FF:1386-42I1: Difference between revisions

Latest revision as of 19:05, 4 June 2020

Name:	stomach, neonate N30
Species:	Mouse (Mus musculus)
Library ID:	CNhs11134
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	stomach
dev stage	30 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		SAMD00005400

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11134		CAGE		DRX009099		DRR009973

Accession ID Mm9

Library id		BAM		CTSS
CNhs11134		DRZ001398		DRZ002781

Accession ID Mm10

Library id		BAM		CTSS
CNhs11134		DRZ012748		DRZ014131

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

CNhs11134

0	0
1	0
10	0
100	0
1000	0.0859
1001	0.0905
1002	0.00605
1003	-0.0798
1004	0
1005	0.25
1006	0
1007	0.0383
1008	0
1009	0.0207
101	-0.13
1010	0
1011	-0.108
1012	0.0835
1013	0.199
1014	-0.0874
1015	-0.376
1016	-0.191
1017	0
1018	0.586
1019	0
102	0
1020	0
1021	-0.0231
1022	0.111
1023	0
1024	0
1025	0.686
1026	0
1027	0
1028	0
1029	0.375
103	0.12
1030	0
1031	-0.185
1032	0.67
1033	0
1034	0.131
1035	0.0624
1036	-0.139
1037	0
1038	0.0428
1039	0.16
104	0.983
1040	-0.0865
1041	0.1

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: CNhs11134

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.643
MA0003.1	MA0003.1	0.226
MA0004.1	MA0004.1	0.443
MA0006.1	MA0006.1	0.0373
MA0007.1	MA0007.1	0.939
MA0009.1	MA0009.1	0.121
MA0014.1	MA0014.1	0.319
MA0017.1	MA0017.1	4.28203e-10
MA0018.2	MA0018.2	0.155
MA0019.1	MA0019.1	0.642
MA0024.1	MA0024.1	5.5036e-4
MA0025.1	MA0025.1	0.519
MA0027.1	MA0027.1	0.493
MA0028.1	MA0028.1	0.618
MA0029.1	MA0029.1	0.614
MA0030.1	MA0030.1	0.425
MA0031.1	MA0031.1	0.0265
MA0035.2	MA0035.2	0.76
MA0038.1	MA0038.1	0.912
MA0039.2	MA0039.2	7.88581e-5
MA0040.1	MA0040.1	0.0211
MA0041.1	MA0041.1	0.357
MA0042.1	MA0042.1	0.665
MA0043.1	MA0043.1	0.921
MA0046.1	MA0046.1	3.29615e-27
MA0047.2	MA0047.2	5.95022e-5
MA0048.1	MA0048.1	0.999
MA0050.1	MA0050.1	7.70974e-4
MA0051.1	MA0051.1	7.03903e-4
MA0052.1	MA0052.1	0.00583
MA0055.1	MA0055.1	0.35
MA0057.1	MA0057.1	0.14
MA0058.1	MA0058.1	0.33
MA0059.1	MA0059.1	0.0996
MA0060.1	MA0060.1	0.0497
MA0061.1	MA0061.1	0.454
MA0062.2	MA0062.2	0.742
MA0065.2	MA0065.2	2.29829e-9
MA0066.1	MA0066.1	0.568
MA0067.1	MA0067.1	0.316
MA0068.1	MA0068.1	0.814
MA0069.1	MA0069.1	0.663
MA0070.1	MA0070.1	0.211
MA0071.1	MA0071.1	0.447
MA0072.1	MA0072.1	0.949
MA0073.1	MA0073.1	0.617
MA0074.1	MA0074.1	0.526
MA0076.1	MA0076.1	0.413
MA0077.1	MA0077.1	0.395
MA0078.1	MA0078.1	0.223
MA0079.2	MA0079.2	0.918
MA0080.2	MA0080.2	9.7886e-4
MA0081.1	MA0081.1	0.244
MA0083.1	MA0083.1	0.0227
MA0084.1	MA0084.1	0.0774
MA0087.1	MA0087.1	0.563
MA0088.1	MA0088.1	0.993
MA0090.1	MA0090.1	0.27
MA0091.1	MA0091.1	0.707
MA0092.1	MA0092.1	0.93
MA0093.1	MA0093.1	0.469
MA0099.2	MA0099.2	2.92515e-4
MA0100.1	MA0100.1	0.159
MA0101.1	MA0101.1	0.957
MA0102.2	MA0102.2	0.198
MA0103.1	MA0103.1	1.1132e-5
MA0104.2	MA0104.2	0.0196
MA0105.1	MA0105.1	0.775
MA0106.1	MA0106.1	0.166
MA0107.1	MA0107.1	0.735
MA0108.2	MA0108.2	0.534
MA0111.1	MA0111.1	0.557
MA0112.2	MA0112.2	2.98904e-4
MA0113.1	MA0113.1	0.267
MA0114.1	MA0114.1	1.69505e-18
MA0115.1	MA0115.1	1.00757e-4
MA0116.1	MA0116.1	0.501
MA0117.1	MA0117.1	0.865
MA0119.1	MA0119.1	0.00698
MA0122.1	MA0122.1	0.77
MA0124.1	MA0124.1	0.339
MA0125.1	MA0125.1	0.307
MA0131.1	MA0131.1	0.538
MA0135.1	MA0135.1	0.0922
MA0136.1	MA0136.1	0.0012
MA0137.2	MA0137.2	0.819
MA0138.2	MA0138.2	0.295
MA0139.1	MA0139.1	0.098
MA0140.1	MA0140.1	0.122
MA0141.1	MA0141.1	0.0343
MA0142.1	MA0142.1	0.103
MA0143.1	MA0143.1	0.0229
MA0144.1	MA0144.1	0.257
MA0145.1	MA0145.1	0.00228
MA0146.1	MA0146.1	0.486
MA0147.1	MA0147.1	0.022
MA0148.1	MA0148.1	1.83387e-5
MA0149.1	MA0149.1	0.0401
MA0150.1	MA0150.1	0.198
MA0152.1	MA0152.1	0.192
MA0153.1	MA0153.1	5.1708e-18
MA0154.1	MA0154.1	0.124
MA0155.1	MA0155.1	0.97
MA0156.1	MA0156.1	0.0111
MA0157.1	MA0157.1	0.0223
MA0159.1	MA0159.1	0.0244
MA0160.1	MA0160.1	0.12
MA0162.1	MA0162.1	0.59
MA0163.1	MA0163.1	0.683
MA0164.1	MA0164.1	0.803
MA0258.1	MA0258.1	0.0554
MA0259.1	MA0259.1	0.0584

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: CNhs11134

Novel motif	Logo	P-value
1	1	0.357
10	10	0.427
100	100	0.695
101	101	0.993
102	102	0.949
103	103	0.793
104	104	0.683
105	105	0.167
106	106	0.00629
107	107	0.0549
108	108	0.866
109	109	0.072
11	11	0.49
110	110	0.331
111	111	0.686
112	112	0.117
113	113	0.455
114	114	0.267
115	115	0.731
116	116	0.657
117	117	0.728
118	118	0.962
119	119	0.136
12	12	0.493
120	120	0.869
121	121	0.399
122	122	0.403
123	123	0.331
124	124	0.707
125	125	0.494
126	126	0.0248
127	127	0.553
128	128	0.0207
129	129	0.423
13	13	2.39791e-4
130	130	0.849
131	131	0.00148
132	132	0.609
133	133	0.928
134	134	0.549
135	135	0.399
136	136	0.219
137	137	0.4
138	138	0.301
139	139	0.144
14	14	0.468
140	140	0.01
141	141	0.322
142	142	0.495
143	143	0.137
144	144	0.287
145	145	0.0925
146	146	0.236
147	147	0.214
148	148	0.199
149	149	0.528
15	15	0.172
150	150	0.4
151	151	0.396
152	152	0.0186
153	153	0.61
154	154	0.399
155	155	0.602
156	156	0.0464
157	157	0.791
158	158	0.667
159	159	0.753
160	160	0.305
161	161	0.53
162	162	0.931
163	163	0.706
164	164	0.202
165	165	0.93
166	166	0.284
167	167	0.773
168	168	0.899
169	169	0.0222
17	17	0.0218
18	18	0.0706
19	19	0.0382
2	2	0.407
20	20	0.976
21	21	0.818
22	22	0.348
23	23	0.35
24	24	0.337
25	25	0.831
26	26	0.0284
27	27	0.941
28	28	0.498
29	29	0.587
3	3	0.467
30	30	0.4
31	31	0.779
32	32	0.318
33	33	0.242
34	34	0.66
35	35	0.665
36	36	0.805
37	37	0.0225
38	38	0.282
39	39	0.217
4	4	0.394
40	40	0.534
41	41	0.85
42	42	0.988
43	43	0.349
44	44	0.997
45	45	0.339
46	46	0.441
47	47	0.651
48	48	0.562
49	49	0.26
5	5	0.556
50	50	0.267
51	51	0.621
52	52	0.0324
53	53	0.915
54	54	0.397
55	55	0.267
56	56	0.386
57	57	0.855
58	58	0.324
59	59	0.875
6	6	0.366
60	60	0.0206
61	61	0.0889
62	62	0.56
63	63	0.173
64	64	0.777
65	65	0.0908
66	66	0.614
67	67	0.0504
68	68	0.209
69	69	0.482
7	7	0.099
70	70	0.089
71	71	0.357
72	72	0.645
73	73	0.0603
74	74	0.642
75	75	0.22
76	76	0.63
77	77	0.135
78	78	0.0412
79	79	0.963
8	8	0.516
80	80	0.721
81	81	0.743
82	82	0.32
83	83	0.0721
84	84	0.365
85	85	0.062
86	86	0.223
87	87	0.746
88	88	0.831
89	89	0.218
9	9	0.76
90	90	0.529
91	91	0.663
92	92	0.509
93	93	0.385
94	94	0.621
95	95	0.165
96	96	0.948
97	97	0.619
98	98	0.537
99	99	0.103

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: CNhs11134

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011494 mouse stomach- neonate N30 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)
0000945 (stomach)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
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)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011494 (mouse stomach- neonate N30 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@DRS008962
+|DRA_sample_Accession=CAGE@SAMD00005400
-|accession_numbers=CAGE;DRX009099;DRR009973;DRZ001398;DRZ002781
+|accession_numbers=CAGE;DRX009099;DRR009973;DRZ001398;DRZ002781;DRZ012748;DRZ014131
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000945,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010039,UBERON:0010317,UBERON:0001555,UBERON:0005409,UBERON:0001041
 |ancestors_in_cell_lineage_facet=
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr5:148118639..148118715,-!p1@Cdx2!2.48!302.26!Cdx2;;chr10:88969376..88969395,-!p1@Nr1h4!2.22!164.87!Nr1h4;;chr1:137155026..137155042,-!p1@Elf3!1.97!512.76!Elf3;;chr2:163372884..163372904,+!p1@Hnf4a!1.90!77.77!Hnf4a;;chr10:30375579..30375616,-!p3@Ncoa7!1.86!163.57!Ncoa7;;chr18:61195843..61195864,-!p2@Cdx1!1.86!72.07!Cdx1;;chr18:61195865..61195880,-!p1@Cdx1!1.84!67.53!Cdx1;;chr15:97738692..97738747,-!p1@Vdr!1.80!322.61!Vdr;;chr2:163332558..163332596,+!p2@Hnf4a!1.77!57.81!Hnf4a;;chr16:38294860..38294924,-!p1@Nr1i2!1.76!56.64!Nr1i2;;chr8:77396591..77396639,+!p1@Isx!1.76!56.64!Isx;;chr6:86619104..86619119,-!p1@Mxd1!1.70!379.25!Mxd1;;chr2:103143336..103143367,-!p1@Ehf!1.64!67.27!Ehf;;chr11:96153767..96153822,+!p1@Hoxb6!1.63!63.77!Hoxb6;;chr6:64679112..64679126,+!p1@Atoh1!1.60!38.75!Atoh1;;chr7:148452314..148452329,-!p1@Irf7!1.59!253.53!Irf7;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.54!93.58!Tfcp2l1;;chr8:79426176..79426275,+!p1@Nr3c2!1.52!153.98!Nr3c2;;chr1:57029281..57029326,-!p1@Satb2!1.52!49.38!Satb2;;chr8:77397095..77397127,+!p2@Isx!1.52!32.40!Isx;;chr3:128916868..128916890,+!p1@Pitx2!1.51!42.64!Pitx2;;chr2:103123925..103123959,-!p3@Ehf!1.44!26.44!Ehf;;chr4:55545337..55545357,-!p1@Klf4!1.38!329.61!Klf4;;chr14:99697871..99697934,+!p1@Klf5!1.36!420.73!Klf5;;chr5:148118840..148118857,-!p2@Cdx2!1.36!22.16!Cdx2;;chr6:52190467..52190500,-!p1@Hoxa10!1.36!22.03!Hoxa10;;chr17:27865882..27865901,-!p1@Spdef!1.36!21.78!Spdef;;chr5:148118792..148118806,-!p3@Cdx2!1.35!21.26!Cdx2;;chr19:5560600..5560617,-!p1@Ovol1!1.29!22.29!Ovol1;;chr8:123608252..123608268,+!p1@Foxf1a!1.28!26.31!Foxf1a;;chr10:22539932..22539956,-!p1@Tcf21!1.27!46.14!Tcf21;;chr8:77397492..77397514,+!p3@Isx!1.26!17.37!Isx;;chr2:103143315..103143328,-!p2@Ehf!1.23!15.81!Ehf;;chr6:115311030..115311065,+!p4@Pparg!1.22!22.55!Pparg;;chr5:148118614..148118625,-!p4@Cdx2!1.21!15.04!Cdx2;;chr3:128902837..128902861,+!p3@Pitx2!1.21!15.04!Pitx2;;chr3:3508024..3508069,+!p2@Hnf4g!1.21!15.04!Hnf4g;;chr8:77397190..77397202,+!p5@Isx!1.21!15.04!Isx;;chr6:52664406..52664434,+!p3@Tax1bp1!1.20!18.02!Tax1bp1;;chr7:19608891..19608895,-!p1@Foxa3!1.17!17.89!Foxa3;;chr5:148118809..148118832,-!p5@Cdx2!1.15!13.09!Cdx2;;chr11:70500401..70500460,-!p3@Camta2!1.14!12.96!Camta2;;chr19:43686789..43686811,+!p1@Nkx2-3!1.11!11.92!Nkx2-3;;chr6:52664439..52664461,+!p4@Tax1bp1!1.10!11.67!Tax1bp1;;chr13:55932591..55932622,-!p1@Pitx1!1.09!13.74!Pitx1;;chr1:194979315..194979359,+!p1@Irf6!1.05!62.99!Irf6;;chr11:96145450..96145517,+!p2@Hoxb7!1.05!15.55!Hoxb7;;chr12:58646974..58647003,-!p1@Foxa1!1.05!13.74!Foxa1;;chr3:90046995..90047031,-!p2@Creb3l4!1.05!12.70!Creb3l4;;chr11:96143666..96143725,+!p1@Hoxb8!1.05!11.79!Hoxb8;;chr11:57645506..57645523,-!p1@Hand1!1.05!10.11!Hand1;;chr4:114581497..114581519,-!p2@Foxd2!1.04!9.98!Foxd2;;chr1:69732511..69732540,-!p2@Ikzf2!1.03!12.57!Ikzf2;;chr19:5560570..5560582,-!p2@Ovol1!1.02!9.46!Ovol1;;chr8:59799772..59799789,+!p1@Hand2!1.01!27.09!Hand2;;chr6:52176164..52176195,-!p1@Hoxa9!1.01!11.54!Hoxa9;;chr10:88996336..88996380,-!p2@Nr1h4!1.01!11.41!Nr1h4;;chr10:80555320..80555378,-!p1@Creb3l3!1.01!10.89!Creb3l3;;chr6:52168685..52168715,-!p9@Hoxa7!1.01!9.20!Hoxa7;;chr10:30375559..30375568,-!p9@Ncoa7!1.00!9.07!Ncoa7;;chr3:89197057..89197114,-!p1@Zbtb7b!0.96!28.26!Zbtb7b;;chr1:57029027..57029056,-!p7@Satb2!0.96!8.04!Satb2;;chr6:52163319..52163342,-!p1@Hoxa3!0.94!11.28!Hoxa3;;chr17:28409136..28409150,+!p3@Ppard!0.94!7.65!Ppard;;chr4:55545051..55545110,-!p2@Klf4!0.93!9.46!Klf4;;chr5:115421065..115421088,-!p1@Hnf1a!0.93!7.52!Hnf1a;;chr8:123260252..123260264,+!p1@Irf8!0.91!52.75!Irf8;;chr10:20880629..20880683,-!p1@Myb!0.91!21.52!Myb;;chr13:31717548..31717596,+!p1@Foxf2!0.91!14.65!Foxf2;;chr3:3634145..3634161,+!p1@Hnf4g!0.90!7.00!Hnf4g;;chr2:74529970..74529997,+!p1@Hoxd10!0.90!6.87!Hoxd10;;chr8:77397026..77397036,+!p6@Isx!0.88!6.61!Isx;;chr4:124805061..124805087,-!p1@Zc3h12a!0.87!20.61!Zc3h12a;;chr16:44173384..44173407,+!p2@Gm608!0.87!17.24!Gm608;;chr2:163372869..163372882,+!p3@Hnf4a!0.87!6.35!Hnf4a;;chr4:102792009..102792021,+!p6@Mier1!0.86!11.02!Mier1;;chr8:77396650..77396662,+!p4@Isx!0.85!6.09!Isx;;chr1:39250584..39250643,+!p1@Npas2!0.84!31.50!Npas2;;chr10:80598209..80598236,+!p4@Zbtb7a!0.84!10.37!Zbtb7a;;chr3:89191234..89191245,-!p15@Zbtb7b!0.83!5.83!Zbtb7b;;chr5:135582751..135582788,+!p1@Mlxipl!0.82!24.24!Mlxipl;;chr4:114581524..114581551,-!p1@Foxd2!0.82!8.55!Foxd2;;chr3:128916838..128916856,+!p4@Pitx2!0.82!5.57!Pitx2;;chr3:3508005..3508021,+!p3@Hnf4g!0.82!5.57!Hnf4g;;chr13:5860776..5860796,+!p1@Klf6!0.81!141.54!Klf6;;chr4:148275237..148275311,+!p2@Casz1!0.81!24.37!Casz1;;chr16:55822241..55822258,-!p1@Nfkbiz!0.80!179.65!Nfkbiz;;chr12:85534957..85535017,-!p2@C130039O16Rik!0.80!28.64!C130039O16Rik;;chr2:133377954..133377973,+!p1@Bmp2!0.80!18.02!Bmp2;;chr6:115310872..115310899,+!p2@Pparg!0.80!9.59!Pparg;;chr1:194979361..194979373,+!p2@Irf6!0.80!7.39!Irf6;;chr4:148178559..148178603,+!p1@Casz1!0.79!15.68!Casz1;;chr3:89197216..89197258,-!p3@Zbtb7b!0.79!11.54!Zbtb7b;;chr4:119486912..119486954,+!p3@Hivep3!0.79!9.46!Hivep3;;chr10:30375530..30375535,-!p12@Ncoa7!0.79!5.18!Ncoa7;;chr1:173144100..173144138,+!p2@Nr1i3!0.79!5.18!Nr1i3;;chr6:52184901..52184959,-!p2@Hoxa10!0.79!5.18!Hoxa10;;chr11:83664334..83664353,+!p2@Hnf1b!0.77!4.93!Hnf1b;;chr18:36441119..36441158,+!p2@Pura!0.76!12.44!Pura;;chr19:5447692..5447711,+!p2@Fosl1!0.76!4.80!Fosl1;;chr11:83664365..83664383,+!p1@Hnf1b!0.76!4.80!Hnf1b;;chr1:138857048..138857071,-!p2@Nr5a2!0.76!4.80!Nr5a2;;chr10:30375647..30375658,-!p7@Ncoa7!0.75!4.67!Ncoa7;;chr3:94176733..94176794,+!p1@Rorc!0.74!39.14!Rorc;;chr15:35225845..35225867,+!p1@Osr2!0.74!12.18!Osr2;;chr11:53583960..53584007,+!p2@Irf1!0.74!10.50!Irf1;;chr13:112476433..112476448,+!p2@Mier3!0.74!9.07!Mier3;;chr11:53583544..53583559,+!p1@Irf1!0.72!80.36!Irf1;;chr3:89197551..89197606,-!p2@Zbtb7b!0.72!15.94!Zbtb7b;;chr15:37162796..37162828,+!p1@Grhl2!0.72!7.52!Grhl2;;chr13:55937467..55937516,-!p3@Pitx1!0.72!4.28!Pitx1;;chr6:72580544..72580553,-!p12@Tcf7l1!0.72!4.28!Tcf7l1;;chr5:65194752..65194769,+!p1@Klf3!0.71!156.83!Klf3;;chr15:102828658..102828678,+!p1@Hoxc6!0.71!4.15!Hoxc6;;chr12:78063146..78063159,-!p2@Max!0.70!11.41!Max;;chr18:11052606..11052633,+!p4@Gata6!0.70!11.02!Gata6;;chr2:147871627..147871641,-!p1@Foxa2!0.70!4.02!Foxa2;;chr14:79915425..79915501,+!p1@Elf1!0.69!39.53!Elf1;;chr19:53384910..53384937,+!p3@Mxi1!0.69!12.31!Mxi1;;chr4:87452200..87452229,-!p2@Mllt3!0.69!9.07!Mllt3;;chr4:55545152..55545194,-!p3@Klf4!0.69!4.80!Klf4;;chr17:28408632..28408682,+!p1@1810013A23Rik,p4@Ppard!0.69!3.89!Ppard;;chr8:77397169..77397182,+!p7@Isx!0.69!3.89!Isx;;chr10:80600749..80600766,+!p2@Zbtb7a!0.68!22.29!Zbtb7a;;chr4:87452180..87452196,-!p3@Mllt3!0.68!8.17!Mllt3;;chr3:128902434..128902444,+!p13@Pitx2!0.68!3.76!Pitx2;;chr3:128918394..128918413,+!p5@Pitx2!0.68!3.76!Pitx2;;chr3:89191265..89191276,-!p16@Zbtb7b!0.68!3.76!Zbtb7b;;chr6:52176144..52176161,-!p2@Hoxa9!0.68!3.76!Hoxa9;;chr6:52195763..52195792,-!p2@Hoxa11!0.67!3.63!Hoxa11;;chr6:115311132..115311147,+!p9@Pparg!0.67!3.63!Pparg;;chr6:99470943..99471024,-!p3@Foxp1!0.66!39.66!Foxp1;;chr19:55816770..55816793,+!p2@Tcf7l2!0.66!35.64!Tcf7l2;;chr8:79423144..79423178,+!p3@Nr3c2!0.66!5.18!Nr3c2;;chr6:115310968..115310980,+!p8@Pparg!0.66!4.02!Pparg;;chr2:74549968..74549996,+!p1@Hoxd3!0.65!4.54!Hoxd3;;chr10:88996295..88996335,-!p3@Nr1h4!0.65!4.28!Nr1h4;;chr9:59797503..59797513,-!p3@Nr2e3!0.65!3.50!Nr2e3;;chr6:52195795..52195825,-!p1@Hoxa11!0.65!3.50!Hoxa11;;chr16:44173352..44173383,+!p1@Gm608!0.64!19.57!Gm608;;chr4:148178529..148178548,+!p3@Casz1!0.64!8.81!Casz1;;chr11:98636400..98636418,-!p4@Nr1d1!0.64!4.67!Nr1d1;;chr2:74549945..74549965,+!p4@Hoxd3!0.64!3.37!Hoxd3;;chr13:5860872..5860883,+!p3@Klf6!0.63!7.26!Klf6;;chr4:102792039..102792052,+!p7@Mier1!0.63!4.93!Mier1;;chr1:57028538..57028553,-!p6@Satb2!0.63!3.24!Satb2;;chr1:57028556..57028583,-!p5@Satb2!0.63!3.24!Satb2;;chr1:57028125..57028149,-!p2@Satb2!0.63!3.24!Satb2;;chr19:6996243..6996293,-!p1@Esrra!0.62!42.00!Esrra;;chr17:28369668..28369734,+!p1@Ppard!0.62!33.83!Ppard;;chr18:11052642..11052659,+!p1@Gata6!0.62!18.92!Gata6;;chr4:135728581..135728668,+!p1@E2f2!0.62!17.63!E2f2;;chr5:104121453..104121479,+!p4@Aff1!0.62!16.98!Aff1;;chr7:133838869..133838945,+!p2@Bola2!0.62!15.42!Bola2;;chr6:52190840..52190853,-!p5@Hoxa10!0.61!3.11!Hoxa10;;chr19:43686882..43686906,+!p2@Nkx2-3!0.61!3.11!Nkx2-3;;chr19:53384985..53385042,+!p1@Mxi1!0.60!111.73!Mxi1;;chr7:120351014..120351109,+!p1@Arntl!0.60!49.51!Arntl;;chr2:166888058..166888105,-!p2@Znfx1!0.60!11.15!Znfx1;;chr11:100948597..100948637,+!p1@Mlx!0.59!83.86!Mlx;;chr2:91864661..91864686,-!p1@Creb3l1!0.59!77.25!Creb3l1;;chr4:102791976..102792008,+!p2@Mier1!0.59!38.63!Mier1;;chr10:107769168..107769215,+!p1@Pawr!0.59!35.64!Pawr;;chr19:6996294..6996324,-!p2@Esrra!0.59!23.07!Esrra;;chr15:37162834..37162849,+!p2@Grhl2!0.59!3.63!Grhl2;;chr6:39068163..39068176,-!p2@Parp12!0.58!5.83!Parp12;;chr3:14578786..14578807,+!p2@E2f5!0.57!12.44!E2f5;;chr5:65213356..65213412,+!p6@Klf3!0.57!6.48!Klf3;;chr5:115420882..115420896,-!p3@Hnf1a!0.57!2.72!Hnf1a;;chr3:128902878..128902893,+!p6@Pitx2!0.57!2.72!Pitx2;;chr1:57029076..57029098,-!p8@Satb2!0.57!2.72!Satb2;;chr2:173044380..173044432,-!p1@Zbp1!0.56!7.26!Zbp1;;chr2:74529998..74530020,+!p2@Hoxd10!0.56!2.59!Hoxd10;;chr2:74549915..74549930,+!p6@Hoxd3!0.56!2.59!Hoxd3;;chr2:79296783..79296801,-!p1@Neurod1!0.56!2.59!Neurod1;;chr2:74536026..74536039,+!p1@Hoxd9!0.56!2.59!Hoxd9;;chr6:52190668..52190682,-!p3@Hoxa10!0.56!2.59!Hoxa10;;chr10:44178521..44178557,-!p1@Prdm1!0.55!5.05!Prdm1;;chr11:96147952..96147967,+!p1@Hoxb7!0.55!3.37!Hoxb7;;chr10:80809447..80809515,-!p5@Hmg20b!0.55!3.24!Hmg20b;;chr6:86619130..86619158,-!p2@Mxd1!0.54!45.24!Mxd1;;chr10:30375665..30375674,-!p11@Ncoa7!0.54!2.46!Ncoa7;;chr11:98822047..98822072,+!p9@Rara!0.54!2.46!Rara;;chr19:5447886..5447905,+!p1@Fosl1!0.54!2.46!Fosl1;;chr2:24278519..24278530,-!p3@Pax8!0.54!2.46!Pax8;;chr4:102787521..102787588,+!p4@Mier1!0.53!4.93!Mier1;;chr9:111020574..111020687,+!p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5;;chr5:67490474..67490494,-!p2@Phox2b!0.14!0.39!Phox2b;;chr6:120314480..120314487,+!p6@Kdm5a!0.14!0.39!Kdm5a;;chr14:17408052..17408073,-!p5@Rarb!0.14!0.39!Rarb;;chr12:39510090..39510114,+!p6@Etv1!0.14!0.39!Etv1;;chr15:102820964..102821006,+!p1@Hoxc8!0.14!0.39!Hoxc8;;chr15:102821007..102821021,+!p2@Hoxc8!0.14!0.39!Hoxc8;;chr15:36937137..36937157,-!p2@Gm10193,p2@Zfp706!0.13!36.42!Zfp706;;chr2:165818125..165818167,+!p1@Ncoa3!0.13!31.63!Ncoa3;;chr10:80813134..80813211,-!p1@Hmg20b!0.13!22.16!Hmg20b;;chr2:75542592..75542609,-!p2@Nfe2l2!0.13!20.09!Nfe2l2;;chr17:46693107..46693137,-!p1@Srf!0.13!11.15!Srf;;chr14:76904356..76904367,+!p3@Tsc22d1!0.13!8.17!Tsc22d1;;chrX:45807329..45807370,-!p1@Elf4!0.13!7.91!Elf4;;chr19:26681929..26681987,+!p4@Smarca2!0.13!6.09!Smarca2;;chr1:133904670..133904731,+!p2@Elk4!0.13!5.57!Elk4;;chr19:5610038..5610066,-!p1@Kat5!0.13!5.05!Kat5;;chr12:110031310..110031342,+!p4@Yy1!0.13!4.15!Yy1;;chr2:83499707..83499708,+!p6@Zc3h15!0.13!3.50!Zc3h15;;chr15:57526206..57526241,+!p2@Zhx2!0.13!3.24!Zhx2;;chr15:100058660..100058711,+!p1@Gm1862,p2@Atf1!0.13!3.24!Atf1;;chr13:42147211..42147244,+!p2@Hivep1!0.13!3.24!Hivep1;;chr11:11586218..11586285,+!p1@Ikzf1!0.13!3.11!Ikzf1;;chr17:23004125..23004157,-!p3@Zfp945!0.13!2.98!Zfp945;;chr14:52634536..52634572,-!p4@Zfp219!0.13!2.85!Zfp219;;chr18:11052485..11052508,+!p2@Gata6!0.13!2.59!Gata6;;chr3:135354349..135354371,-!p6@Nfkb1!0.13!1.68!Nfkb1;;chr11:60036258..60036276,-!p3@Srebf1!0.13!1.30!Srebf1;;chr5:65203599..65203617,+!p8@Klf3!0.13!1.17!Klf3;;chr19:23215469..23215494,+!p2@Klf9!0.13!1.04!Klf9;;chr17:51971960..51971979,-!p1@Satb1!0.13!0.78!Satb1;;chr17:46692970..46692977,-!p5@Srf!0.13!0.78!Srf;;chrX:103070960..103070973,-!p7@Atrx!0.13!0.78!Atrx;;chr9:20385789..20385803,+!p5@Zfp846!0.13!0.65!Zfp846;;chr19:23215430..23215441,+!p7@Klf9!0.13!0.65!Klf9;;chr3:30995296..30995300,+!p6@Skil!0.13!0.65!Skil;;chr4:102787067..102787080,+!p10@Mier1!0.13!0.65!Mier1;;chr11:98636508..98636524,-!p3@Nr1d1!0.13!0.65!Nr1d1;;chr16:11176363..11176458,-!p1@Zc3h7a!0.12!58.33!Zc3h7a;;chr13:48356475..48356492,+!p1@Id4!0.12!25.40!Id4;;chr7:35904304..35904320,+!p1@Cebpa!0.12!23.98!Cebpa;;chr8:108583462..108583523,+!p1@Nfatc3!0.12!21.52!Nfatc3;;chr11:6375995..6376105,-!p1@Purb!0.12!20.61!Purb;;chr4:149943647..149943707,+!p2@Rere!0.12!20.61!Rere;;chr17:23004085..23004108,-!p1@Zfp945!0.12!11.15!Zfp945;;chr8:72662999..72663031,-!p1@LOC100048268,p1@Rfxank!0.12!9.20!Rfxank;;chr10:127176572..127176648,+!p1@Zbtb39!0.12!6.87!Zbtb39;;chr2:120996843..120996894,-!p1@Zscan29!0.12!6.61!Zscan29;;chr4:126698529..126698536,+!p2@Sfpq!0.12!4.80!Sfpq;;chr10:5958538..5958568,+!p1@Zbtb2!0.12!4.54!Zbtb2;;chr13:67552527..67552574,-!p1@Zfp874a!0.12!4.54!Zfp874a;;chrX:137077653..137077669,-!p3@Tsc22d3!0.12!4.54!Tsc22d3;;chr18:69504123..69504155,+!p5@Tcf4!0.12!3.50!Tcf4;;chr9:63869850..63869873,-!p2@Smad6!0.12!2.72!Smad6;;chr6:99216488..99216534,-!p2@Foxp1!0.12!2.59!Foxp1;;chr5:34530277..34530292,-!p3@Mxd4!0.12!2.20!Mxd4;;chr6:92042363..92042413,+!p3@Nr2c2!0.12!2.07!Nr2c2;;chr4:62626682..62626705,+!p2@Zfp618!0.12!1.81!Zfp618;;chr13:5860740..5860747,+!p4@Klf6!0.12!1.68!Klf6;;chr12:9581284..9581303,+!p2@Osr1!0.12!1.43!Osr1;;chr7:13420092..13420160,+!p2@Zfp110!0.12!1.43!Zfp110;;chr4:122673187..122673201,+!p2@Mycl1!0.12!1.30!Mycl1;;chr13:31650026..31650045,+!p2@Foxq1!0.12!1.17!Foxq1;;chr14:47896526..47896539,-!p2@Wdhd1!0.12!1.17!Wdhd1;;chr1:167932722..167932740,-!p2@Pou2f1!0.12!1.17!Pou2f1;;chr10:22451765..22451795,-!p6@Tbpl1!0.12!0.91!Tbpl1;;chr10:41996451..41996462,-!p5@Foxo3!0.12!0.78!Foxo3;;chr2:152758938..152758954,-!p2@Foxs1!0.12!0.78!Foxs1;;chr19:23215554..23215567,+!p5@Klf9!0.12!0.78!Klf9;;chr12:9581243..9581254,+!p4@Osr1!0.12!0.78!Osr1;;chr9:69137648..69137656,+!p5@Rora!0.12!0.78!Rora;;chr11:96213264..96213282,+!p@chr11:96213264..96213282,+!0.12!0.65!Hoxb2;;chr7:38558544..38558566,-!p4@Zfp536!0.12!0.52!Zfp536;;chr18:5593564..5593584,+!p2@Zeb1!0.12!0.52!Zeb1;;chr12:78063165..78063227,-!p1@Max!0.11!99.41!Max;;chr7:51809271..51809325,-!p1@Nr1h2!0.11!64.68!Nr1h2;;chr5:147760216..147760292,+!p1@Gtf3a!0.11!52.11!Gtf3a;;chr11:100800671..100800770,-!p1@Stat3!0.11!37.59!Stat3;;chr12:117285924..117286018,+!p1@Zfp386!0.11!32.40!Zfp386;;chr11:96691218..96691265,-!p2@Nfe2l1!0.11!31.63!Nfe2l1;;chr3:133207232..133207277,-!p1@Tet2!0.11!31.37!Tet2;;chr3:19957802..19957857,+!p1@Hltf!0.11!19.96!Hltf;;chr6:133985839..133985915,+!p1@Etv6!0.11!19.18!Etv6;;chr5:142939972..142940026,+!p1@C330006K01Rik!0.11!14.78!C330006K01Rik;;chr17:48061381..48061399,-!p1@Foxp4!0.11!12.70!Foxp4;;chr6:47827642..47827707,+!p1@Zfp282!0.11!11.67!Zfp282;;chr4:97444446..97444470,+!p3@Nfia!0.11!10.37!Nfia;;chr11:98603119..98603130,+!p2@Thra!0.11!9.07!Thra;;chrX:98728074..98728116,+!p2@Taf1!0.11!6.74!Taf1;;chr10:82226649..82226694,-!p2@Nfyb!0.11!6.61!Nfyb;;chr12:112088483..112088512,+!p1@Zfp839!0.11!6.09!Zfp839;;chr7:28623579..28623631,+!p1@Zfp59!0.11!4.80!Zfp59;;chr10:126725875..126725902,-!p3@Mbd6!0.11!3.37!Mbd6;;chr18:79306158..79306249,-!p1@Setbp1!0.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@@ Line 44: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11134
-|library_ids=CNhs11134
+|library_id_phase_based=2:CNhs11134
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1386
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1386
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N30.CNhs11134.1386-42I1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N30.CNhs11134.1386-42I1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N30.CNhs11134.1386-42I1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N30.CNhs11134.1386-42I1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N30.CNhs11134.1386-42I1.mm9.nobarcode.rdna.fa.gz
 |name=stomach, neonate N30
 |namespace=FANTOM5
@@ Line 50: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11134,LSID735,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.290696836126152,0.0167989261824305,0,0,0.100105043383282,0,0.163257073951971,0,0,0,0,-0.031408799982985,0,0,0,0,0,0,-0.049239596291433,0,0,0,0,0,0.0529304404135566,0,0,0,0,0,0,0,0.276167895037981,0,0,0,0.0529304404135566,0,0.235845456702499,-0.0545836037915545,-0.0495660138728173,-0.444798444489282,-0.216938197596795,0,0,0,0,0,0,0,0,0,0,0.100105043383282,0,0.150971388773078,0,0,0,0,0.207009035164957,0,0.09401251886872,0,0,0.036170453068741,0.0490611755732229,0.0968047796017457,-0.158091042771083,0.0379340060424838,0,0.0954963168125139,0,-0.0273030590566921,0.181403325456646,0,0,0.0810570847740633,-0.0565019587520256,0.230142332030514,0,0,0,0,0.0264652202067783,0,0.0529304404135566,0.193444477540261,-0.0199470119835677,0.0336376687928937,0,0,0,0
@@ Line 87: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1386-42I1;search_select_hide=table117:1386-42I1
 }}

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FF:1386-42I1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:05, 4 June 2020

CNhs11134

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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