FF:827-18D1: Difference between revisions

Latest revision as of 19:21, 4 June 2020

Name:	intestine, neonate N20
Species:	Mouse (Mus musculus)
Library ID:	CNhs11187
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	intestine
dev stage	20 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		SAMD00005244

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11187		CAGE		DRX009001		DRR009875

Accession ID Mm9

Library id		BAM		CTSS
CNhs11187		DRZ001300		DRZ002683

Accession ID Mm10

Library id		BAM		CTSS
CNhs11187		DRZ012650		DRZ014033

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

CNhs11187

0	0
1	0
10	0
100	0
1000	0
1001	0
1002	0.0569
1003	-0.102
1004	0
1005	0
1006	-0.0711
1007	-0.0345
1008	1.889
1009	0.0728
101	-0.0836
1010	0
1011	-0.111
1012	0
1013	0.229
1014	-0.0874
1015	-0.303
1016	-0.163
1017	0
1018	0.278
1019	0
102	0
1020	0
1021	0
1022	0
1023	0
1024	0
1025	0.505
1026	0
1027	-0.048
1028	0
1029	0.63
103	0.226
1030	0
1031	-0.105
1032	0.416
1033	-0.0752
1034	0
1035	0
1036	-0.223
1037	0
1038	0.108
1039	0.166
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: CNhs11187

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.015
MA0003.1	MA0003.1	0.083
MA0004.1	MA0004.1	0.676
MA0006.1	MA0006.1	0.0735
MA0007.1	MA0007.1	0.483
MA0009.1	MA0009.1	0.663
MA0014.1	MA0014.1	0.601
MA0017.1	MA0017.1	3.71966e-18
MA0018.2	MA0018.2	0.0109
MA0019.1	MA0019.1	0.311
MA0024.1	MA0024.1	0.0241
MA0025.1	MA0025.1	0.0778
MA0027.1	MA0027.1	0.653
MA0028.1	MA0028.1	0.167
MA0029.1	MA0029.1	0.591
MA0030.1	MA0030.1	0.632
MA0031.1	MA0031.1	0.663
MA0035.2	MA0035.2	7.80492e-5
MA0038.1	MA0038.1	0.379
MA0039.2	MA0039.2	0.018
MA0040.1	MA0040.1	0.186
MA0041.1	MA0041.1	0.263
MA0042.1	MA0042.1	0.852
MA0043.1	MA0043.1	0.0396
MA0046.1	MA0046.1	7.8573e-29
MA0047.2	MA0047.2	0.0613
MA0048.1	MA0048.1	0.493
MA0050.1	MA0050.1	2.32909e-7
MA0051.1	MA0051.1	2.8158e-5
MA0052.1	MA0052.1	2.67406e-4
MA0055.1	MA0055.1	0.364
MA0057.1	MA0057.1	0.167
MA0058.1	MA0058.1	0.461
MA0059.1	MA0059.1	0.991
MA0060.1	MA0060.1	5.27906e-4
MA0061.1	MA0061.1	0.377
MA0062.2	MA0062.2	0.108
MA0065.2	MA0065.2	9.89822e-15
MA0066.1	MA0066.1	0.216
MA0067.1	MA0067.1	0.279
MA0068.1	MA0068.1	0.295
MA0069.1	MA0069.1	0.197
MA0070.1	MA0070.1	0.217
MA0071.1	MA0071.1	0.354
MA0072.1	MA0072.1	0.306
MA0073.1	MA0073.1	0.891
MA0074.1	MA0074.1	0.0854
MA0076.1	MA0076.1	0.0872
MA0077.1	MA0077.1	0.676
MA0078.1	MA0078.1	0.718
MA0079.2	MA0079.2	0.264
MA0080.2	MA0080.2	0.00559
MA0081.1	MA0081.1	0.384
MA0083.1	MA0083.1	0.586
MA0084.1	MA0084.1	0.65
MA0087.1	MA0087.1	0.894
MA0088.1	MA0088.1	0.728
MA0090.1	MA0090.1	0.779
MA0091.1	MA0091.1	0.759
MA0092.1	MA0092.1	0.308
MA0093.1	MA0093.1	0.619
MA0099.2	MA0099.2	0.0175
MA0100.1	MA0100.1	0.18
MA0101.1	MA0101.1	0.896
MA0102.2	MA0102.2	0.124
MA0103.1	MA0103.1	4.82241e-5
MA0104.2	MA0104.2	0.149
MA0105.1	MA0105.1	0.0933
MA0106.1	MA0106.1	0.505
MA0107.1	MA0107.1	0.868
MA0108.2	MA0108.2	0.487
MA0111.1	MA0111.1	0.962
MA0112.2	MA0112.2	1.12886e-5
MA0113.1	MA0113.1	0.743
MA0114.1	MA0114.1	1.28767e-22
MA0115.1	MA0115.1	1.25129e-11
MA0116.1	MA0116.1	0.223
MA0117.1	MA0117.1	0.768
MA0119.1	MA0119.1	0.0461
MA0122.1	MA0122.1	0.651
MA0124.1	MA0124.1	0.383
MA0125.1	MA0125.1	0.0724
MA0131.1	MA0131.1	0.342
MA0135.1	MA0135.1	0.984
MA0136.1	MA0136.1	0.0828
MA0137.2	MA0137.2	0.68
MA0138.2	MA0138.2	0.405
MA0139.1	MA0139.1	0.0467
MA0140.1	MA0140.1	0.0461
MA0141.1	MA0141.1	5.01623e-5
MA0142.1	MA0142.1	0.39
MA0143.1	MA0143.1	0.332
MA0144.1	MA0144.1	0.0882
MA0145.1	MA0145.1	0.00446
MA0146.1	MA0146.1	0.264
MA0147.1	MA0147.1	0.262
MA0148.1	MA0148.1	0.00327
MA0149.1	MA0149.1	0.0417
MA0150.1	MA0150.1	0.698
MA0152.1	MA0152.1	0.057
MA0153.1	MA0153.1	4.93591e-28
MA0154.1	MA0154.1	0.0103
MA0155.1	MA0155.1	0.202
MA0156.1	MA0156.1	0.448
MA0157.1	MA0157.1	0.327
MA0159.1	MA0159.1	0.00177
MA0160.1	MA0160.1	0.00418
MA0162.1	MA0162.1	0.214
MA0163.1	MA0163.1	0.0125
MA0164.1	MA0164.1	0.947
MA0258.1	MA0258.1	0.00886
MA0259.1	MA0259.1	0.265

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: CNhs11187

Novel motif	Logo	P-value
1	1	0.15
10	10	0.148
100	100	0.913
101	101	0.907
102	102	0.658
103	103	0.116
104	104	0.976
105	105	0.386
106	106	0.00801
107	107	0.014
108	108	0.605
109	109	0.075
11	11	0.165
110	110	0.184
111	111	0.0902
112	112	0.0104
113	113	0.582
114	114	0.0572
115	115	0.685
116	116	0.275
117	117	0.296
118	118	0.648
119	119	0.0581
12	12	0.704
120	120	0.643
121	121	0.718
122	122	0.605
123	123	0.292
124	124	0.978
125	125	0.343
126	126	0.152
127	127	0.11
128	128	0.0623
129	129	0.487
13	13	0.00752
130	130	0.948
131	131	0.0409
132	132	0.729
133	133	0.984
134	134	0.99
135	135	0.86
136	136	0.299
137	137	0.524
138	138	0.913
139	139	0.0825
14	14	0.625
140	140	0.129
141	141	0.149
142	142	0.26
143	143	0.732
144	144	0.46
145	145	0.079
146	146	0.255
147	147	0.442
148	148	0.322
149	149	0.451
15	15	0.159
150	150	0.336
151	151	0.3
152	152	0.0621
153	153	0.962
154	154	0.66
155	155	0.314
156	156	0.302
157	157	0.986
158	158	0.689
159	159	0.611
160	160	0.192
161	161	0.336
162	162	0.917
163	163	0.346
164	164	0.0769
165	165	0.345
166	166	0.498
167	167	0.961
168	168	0.867
169	169	0.00933
17	17	0.0435
18	18	0.0394
19	19	0.0635
2	2	0.304
20	20	0.818
21	21	0.798
22	22	0.289
23	23	0.192
24	24	0.601
25	25	0.753
26	26	0.00307
27	27	0.456
28	28	0.64
29	29	0.291
3	3	0.225
30	30	0.497
31	31	0.565
32	32	0.0046
33	33	0.194
34	34	0.757
35	35	0.444
36	36	0.588
37	37	0.0299
38	38	0.32
39	39	0.249
4	4	0.383
40	40	0.308
41	41	0.299
42	42	0.465
43	43	0.208
44	44	0.103
45	45	0.418
46	46	0.225
47	47	0.296
48	48	0.278
49	49	0.156
5	5	0.479
50	50	0.495
51	51	0.538
52	52	0.0835
53	53	0.948
54	54	0.571
55	55	0.768
56	56	0.406
57	57	0.76
58	58	0.425
59	59	0.0427
6	6	0.873
60	60	0.0381
61	61	0.215
62	62	0.378
63	63	0.138
64	64	0.649
65	65	0.163
66	66	0.478
67	67	0.647
68	68	0.106
69	69	0.882
7	7	0.0749
70	70	0.0524
71	71	0.0735
72	72	0.438
73	73	0.125
74	74	0.855
75	75	0.144
76	76	0.745
77	77	0.097
78	78	0.0676
79	79	0.446
8	8	0.158
80	80	0.923
81	81	0.593
82	82	0.0987
83	83	0.34
84	84	0.483
85	85	0.0251
86	86	0.297
87	87	0.244
88	88	0.67
89	89	0.259
9	9	0.652
90	90	0.117
91	91	0.212
92	92	0.157
93	93	0.404
94	94	0.701
95	95	0.336
96	96	0.726
97	97	0.446
98	98	0.627
99	99	0.0656

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: CNhs11187

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011431 mouse intestine- neonate N20 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)
0000308 (mouse neonate N20 sample)
0011431 (mouse intestine- neonate N20 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@SAMD00005244
+|accession_numbers=CAGE;DRX009001;DRR009875;DRZ001300;DRZ002683;DRZ012650;DRZ014033
+|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:0000308,FF:0011431
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr3:3634145..3634161,+!p1@Hnf4g!2.70!497.95!Hnf4g;;chr5:148118639..148118715,-!p1@Cdx2!2.15!140.22!Cdx2;;chr10:80555320..80555378,-!p1@Creb3l3!2.14!158.19!Creb3l3;;chr1:137155026..137155042,-!p1@Elf3!2.00!538.39!Elf3;;chr2:163372884..163372904,+!p1@Hnf4a!1.98!94.38!Hnf4a;;chr10:88969376..88969395,-!p1@Nr1h4!1.96!90.78!Nr1h4;;chr16:38294860..38294924,-!p1@Nr1i2!1.92!81.79!Nr1i2;;chr2:163332558..163332596,+!p2@Hnf4a!1.82!65.61!Hnf4a;;chr6:86619104..86619119,-!p1@Mxd1!1.79!467.39!Mxd1;;chr2:180069370..180069409,-!p1@Gata5!1.77!67.41!Gata5;;chr14:63864056..63864102,-!p1@Gata4!1.65!74.60!Gata4;;chr3:3508024..3508069,+!p2@Hnf4g!1.65!44.04!Hnf4g;;chr15:97738692..97738747,-!p1@Vdr!1.63!218.41!Vdr;;chr8:77396591..77396639,+!p1@Isx!1.59!37.75!Isx;;chr2:164228702..164228719,+!p1@Rbpjl!1.53!33.26!Rbpjl;;chr18:61195843..61195864,-!p2@Cdx1!1.53!33.26!Cdx1;;chr5:135582751..135582788,+!p1@Mlxipl!1.48!113.25!Mlxipl;;chr18:61195865..61195880,-!p1@Cdx1!1.45!26.96!Cdx1;;chr1:173144100..173144138,+!p2@Nr1i3!1.45!26.96!Nr1i3;;chr6:64679112..64679126,+!p1@Atoh1!1.43!26.07!Atoh1;;chr17:27865882..27865901,-!p1@Spdef!1.42!25.17!Spdef;;chr19:5560600..5560617,-!p1@Ovol1!1.38!27.86!Ovol1;;chr2:173044380..173044432,-!p1@Zbp1!1.37!52.13!Zbp1;;chr5:148118840..148118857,-!p2@Cdx2!1.37!22.47!Cdx2;;chr17:28408632..28408682,+!p1@1810013A23Rik,p4@Ppard!1.35!21.57!Ppard;;chr14:99697871..99697934,+!p1@Klf5!1.34!401.77!Klf5;;chr2:103123925..103123959,-!p3@Ehf!1.34!20.67!Ehf;;chr7:148452314..148452329,-!p1@Irf7!1.33!137.52!Irf7;;chr7:19608891..19608895,-!p1@Foxa3!1.32!26.07!Foxa3;;chr8:77397095..77397127,+!p2@Isx!1.30!18.88!Isx;;chr15:35225845..35225867,+!p1@Osr2!1.29!45.84!Osr2;;chr18:64499674..64499696,+!p1@Onecut2!1.29!31.46!Onecut2;;chr11:70500401..70500460,-!p3@Camta2!1.28!17.98!Camta2;;chr10:22539932..22539956,-!p1@Tcf21!1.27!46.74!Tcf21;;chr8:79426176..79426275,+!p1@Nr3c2!1.26!83.59!Nr3c2;;chr14:63890545..63890560,-!p5@Gata4!1.26!17.08!Gata4;;chr17:28409136..28409150,+!p3@Ppard!1.26!17.08!Ppard;;chr18:64499706..64499721,+!p2@Onecut2!1.25!23.37!Onecut2;;chr5:148118792..148118806,-!p3@Cdx2!1.23!16.18!Cdx2;;chr5:138187583..138187602,+!p6@Tsc22d4!1.22!28.76!Tsc22d4;;chr2:103143336..103143367,-!p1@Ehf!1.22!25.17!Ehf;;chr8:118231678..118231692,-!p2@Maf!1.21!135.72!Maf;;chr11:57645506..57645523,-!p1@Hand1!1.21!15.28!Hand1;;chr2:163372869..163372882,+!p3@Hnf4a!1.19!14.38!Hnf4a;;chr3:89197057..89197114,-!p1@Zbtb7b!1.17!45.84!Zbtb7b;;chr5:144951153..144951203,+!p1@Bhlha15!1.16!19.77!Bhlha15;;chr5:115421065..115421088,-!p1@Hnf1a!1.16!13.48!Hnf1a;;chr8:77397492..77397514,+!p3@Isx!1.16!13.48!Isx;;chr6:39068163..39068176,-!p2@Parp12!1.14!24.27!Parp12;;chr18:11052485..11052508,+!p2@Gata6!1.13!35.05!Gata6;;chr19:43686789..43686811,+!p1@Nkx2-3!1.13!12.58!Nkx2-3;;chr4:148178559..148178603,+!p1@Casz1!1.12!35.05!Casz1;;chr5:120121446..120121461,+!p2@Tbx3!1.11!39.55!Tbx3;;chr2:173044357..173044377,-!p2@Zbp1!1.11!17.08!Zbp1;;chr1:165219345..165219366,-!p7@Prrx1!1.10!11.68!Prrx1;;chr3:30039329..30039355,-!p5@Mecom!1.10!11.68!Mecom;;chr4:55545051..55545110,-!p2@Klf4!1.07!13.48!Klf4;;chr3:3508005..3508021,+!p3@Hnf4g!1.07!10.79!Hnf4g;;chr1:173144144..173144176,+!p1@Nr1i3!1.07!10.79!Nr1i3;;chr1:138857048..138857071,-!p2@Nr5a2!1.07!10.79!Nr5a2;;chr8:77396650..77396662,+!p4@Isx!1.07!10.79!Isx;;chr11:98614335..98614349,+!p8@Thra!1.07!10.79!Thra;;chr4:55545337..55545357,-!p1@Klf4!1.06!157.29!Klf4;;chr13:31650185..31650201,+!p1@Foxq1!1.05!35.95!Foxq1;;chr12:86814833..86814846,+!p1@Fos!1.04!235.49!Fos;;chr14:76887526..76887555,+!p10@Tsc22d1!1.04!9.89!Tsc22d1;;chr19:6996243..6996293,-!p1@Esrra!1.02!105.16!Esrra;;chr5:120121020..120121049,+!p1@Tbx3!1.02!59.32!Tbx3;;chr1:194979315..194979359,+!p1@Irf6!1.02!58.42!Irf6;;chr19:53384910..53384937,+!p3@Mxi1!1.00!26.07!Mxi1;;chr2:180069410..180069421,-!p3@Gata5!1.00!8.99!Gata5;;chr10:80555398..80555409,-!p2@Creb3l3!1.00!8.99!Creb3l3;;chr14:63890519..63890539,-!p3@Gata4!1.00!8.99!Gata4;;chr8:77397190..77397202,+!p5@Isx!1.00!8.99!Isx;;chr11:53583544..53583559,+!p1@Irf1!0.98!145.61!Irf1;;chr11:98636531..98636559,-!p1@Nr1d1!0.98!50.33!Nr1d1;;chr3:90046995..90047031,-!p2@Creb3l4!0.98!10.79!Creb3l4;;chr5:120121169..120121171,+!p4@Tbx3!0.97!15.28!Tbx3;;chr4:124805061..124805087,-!p1@Zc3h12a!0.96!26.07!Zc3h12a;;chr2:79296783..79296801,-!p1@Neurod1!0.96!8.09!Neurod1;;chr4:133109285..133109308,+!p1@Nr0b2!0.96!8.09!Nr0b2;;chr2:180069640..180069660,-!p4@Gata5!0.96!8.09!Gata5;;chr10:61595830..61595846,+!p1@Neurog3!0.96!8.09!Neurog3;;chr14:63890491..63890516,-!p2@Gata4!0.96!8.09!Gata4;;chr2:166888058..166888105,-!p2@Znfx1!0.95!26.07!Znfx1;;chr10:20880629..20880683,-!p1@Myb!0.95!23.37!Myb;;chr8:123260252..123260264,+!p1@Irf8!0.94!55.73!Irf8;;chr8:123608252..123608268,+!p1@Foxf1a!0.94!11.68!Foxf1a;;chr11:98636400..98636418,-!p4@Nr1d1!0.92!9.89!Nr1d1;;chr15:85566014..85566045,+!p3@Ppara!0.91!9.89!Ppara;;chr5:148118809..148118832,-!p5@Cdx2!0.91!7.19!Cdx2;;chr8:77397169..77397182,+!p7@Isx!0.91!7.19!Isx;;chr14:76887566..76887579,+!p18@Tsc22d1!0.91!7.19!Tsc22d1;;chr7:20408047..20408125,-!p1@Bcl3!0.89!80.89!Bcl3;;chr2:133377954..133377973,+!p1@Bmp2!0.89!22.47!Bmp2;;chr18:36441119..36441158,+!p2@Pura!0.89!17.08!Pura;;chr10:88996295..88996335,-!p3@Nr1h4!0.89!8.09!Nr1h4;;chr13:31717548..31717596,+!p1@Foxf2!0.88!13.48!Foxf2;;chr17:87153519..87153533,+!p5@Epas1!0.88!9.89!Epas1;;chr3:94176733..94176794,+!p1@Rorc!0.87!52.13!Rorc;;chr11:98636508..98636524,-!p3@Nr1d1!0.87!8.09!Nr1d1;;chr6:39068181..39068206,-!p3@Parp12!0.86!13.48!Parp12;;chr1:57029281..57029326,-!p1@Satb2!0.86!9.89!Satb2;;chr2:103143315..103143328,-!p2@Ehf!0.86!6.29!Ehf;;chr6:83020355..83020371,-!p1@Tlx2!0.86!6.29!Tlx2;;chr6:99216360..99216372,-!p8@Foxp1!0.86!6.29!Foxp1;;chr7:20213752..20213778,-!p2@Relb!0.86!6.29!Relb;;chr3:128918394..128918413,+!p5@Pitx2!0.86!6.29!Pitx2;;chr15:85566051..85566080,+!p4@Ppara!0.85!7.19!Ppara;;chr1:135557526..135557551,-!p1@Zbed6!0.84!9.89!Zbed6;;chr7:134519473..134519502,-!p3@Zfp747!0.83!8.09!Zfp747;;chr18:11052642..11052659,+!p1@Gata6!0.82!30.56!Gata6;;chr12:78063146..78063159,-!p2@Max!0.82!15.28!Max;;chr6:37391910..37391928,-!p3@Creb3l2!0.81!6.29!Creb3l2;;chr5:148081686..148081715,+!p1@Pdx1!0.81!5.39!Pdx1;;chr2:75543089..75543122,-!p3@Nfe2l2!0.81!5.39!Nfe2l2;;chr1:138857076..138857105,-!p1@Nr5a2!0.81!5.39!Nr5a2;;chr8:118231705..118231722,-!p3@Maf!0.80!45.84!Maf;;chr1:39250584..39250643,+!p1@Npas2!0.80!28.76!Npas2;;chr5:120121091..120121100,+!p7@Tbx3!0.80!6.29!Tbx3;;chr16:55822241..55822258,-!p1@Nfkbiz!0.79!177.07!Nfkbiz;;chr2:70313168..70313184,+!p1@Sp5!0.79!8.09!Sp5;;chr1:194979361..194979373,+!p2@Irf6!0.79!7.19!Irf6;;chr8:79423144..79423178,+!p3@Nr3c2!0.78!7.19!Nr3c2;;chr10:88996336..88996380,-!p2@Nr1h4!0.78!6.29!Nr1h4;;chr8:59799772..59799789,+!p1@Hand2!0.77!15.28!Hand2;;chr1:38721792..38721845,-!p1@Aff3!0.77!6.29!Aff3;;chr6:39068210..39068251,-!p1@Parp12!0.76!24.27!Parp12;;chr13:44825008..44825066,+!p5@Jarid2!0.76!9.89!Jarid2;;chr4:148275237..148275311,+!p2@Casz1!0.75!20.67!Casz1;;chr4:148178529..148178548,+!p3@Casz1!0.75!11.68!Casz1;;chr5:120120981..120120992,+!p5@Tbx3!0.75!6.29!Tbx3;;chr4:55545152..55545194,-!p3@Klf4!0.74!5.39!Klf4;;chr4:44723520..44723544,-!p2@Pax5!0.74!4.49!Pax5;;chr3:128918433..128918448,+!p8@Pitx2!0.74!4.49!Pitx2;;chr5:148118614..148118625,-!p4@Cdx2!0.74!4.49!Cdx2;;chr15:102821007..102821021,+!p2@Hoxc8!0.74!4.49!Hoxc8;;chr15:102828658..102828678,+!p1@Hoxc6!0.74!4.49!Hoxc6;;chr15:35225873..35225889,+!p2@Osr2!0.74!4.49!Osr2;;chr11:98822047..98822072,+!p9@Rara!0.74!4.49!Rara;;chr5:65213356..65213412,+!p6@Klf3!0.73!9.89!Klf3;;chr17:32506357..32506377,-!p3@Wiz!0.73!9.89!Wiz;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.72!13.48!Tfcp2l1;;chr2:77357622..77357704,-!p1@Zfp385b!0.72!12.58!Zfp385b;;chr18:11052606..11052633,+!p4@Gata6!0.72!11.68!Gata6;;chr4:87452180..87452196,-!p3@Mllt3!0.72!8.99!Mllt3;;chr2:91035254..91035271,-!p3@Nr1h3!0.72!5.39!Nr1h3;;chr11:100948597..100948637,+!p1@Mlx!0.71!112.35!Mlx;;chr11:98821937..98821987,+!p4@Rara!0.71!9.89!Rara;;chr7:51787434..51787448,-!p1@Spib!0.71!6.29!Spib;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.68!6.29!Ncoa4;;chr11:98636373..98636387,-!p5@Nr1d1!0.68!4.49!Nr1d1;;chr6:86619130..86619158,-!p2@Mxd1!0.66!60.22!Mxd1;;chr1:52176315..52176343,+!p1@Stat1!0.66!59.32!Stat1;;chr8:124806048..124806094,+!p1@Zfpm1!0.66!37.75!Zfpm1;;chr4:154010918..154010931,-!p1@Prdm16!0.66!11.68!Prdm16;;chr4:154010882..154010889,-!p10@Prdm16!0.66!3.60!Prdm16;;chr3:90046983..90046994,-!p6@Creb3l4!0.66!3.60!Creb3l4;;chr4:151533683..151533698,+!p1@Hes2!0.66!3.60!Hes2;;chr5:148081667..148081678,+!p3@Pdx1!0.66!3.60!Pdx1;;chr5:115421126..115421137,-!p4@Hnf1a!0.66!3.60!Hnf1a;;chr11:98407264..98407295,-!p1@Ikzf3!0.66!3.60!Ikzf3;;chr10:80555285..80555291,-!p4@Creb3l3!0.66!3.60!Creb3l3;;chr11:83664365..83664383,+!p1@Hnf1b!0.66!3.60!Hnf1b;;chr13:31650026..31650045,+!p2@Foxq1!0.65!6.29!Foxq1;;chr14:98568683..98568698,-!p6@Dach1!0.65!4.49!Dach1;;chr11:53583960..53584007,+!p2@Irf1!0.64!8.09!Irf1;;chr2:160192793..160192809,-!p1@Mafb!0.63!58.42!Mafb;;chr16:87699237..87699279,+!p1@Bach1!0.63!40.45!Bach1;;chr16:87699206..87699229,+!p3@Bach1!0.63!20.67!Bach1;;chr10:80600749..80600766,+!p2@Zbtb7a!0.63!19.77!Zbtb7a;;chr4:135728581..135728668,+!p1@E2f2!0.63!17.98!E2f2;;chr3:89197551..89197606,-!p2@Zbtb7b!0.62!12.58!Zbtb7b;;chr9:31720843..31720888,-!p1@Barx2!0.62!3.60!Barx2;;chr18:11052456..11052477,+!p3@Gata6!0.60!10.79!Gata6;;chr13:56804865..56804898,+!p3@Smad5!0.60!8.99!Smad5;;chr5:76733981..76734018,-!p3@Clock!0.60!7.19!Clock;;chr19:53384985..53385042,+!p1@Mxi1!0.59!109.66!Mxi1;;chr12:109242266..109242295,-!p1@Bcl11b!0.59!29.66!Bcl11b;;chr17:84587167..84587239,-!p2@Zfp36l2!0.59!11.68!Zfp36l2;;chr17:15701263..15701277,-!p2@Prdm9!0.59!8.09!Prdm9;;chr4:154010940..154010962,-!p3@Prdm16!0.59!7.19!Prdm16;;chr7:56137011..56137041,-!p2@E2f8!0.59!6.29!E2f8;;chr10:80598209..80598236,+!p4@Zbtb7a!0.59!5.39!Zbtb7a;;chr10:126725815..126725830,-!p10@Mbd6!0.59!3.60!Mbd6;;chr5:140267476..140267493,+!p1@Mafk!0.58!18.88!Mafk;;chr4: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0.19!4.49!Gatad2a;;chr17:34169293..34169320,+!p3@Rxrb!0.19!3.60!Rxrb;;chr18:83080305..83080335,+!p2@Zfp516!0.19!3.60!Zfp516;;chr16:4214034..4214070,-!p@chr16:4214034..4214070,-!0.19!3.60!Crebbp;;chrX:71330995..71331011,-!p2@Mecp2!0.19!3.60!Mecp2;;chrX:92906980..92907024,+!p2@Zc3h12b!0.19!2.70!Zc3h12b;;chr9:48644037..48644067,-!p2@Zbtb16!0.19!2.70!Zbtb16;;chr7:135020412..135020433,+!p2@Zfp646!0.19!2.70!Zfp646;;chr16:43363837..43363842,+!p11@Zbtb20!0.19!1.80!Zbtb20;;chr4:126700576..126700598,+!p7@Sfpq!0.19!1.80!Sfpq;;chr13:112476433..112476448,+!p2@Mier3!0.19!1.80!Mier3;;chr13:29045252..29045271,-!p5@Sox4!0.19!0.90!Sox4;;chr16:55973994..55974005,+!p8@Rpl24,p8@Zbtb11!0.19!0.90!Zbtb11;;chr18:65740031..65740054,+!p5@Zfp532!0.19!0.90!Zfp532;;chr6:108610474..108610491,+!p5@Bhlhe40!0.19!0.90!Bhlhe40;;chr2:74549968..74549996,+!p1@Hoxd3!0.19!0.90!Hoxd3;;chr4:82151500..82151505,-!p11@Nfib!0.19!0.90!Nfib;;chr4:102787067..102787080,+!p10@Mier1!0.19!0.90!Mier1;;chr2:77654815..77654872,-!p2@Zfp385b!0.19!0.90!Zfp385b;;chr4:87678639..87678653,-!p11@Mllt3!0.19!0.90!Mllt3;;chr5:104182694..104182724,+!p8@Aff1!0.19!0.90!Aff1;;chr3:100773602..100773607,-!p2@Ttf2!0.19!0.90!Ttf2;;chr1:13364477..13364492,-!p6@Ncoa2!0.19!0.90!Ncoa2;;chr10:44178575..44178590,-!p5@Prdm1!0.19!0.90!Prdm1;;chr11:96147952..96147967,+!p1@Hoxb7!0.19!0.90!Hoxb7;;chr4:43575485..43575542,+!p1@Creb3!0.18!38.65!Creb3;;chr19:5424906..5425026,-!p1@Drap1!0.18!36.85!Drap1;;chr17:4995902..4995959,+!p1@Arid1b!0.18!31.46!Arid1b;;chr13:59924433..59924504,-!p1@Zcchc6!0.18!29.66!Zcchc6;;chr5:25004592..25004630,-!p2@Mll3!0.18!26.96!Mll3;;chr11:101087728..101087769,-!p1@Ezh1!0.18!19.77!Ezh1;;chr2:160698721..160698745,-!p1@Zhx3!0.18!18.88!Zhx3;;chr16:42907676..42907797,+!p1@Zbtb20!0.18!17.08!Zbtb20;;chr15:10400285..10400360,-!p1@Dnajc21!0.18!17.08!Dnajc21;;chr15:101097270..101097290,+!p1@Nr4a1!0.18!13.48!Nr4a1;;chr7:13483149..13483234,+!p1@Zscan22!0.18!12.58!Zscan22;;chr17:88840082..88840127,+!p1@Foxn2!0.18!8.99!Foxn2;;chr7:56136362..56136400,-!p1@E2f8!0.18!8.09!E2f8;;chr8:109620276..109620306,-!p2@Terf2!0.18!7.19!Terf2;;chr7:30644985..30645072,+!p1@Zfp420!0.18!7.19!Zfp420;;chr4:129055091..129055168,-!p1@Zbtb8a!0.18!7.19!Zbtb8a;;chr4:120488308..120488366,-!p1@Nfyc!0.18!7.19!Nfyc;;chr17:46693153..46693169,-!p2@Srf!0.18!6.29!Srf;;chr10:127984472..127984504,-!p2@Zc3h10!0.18!3.60!Zc3h10;;chr11:59285966..59285990,-!p2@Zfp867!0.18!2.70!Zfp867;;chr3:135354452..135354475,-!p5@Nfkb1!0.18!2.70!Nfkb1;;chr15:78994907..78994926,-!p1@Sox10!0.18!2.70!Sox10;;chr19:41557591..41557634,+!p3@Lcor!0.18!2.70!Lcor;;chr5:34530277..34530292,-!p3@Mxd4!0.18!2.70!Mxd4;;chr5:65194789..65194800,+!p7@Klf3!0.18!2.70!Klf3;;chr13:67182439..67182491,-!p2@Zfp708!0.18!2.70!Zfp708;;chr13:44826634..44826645,+!p7@Jarid2!0.18!1.80!Jarid2;;chr2:165818215..165818226,+!p4@Ncoa3!0.18!1.80!Ncoa3;;chr6:72185553..72185612,-!p2@Atoh8!0.18!1.80!Atoh8;;chr6:14851250..14851277,+!p4@Foxp2!0.18!0.90!Foxp2;;chr6:145813964..145813994,-!p3@Bhlhe41!0.18!0.90!Bhlhe41;;chr7:119822940..119822945,+!p6@Tead1!0.18!0.90!Tead1;;chr6:52154386..52154407,-!p2@Hoxa5!0.18!0.90!Hoxa5;;chr6:52141694..52141715,-!p1@Hoxa4!0.18!0.90!Hoxa4;;chr13:67433434..67433446,-!p3@Zfp595!0.18!0.90!Zfp595;;chr15:102865048..102865073,+!p3@Hoxc4!0.18!0.90!Hoxc4;;chr8:79423672..79423727,+!p2@Nr3c2!0.18!0.90!Nr3c2;;chr7:52960730..52960762,+!p3@Dbp!0.18!0.90!Dbp;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!0.18!0.90!Pou3f3;;chr2:115891680..115891701,-!p12@Meis2!0.18!0.90!Meis2;;chr2:162880418..162880429,+!p4@Mybl2!0.18!0.90!Mybl2;;chr2:77654650..77654685,-!p3@Zfp385b!0.18!0.90!Zfp385b;;chr4:99322820..99322845,+!p1@Foxd3!0.18!0.90!Foxd3;;chr5:104182943..104182954,+!p12@Aff1!0.18!0.90!Aff1;;chr16:95923586..95923598,+!p5@Ets2!0.18!0.90!Ets2;;chr16:98073382..98073395,-!p4@Prdm15!0.18!0.90!Prdm15;;chr8:73222830..73222844,+!p1@Jund!0.17!342.45!Jund;;chr17:87153028..87153049,+!p2@Epas1!0.17!26.96!Epas1;;chr1:179372411..179372509,+!p1@Zfp238!0.17!16.18!Zfp238;;chr16:98073403..98073460,-!p1@Prdm15!0.17!9.89!Prdm15;;chr18:55147667..55147746,-!p2@Zfp608!0.17!5.39!Zfp608;;chr3:5218629..5218684,+!p1@Zfhx4!0.17!3.60!Zfhx4;;chr3:152059326..152059358,+!p3@Gm8261,p3@Zzz3!0.17!3.60!Zzz3;;chr2:90936947..90936977,+!p2@Sfpi1!0.17!1.80!Sfpi1;;chr13:67229127..67229153,+!p2@Zfp759!0.17!1.80!Zfp759;;chr6:72849280..72849297,-!p6@Kcmf1!0.17!1.80!Kcmf1;;chr18:3337465..3337498,-!p6@Crem!0.17!1.80!Crem;;chr18:14131020..14131033,-!p4@Zfp521!0.17!0.90!Zfp521;;chr17:84587077..84587097,-!p4@Zfp36l2!0.17!0.90!Zfp36l2;;chr17:27693922..27693934,+!p10@Hmga1-rs1,p11@Hmga1!0.17!0.90!Hmga1;;chr16:43619156..43619171,+!p16@Zbtb20!0.17!0.90!Zbtb20;;chr12:25257114..25257131,+!p4@Grhl1!0.17!0.90!Grhl1;;chr10:88145766..88145770,-!p1@Spic!0.17!0.90!Spic;;chr10:126723307..126723319,-!p6@Mbd6!0.17!0.90!Mbd6;;chr10:13685657..13685677,+!p7@Hivep2!0.17!0.90!Hivep2;;chr2:91490176..91490193,-!p2@Zfp408!0.17!0.90!Zfp408;;chr6:134780337..134780355,+!p3@Crebl2!0.17!0.90!Crebl2;;chr2:32219200..32219213,+!p5@Ciz1!0.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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:0011431
 |is_obsolete=
+|library_id=CNhs11187
+|library_id_phase_based=2:CNhs11187
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;827
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;827
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N20.CNhs11187.827-18D1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N20.CNhs11187.827-18D1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N20.CNhs11187.827-18D1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N20.CNhs11187.827-18D1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N20.CNhs11187.827-18D1.mm9.nobarcode.rdna.fa.gz
 |name=intestine, neonate N20
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11187,LSID746,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,0.172408762146572,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.0865903112981225,0,0,0,0,0,0,0,0,0,0,0,0,0,0.478485968934179,0,0.278483662180697,0,0.278483662180697,0,0.213812006872867,0,0.116080932250236,-0.244315040300284,0.00861502417034582,0,0,0,0,0,0,0,0,0,0,0,0,0.212478114617257,0,0,0,0,0.136778961585482,0,0,0,0,0,0.0817151924388893,0.136140987850387,-0.158091042771083,-0.0265518813377336,0.278483662180697,0,0,-0.0536726320041341,0,0,0,-0.0196042359821261,1.03089436180925,0.19965206734079,0,0,0,0,0,0,0.751278191965309,1.05648944501529,0.709207487202989,0,0,0,0,0
 |rna_box=18
 |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: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:827-18D1;search_select_hide=table117:827-18D1
 }}

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FF:827-18D1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:21, 4 June 2020

CNhs11187

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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