0.58!8.38!Max;;chr15:35225845..35225867,+!p1@Osr2!0.58!8.19!Osr2;;chr18:11052606..11052633,+!p4@Gata6!0.58!8.19!Gata6;;chr10:80598968..80599012,+!p5@Zbtb7a!0.58!3.90!Zbtb7a;;chr11:96145450..96145517,+!p2@Hoxb7!0.57!4.48!Hoxb7;;chr5:42155788..42155800,-!p1@Nkx3-2!0.57!2.73!Nkx3-2;;chr6:52168685..52168715,-!p9@Hoxa7!0.57!2.73!Hoxa7;;chr2:147871627..147871641,-!p1@Foxa2!0.57!2.73!Foxa2;;chr15:102828658..102828678,+!p1@Hoxc6!0.57!2.73!Hoxc6;;chr12:39507680..39507715,+!p2@Etv1!0.56!5.85!Etv1;;chr6:52154414..52154462,-!p1@Hoxa5!0.56!3.90!Hoxa5;;chr6:52154386..52154407,-!p2@Hoxa5!0.56!3.51!Hoxa5;;chr8:124806048..124806094,+!p1@Zfpm1!0.55!29.24!Zfpm1;;chr6:39068210..39068251,-!p1@Parp12!0.55!14.43!Parp12;;chr10:79390075..79390115,+!p2@Arid3a!0.55!10.33!Arid3a;;chr2:153067138..153067147,-!p3@Plagl2!0.55!4.68!Plagl2;;chr7:134519473..134519502,-!p3@Zfp747!0.55!3.70!Zfp747;;chr15:85566014..85566045,+!p3@Ppara!0.55!3.70!Ppara;;chr2:91035254..91035271,-!p3@Nr1h3!0.55!3.31!Nr1h3;;chr4:114581497..114581519,-!p2@Foxd2!0.55!2.53!Foxd2;;chr9:59797875..59797929,-!p1@Nr2e3!0.55!2.53!Nr2e3;;chr7:150155143..150155156,-!p1@Ascl2!0.55!2.53!Ascl2;;chr11:96164821..96164865,+!p1@Hoxb5!0.55!2.53!Hoxb5;;chr14:79915425..79915501,+!p1@Elf1!0.54!27.49!Elf1;;chr6:52163319..52163342,-!p1@Hoxa3!0.54!3.90!Hoxa3;;chr7:20408047..20408125,-!p1@Bcl3!0.52!33.73!Bcl3;;chr1:135320989..135321043,-!p1@Sox13!0.52!32.75!Sox13;;chr4:94718861..94718872,-!p2@Jun!0.52!22.42!Jun;;chr2:74549968..74549996,+!p1@Hoxd3!0.52!3.12!Hoxd3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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011418
 |is_obsolete=
+|library_id=CNhs11098
+|library_id_phase_based=2:CNhs11098
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;755
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;755
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N10.CNhs11098.755-23A5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N10.CNhs11098.755-23A5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N10.CNhs11098.755-23A5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N10.CNhs11098.755-23A5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N10.CNhs11098.755-23A5.mm9.nobarcode.rdna.fa.gz
 |name=intestine, neonate N10
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11098,LSID733,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.211492490992178,0,0,0,0,0,0.0717498489957865,0,0.0770667629889114,0,0.000645396235375906,0.252077366612137,0,0,0,0,0,0,0.0584916010996163,0,0,0,0,0,0,0,0,0,0,0,0.0386774267005042,0,0.224699087036416,0,0,0,0.754282428882241,0,0.00993725998827295,-0.0150617932830232,0.0115144141016268,0.0228238956039449,0.0256589746735024,0,0,0,0,0,0,0,0,0,0,0.0773548534010084,0,0.229522065120413,0,0,0,0,0,0,0,0,0,0.0230668657382024,0.00998635147200776,0.129419991536714,-0.0150986844867382,0.00208471770365073,0,0,0.0068902673130472,0,0.0773548534010084,0,0,0.0934232539729186,0.0581994079423526,0.216696017843946,0,0,0,0,0,0.0773548534010084,-0.00151549782172629,0.0145180315843212,-0.0446106538114684,0,0,0.0773548534010084,0,0
 |rna_box=23
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
 |top_motifs=HNF4A_NR2F1,2:2.33740143994;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.8625486815;RXRA_VDR{dimer}:1.85267254968;FOXM1:1.75191165205;DMAP1_NCOR{1,2}_SMARC:1.74084853199;CDX1,2,4:1.74075322701;SNAI1..3:1.6462647646;HNF1A:1.63807212431;NR6A1:1.62208120276;ARID5B:1.33515736286;IRF1,2:1.29463277395;MYBL2:1.21099828655;NFIX:1.18323176957;ATF6:1.1288474286;ZEB1:1.09273890901;TLX1..3_NFIC{dimer}:1.07206878401;PDX1:1.04170439877;XCPE1{core}:0.986480721103;ESRRA:0.966107470295;SREBF1,2:0.941242132104;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.915336745494;SP1:0.908233615904;ZNF148:0.852118273146;FOSL2:0.849571498745;MYOD1:0.840419797041;SRF:0.823308051255;TOPORS:0.821193562805;NR1H4:0.700816497808;GZF1:0.654471040881;AR:0.611887317656;TAL1_TCF{3,4,12}:0.583032384681;TP53:0.557583879347;ZNF423:0.537889554756;TBP:0.537661008764;TBX4,5:0.528055991328;NKX2-1,4:0.513734304861;TLX2:0.476805609098;FOXA2:0.450912184615;POU1F1:0.446361416084;RBPJ:0.443161685527;MAZ:0.440931006922;STAT2,4,6:0.435799927597;TFAP4:0.43395007659;GATA6:0.432831432298;ESR1:0.410778586111;ETS1,2:0.357447025024;ZNF238:0.356683176678;LMO2:0.325500875976;EVI1:0.306404056844;EBF1:0.296347718224;FOS_FOS{B,L1}_JUN{B,D}:0.292018684758;STAT1,3:0.286803352718;TEAD1:0.270827776958;FOX{D1,D2}:0.256512668542;T:0.211766662385;GTF2A1,2:0.20365405573;FOXP1:0.187306617717;ELF1,2,4:0.170212409955;GTF2I:0.150309525827;TFCP2:0.136937056746;FOX{I1,J2}:0.104843606817;CDC5L:0.100387187844;STAT5{A,B}:0.100235973321;IRF7:0.0968996460965;FOXD3:0.0756863157058;MYFfamily:0.0721408275437;SPI1:0.0720786924376;GFI1:0.0667293173032;HAND1,2:0.062977361672;ADNP_IRX_SIX_ZHX:0.0544202865007;BPTF:0.0364161685793;REST:-0.0058309161139;HBP1_HMGB_SSRP1_UBTF:-0.0138134259256;IKZF1:-0.0372661520499;NKX2-3_NKX2-5:-0.0445967505603;IKZF2:-0.0487887678225;LEF1_TCF7_TCF7L1,2:-0.0547912095422;TFAP2B:-0.0551850311744;DBP:-0.0725955271771;FOXN1:-0.074028472898;bHLH_family:-0.0921375937018;SMAD1..7,9:-0.0955024032806;NKX3-2:-0.104879891997;POU6F1:-0.112633795947;HIF1A:-0.114796455913;CEBPA,B_DDIT3:-0.120617562942;HIC1:-0.135182908215;FOX{F1,F2,J1}:-0.142995355579;NFKB1_REL_RELA:-0.143514652167;NR5A1,2:-0.145545649353;JUN:-0.15304079326;EN1,2:-0.154630732401;VSX1,2:-0.158127363815;GLI1..3:-0.176067685909;HMX1:-0.187057656927;NANOG:-0.203815278761;TFAP2{A,C}:-0.208885133856;ZBTB6:-0.218420146668;SPIB:-0.223067654335;ATF5_CREB3:-0.224433153404;GFI1B:-0.230797534601;SPZ1:-0.235845620729;E2F1..5:-0.237395037851;FOXQ1:-0.255455547345;PBX1:-0.264222481026;FOXO1,3,4:-0.279343273976;GCM1,2:-0.285618207746;BACH2:-0.292897432194;LHX3,4:-0.294181401328;EP300:-0.295090906912;RUNX1..3:-0.296758299022;HES1:-0.300324941085;MTF1:-0.310595635991;NKX6-1,2:-0.311065835776;MTE{core}:-0.322939511877;PATZ1:-0.325904142005;PAX5:-0.339707668963;MED-1{core}:-0.352402544748;RREB1:-0.360394568987;CUX2:-0.3625160778;NFY{A,B,C}:-0.382661658625;TGIF1:-0.39289968438;MAFB:-0.397024019502;NR3C1:-0.397237124513;PRDM1:-0.408378836822;NFIL3:-0.414436544967;PAX1,9:-0.422255675886;ELK1,4_GABP{A,B1}:-0.423365363854;GATA4:-0.427227799626;TEF:-0.441367341412;PRRX1,2:-0.443847320978;ALX4:-0.448562166326;HOXA9_MEIS1:-0.456727130016;NFE2:-0.462052250819;NKX2-2,8:-0.468733771921;NFATC1..3:-0.475846798366;PITX1..3:-0.484687375405;ZNF384:-0.5092049508;EGR1..3:-0.509812645332;ZFP161:-0.510278655063;POU2F1..3:-0.519375340399;ATF2:-0.521721708709;FOXL1:-0.525988931314;BREu{core}:-0.52895410501;ONECUT1,2:-0.535307336572;SOX5:-0.536893955622;PPARG:-0.543055369459;PAX6:-0.57309111573;PAX2:-0.586270245696;YY1:-0.603970580874;MYB:-0.606541705091;PAX4:-0.634240063471;RFX1:-0.647326089622;NFE2L2:-0.64930917512;SOX2:-0.64979133112;MEF2{A,B,C,D}:-0.664235872066;HLF:-0.66853379439;NKX3-1:-0.671535280363;CREB1:-0.67280078931;KLF4:-0.675345597406;TFDP1:-0.677070168933;HSF1,2:-0.683343239711;NHLH1,2:-0.686461340607;CRX:-0.689810919862;HMGA1,2:-0.70993265044;UFEwm:-0.710364324638;OCT4_SOX2{dimer}:-0.746325316108;RFX2..5_RFXANK_RFXAP:-0.750647196666;MZF1:-0.799669151424;ZIC1..3:-0.817295625242;RORA:-0.821178238714;ZNF143:-0.857181523921;AHR_ARNT_ARNT2:-0.927749738158;SOX{8,9,10}:-0.947969474388;POU3F1..4:-0.957512760299;ATF4:-0.963495291677;NFE2L1:-0.974595348835;SOX17:-1.00732656209;POU5F1:-1.04338031357;NANOG{mouse}:-1.0710858082;NRF1:-1.08754308231;ZBTB16:-1.09915389784;AIRE:-1.17126418217;RXR{A,B,G}:-1.18516695974;PAX8:-1.20000491335;ALX1:-1.24401858907;FOXP3:-1.40950417581;HOX{A4,D4}:-1.72638267006;HOX{A5,B5}:-1.85803073576
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:755-23A5;search_select_hide=table117:755-23A5
 }}

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FF:755-23A5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:20, 4 June 2020

CNhs11098

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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