FF:12971-138H1: Difference between revisions

Latest revision as of 18:47, 4 June 2020

Name:	TSt-4/DLL1 feeder cells, biol_rep1
Species:	Mouse (Mus musculus)
Library ID:	CNhs13407
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	NA
dev stage	NA
sex	NA
age	NA
cell type	unclassifiable
cell line	NA
company	NA
collaboration	Tomokatsu Ikawa (RCAI)
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		SAMD00005333

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13407		CAGE		DRX008908		DRR009782

Accession ID Mm9

Library id		BAM		CTSS
CNhs13407		DRZ001207		DRZ002590

Accession ID Mm10

Library id		BAM		CTSS
CNhs13407		DRZ012557		DRZ013940

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

CNhs13407

0	0
1	0
10	0
100	0
1000	0
1001	-0.0668
1002	0.361
1003	-0.102
1004	0
1005	0
1006	-0.143
1007	0.315
1008	0
1009	0.882
101	-0.0812
1010	0
1011	-0.337
1012	0
1013	0.115
1014	-0.0874
1015	-0.00444
1016	0.405
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	-0.124
1023	0
1024	-0.307
1025	0
1026	0
1027	-0.048
1028	0.359
1029	-0.115
103	0.321
1030	0
1031	0.0949
1032	-0.184
1033	-0.0752
1034	0
1035	0
1036	0.0168
1037	0
1038	0.554
1039	0.0102
104	0
1040	0.883
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: CNhs13407

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	1.92641e-4
MA0003.1	MA0003.1	0.765
MA0004.1	MA0004.1	0.59
MA0006.1	MA0006.1	0.207
MA0007.1	MA0007.1	0.594
MA0009.1	MA0009.1	0.304
MA0014.1	MA0014.1	0.246
MA0017.1	MA0017.1	0.123
MA0018.2	MA0018.2	0.72
MA0019.1	MA0019.1	0.999
MA0024.1	MA0024.1	0.00964
MA0025.1	MA0025.1	0.925
MA0027.1	MA0027.1	0.495
MA0028.1	MA0028.1	0.805
MA0029.1	MA0029.1	0.543
MA0030.1	MA0030.1	0.579
MA0031.1	MA0031.1	0.845
MA0035.2	MA0035.2	6.39194e-4
MA0038.1	MA0038.1	0.116
MA0039.2	MA0039.2	0.148
MA0040.1	MA0040.1	0.991
MA0041.1	MA0041.1	0.755
MA0042.1	MA0042.1	0.493
MA0043.1	MA0043.1	0.441
MA0046.1	MA0046.1	3.71484e-5
MA0047.2	MA0047.2	0.844
MA0048.1	MA0048.1	0.00485
MA0050.1	MA0050.1	0.0156
MA0051.1	MA0051.1	0.0222
MA0052.1	MA0052.1	1.71128e-4
MA0055.1	MA0055.1	0.148
MA0057.1	MA0057.1	0.502
MA0058.1	MA0058.1	0.441
MA0059.1	MA0059.1	0.796
MA0060.1	MA0060.1	8.48182e-5
MA0061.1	MA0061.1	0.0759
MA0062.2	MA0062.2	0.709
MA0065.2	MA0065.2	0.841
MA0066.1	MA0066.1	0.291
MA0067.1	MA0067.1	0.165
MA0068.1	MA0068.1	0.164
MA0069.1	MA0069.1	0.57
MA0070.1	MA0070.1	0.2
MA0071.1	MA0071.1	0.5
MA0072.1	MA0072.1	0.22
MA0073.1	MA0073.1	0.591
MA0074.1	MA0074.1	0.797
MA0076.1	MA0076.1	0.843
MA0077.1	MA0077.1	0.246
MA0078.1	MA0078.1	0.00548
MA0079.2	MA0079.2	0.147
MA0080.2	MA0080.2	0.961
MA0081.1	MA0081.1	0.238
MA0083.1	MA0083.1	0.00462
MA0084.1	MA0084.1	0.182
MA0087.1	MA0087.1	0.682
MA0088.1	MA0088.1	0.00544
MA0090.1	MA0090.1	1.98238e-5
MA0091.1	MA0091.1	0.23
MA0092.1	MA0092.1	0.257
MA0093.1	MA0093.1	0.676
MA0099.2	MA0099.2	3.4467e-4
MA0100.1	MA0100.1	0.0839
MA0101.1	MA0101.1	0.294
MA0102.2	MA0102.2	0.00734
MA0103.1	MA0103.1	1.60612e-6
MA0104.2	MA0104.2	0.188
MA0105.1	MA0105.1	0.0186
MA0106.1	MA0106.1	3.06164e-6
MA0107.1	MA0107.1	0.215
MA0108.2	MA0108.2	1.97756e-4
MA0111.1	MA0111.1	0.518
MA0112.2	MA0112.2	0.179
MA0113.1	MA0113.1	0.833
MA0114.1	MA0114.1	0.0752
MA0115.1	MA0115.1	0.199
MA0116.1	MA0116.1	0.303
MA0117.1	MA0117.1	0.494
MA0119.1	MA0119.1	0.0103
MA0122.1	MA0122.1	0.635
MA0124.1	MA0124.1	0.238
MA0125.1	MA0125.1	0.0967
MA0131.1	MA0131.1	0.868
MA0135.1	MA0135.1	0.181
MA0136.1	MA0136.1	0.254
MA0137.2	MA0137.2	0.183
MA0138.2	MA0138.2	0.00463
MA0139.1	MA0139.1	0.623
MA0140.1	MA0140.1	0.00195
MA0141.1	MA0141.1	0.448
MA0142.1	MA0142.1	0.906
MA0143.1	MA0143.1	0.029
MA0144.1	MA0144.1	0.0892
MA0145.1	MA0145.1	0.17
MA0146.1	MA0146.1	0.0481
MA0147.1	MA0147.1	0.169
MA0148.1	MA0148.1	0.852
MA0149.1	MA0149.1	0.379
MA0150.1	MA0150.1	0.0395
MA0152.1	MA0152.1	0.664
MA0153.1	MA0153.1	5.37938e-4
MA0154.1	MA0154.1	0.0673
MA0155.1	MA0155.1	0.849
MA0156.1	MA0156.1	0.832
MA0157.1	MA0157.1	0.0727
MA0159.1	MA0159.1	0.794
MA0160.1	MA0160.1	0.609
MA0162.1	MA0162.1	0.0942
MA0163.1	MA0163.1	0.342
MA0164.1	MA0164.1	0.977
MA0258.1	MA0258.1	0.294
MA0259.1	MA0259.1	0.969

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: CNhs13407

Novel motif	Logo	P-value
1	1	0.185
10	10	0.0374
100	100	0.448
101	101	0.675
102	102	0.356
103	103	0.428
104	104	0.92
105	105	0.222
106	106	0.198
107	107	0.25
108	108	0.897
109	109	0.228
11	11	0.214
110	110	0.0308
111	111	0.513
112	112	0.5
113	113	0.428
114	114	0.173
115	115	0.456
116	116	0.244
117	117	0.00158
118	118	0.705
119	119	0.894
12	12	0.257
120	120	0.353
121	121	0.89
122	122	0.909
123	123	0.652
124	124	0.206
125	125	0.146
126	126	0.494
127	127	0.105
128	128	0.183
129	129	0.0692
13	13	0.428
130	130	0.792
131	131	0.186
132	132	0.795
133	133	0.802
134	134	0.75
135	135	0.216
136	136	0.168
137	137	0.252
138	138	0.516
139	139	0.737
14	14	0.951
140	140	0.877
141	141	0.283
142	142	0.72
143	143	0.0503
144	144	0.0368
145	145	0.112
146	146	0.922
147	147	0.432
148	148	0.819
149	149	0.273
15	15	0.392
150	150	0.0511
151	151	0.921
152	152	0.191
153	153	0.678
154	154	0.401
155	155	0.609
156	156	0.0635
157	157	0.564
158	158	0.851
159	159	0.125
160	160	0.721
161	161	0.249
162	162	0.924
163	163	0.56
164	164	0.0092
165	165	0.884
166	166	0.526
167	167	0.465
168	168	0.49
169	169	0.0132
17	17	0.174
18	18	0.207
19	19	0.169
2	2	0.755
20	20	0.124
21	21	0.0435
22	22	0.147
23	23	0.609
24	24	0.583
25	25	0.895
26	26	0.00495
27	27	0.451
28	28	0.891
29	29	0.0823
3	3	0.0448
30	30	0.554
31	31	0.439
32	32	0.888
33	33	0.816
34	34	0.743
35	35	0.664
36	36	0.415
37	37	0.0622
38	38	0.315
39	39	0.212
4	4	0.197
40	40	0.69
41	41	0.155
42	42	0.264
43	43	0.118
44	44	0.485
45	45	0.71
46	46	0.156
47	47	0.306
48	48	0.693
49	49	0.196
5	5	0.247
50	50	0.875
51	51	0.626
52	52	0.705
53	53	0.689
54	54	0.973
55	55	0.294
56	56	0.575
57	57	0.0217
58	58	0.816
59	59	0.0978
6	6	0.763
60	60	0.151
61	61	0.492
62	62	0.435
63	63	0.557
64	64	0.788
65	65	0.635
66	66	0.291
67	67	0.441
68	68	0.44
69	69	0.175
7	7	0.125
70	70	0.0274
71	71	0.00407
72	72	0.561
73	73	0.0404
74	74	0.21
75	75	0.0424
76	76	0.408
77	77	0.173
78	78	0.0409
79	79	0.362
8	8	0.6
80	80	0.171
81	81	0.203
82	82	0.138
83	83	0.25
84	84	0.645
85	85	0.185
86	86	0.52
87	87	0.171
88	88	0.613
89	89	0.427
9	9	0.494
90	90	0.00158
91	91	0.0442
92	92	0.21
93	93	0.00574
94	94	0.123
95	95	0.932
96	96	0.575
97	97	0.128
98	98	0.264
99	99	0.944

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: CNhs13407

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011508 mouse TSt-4/DLL1 feeder cells 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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002293 (epithelial cell of thymus)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002370 (thymus)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0000350 (experimentally modified sample)
0011508 (mouse TSt-4/DLL1 feeder cells 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
CL:0000223 (endodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008771
+|DRA_sample_Accession=CAGE@SAMD00005333
-|accession_numbers=CAGE;DRX008908;DRR009782;DRZ001207;DRZ002590
+|accession_numbers=CAGE;DRX008908;DRR009782;DRZ001207;DRZ002590;DRZ012557;DRZ013940
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002370,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0004177,UBERON:0005057,UBERON:0002530,UBERON:0005058,UBERON:0010317,UBERON:0000153,UBERON:0002390,UBERON:0000949,UBERON:0002193,UBERON:0002405,UBERON:0009113
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000255,CL:0002076,CL:0002293
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr17:44951553..44951586,-!p2@Runx2!1.84!75.71!Runx2;;chr16:14705925..14705951,+!p1@Snai2!1.72!346.48!Snai2;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.72!65.45!Zbtb11;;chr16:14705961..14705978,+!p2@Snai2!1.63!186.07!Snai2;;chr15:102828658..102828678,+!p1@Hoxc6!1.62!41.06!Hoxc6;;chr3:99057269..99057306,+!p1@Tbx15!1.54!41.06!Tbx15;;chr16:25684232..25684285,+!p2@Trp63!1.52!32.08!Trp63;;chr15:102751603..102751630,+!p1@Hoxc13!1.45!26.95!Hoxc13;;chr1:140739014..140739032,-!p1@Lhx9!1.42!32.08!Lhx9;;chr13:99124189..99124205,+!p1@Foxd1!1.40!35.93!Foxd1;;chr6:6831950..6831985,-!p2@Dlx5!1.38!25.67!Dlx5;;chr16:92697560..92697592,-!p2@Runx1!1.36!134.74!Runx1;;chr15:102751578..102751600,+!p2@Hoxc13!1.36!21.82!Hoxc13;;chr19:28754692..28754757,-!p1@Glis3!1.35!85.98!Glis3;;chr2:30700881..30700916,+!p1@Prrx2!1.31!35.93!Prrx2;;chr16:14705668..14705683,+!p3@Snai2!1.31!19.25!Snai2;;chr7:35904304..35904320,+!p1@Cebpa!1.30!372.15!Cebpa;;chr13:31898637..31898653,+!p2@Foxc1!1.30!33.36!Foxc1;;chr15:97738692..97738747,-!p1@Vdr!1.29!100.09!Vdr;;chr8:94881733..94881790,+!p1@Irx5!1.29!35.93!Irx5;;chr6:6832076..6832092,-!p1@Dlx5!1.29!21.82!Dlx5;;chr9:96653072..96653154,-!p1@Zbtb38!1.27!46.20!Zbtb38;;chr9:87626083..87626108,-!p1@Tbx18!1.23!34.65!Tbx18;;chr13:31898496..31898519,+!p3@Foxc1!1.23!25.67!Foxc1;;chr11:96153767..96153822,+!p1@Hoxb6!1.23!24.38!Hoxb6;;chr2:30700857..30700873,+!p3@Prrx2!1.23!21.82!Prrx2;;chr16:14705746..14705761,+!p4@Snai2!1.21!15.40!Snai2;;chr12:74147689..74147711,-!p1@Six1!1.20!32.08!Six1;;chr11:44430812..44430838,+!p1@Ebf1!1.19!139.88!Ebf1;;chr10:67000609..67000625,+!p1@Egr2!1.19!33.36!Egr2;;chr6:83661226..83661282,+!p1@Vax2!1.18!14.12!Vax2;;chr1:87497610..87497645,+!p1@Gm2427,p1@Sp140!1.18!14.12!Sp140;;chr18:35020854..35020869,+!p1@Egr1!1.16!512.02!Egr1;;chr7:144506077..144506128,-!p1@Ebf3!1.14!29.52!Ebf3;;chr15:102197405..102197454,-!p1@Sp7!1.14!12.83!Sp7;;chr17:44951431..44951445,-!p3@Runx2!1.14!12.83!Runx2;;chr3:66785181..66785199,-!p2@Shox2!1.14!12.83!Shox2;;chr11:44431687..44431706,+!p2@Ebf1!1.11!55.18!Ebf1;;chr3:66785201..66785226,-!p3@Shox2!1.10!11.55!Shox2;;chr15:102797225..102797243,+!p2@Hoxc10!1.10!11.55!Hoxc10;;chr9:87625971..87625992,-!p2@Tbx18!1.10!11.55!Tbx18;;chr11:44431710..44431725,+!p7@Ebf1!1.08!17.97!Ebf1;;chr8:94881872..94881887,+!p2@Irx5!1.07!11.55!Irx5;;chr6:72185210..72185228,-!p3@Atoh8!1.06!17.97!Atoh8;;chr6:52176164..52176195,-!p1@Hoxa9!1.05!12.83!Hoxa9;;chr6:52190467..52190500,-!p1@Hoxa10!1.05!10.27!Hoxa10;;chr15:50720601..50720630,-!p2@Trps1!1.04!24.38!Trps1;;chr6:72185232..72185272,-!p1@Atoh8!1.03!28.23!Atoh8;;chr13:31898729..31898761,+!p1@Foxc1!1.03!24.38!Foxc1;;chr6:52163319..52163342,-!p1@Hoxa3!1.03!14.12!Hoxa3;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!1.02!17.97!Zbtb38;;chr16:43363152..43363186,+!p3@Zbtb20!0.99!20.53!Zbtb20;;chr15:40486566..40486600,+!p1@Zfpm2!0.98!51.33!Zfpm2;;chr11:44430788..44430804,+!p3@Ebf1!0.98!21.82!Ebf1;;chr15:101097270..101097290,+!p1@Nr4a1!0.97!87.26!Nr4a1;;chr6:115311030..115311065,+!p4@Pparg!0.95!11.55!Pparg;;chr17:87153028..87153049,+!p2@Epas1!0.94!162.97!Epas1;;chr17:44872561..44872615,-!p1@Runx2!0.94!17.97!Runx2;;chr19:28754622..28754633,-!p4@Glis3!0.94!8.98!Glis3;;chr19:5447886..5447905,+!p1@Fosl1!0.94!7.70!Fosl1;;chr17:44873599..44873623,-!p7@Runx2!0.94!7.70!Runx2;;chr19:5447692..5447711,+!p2@Fosl1!0.94!7.70!Fosl1;;chr15:102828642..102828653,+!p2@Hoxc6!0.94!7.70!Hoxc6;;chr9:63869751..63869767,-!p1@Smad6!0.93!20.53!Smad6;;chr5:104121453..104121479,+!p4@Aff1!0.92!34.65!Aff1;;chr10:67375368..67375433,-!p1@Zfp365!0.91!12.83!Zfp365;;chr19:28754600..28754612,-!p2@Glis3!0.91!11.55!Glis3;;chr11:44430877..44430899,+!p6@Ebf1!0.90!8.98!Ebf1;;chr8:109817400..109817417,+!p1@Nfat5!0.88!145.01!Nfat5;;chr10:119913278..119913298,-!p2@Hmga2!0.88!15.40!Hmga2;;chr1:165243591..165243625,-!p2@Prrx1!0.88!10.27!Prrx1;;chr1:57029281..57029326,-!p1@Satb2!0.87!10.27!Satb2;;chr6:6831986..6832007,-!p4@Dlx5!0.87!6.42!Dlx5;;chr15:102797288..102797302,+!p1@Hoxc10!0.87!6.42!Hoxc10;;chr15:102820964..102821006,+!p1@Hoxc8!0.87!6.42!Hoxc8;;chr15:102751552..102751563,+!p3@Hoxc13!0.87!6.42!Hoxc13;;chr1:165243792..165243808,-!p1@Prrx1!0.86!23.10!Prrx1;;chr9:63869850..63869873,-!p2@Smad6!0.86!19.25!Smad6;;chr6:72739034..72739055,-!p3@Tcf7l1!0.86!14.12!Tcf7l1;;chr10:5734525..5734569,-!p3@Esr1!0.85!10.27!Esr1;;chr11:98603185..98603208,+!p1@Thra!0.84!381.13!Thra;;chr2:167363692..167363710,+!p1@Snai1!0.82!73.15!Snai1;;chr3:5218563..5218587,+!p5@Zfhx4!0.80!8.98!Zfhx4;;chr11:112643496..112643562,+!p1@Sox9!0.79!210.46!Sox9;;chr7:144505980..144506010,-!p3@Ebf3!0.79!6.42!Ebf3;;chr13:31898767..31898785,+!p4@Foxc1!0.79!6.42!Foxc1;;chr15:102797183..102797205,+!p4@Hoxc10!0.79!5.13!Hoxc10;;chr17:44951598..44951609,-!p12@Runx2!0.79!5.13!Runx2;;chr6:6831928..6831949,-!p3@Dlx5!0.79!5.13!Dlx5;;chr4:107107224..107107259,+!p2@Glis1!0.79!5.13!Glis1;;chr4:134676555..134676575,+!p2@Runx3!0.79!5.13!Runx3;;chr2:71367871..71367898,+!p1@Dlx1!0.79!5.13!Dlx1;;chr17:34784073..34784118,+!p2@Atf6b!0.78!21.82!Atf6b;;chr19:55816546..55816556,+!p3@Tcf7l2!0.78!20.53!Tcf7l2;;chr6:72185553..72185612,-!p2@Atoh8!0.78!10.27!Atoh8;;chr8:94325321..94325366,-!p1@Irx3!0.77!12.83!Irx3;;chr9:63869802..63869815,-!p3@Smad6!0.77!10.27!Smad6;;chr16:43363190..43363242,+!p2@Zbtb20!0.75!15.40!Zbtb20;;chr11:98603160..98603171,+!p3@Thra!0.74!23.10!Thra;;chr12:34642510..34642530,+!p1@Twist1!0.74!15.40!Twist1;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.74!12.83!Zfhx3;;chr8:87502608..87502623,-!p1@Junb!0.73!79.56!Junb;;chr15:102087737..102087801,-!p3@Rarg!0.73!7.70!Rarg;;chr10:107769229..107769238,+!p3@Pawr!0.73!6.42!Pawr;;chr11:44431016..44431045,+!p5@Ebf1!0.73!6.42!Ebf1;;chr1:165243653..165243664,-!p4@Prrx1!0.73!6.42!Prrx1;;chr11:44431626..44431637,+!p10@Ebf1!0.73!5.13!Ebf1;;chr3:54559496..54559511,+!p1@Smad9!0.72!10.27!Smad9;;chr4:135699731..135699747,+!p1@Id3!0.71!532.55!Id3;;chr15:102087880..102087927,-!p2@Rarg!0.71!10.27!Rarg;;chr3:5218516..5218544,+!p2@Zfhx4!0.71!6.42!Zfhx4;;chr2:38206744..38206766,+!p1@Lhx2!0.71!5.13!Lhx2;;chr10:107769168..107769215,+!p1@Pawr!0.70!46.20!Pawr;;chr12:34642682..34642753,+!p2@Twist1!0.70!11.55!Twist1;;chr10:67375146..67375208,-!p2@Zfp365!0.70!6.42!Zfp365;;chr19:28754655..28754673,-!p3@Glis3!0.70!6.42!Glis3;;chr2:30700788..30700824,+!p2@Prrx2!0.70!6.42!Prrx2;;chr1:165243379..165243402,-!p3@Prrx1!0.70!6.42!Prrx1;;chr19:59533221..59533271,+!p1@Emx2!0.70!5.13!Emx2;;chr14:22807083..22807104,-!p1@Zfp503!0.69!78.28!Zfp503;;chr13:99124236..99124243,+!p2@Foxd1!0.69!3.85!Foxd1;;chr15:102839948..102839975,+!p3@Hoxc6!0.69!3.85!Hoxc6;;chr1:57029027..57029056,-!p7@Satb2!0.69!3.85!Satb2;;chr1:87497443..87497454,+!p3@Gm2427,p3@Sp140!0.69!3.85!Sp140;;chr11:96685444..96685473,-!p5@Nfe2l1!0.69!3.85!Nfe2l1;;chr11:21901608..21901634,-!p1@Otx1!0.69!3.85!Otx1;;chr2:71367142..71367167,+!p2@Dlx1!0.69!3.85!Dlx1;;chr3:99057256..99057268,+!p3@Tbx15!0.69!3.85!Tbx15;;chr6:52190858..52190873,-!p4@Hoxa10!0.69!3.85!Hoxa10;;chr18:83080255..83080277,+!p4@Zfp516!0.68!10.27!Zfp516;;chr15:40486427..40486437,+!p5@Zfpm2!0.68!5.13!Zfpm2;;chr17:84587279..84587294,-!p1@Zfp36l2!0.67!447.86!Zfp36l2;;chr16:15887371..15887385,+!p1@Cebpd!0.67!146.29!Cebpd;;chr18:75527009..75527027,+!p1@Smad7!0.67!89.83!Smad7;;chr5:104121391..104121450,+!p3@Aff1!0.67!21.82!Aff1;;chr5:65203599..65203617,+!p8@Klf3!0.67!6.42!Klf3;;chr12:86940338..86940357,+!p1@Jdp2!0.66!41.06!Jdp2;;chr2:152758901..152758925,-!p1@Foxs1!0.66!17.97!Foxs1;;chr19:26681865..26681900,+!p6@Smarca2!0.66!11.55!Smarca2;;chr18:75979828..75979864,+!p2@Zbtb7c!0.66!8.98!Zbtb7c;;chr17:37140628..37140631,+!p2@Zfp57!0.66!7.70!Zfp57;;chr11:98636531..98636559,-!p1@Nr1d1!0.65!23.10!Nr1d1;;chr1:93698030..93698064,+!p1@Twist2!0.65!7.70!Twist2;;chr9:63869834..63869849,-!p5@Smad6!0.65!6.42!Smad6;;chr3:5218590..5218614,+!p3@Zfhx4!0.65!6.42!Zfhx4;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.65!5.13!Carhsp1;;chr15:81977802..81977828,+!p2@Srebf2!0.64!33.36!Srebf2;;chr10:119913546..119913583,-!p3@Hmga2!0.64!7.70!Hmga2;;chr5:92391466..92391471,+!p2@Thap6!0.64!5.13!Thap6;;chr15:75578637..75578669,-!p2@Mafa!0.64!3.85!Mafa;;chr8:123640090..123640101,+!p2@Foxc2!0.64!3.85!Foxc2;;chr1:52176406..52176433,+!p2@Stat1!0.63!8.98!Stat1;;chr11:44430989..44431015,+!p4@Ebf1!0.63!6.42!Ebf1;;chr8:123640063..123640077,+!p1@Foxc2!0.63!6.42!Foxc2;;chr2:92886587..92886622,-!p3@Prdm11!0.63!5.13!Prdm11;;chr11:98798983..98799049,+!p1@Rara!0.62!96.24!Rara;;chr10:107769750..107769799,+!p2@Pawr!0.62!7.70!Pawr;;chr7:122968213..122968266,-!p4@Sox6!0.62!3.85!Sox6;;chr15:50721588..50721610,-!p1@Trps1!0.61!37.21!Trps1;;chr14:56443698..56443726,+!p2@Nfatc4!0.61!6.42!Nfatc4;;chr9:68501522..68501538,+!p4@Rora!0.61!6.42!Rora;;chr17:37139455..37139469,+!p3@Zfp57!0.61!5.13!Zfp57;;chr13:55932591..55932622,-!p1@Pitx1!0.61!3.85!Pitx1;;chr1:165243272..165243283,-!p6@Prrx1!0.61!3.85!Prrx1;;chr1:165243638..165243649,-!p5@Prrx1!0.61!3.85!Prrx1;;chr9:63869705..63869713,-!p8@Smad6!0.61!3.85!Smad6;;chr3:135354903..135354945,-!p7@Nfkb1!0.60!7.70!Nfkb1;;chr18:14131045..14131062,-!p3@Zfp521!0.60!5.13!Zfp521;;chr7:144505957..144505972,-!p2@Ebf3!0.60!3.85!Ebf3;;chr15:102455867..102455930,-!p1@Atf7!0.59!44.91!Atf7;;chr19:55816414..55816425,+!p4@Tcf7l2!0.59!17.97!Tcf7l2;;chr15:50721616..50721632,-!p4@Trps1!0.59!8.98!Trps1;;chr10:92773736..92773761,-!p4@Elk3!0.59!5.13!Elk3;;chr9:63605740..63605771,-!p1@Smad3!0.58!50.05!Smad3;;chr8:118231705..118231722,-!p3@Maf!0.58!26.95!Maf;;chr6:65728988..65729056,+!p1@Prdm5!0.58!16.68!Prdm5;;chr9:69137672..69137702,+!p2@Rora!0.58!14.12!Rora;;chr1:186556323..186556370,-!p2@Hlx!0.58!8.98!Hlx;;chr5:24107993..24108036,-!p2@Smarcd3!0.58!7.70!Smarcd3;;chr11:98821858..98821907,+!p6@Rara!0.58!5.13!Rara;;chr11:44431369..44431389,+!p8@Ebf1!0.58!3.85!Ebf1;;chr18:14131020..14131033,-!p4@Zfp521!0.58!3.85!Zfp521;;chr7:52071956..52071978,-!p1@Atf5!0.57!110.36!Atf5;;chr17:87153240..87153254,+!p1@Epas1!0.57!65.45!Epas1;;chr15:81977766..81977789,+!p3@Srebf2!0.57!20.53!Srebf2;;chr3:52072315..52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chr5:139060892..139060911,-!p2@Zfp68!0.13!5.13!Zfp68;;chr6:133985709..133985735,+!p5@Etv6!0.13!2.57!Etv6;;chr5:130175949..130175975,-!p1@Zfp11!0.13!2.57!Zfp11;;chr18:65741935..65741964,+!p2@Zfp532!0.13!2.57!Zfp532;;chr7:87171233..87171255,+!p3@Zfp710!0.13!2.57!Zfp710;;chr2:153475210..153475252,+!p2@Dnmt3b!0.13!2.57!Dnmt3b;;chr18:69839537..69839544,+!p13@Tcf4!0.13!1.28!Tcf4;;chr18:76219118..76219155,+!p1@Zbtb7c!0.13!1.28!Zbtb7c;;chr17:44873393..44873418,-!p4@Runx2!0.13!1.28!Runx2;;chr5:24108047..24108106,-!p3@Smarcd3!0.13!1.28!Smarcd3;;chr6:115310872..115310899,+!p2@Pparg!0.13!1.28!Pparg;;chr13:59924173..59924194,-!p4@Zcchc6!0.13!1.28!Zcchc6;;chr13:37917716..37917742,+!p9@Rreb1!0.13!1.28!Rreb1;;chr4:133309830..133309841,-!p10@Arid1a!0.13!1.28!Arid1a;;chr7:4946990..4947016,-!p4@Zfp579!0.13!1.28!Zfp579;;chr7:71083729..71083742,-!p4@Klf13!0.13!1.28!Klf13;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.13!1.28!Zfhx3;;chr1:170362273..170362317,-!p1@Pbx1!0.12!33.36!Pbx1;;chr1:162836503..162836591,+!p1@Rc3h1!0.12!20.53!Rc3h1;;chr1:95651138..95651255,-!p1@Thap4!0.12!16.68!Thap4;;chr7:134488857..134488914,-!p1@Zfp768!0.12!15.40!Zfp768;;chr11:18918959..18918976,-!p2@Meis1!0.12!15.40!Meis1;;chr11:115891618..115891699,+!p1@Unk!0.12!14.12!Unk;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.12!11.55!Camta2;;chr2:181022663..181022712,-!p1@Gmeb2!0.12!11.55!Gmeb2;;chr15:57908011..57908070,-!p2@Zhx1,p3@9130401M01Rik!0.12!10.27!Zhx1;;chr15:75771454..75771521,+!p1@Zfp623!0.12!10.27!Zfp623;;chr3:94758041..94758142,+!p1@Rfx5!0.12!10.27!Rfx5;;chr2:91489908..91489941,-!p1@Zfp408!0.12!8.98!Zfp408;;chr13:67601387..67601448,-!p2@Zfp58!0.12!8.98!Zfp58;;chr7:13551180..13551243,+!p1@Zfp324!0.12!8.98!Zfp324;;chr18:76401314..76401395,+!p2@Smad2!0.12!7.70!Smad2;;chr17:21587325..21587361,+!p1@Zfp51!0.12!6.42!Zfp51;;chr2:48805015..48805042,+!p2@Mbd5!0.12!6.42!Mbd5;;chr13:67825201..67825277,-!p1@Zfp71-rs1!0.12!5.13!Zfp71-rs1;;chr13:44826095..44826185,+!p4@Jarid2!0.12!5.13!Jarid2;;chr7:16986617..16986632,+!p2@Zc3h4!0.12!2.57!Zc3h4;;chr13:67295432..67295453,+!p1@Zfp455!0.12!1.28!Zfp455;;chr14:75684203..75684214,+!p4@Zc3h13!0.12!1.28!Zc3h13;;chr10:80599248..80599261,+!p3@Zbtb7a!0.12!1.28!Zbtb7a;;chr10:127896265..127896276,+!p4@Smarcc2!0.12!1.28!Smarcc2;;chr17:15636872..15636923,+!p1@Tbp!0.11!43.63!Tbp;;chr5:145992579..145992623,+!p1@Zfp655!0.11!34.65!Zfp655;;chr5:53981912..53981942,+!p1@Rbpj!0.11!21.82!Rbpj;;chr5:123844791..123844835,+!p1@Mlxip!0.11!19.25!Mlxip;;chr15:102034070..102034124,+!p1@Zfp740!0.11!19.25!Zfp740;;chr11:59319701..59319741,-!p1@Zkscan17!0.11!12.83!Zkscan17;;chr6:88148650..88148669,+!p1@Gata2!0.11!8.98!Gata2;;chr18:80348206..80348256,-!p1@Adnp2!0.11!8.98!Adnp2;;chr17:34169016..34169068,+!p2@Rxrb!0.11!7.70!Rxrb;;chr6:120314411..120314466,+!p2@Kdm5a!0.11!7.70!Kdm5a;;chr9:44113678..44113771,-!p1@Hinfp!0.11!7.70!Hinfp;;chr9:65675351..65675383,-!p1@Zfp609!0.11!5.13!Zfp609;;chr19:12870598..12870636,-!p1@U05342,p1@Zfp91!0.11!5.13!Zfp91;;chr19:5424822..5424845,-!p3@Drap1!0.11!3.85!Drap1;;chr2:83484738..83484749,+!p5@Zc3h15!0.11!3.85!Zc3h15;;chr7:88138532..88138543,+!p3@Zfp592!0.11!2.57!Zfp592;;chr10:41996471..41996487,-!p4@Foxo3!0.11!2.57!Foxo3;;chr9:72122708..72122720,+!p3@Zfp280d!0.11!1.28!Zfp280d;;chr4:102787521..102787588,+!p4@Mier1!0.11!1.28!Mier1;;chr3:135271185..135271254,-!p4@Nfkb1!0.11!1.28!Nfkb1;;chr3:54611738..54611749,-!p3@Rfxap!0.11!1.28!Rfxap;;chr15:100058358..100058374,+!p2@Gm1862,p4@Atf1!0.11!1.28!Atf1;;chr19:28085997..28086028,-!p7@Rfx3!0.11!1.28!Rfx3;;chr2:168055853..168055886,-!p1@Adnp,p1@Dpm1!0.10!77.00!Adnp;;chr2:83484681..83484704,+!p1@Zc3h15!0.10!51.33!Zc3h15;;chr4:118967105..118967123,-!p1@Ybx1!0.10!33.36!Ybx1;;chr19:4397052..4397098,-!p1@Kdm2a!0.10!29.52!Kdm2a;;chr1:13364108..13364150,-!p1@Ncoa2!0.10!24.38!Ncoa2;;chr18:24179250..24179314,-!p1@Zfp191!0.10!17.97!Zfp191;;chr6:122769906..122769956,+!p1@Foxj2!0.10!17.97!Foxj2;;chr5:138187341..138187406,+!p3@Tsc22d4!0.10!11.55!Tsc22d4;;
@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs13407
-|library_id_phase_based=1:CNhs13407
+|library_id_phase_based=2:CNhs13407
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12971
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12971
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/TSt-4%252fDLL1%2520feeder%2520cells%252c%2520biol_rep1.CNhs13407.12971-138H1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/TSt-4%252fDLL1%2520feeder%2520cells%252c%2520biol_rep1.CNhs13407.12971-138H1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/TSt-4%252fDLL1%2520feeder%2520cells%252c%2520biol_rep1.CNhs13407.12971-138H1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/TSt-4%252fDLL1%2520feeder%2520cells%252c%2520biol_rep1.CNhs13407.12971-138H1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/TSt-4%252fDLL1%2520feeder%2520cells%252c%2520biol_rep1.CNhs13407.12971-138H1.mm9.nobarcode.rdna.fa.gz
 |name=TSt-4/DLL1 feeder cells, biol_rep1
 |namespace=FANTOM5
@@ Line 51: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13407,LSID1023,release014,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,0.0279378398512975,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,1.05177430311818,0,0,0,0,0,0,0,0.229254357133032,0,0,0,0,0,-0.030044587253602,0,-0.0836083681943256,-0.984211366477826,-0.269868638010351,0.358556276484448,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0428469550828748,0,0.358556276484448,0,0,0,-0.117389802908326,-0.310650657339386,-0.158091042771083,0.0134844258141419,0,0,-0.0520493595414002,-0.109046983543123,0,0,-0.0099362574738705,-0.118426961692612,-0.043669054289221,-0.0788315948399074,0,0,0,0,0,0,0.256298033920771,-0.201084779719118,0.383398483531338,0,0,0,0,0
@@ Line 89: / Line 98: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12971-138H1;search_select_hide=table117:12971-138H1
 }}

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FF:12971-138H1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:47, 4 June 2020

CNhs13407

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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