FF:1322-23E9: Difference between revisions

Latest revision as of 18:53, 4 June 2020

Name:	intestine, neonate N01
Species:	Mouse (Mus musculus)
Library ID:	CNhs11192
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	intestine
dev stage	1 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		SAMD00005547

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11192		CAGE		DRX008997		DRR009871

Accession ID Mm9

Library id		BAM		CTSS
CNhs11192		DRZ001296		DRZ002679

Accession ID Mm10

Library id		BAM		CTSS
CNhs11192		DRZ012646		DRZ014029

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

CNhs11192

0	0
1	0
10	0
100	0
1000	0.106
1001	0.0318
1002	0.3
1003	-0.0445
1004	0
1005	0.174
1006	-0.0532
1007	-0.158
1008	0.174
1009	0.117
101	-0.0476
1010	0
1011	-0.108
1012	0
1013	0.273
1014	0.365
1015	-0.173
1016	-0.0993
1017	0
1018	0.298
1019	0
102	0
1020	0
1021	0.0662
1022	-0.00418
1023	0
1024	0.0338
1025	0.642
1026	0.0942
1027	0
1028	0
1029	0.146
103	0.085
1030	0
1031	0.126
1032	0.307
1033	0
1034	0
1035	0
1036	-0.0474
1037	0
1038	0.0371
1039	-0.0257
104	0.0662
1040	-0.0865
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: CNhs11192

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.227
MA0003.1	MA0003.1	0.166
MA0004.1	MA0004.1	0.572
MA0006.1	MA0006.1	0.0497
MA0007.1	MA0007.1	0.883
MA0009.1	MA0009.1	0.447
MA0014.1	MA0014.1	0.573
MA0017.1	MA0017.1	2.67145e-32
MA0018.2	MA0018.2	6.04303e-4
MA0019.1	MA0019.1	0.137
MA0024.1	MA0024.1	0.00825
MA0025.1	MA0025.1	0.142
MA0027.1	MA0027.1	0.22
MA0028.1	MA0028.1	0.263
MA0029.1	MA0029.1	0.836
MA0030.1	MA0030.1	0.422
MA0031.1	MA0031.1	0.277
MA0035.2	MA0035.2	1.52642e-6
MA0038.1	MA0038.1	0.354
MA0039.2	MA0039.2	4.89281e-4
MA0040.1	MA0040.1	0.245
MA0041.1	MA0041.1	0.261
MA0042.1	MA0042.1	0.868
MA0043.1	MA0043.1	0.00918
MA0046.1	MA0046.1	2.08841e-71
MA0047.2	MA0047.2	0.00384
MA0048.1	MA0048.1	0.496
MA0050.1	MA0050.1	0.00157
MA0051.1	MA0051.1	0.0194
MA0052.1	MA0052.1	6.51544e-5
MA0055.1	MA0055.1	0.24
MA0057.1	MA0057.1	0.115
MA0058.1	MA0058.1	0.386
MA0059.1	MA0059.1	0.994
MA0060.1	MA0060.1	1.13221e-4
MA0061.1	MA0061.1	0.717
MA0062.2	MA0062.2	0.169
MA0065.2	MA0065.2	2.40831e-14
MA0066.1	MA0066.1	0.296
MA0067.1	MA0067.1	0.28
MA0068.1	MA0068.1	0.389
MA0069.1	MA0069.1	0.0783
MA0070.1	MA0070.1	0.118
MA0071.1	MA0071.1	0.805
MA0072.1	MA0072.1	0.485
MA0073.1	MA0073.1	0.805
MA0074.1	MA0074.1	0.0345
MA0076.1	MA0076.1	0.134
MA0077.1	MA0077.1	0.219
MA0078.1	MA0078.1	0.174
MA0079.2	MA0079.2	0.555
MA0080.2	MA0080.2	0.125
MA0081.1	MA0081.1	0.0701
MA0083.1	MA0083.1	0.294
MA0084.1	MA0084.1	0.659
MA0087.1	MA0087.1	0.499
MA0088.1	MA0088.1	0.965
MA0090.1	MA0090.1	0.204
MA0091.1	MA0091.1	0.708
MA0092.1	MA0092.1	0.114
MA0093.1	MA0093.1	0.557
MA0099.2	MA0099.2	0.0025
MA0100.1	MA0100.1	0.00871
MA0101.1	MA0101.1	0.514
MA0102.2	MA0102.2	0.979
MA0103.1	MA0103.1	1.09265e-5
MA0104.2	MA0104.2	0.175
MA0105.1	MA0105.1	0.423
MA0106.1	MA0106.1	0.936
MA0107.1	MA0107.1	0.334
MA0108.2	MA0108.2	0.0882
MA0111.1	MA0111.1	0.383
MA0112.2	MA0112.2	2.63798e-4
MA0113.1	MA0113.1	0.929
MA0114.1	MA0114.1	3.14273e-39
MA0115.1	MA0115.1	1.52012e-10
MA0116.1	MA0116.1	0.392
MA0117.1	MA0117.1	0.698
MA0119.1	MA0119.1	0.24
MA0122.1	MA0122.1	0.72
MA0124.1	MA0124.1	0.282
MA0125.1	MA0125.1	0.66
MA0131.1	MA0131.1	0.708
MA0135.1	MA0135.1	0.00977
MA0136.1	MA0136.1	0.407
MA0137.2	MA0137.2	0.472
MA0138.2	MA0138.2	0.61
MA0139.1	MA0139.1	0.0183
MA0140.1	MA0140.1	0.0402
MA0141.1	MA0141.1	4.77283e-4
MA0142.1	MA0142.1	0.0159
MA0143.1	MA0143.1	0.141
MA0144.1	MA0144.1	0.0312
MA0145.1	MA0145.1	0.0132
MA0146.1	MA0146.1	0.125
MA0147.1	MA0147.1	0.102
MA0148.1	MA0148.1	1.314e-4
MA0149.1	MA0149.1	0.0526
MA0150.1	MA0150.1	0.648
MA0152.1	MA0152.1	0.328
MA0153.1	MA0153.1	2.6911e-57
MA0154.1	MA0154.1	0.0161
MA0155.1	MA0155.1	0.0557
MA0156.1	MA0156.1	0.318
MA0157.1	MA0157.1	0.574
MA0159.1	MA0159.1	0.0153
MA0160.1	MA0160.1	0.00991
MA0162.1	MA0162.1	0.232
MA0163.1	MA0163.1	0.00395
MA0164.1	MA0164.1	0.922
MA0258.1	MA0258.1	0.0499
MA0259.1	MA0259.1	0.155

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: CNhs11192

Novel motif	Logo	P-value
1	1	0.373
10	10	0.276
100	100	0.609
101	101	0.898
102	102	0.454
103	103	0.227
104	104	0.812
105	105	0.717
106	106	0.0148
107	107	0.0287
108	108	0.503
109	109	0.0536
11	11	0.242
110	110	0.494
111	111	0.265
112	112	0.0213
113	113	0.392
114	114	0.128
115	115	0.696
116	116	0.18
117	117	0.541
118	118	0.337
119	119	0.211
12	12	0.768
120	120	0.847
121	121	0.989
122	122	0.826
123	123	0.258
124	124	0.364
125	125	0.721
126	126	0.0783
127	127	0.4
128	128	0.066
129	129	0.437
13	13	0.00149
130	130	0.969
131	131	0.127
132	132	0.424
133	133	0.932
134	134	0.373
135	135	0.963
136	136	0.037
137	137	0.925
138	138	0.17
139	139	0.0258
14	14	0.764
140	140	0.411
141	141	0.334
142	142	0.882
143	143	0.195
144	144	0.732
145	145	0.142
146	146	0.161
147	147	0.31
148	148	0.09
149	149	0.0781
15	15	0.209
150	150	0.302
151	151	0.686
152	152	0.0301
153	153	0.369
154	154	0.985
155	155	0.488
156	156	0.00216
157	157	0.621
158	158	0.442
159	159	0.761
160	160	0.0882
161	161	0.487
162	162	0.287
163	163	0.061
164	164	0.124
165	165	0.49
166	166	0.72
167	167	0.49
168	168	0.357
169	169	0.0297
17	17	0.0757
18	18	0.507
19	19	0.0427
2	2	0.0752
20	20	0.633
21	21	0.727
22	22	0.331
23	23	0.243
24	24	0.818
25	25	0.73
26	26	0.0135
27	27	0.54
28	28	0.892
29	29	0.581
3	3	0.264
30	30	0.251
31	31	0.568
32	32	0.0195
33	33	0.109
34	34	0.432
35	35	0.909
36	36	0.924
37	37	0.0407
38	38	0.383
39	39	0.162
4	4	0.392
40	40	0.254
41	41	0.894
42	42	0.93
43	43	0.256
44	44	0.316
45	45	0.206
46	46	0.43
47	47	0.465
48	48	0.407
49	49	0.424
5	5	0.819
50	50	0.34
51	51	0.788
52	52	0.0264
53	53	0.851
54	54	0.725
55	55	0.125
56	56	0.392
57	57	0.602
58	58	0.6
59	59	0.0926
6	6	0.74
60	60	0.023
61	61	0.338
62	62	0.695
63	63	0.29
64	64	0.567
65	65	0.185
66	66	0.376
67	67	0.243
68	68	0.232
69	69	0.807
7	7	0.0465
70	70	0.0546
71	71	0.0888
72	72	0.554
73	73	0.128
74	74	0.825
75	75	0.206
76	76	0.912
77	77	0.0249
78	78	0.0438
79	79	0.596
8	8	0.466
80	80	0.212
81	81	0.416
82	82	0.122
83	83	0.652
84	84	0.241
85	85	0.0612
86	86	0.381
87	87	0.287
88	88	0.796
89	89	0.163
9	9	0.712
90	90	0.595
91	91	0.626
92	92	0.167
93	93	0.928
94	94	0.229
95	95	0.107
96	96	0.736
97	97	0.553
98	98	0.866
99	99	0.0395

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: CNhs11192

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000304 mouse neonate N0 sample
FF:0011504 mouse intestine- neonate N01 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)
0000734 (mouse neonate N1 sample)
0011504 (mouse intestine- neonate N01 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@SAMD00005547
+|accession_numbers=CAGE;DRX008997;DRR009871;DRZ001296;DRZ002679;DRZ012646;DRZ014029
+|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:0000304,FF:0000734,FF:0011504
 |comment=fantom:1322-23E9
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:80555320..80555378,-!p1@Creb3l3!2.31!235.52!Creb3l3;;chr10:88969376..88969395,-!p1@Nr1h4!2.21!161.73!Nr1h4;;chr5:148118639..148118715,-!p1@Cdx2!2.19!153.66!Cdx2;;chr3:3634145..3634161,+!p1@Hnf4g!2.18!150.53!Hnf4g;;chr16:38294860..38294924,-!p1@Nr1i2!1.81!63.24!Nr1i2;;chr1:137155026..137155042,-!p1@Elf3!1.76!313.26!Elf3;;chr2:163372884..163372904,+!p1@Hnf4a!1.59!37.55!Hnf4a;;chr2:180069370..180069409,-!p1@Gata5!1.53!38.54!Gata5;;chr8:77396591..77396639,+!p1@Isx!1.52!32.45!Isx;;chr8:77397095..77397127,+!p2@Isx!1.46!28.00!Isx;;chr18:61195865..61195880,-!p1@Cdx1!1.38!23.22!Cdx1;;chr18:61195843..61195864,-!p2@Cdx1!1.38!23.22!Cdx1;;chr19:43686789..43686811,+!p1@Nkx2-3!1.38!23.22!Nkx2-3;;chr10:22539932..22539956,-!p1@Tcf21!1.37!58.63!Tcf21;;chr10:80555398..80555409,-!p2@Creb3l3!1.35!21.41!Creb3l3;;chr14:63864056..63864102,-!p1@Gata4!1.34!35.57!Gata4;;chr17:27865882..27865901,-!p1@Spdef!1.32!19.76!Spdef;;chr11:57645506..57645523,-!p1@Hand1!1.28!18.12!Hand1;;chr8:59799772..59799789,+!p1@Hand2!1.27!49.90!Hand2;;chr8:123608252..123608268,+!p1@Foxf1a!1.27!25.69!Foxf1a;;chr2:163332558..163332596,+!p2@Hnf4a!1.27!17.46!Hnf4a;;chr7:148452314..148452329,-!p1@Irf7!1.26!116.28!Irf7;;chr1:173144144..173144176,+!p1@Nr1i3!1.23!15.98!Nr1i3;;chr1:165219345..165219366,-!p7@Prrx1!1.22!15.65!Prrx1;;chr5:148118840..148118857,-!p2@Cdx2!1.20!14.82!Cdx2;;chr6:64679112..64679126,+!p1@Atoh1!1.19!14.49!Atoh1;;chr2:103123925..103123959,-!p3@Ehf!1.18!14.16!Ehf;;chr18:64499706..64499721,+!p2@Onecut2!1.16!18.94!Onecut2;;chr3:30039329..30039355,-!p5@Mecom!1.16!13.51!Mecom;;chr3:3508024..3508069,+!p2@Hnf4g!1.15!13.18!Hnf4g;;chr1:173144100..173144138,+!p2@Nr1i3!1.15!13.01!Nr1i3;;chr18:64499674..64499696,+!p1@Onecut2!1.13!21.74!Onecut2;;chr5:148118792..148118806,-!p3@Cdx2!1.13!12.35!Cdx2;;chr5:115421065..115421088,-!p1@Hnf1a!1.12!12.19!Hnf1a;;chr2:103143336..103143367,-!p1@Ehf!1.10!18.78!Ehf;;chr10:127095407..127095440,+!p3@Stat6!1.07!13.34!Stat6;;chr2:77357622..77357704,-!p1@Zfp385b!1.06!28.66!Zfp385b;;chr8:77397492..77397514,+!p3@Isx!1.06!10.38!Isx;;chr14:99697871..99697934,+!p1@Klf5!1.05!205.38!Klf5;;chr10:44178375..44178390,-!p2@Prdm1!1.05!14.00!Prdm1;;chr3:94176733..94176794,+!p1@Rorc!1.04!78.23!Rorc;;chr13:31717548..31717596,+!p1@Foxf2!1.04!19.76!Foxf2;;chr18:11052485..11052508,+!p2@Gata6!1.03!27.83!Gata6;;chr10:44178521..44178557,-!p1@Prdm1!1.03!17.62!Prdm1;;chr10:88996336..88996380,-!p2@Nr1h4!1.02!11.86!Nr1h4;;chr14:63890545..63890560,-!p5@Gata4!1.02!9.39!Gata4;;chr8:77397190..77397202,+!p5@Isx!1.02!9.39!Isx;;chr7:19608891..19608895,-!p1@Foxa3!1.00!11.86!Foxa3;;chr5:148118614..148118625,-!p4@Cdx2!1.00!8.89!Cdx2;;chr4:133109285..133109308,+!p1@Nr0b2!1.00!8.89!Nr0b2;;chr14:63890519..63890539,-!p3@Gata4!1.00!8.89!Gata4;;chr7:17642177..17642223,-!p3@Hif3a!0.98!8.56!Hif3a;;chr8:77396650..77396662,+!p4@Isx!0.97!8.40!Isx;;chr5:67490284..67490302,-!p1@Phox2b!0.97!8.23!Phox2b;;chr2:160192793..160192809,-!p1@Mafb!0.94!121.38!Mafb;;chr19:5560600..5560617,-!p1@Ovol1!0.94!9.39!Ovol1;;chr1:194979315..194979359,+!p1@Irf6!0.90!44.14!Irf6;;chr2:153067079..153067090,-!p2@Plagl2!0.90!14.99!Plagl2;;chr3:90046995..90047031,-!p2@Creb3l4!0.90!8.89!Creb3l4;;chr7:17642018..17642045,-!p4@Hif3a!0.90!8.07!Hif3a;;chr6:16848443..16848459,-!p3@Tfec!0.89!6.75!Tfec;;chr8:118231678..118231692,-!p2@Maf!0.88!62.09!Maf;;chr6:83020355..83020371,-!p1@Tlx2!0.88!6.59!Tlx2;;chr5:120121020..120121049,+!p1@Tbx3!0.87!41.17!Tbx3;;chr18:11052642..11052659,+!p1@Gata6!0.87!34.09!Gata6;;chr5:148118809..148118832,-!p5@Cdx2!0.86!6.26!Cdx2;;chr19:53384910..53384937,+!p3@Mxi1!0.84!17.62!Mxi1;;chr10:44178474..44178487,-!p4@Prdm1!0.84!8.73!Prdm1;;chr10:44178493..44178520,-!p3@Prdm1!0.84!8.40!Prdm1;;chr7:108966820..108966835,+!p1@Phox2a!0.84!5.93!Phox2a;;chr18:11052456..11052477,+!p3@Gata6!0.83!18.94!Gata6;;chr3:3508005..3508021,+!p3@Hnf4g!0.83!5.76!Hnf4g;;chr2:180069410..180069421,-!p3@Gata5!0.83!5.76!Gata5;;chr2:163372869..163372882,+!p3@Hnf4a!0.83!5.76!Hnf4a;;chr9:59797525..59797538,-!p2@Nr2e3!0.83!5.76!Nr2e3;;chr7:17647736..17647772,-!p1@Hif3a!0.82!21.08!Hif3a;;chr7:17642053..17642066,-!p2@Hif3a!0.82!8.07!Hif3a;;chr6:16848395..16848416,-!p2@Tfec!0.82!6.59!Tfec;;chr2:79296783..79296801,-!p1@Neurod1!0.82!5.60!Neurod1;;chr2:153067094..153067130,-!p1@Plagl2!0.81!145.76!Plagl2;;chr5:120121446..120121461,+!p2@Tbx3!0.81!19.43!Tbx3;;chr1:194982959..194983007,+!p5@Irf6!0.81!5.44!Irf6;;chr2:180069640..180069660,-!p4@Gata5!0.81!5.44!Gata5;;chr9:59796270..59796294,-!p4@Nr2e3!0.80!5.27!Nr2e3;;chr11:96164821..96164865,+!p1@Hoxb5!0.80!5.27!Hoxb5;;chr10:12810631..12810649,+!p1@Plagl1!0.77!139.99!Plagl1;;chr19:6996243..6996293,-!p1@Esrra!0.77!59.62!Esrra;;chr8:123260252..123260264,+!p1@Irf8!0.77!37.55!Irf8;;chr8:77397169..77397182,+!p7@Isx!0.77!4.94!Isx;;chr6:99216360..99216372,-!p8@Foxp1!0.77!4.94!Foxp1;;chr15:35225845..35225867,+!p1@Osr2!0.76!12.85!Osr2;;chr10:80555285..80555291,-!p4@Creb3l3!0.76!4.78!Creb3l3;;chr2:103143315..103143328,-!p2@Ehf!0.76!4.78!Ehf;;chr11:986143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2.47!Gm4944;;chr4:102792072..102792091,+!p5@Mier1!0.09!2.14!Mier1;;chr4:87678743..87678767,-!p7@Mllt3!0.09!1.81!Mllt3;;chr7:30954700..30954715,-!p2@LOC677248,p2@Zfp146!0.09!1.81!Zfp146;;chr2:91077034..91077078,-!p2@Ddb2!0.09!1.65!Ddb2;;chr14:52639709..52639753,-!p5@Zfp219!0.09!1.65!Zfp219;;chr5:134790276..134790294,-!p7@Gtf2i!0.09!1.65!Gtf2i;;chr6:99471044..99471066,-!p4@Foxp1!0.09!1.48!Foxp1;;chr15:76709662..76709676,+!p2@Zfp7!0.09!1.48!Zfp7;;chr1:120949925..120949947,-!p4@Gli2!0.09!1.32!Gli2;;chr5:65194810..65194819,+!p9@Klf3!0.09!1.32!Klf3;;chr5:147760297..147760304,+!p4@Gtf3a!0.09!1.15!Gtf3a;;chr5:3648045..3648074,-!p2@Gatad1!0.09!0.99!Gatad1;;chr7:119822915..119822936,+!p5@Tead1!0.09!0.99!Tead1;;chr2:127347094..127347111,-!p2@Kcnip3!0.09!0.99!Kcnip3;;chr5:32438395..32438406,+!p3@Fosl2!0.09!0.82!Fosl2;;chr18:61336630..61336641,-!p3@Hmgxb3!0.09!0.49!Hmgxb3;;chr3:95032184..95032195,-!p4@Mllt11!0.09!0.49!Mllt11;;chr2:71384802..71384815,-!p1@Dlx2!0.09!0.49!Dlx2;;chr2:120389480..120389491,-!p6@Zfp106!0.09!0.49!Zfp106;;chr12:39506841..39506848,+!p7@Etv1!0.09!0.49!Etv1;;chrX:45245582..45245591,-!p4@Smarca1!0.09!0.49!Smarca1;;chr19:53403997..53404008,+!p7@Mxi1!0.09!0.33!Mxi1;;chr2:34227273..34227292,-!p4@Pbx3!0.09!0.33!Pbx3;;chr14:76904313..76904328,+!p1@Tsc22d1!0.08!210.16!Tsc22d1;;chr16:15887371..15887385,+!p1@Cebpd!0.08!36.89!Cebpd;;chr13:5860776..5860796,+!p1@Klf6!0.08!25.53!Klf6;;chr10:80040030..80040072,-!p1@Klf16!0.08!20.92!Klf16;;chr17:28487692..28487765,-!p1@Tead3!0.08!20.92!Tead3;;chr13:48608763..48608821,-!p1@Zfp169!0.08!16.47!Hkr1;;chr12:85559785..85559840,-!p1@C130039O16Rik!0.08!14.00!C130039O16Rik;;chr5:142939972..142940026,+!p1@C330006K01Rik!0.08!13.67!C330006K01Rik;;chr5:104183173..104183207,+!p1@Aff1!0.08!13.51!Aff1;;chr11:120494853..120494905,-!p1@Mafg!0.08!9.72!Mafg;;chr11:100721761..100721851,+!p1@Stat5a!0.08!7.25!Stat5a;;chr17:48061692..48061723,-!p5@Foxp4!0.08!4.45!Foxp4;;chr2:126501274..126501308,-!p2@Gabpb1!0.08!3.62!Gabpb1;;chr6:48395825..48395846,-!p3@Zfp467!0.08!3.29!Zfp467;;chrX:48558950..48559016,-!p1@Mbnl3!0.08!2.64!Mbnl3;;chr15:102301130..102301147,+!p3@Pcbp2!0.08!2.47!Pcbp2;;chr2:38781916..38781974,-!p1@Nr6a1!0.08!2.47!Nr6a1;;chr7:119822828..119822839,+!p4@Tead1!0.08!2.31!Tead1;;chr19:5912834..5912852,-!p2@Dpf2!0.08!1.98!Dpf2;;chr15:78994907..78994926,-!p1@Sox10!0.08!1.98!Sox10;;chr6:14851440..14851497,+!p2@Foxp2!0.08!1.81!Foxp2;;chr5:134790326..134790343,-!p8@Gtf2i!0.08!1.81!Gtf2i;;chrX:48559079..48559108,-!p2@Mbnl3!0.08!1.65!Mbnl3;;chr15:75672367..75672384,-!p2@Zc3h3!0.08!1.48!Zc3h3;;chr6:47545052..47545064,-!p2@Ezh2!0.08!1.32!Ezh2;;chr2:169458838..169458859,+!p4@Tshz2!0.08!1.32!Tshz2;;chr1:133914326..133914346,+!p8@Elk4!0.08!1.15!Elk4;;chr13:117099847..117099907,-!p1@Isl1!0.08!1.15!Isl1;;chr5:3647720..3647733,-!p3@Gatad1!0.08!1.15!Gatad1;;chr3:54559463..54559493,+!p3@Smad9!0.08!1.15!Smad9;;chr11:98602203..98602266,+!p4@Thra!0.08!0.82!Thra;;chr10:67599361..67599372,-!p5@Arid5b!0.08!0.82!Arid5b;;chr13:67476665..67476693,-!p2@Zfp456!0.08!0.82!Zfp456;;chr13:112476264..112476282,+!p3@Mier3!0.08!0.66!Mier3;;chr12:75009147..75009157,+!p5@Hif1a!0.08!0.66!Hif1a;;chr2:77654650..77654685,-!p3@Zfp385b!0.08!0.49!Zfp385b;;chr4:55545051..55545110,-!p2@Klf4!0.08!0.49!Klf4;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!0.08!0.49!Pou3f3;;chr16:43364215..43364252,+!p14@Zbtb20!0.08!0.49!Zbtb20;;chr18:3337307..3337326,-!p14@Crem!0.08!0.49!Crem;;chr17:71202982..71202985,-!p7@Tgif1!0.08!0.49!Tgif1;;chrX:90531838..90531861,+!p1@Arx!0.08!0.49!Arx;;chr5:31262543..31262555,-!p3@Preb!0.08!0.49!Preb;;chr2:74550178..74550214,+!p5@Hoxd3!0.08!0.33!Hoxd3;;chr7:26067803..26067814,+!p11@Cic!0.08!0.33!Cic;;chr7:4947786..4947797,-!p9@Zfp579!0.08!0.33!Zfp579;;
+|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:0000304;;FF:0011504
 |is_obsolete=
+|library_id=CNhs11192
+|library_id_phase_based=2:CNhs11192
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1322
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1322
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N01.CNhs11192.1322-23E9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N01.CNhs11192.1322-23E9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N01.CNhs11192.1322-23E9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N01.CNhs11192.1322-23E9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N01.CNhs11192.1322-23E9.mm9.nobarcode.rdna.fa.gz
 |name=intestine, neonate N01
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11192,LSID746,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.228945602489142,0,0,0,0,0.0256350442579473,0.0197461284708924,0,0,0,0,-0.0181255546890116,0,0,0,0,0,0,0.0690111720229296,0,0,0,0.0662136857075299,0,0,0.123654991486488,0,0,0,0,0,0,0.238870137102648,0,0,0,0.560526311637518,0,0.0980000512052564,-0.0404487346519462,-0.126239853968407,-0.153978014176731,0.0951682771904872,0,0,0,0,0,0,0,0,0,0,0.0662136857075299,0.123654991486488,0.0576494439230477,0,0,0,0,0.0780882314303404,0,0.033106842853765,0,0,0,0.00275889362371365,0.0223717244056244,0.174931338973928,0.0625449741876671,0,0,-0.00674461603264537,-0.0719576978972953,0.0662136857075299,0.033106842853765,-0.027762471349048,0.0924171316679703,-0.230877965539731,-0.0126179091323775,0,0,0,0,0.061827495743244,0.219792932025556,0.036654330773128,0.192854182312336,0.0974939920380969,0,0,0,0,0
 |rna_box=23
 |rna_catalog_number=
@@ Line 55: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=23E9
+|rna_tube_id=2.30E+10
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
 |top_motifs=HNF4A_NR2F1,2:2.55040845708;FOXM1:2.01415285087;DMAP1_NCOR{1,2}_SMARC:1.87147745288;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.74647633008;HNF1A:1.71121814721;SNAI1..3:1.59227982021;ESRRA:1.53207936218;CDX1,2,4:1.32571144355;ATF6:1.32132820835;ZNF423:1.23027971139;XCPE1{core}:1.20057863798;GZF1:1.16748756392;NFIX:1.12680417779;ARID5B:1.09476385861;SREBF1,2:1.05290080537;ZEB1:1.03629716619;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.995543385982;AR:0.944367687083;NR6A1:0.893040136665;MYBL2:0.889203255295;NR1H4:0.85475884035;IRF1,2:0.78038655273;PDX1:0.756520600609;EVI1:0.753699747076;SRF:0.731226381037;EBF1:0.721732157872;ZNF148:0.716824395258;TOPORS:0.701371389292;RXRA_VDR{dimer}:0.646494912046;TLX1..3_NFIC{dimer}:0.613529548154;FOSL2:0.610692514053;TBX4,5:0.595967594834;ADNP_IRX_SIX_ZHX:0.548794895813;SP1:0.547804289478;TFAP4:0.538336778281;TP53:0.453922739471;FOX{D1,D2}:0.441040324838;JUN:0.435809856625;TBP:0.40911886621;HIF1A:0.385763254681;TFCP2:0.334673801437;STAT2,4,6:0.319957480128;TEAD1:0.279156130285;FOXA2:0.260071410848;MYOD1:0.257095040896;FOXO1,3,4:0.251762497614;IKZF2:0.236309716224;NKX2-1,4:0.182373252093;FOXP3:0.165076518409;GATA6:0.160402603683;GLI1..3:0.157162765092;MAZ:0.145004854144;LMO2:0.125608504954;HOXA9_MEIS1:0.122125479365;FOS_FOS{B,L1}_JUN{B,D}:0.115296067667;FOX{I1,J2}:0.0944867196019;GCM1,2:0.0792585081548;ETS1,2:0.0768384104698;GTF2A1,2:0.051619393358;VSX1,2:0.0508985363296;LEF1_TCF7_TCF7L1,2:0.0431403314162;ZBTB6:0.0419381608079;ELF1,2,4:0.0347730447375;REST:-0.00031920744591;ESR1:-0.00303123317599;PAX2:-0.00646351336257;GFI1B:-0.0172691624523;CUX2:-0.0212812983637;MYFfamily:-0.0594209059043;STAT1,3:-0.0600602934979;SPI1:-0.0642850032108;CDC5L:-0.079498909436;NR5A1,2:-0.0864479445781;ZNF238:-0.088179824197;GFI1:-0.0890965409452;NKX3-2:-0.0921801340602;FOXP1:-0.0949858728239;FOXN1:-0.095251358619;HES1:-0.0995268845055;NKX6-1,2:-0.103664478184;NANOG:-0.116488408519;PRRX1,2:-0.117366176643;FOXL1:-0.125455529594;UFEwm:-0.145295326357;GTF2I:-0.156365995496;TAL1_TCF{3,4,12}:-0.176607980809;T:-0.181630696829;HMGA1,2:-0.185240022373;PBX1:-0.187236329545;NFE2:-0.193932594063;PAX4:-0.230127508272;FOXQ1:-0.23435461164;NR3C1:-0.236896063722;HIC1:-0.242560748236;PAX5:-0.246415865912;RXR{A,B,G}:-0.246879981945;E2F1..5:-0.253296647492;ALX4:-0.257421800841;TLX2:-0.268978217515;GATA4:-0.27414229016;MTF1:-0.280861191327;IKZF1:-0.288946887237;RBPJ:-0.289423463595;MED-1{core}:-0.290099565456;HMX1:-0.290286472101;NKX2-3_NKX2-5:-0.291746884123;NKX2-2,8:-0.301886625613;ELK1,4_GABP{A,B1}:-0.3027751711;NFE2L1:-0.304387144927;BACH2:-0.307091457533;POU1F1:-0.314059692127;NKX3-1:-0.314784731665;ONECUT1,2:-0.317093493766;TFAP2{A,C}:-0.325865033159;BPTF:-0.355899384427;FOXD3:-0.361484055093;ZNF384:-0.372125022043;POU6F1:-0.377599942189;NFKB1_REL_RELA:-0.388158468866;TFAP2B:-0.395463085861;PAX1,9:-0.397438837772;IRF7:-0.405245279761;PATZ1:-0.427328374957;EP300:-0.429405270896;ATF5_CREB3:-0.437388481617;NANOG{mouse}:-0.438662630392;DBP:-0.448571199122;PAX6:-0.45407808552;MAFB:-0.455564629586;PITX1..3:-0.457259927896;STAT5{A,B}:-0.463760046584;KLF4:-0.466107300487;HAND1,2:-0.468846098702;ZIC1..3:-0.472835923533;ATF2:-0.477704796161;HBP1_HMGB_SSRP1_UBTF:-0.486955911537;SPIB:-0.50050698468;RREB1:-0.521033518956;NFE2L2:-0.534434333734;YY1:-0.536907964652;bHLH_family:-0.537213743885;POU2F1..3:-0.545498694124;OCT4_SOX2{dimer}:-0.550864338093;CEBPA,B_DDIT3:-0.561192686287;LHX3,4:-0.566928788357;POU3F1..4:-0.569069291922;ZFP161:-0.569822949054;MYB:-0.579535580414;FOX{F1,F2,J1}:-0.579543043953;TGIF1:-0.597055383207;RUNX1..3:-0.598327033231;BREu{core}:-0.628479437247;PRDM1:-0.641658916256;CREB1:-0.645928294606;SOX5:-0.647175351035;EGR1..3:-0.651564193294;MTE{core}:-0.67588694136;HLF:-0.677446614763;AHR_ARNT_ARNT2:-0.68438651696;RFX1:-0.735028113298;SPZ1:-0.73669642724;NHLH1,2:-0.745073516305;NFY{A,B,C}:-0.748195182021;SMAD1..7,9:-0.752341036601;MEF2{A,B,C,D}:-0.754425539823;TEF:-0.826776545811;SOX2:-0.84379276623;PAX8:-0.877842804719;EN1,2:-0.908721517668;RORA:-0.918969404344;HSF1,2:-0.921648623453;TFDP1:-0.924991216295;MZF1:-0.942235594273;SOX17:-0.946476131964;AIRE:-0.954676203633;ATF4:-1.02422198484;ZBTB16:-1.06612008914;PPARG:-1.08243249176;NRF1:-1.08487982785;NFIL3:-1.11305160004;NFATC1..3:-1.12614634881;CRX:-1.15000308335;ZNF143:-1.23087315367;SOX{8,9,10}:-1.26177883156;RFX2..5_RFXANK_RFXAP:-1.30910688874;POU5F1:-1.40762619188;ALX1:-1.6811050149;HOX{A4,D4}:-1.82302333095;HOX{A5,B5}:-2.03146240975
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1322-23E9;search_select_hide=table117:1322-23E9
 }}

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FF:1322-23E9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:53, 4 June 2020

CNhs11192

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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