FF:644-26D1: Difference between revisions

Latest revision as of 19:19, 4 June 2020

Name:	intestine, neonate N00
Species:	Mouse (Mus musculus)
Library ID:	CNhs11126
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	intestine
dev stage	0 day 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		SAMD00006001

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11126		CAGE		DRX008996		DRR009870

Accession ID Mm9

Library id		BAM		CTSS
CNhs11126		DRZ001295		DRZ002678

Accession ID Mm10

Library id		BAM		CTSS
CNhs11126		DRZ012645		DRZ014028

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

CNhs11126

0	0
1	0
10	0
100	0
1000	0.0961
1001	0.0453
1002	0.0516
1003	-0.058
1004	0
1005	0.229
1006	-0.0512
1007	-0.0584
1008	1.878
1009	0.1
101	-0.105
1010	0
1011	-0.154
1012	0
1013	0.304
1014	-0.0874
1015	-0.342
1016	-0.222
1017	0
1018	0.585
1019	0
102	0
1020	0
1021	0
1022	0.0983
1023	0
1024	0
1025	0.584
1026	0
1027	-0.0134
1028	0
1029	0.582
103	0.169
1030	0
1031	-0.172
1032	0.64
1033	0
1034	0
1035	0
1036	-0.183
1037	0
1038	0.0862
1039	-0.043
104	0
1040	-0.216
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: CNhs11126

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0106
MA0003.1	MA0003.1	0.15
MA0004.1	MA0004.1	0.722
MA0006.1	MA0006.1	0.0441
MA0007.1	MA0007.1	0.578
MA0009.1	MA0009.1	0.347
MA0014.1	MA0014.1	0.359
MA0017.1	MA0017.1	3.73907e-22
MA0018.2	MA0018.2	0.00692
MA0019.1	MA0019.1	0.384
MA0024.1	MA0024.1	0.0286
MA0025.1	MA0025.1	0.163
MA0027.1	MA0027.1	0.875
MA0028.1	MA0028.1	0.343
MA0029.1	MA0029.1	0.96
MA0030.1	MA0030.1	0.382
MA0031.1	MA0031.1	0.576
MA0035.2	MA0035.2	4.33673e-6
MA0038.1	MA0038.1	0.387
MA0039.2	MA0039.2	0.00661
MA0040.1	MA0040.1	0.206
MA0041.1	MA0041.1	0.21
MA0042.1	MA0042.1	0.842
MA0043.1	MA0043.1	0.0388
MA0046.1	MA0046.1	6.40895e-33
MA0047.2	MA0047.2	0.0504
MA0048.1	MA0048.1	0.381
MA0050.1	MA0050.1	1.5073e-6
MA0051.1	MA0051.1	5.58828e-5
MA0052.1	MA0052.1	9.27913e-5
MA0055.1	MA0055.1	0.387
MA0057.1	MA0057.1	0.135
MA0058.1	MA0058.1	0.51
MA0059.1	MA0059.1	0.97
MA0060.1	MA0060.1	0.00217
MA0061.1	MA0061.1	0.402
MA0062.2	MA0062.2	0.236
MA0065.2	MA0065.2	2.03617e-13
MA0066.1	MA0066.1	0.127
MA0067.1	MA0067.1	0.164
MA0068.1	MA0068.1	0.0793
MA0069.1	MA0069.1	0.218
MA0070.1	MA0070.1	0.239
MA0071.1	MA0071.1	0.472
MA0072.1	MA0072.1	0.401
MA0073.1	MA0073.1	0.693
MA0074.1	MA0074.1	0.101
MA0076.1	MA0076.1	0.129
MA0077.1	MA0077.1	0.793
MA0078.1	MA0078.1	0.583
MA0079.2	MA0079.2	0.376
MA0080.2	MA0080.2	0.00447
MA0081.1	MA0081.1	0.311
MA0083.1	MA0083.1	0.756
MA0084.1	MA0084.1	0.883
MA0087.1	MA0087.1	0.735
MA0088.1	MA0088.1	0.866
MA0090.1	MA0090.1	0.711
MA0091.1	MA0091.1	0.846
MA0092.1	MA0092.1	0.286
MA0093.1	MA0093.1	0.659
MA0099.2	MA0099.2	0.0211
MA0100.1	MA0100.1	0.148
MA0101.1	MA0101.1	0.995
MA0102.2	MA0102.2	0.16
MA0103.1	MA0103.1	1.28856e-5
MA0104.2	MA0104.2	0.11
MA0105.1	MA0105.1	0.198
MA0106.1	MA0106.1	0.745
MA0107.1	MA0107.1	0.869
MA0108.2	MA0108.2	0.724
MA0111.1	MA0111.1	0.951
MA0112.2	MA0112.2	3.47894e-5
MA0113.1	MA0113.1	0.677
MA0114.1	MA0114.1	2.22337e-26
MA0115.1	MA0115.1	1.9569e-10
MA0116.1	MA0116.1	0.208
MA0117.1	MA0117.1	0.973
MA0119.1	MA0119.1	0.0637
MA0122.1	MA0122.1	0.712
MA0124.1	MA0124.1	0.358
MA0125.1	MA0125.1	0.0949
MA0131.1	MA0131.1	0.42
MA0135.1	MA0135.1	0.267
MA0136.1	MA0136.1	0.0248
MA0137.2	MA0137.2	0.862
MA0138.2	MA0138.2	0.581
MA0139.1	MA0139.1	0.0551
MA0140.1	MA0140.1	0.0347
MA0141.1	MA0141.1	4.98095e-5
MA0142.1	MA0142.1	0.42
MA0143.1	MA0143.1	0.294
MA0144.1	MA0144.1	0.0902
MA0145.1	MA0145.1	0.00907
MA0146.1	MA0146.1	0.335
MA0147.1	MA0147.1	0.182
MA0148.1	MA0148.1	0.00428
MA0149.1	MA0149.1	0.0236
MA0150.1	MA0150.1	0.88
MA0152.1	MA0152.1	0.157
MA0153.1	MA0153.1	6.91296e-29
MA0154.1	MA0154.1	0.0183
MA0155.1	MA0155.1	0.249
MA0156.1	MA0156.1	0.175
MA0157.1	MA0157.1	0.45
MA0159.1	MA0159.1	0.00175
MA0160.1	MA0160.1	0.00804
MA0162.1	MA0162.1	0.127
MA0163.1	MA0163.1	0.018
MA0164.1	MA0164.1	0.987
MA0258.1	MA0258.1	0.00945
MA0259.1	MA0259.1	0.25

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: CNhs11126

Novel motif	Logo	P-value
1	1	0.139
10	10	0.186
100	100	0.969
101	101	0.713
102	102	0.767
103	103	0.19
104	104	0.925
105	105	0.412
106	106	0.00942
107	107	0.0231
108	108	0.854
109	109	0.0786
11	11	0.141
110	110	0.27
111	111	0.0395
112	112	0.0239
113	113	0.435
114	114	0.047
115	115	0.561
116	116	0.25
117	117	0.224
118	118	0.514
119	119	0.0915
12	12	0.794
120	120	0.696
121	121	0.755
122	122	0.733
123	123	0.315
124	124	0.903
125	125	0.591
126	126	0.097
127	127	0.251
128	128	0.0757
129	129	0.408
13	13	0.00234
130	130	0.585
131	131	0.0339
132	132	0.602
133	133	0.684
134	134	0.838
135	135	0.473
136	136	0.158
137	137	0.454
138	138	0.639
139	139	0.048
14	14	0.676
140	140	0.525
141	141	0.298
142	142	0.868
143	143	0.692
144	144	0.637
145	145	0.121
146	146	0.266
147	147	0.312
148	148	0.163
149	149	0.552
15	15	0.206
150	150	0.225
151	151	0.504
152	152	0.0324
153	153	0.71
154	154	0.346
155	155	0.193
156	156	0.738
157	157	0.869
158	158	0.731
159	159	0.399
160	160	0.237
161	161	0.35
162	162	0.919
163	163	0.396
164	164	0.141
165	165	0.398
166	166	0.614
167	167	0.942
168	168	0.801
169	169	0.0122
17	17	0.0961
18	18	0.0823
19	19	0.0899
2	2	0.274
20	20	0.858
21	21	0.982
22	22	0.366
23	23	0.203
24	24	0.762
25	25	0.755
26	26	0.00595
27	27	0.491
28	28	0.662
29	29	0.227
3	3	0.179
30	30	0.419
31	31	0.584
32	32	0.00355
33	33	0.282
34	34	0.809
35	35	0.533
36	36	0.774
37	37	0.0401
38	38	0.399
39	39	0.165
4	4	0.457
40	40	0.31
41	41	0.404
42	42	0.462
43	43	0.216
44	44	0.296
45	45	0.4
46	46	0.232
47	47	0.284
48	48	0.259
49	49	0.154
5	5	0.68
50	50	0.526
51	51	0.565
52	52	0.0753
53	53	0.994
54	54	0.48
55	55	0.609
56	56	0.484
57	57	0.786
58	58	0.48
59	59	0.105
6	6	0.797
60	60	0.043
61	61	0.194
62	62	0.353
63	63	0.166
64	64	0.628
65	65	0.181
66	66	0.582
67	67	0.556
68	68	0.11
69	69	0.992
7	7	0.0827
70	70	0.0223
71	71	0.091
72	72	0.589
73	73	0.0976
74	74	0.969
75	75	0.144
76	76	0.897
77	77	0.106
78	78	0.0441
79	79	0.579
8	8	0.136
80	80	0.492
81	81	0.641
82	82	0.061
83	83	0.785
84	84	0.466
85	85	0.0358
86	86	0.159
87	87	0.31
88	88	0.74
89	89	0.306
9	9	0.653
90	90	0.209
91	91	0.112
92	92	0.241
93	93	0.585
94	94	0.363
95	95	0.146
96	96	0.723
97	97	0.334
98	98	0.995
99	99	0.0358

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: CNhs11126

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011265 mouse intestine- neonate N00 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)
0000304 (mouse neonate N0 sample)
0011265 (mouse intestine- neonate N00 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@SAMD00006001
+|accession_numbers=CAGE;DRX008996;DRR009870;DRZ001295;DRZ002678;DRZ012645;DRZ014028
 |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!2.60!396.71!Hnf4g;;chr10:80555320..80555378,-!p1@Creb3l3!2.23!194.08!Creb3l3;;chr5:148118639..148118715,-!p1@Cdx2!2.23!169.41!Cdx2;;chr2:163372884..163372904,+!p1@Hnf4a!2.07!115.79!Hnf4a;;chr1:137155026..137155042,-!p1@Elf3!1.94!474.53!Elf3;;chr16:38294860..38294924,-!p1@Nr1i2!1.91!80.20!Nr1i2;;chr10:88969376..88969395,-!p1@Nr1h4!1.80!62.64!Nr1h4;;chr2:163332558..163332596,+!p2@Hnf4a!1.80!61.69!Hnf4a;;chr6:86619104..86619119,-!p1@Mxd1!1.74!419.48!Mxd1;;chr2:180069370..180069409,-!p1@Gata5!1.71!58.37!Gata5;;chr15:97738692..97738747,-!p1@Vdr!1.63!216.86!Vdr;;chr1:173144100..173144138,+!p2@Nr1i3!1.57!36.54!Nr1i3;;chr8:77396591..77396639,+!p1@Isx!1.57!36.06!Isx;;chr2:164228702..164228719,+!p1@Rbpjl!1.55!34.17!Rbpjl;;chr14:63864056..63864102,-!p1@Gata4!1.54!57.89!Gata4;;chr18:61195843..61195864,-!p2@Cdx1!1.46!28.00!Cdx1;;chr18:61195865..61195880,-!p1@Cdx1!1.46!27.52!Cdx1;;chr5:135582751..135582788,+!p1@Mlxipl!1.45!104.87!Mlxipl;;chr17:27865882..27865901,-!p1@Spdef!1.45!27.05!Spdef;;chr3:3508024..3508069,+!p2@Hnf4g!1.44!26.57!Hnf4g;;chr6:64679112..64679126,+!p1@Atoh1!1.43!25.62!Atoh1;;chr5:148118840..148118857,-!p2@Cdx2!1.41!24.68!Cdx2;;chr8:77397095..77397127,+!p2@Isx!1.41!24.68!Isx;;chr2:103123925..103123959,-!p3@Ehf!1.38!23.25!Ehf;;chr10:80555398..80555409,-!p2@Creb3l3!1.33!20.40!Creb3l3;;chr14:99697871..99697934,+!p1@Klf5!1.32!383.42!Klf5;;chr7:19608891..19608895,-!p1@Foxa3!1.30!24.68!Foxa3;;chr17:28408632..28408682,+!p1@1810013A23Rik,p4@Ppard!1.30!18.98!Ppard;;chr5:115421065..115421088,-!p1@Hnf1a!1.29!18.51!Hnf1a;;chr8:77397492..77397514,+!p3@Isx!1.27!17.56!Isx;;chr18:64499674..64499696,+!p1@Onecut2!1.25!28.95!Onecut2;;chr19:5560600..5560617,-!p1@Ovol1!1.22!18.98!Ovol1;;chr15:35225845..35225867,+!p1@Osr2!1.21!38.44!Osr2;;chr18:64499706..64499721,+!p2@Onecut2!1.21!21.35!Onecut2;;chr17:28409136..28409150,+!p3@Ppard!1.21!15.18!Ppard;;chr8:79426176..79426275,+!p1@Nr3c2!1.20!74.03!Nr3c2;;chr10:22539932..22539956,-!p1@Tcf21!1.19!37.96!Tcf21;;chr7:148452314..148452329,-!p1@Irf7!1.17!93.96!Irf7;;chr8:123608252..123608268,+!p1@Foxf1a!1.17!20.40!Foxf1a;;chr19:43686789..43686811,+!p1@Nkx2-3!1.17!13.76!Nkx2-3;;chr1:173144144..173144176,+!p1@Nr1i3!1.17!13.76!Nr1i3;;chr8:77397190..77397202,+!p5@Isx!1.13!12.34!Isx;;chr1:165219345..165219366,-!p7@Prrx1!1.11!11.86!Prrx1;;chr3:89197057..89197114,-!p1@Zbtb7b!1.10!39.39!Zbtb7b;;chr5:144951153..144951203,+!p1@Bhlha15!1.10!17.08!Bhlha15;;chr5:148118809..148118832,-!p5@Cdx2!1.09!11.39!Cdx2;;chr8:118231678..118231692,-!p2@Maf!1.08!99.18!Maf;;chr5:120121020..120121049,+!p1@Tbx3!1.08!67.38!Tbx3;;chr11:98636531..98636559,-!p1@Nr1d1!1.08!62.64!Nr1d1;;chr8:77396650..77396662,+!p4@Isx!1.08!10.91!Isx;;chr3:3508005..3508021,+!p3@Hnf4g!1.08!10.91!Hnf4g;;chr2:103143336..103143367,-!p1@Ehf!1.06!17.08!Ehf;;chr1:194979315..194979359,+!p1@Irf6!1.05!63.59!Irf6;;chr4:55545337..55545357,-!p1@Klf4!1.04!147.58!Klf4;;chr2:163372869..163372882,+!p3@Hnf4a!1.04!9.97!Hnf4a;;chr5:148118792..148118806,-!p3@Cdx2!1.04!9.97!Cdx2;;chr14:63890545..63890560,-!p5@Gata4!1.04!9.97!Gata4;;chr13:31650185..31650201,+!p1@Foxq1!1.03!34.17!Foxq1;;chr5:120121446..120121461,+!p2@Tbx3!1.03!32.74!Tbx3;;chr13:31717548..31717596,+!p1@Foxf2!1.03!19.46!Foxf2;;chr19:6996243..6996293,-!p1@Esrra!1.02!105.35!Esrra;;chr18:11052485..11052508,+!p2@Gata6!1.00!26.10!Gata6;;chr1:138857048..138857071,-!p2@Nr5a2!1.00!9.02!Nr5a2;;chr6:39068163..39068176,-!p2@Parp12!0.99!16.61!Parp12;;chr5:148081722..148081744,+!p2@Pdx1!0.98!8.54!Pdx1;;chr11:57645506..57645523,-!p1@Hand1!0.98!8.54!Hand1;;chr8:123260252..123260264,+!p1@Irf8!0.96!58.84!Irf8;;chr4:124805061..124805087,-!p1@Zc3h12a!0.96!25.62!Zc3h12a;;chr2:173044380..173044432,-!p1@Zbp1!0.96!19.93!Zbp1;;chr14:63890519..63890539,-!p3@Gata4!0.96!8.07!Gata4;;chr5:148081686..148081715,+!p1@Pdx1!0.96!8.07!Pdx1;;chr1:194979361..194979373,+!p2@Irf6!0.95!10.91!Irf6;;chr3:90046995..90047031,-!p2@Creb3l4!0.95!9.97!Creb3l4;;chr12:86814833..86814846,+!p1@Fos!0.94!186.02!Fos;;chr10:20880629..20880683,-!p1@Myb!0.93!22.30!Myb;;chr11:70500401..70500460,-!p3@Camta2!0.93!7.59!Camta2;;chr2:79296783..79296801,-!p1@Neurod1!0.93!7.59!Neurod1;;chr4:151533683..151533698,+!p1@Hes2!0.93!7.59!Hes2;;chr14:63890491..63890516,-!p2@Gata4!0.93!7.59!Gata4;;chr14:76887526..76887555,+!p10@Tsc22d1!0.93!7.59!Tsc22d1;;chr5:138187583..138187602,+!p6@Tsc22d4!0.92!13.76!Tsc22d4;;chr19:53384910..53384937,+!p3@Mxi1!0.91!20.88!Mxi1;;chr2:70313168..70313184,+!p1@Sp5!0.91!10.91!Sp5;;chr5:120121091..120121100,+!p7@Tbx3!0.91!8.54!Tbx3;;chr8:118231705..118231722,-!p3@Maf!0.90!58.37!Maf;;chr12:78063146..78063159,-!p2@Max!0.90!18.98!Max;;chr4:148178559..148178603,+!p1@Casz1!0.88!19.93!Casz1;;chr4:148178529..148178548,+!p3@Casz1!0.88!16.13!Casz1;;chr3:30039329..30039355,-!p5@Mecom!0.88!6.64!Mecom;;chr2:19367259..19367278,+!p1@Ptf1a!0.88!6.64!Ptf1a;;chr8:59799772..59799789,+!p1@Hand2!0.87!19.46!Hand2;;chr18:36441119..36441158,+!p2@Pura!0.87!16.13!Pura;;chr10:88996336..88996380,-!p2@Nr1h4!0.87!8.07!Nr1h4;;chr2:166888058..166888105,-!p2@Znfx1!0.86!20.88!Znfx1;;chr2:180069640..180069660,-!p4@Gata5!0.86!6.17!Gata5;;chr2:103143315..103143328,-!p2@Ehf!0.86!6.17!Ehf;;chr5:148118614..148118625,-!p4@Cdx2!0.86!6.17!Cdx2;;chr4:133109285..133109308,+!p1@Nr0b2!0.86!6.17!Nr0b2;;chr4:154010918..154010931,-!p1@Prdm16!0.85!18.51!Prdm16;;chr11:53583544..53583559,+!p1@Irf1!0.83!103.92!Irf1;;chr11:98636400..98636418,-!p4@Nr1d1!0.82!7.59!Nr1d1;;chr3:94176733..94176794,+!p1@Rorc!0.81!46.03!Rorc;;chr6:39068181..39068206,-!p3@Parp12!0.81!11.86!Parp12;;chr7:51787434..51787448,-!p1@Spib!0.81!8.07!Spib;;chr10:127095407..127095440,+!p3@Stat6!0.80!6.64!Stat6;;chr1:135557526..135557551,-!p1@Zbed6!0.79!8.54!Zbed6;;chr2:173044357..173044377,-!p2@Zbp1!0.79!7.59!Zbp1;;chr4:55545051..55545110,-!p2@Klf4!0.79!6.64!Klf4;;chr11:98822047..98822072,+!p9@Rara!0.79!5.22!Rara;;chr7:20213752..20213778,-!p2@Relb!0.79!5.22!Relb;;chr17:28409059..28409076,+!p6@Ppard!0.79!5.22!Ppard;;chr2:180069410..180069421,-!p3@Gata5!0.79!5.22!Gata5;;chr7:20408047..20408125,-!p1@Bcl3!0.77!61.21!Bcl3;;chr11:98636373..98636387,-!p5@Nr1d1!0.77!5.69!Nr1d1;;chr18:11052642..11052659,+!p1@Gata6!0.76!26.57!Gata6;;chr19:5560570..5560582,-!p2@Ovol1!0.76!4.75!Ovol1;;chr8:77397026..77397036,+!p6@Isx!0.76!4.75!Isx;;chr2:180069423..180069434,-!p2@Gata5!0.76!4.75!Gata5;;chr10:80555299..80555306,-!p3@Creb3l3!0.76!4.75!Creb3l3;;chr13:31717597..31717613,+!p2@Foxf2!0.76!4.75!Foxf2;;chr2:160192793..160192809,-!p1@Mafb!0.75!77.82!Mafb;;chr4:148275237..148275311,+!p2@Casz1!0.75!20.88!Casz1;;chr10:88996295..88996335,-!p3@Nr1h4!0.75!5.69!Nr1h4;;chr15:85566051..85566080,+!p4@Ppara!0.73!5.22!Ppara;;chr8:79423144..79423178,+!p3@Nr3c2!0.72!6.17!Nr3c2;;chr9:59797503..59797513,-!p3@Nr2e3!0.72!4.27!Nr2e3;;chr8:77397169..77397182,+!p7@Isx!0.72!4.27!Isx;;chr10:80555285..80555291,-!p4@Creb3l3!0.72!4.27!Creb3l3;;chr1:194982959..194983007,+!p5@Irf6!0.72!4.27!Irf6;;chr2:75543089..75543122,-!p3@Nfe2l2!0.72!4.27!Nfe2l2;;chr14:76887566..76887579,+!p18@Tsc22d1!0.72!4.27!Tsc22d1;;chr6:99216360..99216372,-!p8@Foxp1!0.72!4.27!Foxp1;;chr6:37391910..37391928,-!p3@Creb3l2!0.71!4.75!Creb3l2;;chr19:6996294..6996324,-!p2@Esrra!0.70!29.90!Esrra;;chr3:89197551..89197606,-!p2@Zbtb7b!0.70!15.18!Zbtb7b;;chr17:32506357..32506377,-!p3@Wiz!0.70!9.02!Wiz;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.70!6.64!Ncoa4;;chr15:85566014..85566045,+!p3@Ppara!0.70!5.69!Ppara;;chr11:100948597..100948637,+!p1@Mlx!0.69!105.82!Mlx;;chr11:98821937..98821987,+!p4@Rara!0.69!9.49!Rara;;chr13:31650026..31650045,+!p2@Foxq1!0.69!7.12!Foxq1;;chr2:91035197..91035237,-!p1@Nr1h3!0.68!8.54!Nr1h3;;chr19:43686882..43686906,+!p2@Nkx2-3!0.68!3.80!Nkx2-3;;chr8:124806048..124806094,+!p1@Zfpm1!0.67!38.91!Zfpm1;;chr1:193007123..193007139,-!p1@Atf3!0.67!23.73!Atf3;;chr17:87153519..87153533,+!p5@Epas1!0.67!5.69!Epas1;;chr11:53583960..53584007,+!p2@Irf1!0.66!8.54!Irf1;;chr1:135320989..135321043,-!p1@Sox13!0.65!44.61!Sox13;;chr6:39068210..39068251,-!p1@Parp12!0.65!18.51!Parp12;;chr1:138846047..138846074,-!p5@Nr5a2!0.65!3.80!Nr5a2;;chr5:77524250..77524300,-!p1@Hopx!0.64!80.67!Hopx;;chr1:39250584..39250643,+!p1@Npas2!0.64!19.93!Npas2;;chr5:120121169..120121171,+!p4@Tbx3!0.64!6.64!Tbx3;;chr5:115421126..115421137,-!p4@Hnf1a!0.64!3.32!Hnf1a;;chr5:29805118..29805137,-!p1@Mnx1!0.64!3.32!Mnx1;;chr11:98822093..98822104,+!p16@Rara!0.64!3.32!Rara;;chr10:79884592..79884621,-!p5@Tcf3!0.64!3.32!Tcf3;;chr15:35225873..35225889,+!p2@Osr2!0.64!3.32!Osr2;;chr3:128918394..128918413,+!p5@Pitx2!0.64!3.32!Pitx2;;chr1:138846079..138846103,-!p6@Nr5a2!0.64!3.32!Nr5a2;;chr2:147871627..147871641,-!p1@Foxa2!0.64!3.32!Foxa2;;chr5:32438894..32438908,+!p2@Fosl2!0.63!7.59!Fosl2;;chr17:87153505..87153516,+!p6@Epas1!0.63!4.75!Epas1;;chr1:138846009..138846038,-!p3@Nr5a2!0.63!3.80!Nr5a2;;chr16:55822241..55822258,-!p1@Nfkbiz!0.62!118.16!Nfkbiz;;chr13:37918094..37918119,+!p6@Rreb1!0.61!7.59!Rreb1;;chr10:80598209..80598236,+!p4@Zbtb7a!0.61!5.69!Zbtb7a;;chr11:53164556..53164567,+!p5@Aff4!0.61!5.22!Aff4;;chr2:75542527..75542590,-!p1@Nfe2l2!0.60!324.10!Nfe2l2;;chr19:55816770..55816793,+!p2@Tcf7l2!0.60!30.84!Tcf7l2;;chr7:52960555..52960662,+!p1@Dbp!0.60!30.37!Dbp;;chr18:11052606..11052633,+!p4@Gata6!0.60!8.54!Gata6;;chr5:76733981..76734018,-!p3@Clock!0.60!7.12!Clock;;chr7:134519473..134519502,-!p3@Zfp747!0.60!4.27!Zfp747;;chr12:58646974..58647003,-!p1@Foxa1!0.60!4.27!Foxa1;;chr19:53384985..53385042,+!p1@Mxi1!0.59!109.14!Mxi1;;chr1:133904946..133904974,+!p7@Elk4!0.59!4.75!Elk4;;chr2:91035254..91035271,-!p3@Nr1h3!0.59!3.80!Nr1h3;;chr9:31720843..31720888,-!p1@Barx2!0.59!3.32!Barx2;;chr9:31720903..31720918,-!p2@Barx2!0.59!2.85!Barx2;;chr2:24278519..24278530,-!p3@Pax8!0.59!2.85!Pax8;;chr5:138526401..138526410,+!p3@Zkscan1!0.59!2.85!Zkscan1;;chr4:148178459..148178482,+!p4@Casz1!0.59!2.85!Casz1;;chr11:98614335..98614349,+!p8@Thra!0.59!2.85!Thra;;chr10:61595830..61595846,+!p1@Neurog3!0.59!2.85!Neurog3;;chr12:109242266..109242295,-!p1@Bcl11b!0.58!28.47!Bcl11b;;chr1:120524520..120524528,+!p1@Tfcp2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62272010..62272050,-!p2@Ncor1!0.15!3.32!Ncor1;;chr4:133310175..133310212,-!p5@Arid1a!0.15!3.32!Arid1a;;chr6:99216488..99216534,-!p2@Foxp1!0.15!2.85!Foxp1;;chr7:88138585..88138600,+!p2@Zfp592!0.15!2.85!Zfp592;;chr2:169458352..169458397,+!p3@Tshz2!0.15!2.37!Tshz2;;chr1:15795704..15795713,+!p2@Terf1!0.15!2.37!Terf1;;chr5:139060915..139060929,-!p3@Zfp68!0.15!2.37!Zfp68;;chr7:148514080..148514108,-!p4@Deaf1!0.15!1.90!Deaf1;;chr13:5860740..5860747,+!p4@Klf6!0.15!1.90!Klf6;;chr18:3337503..3337536,-!p7@Crem!0.15!1.42!Crem;;chr11:106993257..106993268,-!p4@Bptf!0.15!1.42!Bptf;;chr10:44178521..44178557,-!p1@Prdm1!0.15!1.42!Prdm1;;chr7:91558472..91558512,-!p2@Arnt2!0.15!0.95!Arnt2;;chr16:30065394..30065398,+!p3@Hes1!0.15!0.95!Hes1;;chr7:135020660..135020688,+!p3@Zfp646!0.15!0.95!Zfp646;;chr15:81641878..81641921,+!p1@Tef!0.14!31.79!Tef;;chr12:110031156..110031198,+!p2@Yy1!0.14!17.08!Yy1;;chr11:72990702..72990737,+!p1@LOC100047518,p1@Tax1bp3!0.14!11.39!Tax1bp3;;chr16:87699149..87699204,+!p2@Bach1!0.14!9.49!Bach1;;chr8:72520015..72520053,-!p2@Gatad2a!0.14!7.59!Gatad2a;;chr4:120498356..120498401,-!p2@Nfyc!0.14!6.17!Nfyc;;chr11:98636575..98636607,-!p2@Nr1d1!0.14!3.80!Nr1d1;;chr8:108160826..108160879,+!p3@Ctcf!0.14!2.85!Ctcf;;chr16:42907656..42907675,+!p10@Zbtb20!0.14!1.90!Zbtb20;;chr11:101755669..101755686,-!p1@Meox1!0.14!1.42!Meox1;;chr8:72663049..72663061,-!p4@LOC100048268,p4@Rfxank!0.14!1.42!Rfxank;;chr1:186556375..186556404,-!p3@Hlx!0.14!1.42!Hlx;;chr6:108610766..108610781,+!p2@Bhlhe40!0.14!1.42!Bhlhe40;;chr3:9610233..9610247,-!p4@Zfp704!0.14!0.95!Zfp704;;chr3:54559550..54559570,+!p4@Smad9!0.14!0.95!Smad9;;chr13:59924319..59924331,-!p5@Zcchc6!0.14!0.95!Zcchc6;;chr12:37835120..37835133,+!p2@Meox2!0.14!0.95!Meox2;;chr2:115891521..115891532,-!p8@Meis2!0.14!0.95!Meis2;;chr11:120494908..120494919,-!p4@Mafg!0.14!0.95!Mafg;;chr11:11585678..11585745,+!p5@Ikzf1!0.14!0.95!Ikzf1;;chr9:20385868..20385902,+!p3@Zfp846!0.14!0.95!Zfp846;;chr8:94881872..94881887,+!p2@Irx5!0.14!0.47!Irx5;;chr16:30065419..30065437,+!p1@Hes1!0.13!64.54!Hes1;;chr10:126727842..126727859,+!p1@Ddit3!0.13!35.12!Ddit3;;chr17:87153028..87153049,+!p2@Epas1!0.13!24.68!Epas1;;chr17:28487692..28487765,-!p1@Tead3!0.13!23.25!Tead3;;chr11:6375995..6376105,-!p1@Purb!0.13!20.88!Purb;;chr8:74474953..74475029,+!p1@Zfp961!0.13!19.46!Zfp961;;chr12:3807017..3807063,+!p1@Dnmt3a!0.13!19.46!Dnmt3a;;chr8:81923316..81923334,-!p1@Smad1!0.13!18.51!Smad1;;chr7:120351014..120351109,+!p1@Arntl!0.13!16.13!Arntl;;chr1:75188717..75188804,+!p1@ENSMUST00000125384,p1@ENSMUST00000127625,p1@ENSMUST00000131788,p1@ENSMUST00000134233,p1@ENSMUST00000134378,p1@ENSMUST00000145459,p1@ENSMUST00000151887,p1@ENSMUST00000152233!0.13!16.13!Ankzf1;;chr1:193961880..193961929,-!p1@Rcor3!0.13!12.81!Rcor3;;chr6:99470943..99471024,-!p3@Foxp1!0.13!10.91!Foxp1;;chr7:6107541..6107572,-!p1@Zfp787!0.13!8.54!Zfp787;;chrX:98728074..98728116,+!p2@Taf1!0.13!7.12!Taf1;;chr7:6124098..6124133,+!p1@Zfp444!0.13!4.75!Zfp444;;chr8:81923350..81923361,-!p3@Smad1!0.13!3.80!Smad1;;chr9:96096665..96096699,+!p4@Tfdp2!0.13!3.32!Tfdp2;;chr9:63869850..63869873,-!p2@Smad6!0.13!2.85!Smad6;;chr4:149611311..149611317,+!p2@Eno1!0.13!2.85!Eno1;;chr14:52634536..52634572,-!p4@Zfp219!0.13!2.85!Zfp219;;chr8:124900562..124900573,+!p3@Zc3h18!0.13!2.37!Zc3h18;;chr5:138187181..138187192,+!p5@Tsc22d4!0.13!2.37!Tsc22d4;;chr18:74427866..74427881,+!p3@Mbd1!0.13!2.37!Mbd1;;chr1:170362322..170362333,-!p8@Pbx1!0.13!2.37!Pbx1;;chr14:52639709..52639753,-!p5@Zfp219!0.13!1.90!Zfp219;;chr4:13670499..13670526,+!p2@Runx1t1!0.13!1.90!Runx1t1;;chr2:160698668..160698679,-!p4@Zhx3!0.13!1.42!Zhx3;;chr8:112603658..112603674,+!p2@Zfp612!0.13!1.42!Zfp612;;chr2:44965761..44965785,-!p13@Zeb2!0.13!0.95!Zeb2;;chr2:92886587..92886622,-!p3@Prdm11!0.13!0.95!Prdm11;;chr11:120491440..120491474,-!p3@Mafg!0.13!0.95!Mafg;;chr12:25336286..25336297,+!p2@Klf11!0.13!0.95!Klf11;;
+|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:0011265
 |is_obsolete=
+|library_id=CNhs11126
+|library_id_phase_based=2:CNhs11126
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;644
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;644
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N00.CNhs11126.644-26D1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N00.CNhs11126.644-26D1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N00.CNhs11126.644-26D1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N00.CNhs11126.644-26D1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N00.CNhs11126.644-26D1.mm9.nobarcode.rdna.fa.gz
 |name=intestine, neonate N00
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11126,LSID735,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.230516406896742,0,0,0,0.168653336497203,0,0.0966754890155125,0,0.0478809972689597,0,0,-0.0843392403965415,0,0,0,0,0.0843266682486015,0,-0.0232400143853716,0,0,0,0,0,0,0.168653336497203,0,0,0,0,0,0,0.297028385187985,0,0,0,0,0,0.0805020649611742,-0.0580636980014754,0.128583424819642,-0.694386576020826,-0.101215301513148,0,0,0,0,0,0,0,0,0,0,0,0,0.102647788933763,0,0,0,0,0.242753946786936,0,0,0,0,0,0.0998010043277981,0.217320012637654,0.0105622937261205,-0.104094974270439,0,0,0,-0.113870077396501,0,0,0,0.107712505723076,0.805502585800365,0.0898217416572956,0,0,0,0,0,0.168653336497203,0.700359103244261,1.05889356418959,0.705592541835188,0,0,0,0,0
 |rna_box=26
 |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=table111:644-26D1;search_select_hide=table117:644-26D1
 }}

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FF:644-26D1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:19, 4 June 2020

CNhs11126

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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