FF:13369-143G3: Difference between revisions

Latest revision as of 18:57, 4 June 2020

Name:	Tracheal epithelial cells, differentiation to ciliated epithelial cells
Species:	Mouse (Mus musculus)
Library ID:	CNhs13741
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	NA
dev stage	NA
sex	female
age	NA
cell type	SELECT CELL TYPE
cell line	NA
company	NA
collaboration	Mitsuru Morimoto
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	0-3
catalog number	NA
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005581

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13741		CAGE		DRX008913		DRR009787

Accession ID Mm9

Library id		BAM		CTSS
CNhs13741		DRZ001212		DRZ002595

Accession ID Mm10

Library id		BAM		CTSS
CNhs13741		DRZ012562		DRZ013945

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

CNhs13741

0	0
1	0
10	0
100	0
1000	0
1001	-0.0356
1002	-0.116
1003	-0.102
1004	0
1005	0.0457
1006	-0.362
1007	-0.306
1008	0
1009	-0.19
101	0.0376
1010	0
1011	-0.12
1012	0
1013	0.0241
1014	0
1015	-0.0805
1016	-0.486
1017	0
1018	0.744
1019	0
102	0
1020	0.178
1021	0.178
1022	-0.138
1023	0
1024	-0.14
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.148
103	-0.0861
1030	0
1031	-0.627
1032	-0.162
1033	0
1034	0
1035	0
1036	0.255
1037	0
1038	-0.159
1039	-0.0104
104	0
1040	0.0568
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: CNhs13741

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.225
MA0003.1	MA0003.1	0.479
MA0004.1	MA0004.1	0.651
MA0006.1	MA0006.1	0.247
MA0007.1	MA0007.1	0.622
MA0009.1	MA0009.1	0.175
MA0014.1	MA0014.1	0.106
MA0017.1	MA0017.1	0.914
MA0018.2	MA0018.2	0.051
MA0019.1	MA0019.1	0.124
MA0024.1	MA0024.1	0.886
MA0025.1	MA0025.1	0.425
MA0027.1	MA0027.1	0.877
MA0028.1	MA0028.1	6.10034e-5
MA0029.1	MA0029.1	0.47
MA0030.1	MA0030.1	0.916
MA0031.1	MA0031.1	0.824
MA0035.2	MA0035.2	3.79235e-4
MA0038.1	MA0038.1	0.0213
MA0039.2	MA0039.2	0.0236
MA0040.1	MA0040.1	0.91
MA0041.1	MA0041.1	0.596
MA0042.1	MA0042.1	0.728
MA0043.1	MA0043.1	0.546
MA0046.1	MA0046.1	4.84586e-5
MA0047.2	MA0047.2	0.0274
MA0048.1	MA0048.1	0.00607
MA0050.1	MA0050.1	0.202
MA0051.1	MA0051.1	0.136
MA0052.1	MA0052.1	0.0243
MA0055.1	MA0055.1	6.45399e-5
MA0057.1	MA0057.1	0.0987
MA0058.1	MA0058.1	0.756
MA0059.1	MA0059.1	0.0448
MA0060.1	MA0060.1	0.00189
MA0061.1	MA0061.1	0.102
MA0062.2	MA0062.2	5.39378e-7
MA0065.2	MA0065.2	0.16
MA0066.1	MA0066.1	0.231
MA0067.1	MA0067.1	0.29
MA0068.1	MA0068.1	0.716
MA0069.1	MA0069.1	0.343
MA0070.1	MA0070.1	0.0705
MA0071.1	MA0071.1	0.26
MA0072.1	MA0072.1	0.671
MA0073.1	MA0073.1	0.605
MA0074.1	MA0074.1	0.484
MA0076.1	MA0076.1	9.5507e-4
MA0077.1	MA0077.1	0.521
MA0078.1	MA0078.1	0.306
MA0079.2	MA0079.2	0.246
MA0080.2	MA0080.2	0.444
MA0081.1	MA0081.1	0.715
MA0083.1	MA0083.1	0.0238
MA0084.1	MA0084.1	0.698
MA0087.1	MA0087.1	0.183
MA0088.1	MA0088.1	0.138
MA0090.1	MA0090.1	4.73441e-4
MA0091.1	MA0091.1	0.641
MA0092.1	MA0092.1	0.456
MA0093.1	MA0093.1	0.812
MA0099.2	MA0099.2	1.03311e-19
MA0100.1	MA0100.1	0.265
MA0101.1	MA0101.1	8.01223e-4
MA0102.2	MA0102.2	0.332
MA0103.1	MA0103.1	2.61764e-6
MA0104.2	MA0104.2	0.572
MA0105.1	MA0105.1	0.24
MA0106.1	MA0106.1	9.58631e-4
MA0107.1	MA0107.1	0.012
MA0108.2	MA0108.2	0.528
MA0111.1	MA0111.1	0.701
MA0112.2	MA0112.2	0.0048
MA0113.1	MA0113.1	0.305
MA0114.1	MA0114.1	0.926
MA0115.1	MA0115.1	0.488
MA0116.1	MA0116.1	0.0987
MA0117.1	MA0117.1	0.878
MA0119.1	MA0119.1	0.318
MA0122.1	MA0122.1	0.763
MA0124.1	MA0124.1	0.0888
MA0125.1	MA0125.1	0.0756
MA0131.1	MA0131.1	0.278
MA0135.1	MA0135.1	0.098
MA0136.1	MA0136.1	0.00285
MA0137.2	MA0137.2	0.0575
MA0138.2	MA0138.2	0.039
MA0139.1	MA0139.1	0.4
MA0140.1	MA0140.1	6.64163e-4
MA0141.1	MA0141.1	0.491
MA0142.1	MA0142.1	0.53
MA0143.1	MA0143.1	0.578
MA0144.1	MA0144.1	0.128
MA0145.1	MA0145.1	0.0841
MA0146.1	MA0146.1	0.114
MA0147.1	MA0147.1	0.28
MA0148.1	MA0148.1	0.385
MA0149.1	MA0149.1	0.00532
MA0150.1	MA0150.1	0.00345
MA0152.1	MA0152.1	0.311
MA0153.1	MA0153.1	0.0169
MA0154.1	MA0154.1	0.615
MA0155.1	MA0155.1	0.444
MA0156.1	MA0156.1	0.00824
MA0157.1	MA0157.1	0.725
MA0159.1	MA0159.1	3.48039e-4
MA0160.1	MA0160.1	0.572
MA0162.1	MA0162.1	0.343
MA0163.1	MA0163.1	0.05
MA0164.1	MA0164.1	0.161
MA0258.1	MA0258.1	0.0346
MA0259.1	MA0259.1	0.575

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: CNhs13741

Novel motif	Logo	P-value
1	1	0.521
10	10	0.0388
100	100	0.392
101	101	0.0837
102	102	0.308
103	103	0.0405
104	104	0.905
105	105	0.68
106	106	0.126
107	107	0.682
108	108	0.575
109	109	0.0132
11	11	0.252
110	110	0.132
111	111	0.0767
112	112	0.875
113	113	0.359
114	114	0.266
115	115	0.477
116	116	0.0612
117	117	0.00209
118	118	0.525
119	119	0.197
12	12	0.516
120	120	0.552
121	121	0.785
122	122	0.134
123	123	0.0856
124	124	0.709
125	125	0.0372
126	126	0.809
127	127	0.963
128	128	0.0737
129	129	0.881
13	13	2.09184e-6
130	130	0.401
131	131	0.0632
132	132	0.596
133	133	0.0709
134	134	0.269
135	135	0.025
136	136	0.0186
137	137	0.816
138	138	0.221
139	139	0.209
14	14	0.639
140	140	0.295
141	141	0.135
142	142	0.846
143	143	0.187
144	144	0.112
145	145	0.0335
146	146	0.368
147	147	0.477
148	148	0.745
149	149	0.172
15	15	0.168
150	150	0.352
151	151	0.656
152	152	0.0174
153	153	0.536
154	154	0.323
155	155	0.273
156	156	0.00778
157	157	0.705
158	158	0.329
159	159	0.295
160	160	0.934
161	161	0.684
162	162	0.418
163	163	0.771
164	164	0.0574
165	165	0.22
166	166	0.996
167	167	0.659
168	168	0.479
169	169	0.0309
17	17	0.151
18	18	0.929
19	19	0.515
2	2	0.185
20	20	0.067
21	21	0.295
22	22	0.468
23	23	0.779
24	24	0.104
25	25	0.972
26	26	0.00698
27	27	0.686
28	28	0.683
29	29	0.00143
3	3	0.0725
30	30	0.719
31	31	0.613
32	32	0.127
33	33	0.0837
34	34	0.384
35	35	0.825
36	36	0.0421
37	37	0.0301
38	38	0.559
39	39	0.0562
4	4	0.284
40	40	0.0484
41	41	0.101
42	42	0.486
43	43	0.431
44	44	0.148
45	45	0.963
46	46	0.189
47	47	0.498
48	48	0.479
49	49	0.516
5	5	0.619
50	50	0.566
51	51	0.712
52	52	0.68
53	53	0.151
54	54	0.691
55	55	0.95
56	56	0.972
57	57	0.208
58	58	0.578
59	59	0.743
6	6	0.887
60	60	0.289
61	61	0.0904
62	62	0.441
63	63	0.172
64	64	0.907
65	65	0.321
66	66	0.477
67	67	0.25
68	68	0.225
69	69	0.388
7	7	0.226
70	70	0.00433
71	71	0.00741
72	72	0.818
73	73	5.88387e-4
74	74	0.46
75	75	0.00999
76	76	0.302
77	77	0.386
78	78	0.00103
79	79	0.163
8	8	0.165
80	80	0.0712
81	81	0.765
82	82	0.99
83	83	0.468
84	84	0.724
85	85	0.937
86	86	0.24
87	87	0.0548
88	88	0.962
89	89	0.698
9	9	0.781
90	90	0.663
91	91	0.337
92	92	0.846
93	93	0.525
94	94	0.278
95	95	0.00261
96	96	0.457
97	97	0.884
98	98	0.314
99	99	0.3

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: CNhs13741

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011232 mouse tracheal ciliated cells differentiation after 0hr 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)
0002202 (epithelial cell of tracheobronchial tree)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002632 (epithelial cell of lower respiratory tract)
0002368 (respiratory epithelial cell)
0000307 (tracheal epithelial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0003126 (trachea)
0002100 (trunk)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0000072 (segment of respiratory tract)
0005177 (trunk region element)
0000464 (anatomical space)
0001005 (respiratory airway)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0007196 (tracheobronchial tree)
0000065 (respiratory tract)
0001558 (lower respiratory tract)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000357 (0 hr sample)
0000645 (tracheal ciliated cell differentiation sample)
0000652 (tracheal ciliated cell line sample)
0011232 (mouse tracheal ciliated cells differentiation after 0hr 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)
CL:0000377 (tracheoblast)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0003126,UBERON:0002100,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0000077,UBERON:0000466,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004921,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0003103,UBERON:0009569,UBERON:0005291,UBERON:0005178,UBERON:0000072,UBERON:0005177,UBERON:0003104,UBERON:0000464,UBERON:0001048,UBERON:0001005,UBERON:0000925,UBERON:0005181,UBERON:0006598,UBERON:0004185,UBERON:0002532,UBERON:0007196,UBERON:0001555,UBERON:0000065,UBERON:0001558,UBERON:0001004,UBERON:0007026,UBERON:0001041,UBERON:0002224,UBERON:0000915,UBERON:0009142,UBERON:0008947,UBERON:0003258,UBERON:0006595,UBERON:0006603
+|DRA_sample_Accession=CAGE@SAMD00005581
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000012,CL:0002321,CL:0000063,CL:0000066,CL:0002371,CL:0000068,CL:0000220,CL:0000004,CL:0002202,CL:0000069,CL:0000255,CL:0002076,CL:0002632,CL:0002368,CL:0000307,CL:0000223,CL:0000377
+|accession_numbers=CAGE;DRX008913;DRR009787;DRZ001212;DRZ002595;DRZ012562;DRZ013945
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0003126,UBERON:0002100,UBERON:0000064,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0005178,UBERON:0000072,UBERON:0005177,UBERON:0000464,UBERON:0001005,UBERON:0005181,UBERON:0010317,UBERON:0007196,UBERON:0000065,UBERON:0001558,UBERON:0001004,UBERON:0002224,UBERON:0000915
+|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002202,CL:0000255,CL:0002076,CL:0002632,CL:0002368,CL:0000307
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000101,FF:0000103,FF:0000001,FF:0000350,FF:0000357,FF:0000645,FF:0000652,FF:0011232
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
+|donor= biol_rep3
 |expression_enrichment_score=chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.87!92.51!Zbtb11;;chr19:5447886..5447905,+!p1@Fosl1!1.82!65.72!Fosl1;;chr13:31650185..31650201,+!p1@Foxq1!1.72!171.88!Foxq1;;chr12:58646974..58647003,-!p1@Foxa1!1.66!59.15!Foxa1;;chr1:137155026..137155042,-!p1@Elf3!1.57!199.18!Elf3;;chr14:118636214..118636235,-!p1@Sox21!1.50!36.90!Sox21;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!1.40!58.64!Hmga1;;chr3:34548909..34548927,+!p1@Sox2!1.39!38.93!Sox2;;chr10:119913278..119913298,-!p2@Hmga2!1.38!50.55!Hmga2;;chr13:72766279..72766296,+!p2@Irx2!1.35!31.85!Irx2;;chr19:5447692..5447711,+!p2@Fosl1!1.34!20.73!Fosl1;;chr2:103143336..103143367,-!p1@Ehf!1.33!32.35!Ehf;;chr13:72101178..72101203,-!p1@Irx1!1.30!29.32!Irx1;;chr13:72766250..72766273,+!p1@Irx2!1.27!26.79!Irx2;;chr9:96653072..96653154,-!p1@Zbtb38!1.24!42.97!Zbtb38;;chr12:57796615..57796687,+!p1@Pax9!1.23!16.18!Pax9;;chr16:92697560..92697592,-!p2@Runx1!1.21!93.52!Runx1;;chr5:77543897..77543911,-!p2@Hopx!1.21!29.32!Hopx;;chr6:108610766..108610781,+!p2@Bhlhe40!1.19!25.78!Bhlhe40;;chr10:119913310..119913366,-!p1@Hmga2!1.17!106.67!Hmga2;;chr8:87502608..87502623,-!p1@Junb!1.16!214.34!Junb;;chr1:194979315..194979359,+!p1@Irf6!1.16!80.88!Irf6;;chr11:21901608..21901634,-!p1@Otx1!1.13!12.64!Otx1;;chr15:79178060..79178074,+!p2@Maff!1.10!15.17!Maff;;chr14:118636238..118636257,-!p2@Sox21!1.10!11.63!Sox21;;chr15:79177964..79177986,+!p1@Maff!1.08!37.91!Maff;;chr14:118635860..118635885,-!p3@Sox21!1.08!11.12!Sox21;;chr15:79178029..79178044,+!p4@Maff!1.07!13.14!Maff;;chr1:194979361..194979373,+!p2@Irf6!1.04!13.65!Irf6;;chr15:79178013..79178028,+!p3@Maff!1.01!12.13!Maff;;chr15:37162834..37162849,+!p2@Grhl2!0.99!10.62!Grhl2;;chr1:193007123..193007139,-!p1@Atf3!0.97!48.02!Atf3;;chr2:30700881..30700916,+!p1@Prrx2!0.97!16.18!Prrx2;;chr19:25746898..25746910,+!p1@Dmrt2!0.97!12.64!Dmrt2;;chr13:72101141..72101158,-!p3@Irx1!0.97!10.62!Irx1;;chr16:92697354..92697362,-!p3@Runx1!0.96!12.64!Runx1;;chr15:35225845..35225867,+!p1@Osr2!0.95!20.22!Osr2;;chr6:52154414..52154462,-!p1@Hoxa5!0.94!10.62!Hoxa5;;chr16:25801993..25802014,+!p1@Trp63!0.93!7.58!Trp63;;chr11:69468531..69468557,+!p1@Sox15!0.93!7.58!Sox15;;chr8:94881733..94881790,+!p1@Irx5!0.90!14.15!Irx5;;chr12:74147689..74147711,-!p1@Six1!0.87!14.66!Six1;;chr6:51382677..51382783,+!p1@Nfe2l3!0.86!16.68!Nfe2l3;;chr6:146744595..146744613,+!p2@Arntl2!0.86!10.62!Arntl2;;chr1:36364590..36364608,+!p1@Arid5a!0.85!66.22!Arid5a;;chr7:20214704..20214800,-!p1@Relb!0.85!21.23!Relb;;chr13:72101161..72101177,-!p2@Irx1!0.83!8.09!Irx1;;chr6:128250471..128250519,-!p1@Tead4!0.80!11.12!Tead4;;chr15:37162796..37162828,+!p1@Grhl2!0.79!9.10!Grhl2;;chr2:30700788..30700824,+!p2@Prrx2!0.78!8.09!Prrx2;;chr6:128250380..128250442,-!p2@Tead4!0.78!6.57!Tead4;;chr3:98186461..98186476,+!p2@Zfp697!0.78!5.06!Zfp697;;chr13:40825465..40825469,-!p2@Tfap2a!0.78!5.06!Tfap2a;;chr11:116196664..116196679,-!p1@Foxj1!0.76!7.58!Foxj1;;chr16:55966451..55966484,+!p3@Rpl24,p3@Zbtb11!0.75!30.33!Zbtb11;;chr6:52141694..52141715,-!p1@Hoxa4!0.75!6.07!Hoxa4;;chr19:5637528..5637548,+!p2@Rela!0.74!29.32!Rela;;chr13:5860872..5860883,+!p3@Klf6!0.74!9.60!Klf6;;chr5:107003725..107003746,-!p5@Zfp644!0.74!6.07!Zfp644;;chr3:34548946..34548972,+!p2@Sox2!0.74!5.06!Sox2;;chr4:109650609..109650653,+!p1@Dmrta2!0.74!4.55!Dmrta2;;chr11:21901587..21901604,-!p2@Otx1!0.74!4.55!Otx1;;chr8:94881686..94881700,+!p4@Irx5!0.74!4.55!Irx5;;chr19:46379199..46379301,+!p1@Nfkb2!0.72!26.79!Nfkb2;;chr6:108610610..108610676,+!p1@Bhlhe40!0.71!225.97!Bhlhe40;;chr14:99697871..99697934,+!p1@Klf5!0.71!92.51!Klf5;;chr8:94325321..94325366,-!p1@Irx3!0.70!10.62!Irx3;;chr17:27693746..27693759,+!p6@Hmga1-rs1,p7@Hmga1!0.70!8.59!Hmga1;;chr8:77540128..77540145,+!p2@Hmgxb4!0.70!4.04!Hmgxb4;;chr8:77540157..77540170,+!p3@Hmgxb4!0.70!4.04!Hmgxb4;;chr1:194979383..194979393,+!p3@Irf6!0.70!4.04!Irf6;;chr12:57636240..57636256,-!p4@Nkx2-1!0.70!4.04!Nkx2-1;;chr12:57636178..57636194,-!p2@Nkx2-1!0.70!4.04!Nkx2-1;;chr10:119913266..119913277,-!p6@Hmga2!0.70!4.04!Hmga2;;chr11:101646566..101646603,-!p1@Etv4!0.69!14.15!Etv4;;chr17:71200529..71200556,-!p1@Tgif1!0.68!69.26!Tgif1;;chr18:3281034..3281104,-!p1@Crem!0.68!30.33!Crem;;chr17:71200415..71200427,-!p5@Tgif1!0.68!6.57!Tgif1;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.68!5.56!Carhsp1;;chr6:52154386..52154407,-!p2@Hoxa5!0.68!5.06!Hoxa5;;chr15:101097270..101097290,+!p1@Nr4a1!0.67!43.48!Nr4a1;;chr16:18587076..18587106,-!p1@Tbx1!0.67!5.56!Tbx1;;chr13:5860776..5860796,+!p1@Klf6!0.66!101.61!Klf6;;chr9:63605740..63605771,-!p1@Smad3!0.66!59.65!Smad3;;chr8:94325847..94325869,-!p3@Irx3!0.66!6.07!Irx3;;chr19:5560600..5560617,-!p1@Ovol1!0.66!4.55!Ovol1;;chr12:57636220..57636236,-!p3@Nkx2-1!0.66!3.54!Nkx2-1;;chrX:7339938..7339963,+!p1@Tfe3!0.65!20.22!Tfe3;;chr5:32438395..32438406,+!p3@Fosl2!0.65!5.56!Fosl2;;chr15:80085920..80085941,+!p1@Atf4!0.64!460.53!Atf4;;chr12:36219645..36219730,-!p1@Ahr!0.63!37.41!Ahr;;chr7:20162663..20162678,+!p1@Zfp296!0.63!4.55!Zfp296;;chr6:29490887..2949089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f1;;chr16:14705961..14705978,+!p2@Snai2!0.21!6.07!Snai2;;chr10:79896347..79896358,-!p2@Tcf3!0.21!4.55!Tcf3;;chr1:133904217..133904250,+!p5@Elk4!0.21!4.04!Elk4;;chr17:71202822..71202877,-!p3@Tgif1!0.21!3.54!Tgif1;;chr8:13338745..13338756,+!p2@Tfdp1!0.21!2.53!Tfdp1;;chr8:13339656..13339661,+!p3@Tfdp1!0.21!2.53!Tfdp1;;chr6:72849280..72849297,-!p6@Kcmf1!0.21!2.02!Kcmf1;;chr8:81552528..81552553,+!p6@Zfp827!0.21!1.52!Zfp827;;chr19:28754600..28754612,-!p2@Glis3!0.21!1.52!Glis3;;chr17:27693622..27693635,+!p11@Hmga1-rs1,p12@Hmga1!0.21!1.01!Hmga1;;chr15:102865048..102865073,+!p3@Hoxc4!0.21!1.01!Hoxc4;;chr3:30995296..30995300,+!p6@Skil!0.21!1.01!Skil;;chr5:53981578..53981590,+!p4@Rbpj!0.21!1.01!Rbpj;;chr11:72990702..72990737,+!p1@LOC100047518,p1@Tax1bp3!0.20!13.14!Tax1bp3;;chr11:120494853..120494905,-!p1@Mafg!0.20!13.14!Mafg;;chr1:170362242..170362256,-!p3@Pbx1!0.20!9.60!Pbx1;;chr14:19071466..19071550,-!p1@Nr1d2!0.20!9.10!Nr1d2;;chr17:37139472..37139514,+!p1@Zfp57!0.20!9.10!Zfp57;;chr7:135020060..135020124,-!p2@Zfp668!0.20!5.56!Zfp668;;chr18:84255771..84255795,-!p3@Tshz1!0.20!3.54!Tshz1;;chr18:3337339..3337397,-!p5@Crem!0.20!2.02!Crem;;chr13:44825008..44825066,+!p5@Jarid2!0.20!2.02!Jarid2;;chr5:31262699..31262712,-!p2@Preb!0.20!1.52!Preb;;chr10:5734525..5734569,-!p3@Esr1!0.20!1.52!Esr1;;chr7:4947625..4947634,-!p6@Zfp579!0.20!1.52!Zfp579;;chr8:81923366..81923371,-!p5@Smad1!0.20!1.52!Smad1;;chr3:30408674..30408716,-!p2@Mecom!0.20!1.52!Mecom;;chr5:104183237..104183248,+!p7@Aff1!0.20!1.52!Aff1;;chr3:96002383..96002407,-!p4@Bola1!0.20!1.01!Bola1;;chr17:21626041..21626052,+!p3@Zfp53!0.20!1.01!Zfp53;;chr2:162880418..162880429,+!p4@Mybl2!0.20!1.01!Mybl2;;chrX:48559055..48559077,-!p6@Mbnl3!0.20!1.01!Mbnl3;;chr7:119822940..119822945,+!p6@Tead1!0.20!1.01!Tead1;;chr16:95924055..95924077,+!p1@Ets2!0.19!75.83!Ets2;;chr11:95528303..95528319,+!p1@1700071K01Rik,p1@Phb!0.19!18.20!Phb;;chr12:86940338..86940357,+!p1@Jdp2!0.19!13.14!Jdp2;;chr10:79862223..79862261,-!p4@Mbd3!0.19!12.64!Mbd3;;chr17:34169016..34169068,+!p2@Rxrb!0.19!9.60!Rxrb;;chr11:72990738..72990763,+!p2@LOC100047518,p2@Tax1bp3!0.19!7.08!Tax1bp3;;chr7:134519542..134519569,-!p1@Zfp747!0.19!3.54!Zfp747;;chr5:3648045..3648074,-!p2@Gatad1!0.19!1.52!Gatad1;;chr13:31650026..31650045,+!p2@Foxq1!0.19!1.52!Foxq1;;chr17:69733108..69733129,+!p3@Zfp161!0.19!1.52!Zfp161;;chr11:98636400..98636418,-!p4@Nr1d1!0.19!1.01!Nr1d1;;chr3:103772250..103772317,+!p1@Phtf1!0.18!26.29!Phtf1;;chrX:70587953..70587968,+!p1@Zfp275!0.18!14.15!Zfp275;;chr7:29551464..29551487,-!p2@Nfkbib!0.18!4.55!Nfkbib;;chrX:48558950..48559016,-!p1@Mbnl3!0.18!3.54!Mbnl3;;chr18:36441119..36441158,+!p2@Pura!0.18!2.53!Pura;;chr1:133904862..133904893,+!p6@Elk4!0.18!2.02!Elk4;;chr8:87324171..87324182,-!p6@Nfix!0.18!1.52!Nfix;;chr14:47896526..47896539,-!p2@Wdhd1!0.18!1.52!Wdhd1;;chr12:3807076..3807086,+!p8@Dnmt3a!0.18!1.52!Dnmt3a;;chr12:85534690..85534708,-!p9@C130039O16Rik!0.18!1.01!C130039O16Rik;;chr5:108494765..108494786,+!p2@Mtf2!0.18!1.01!Mtf2;;chr7:17200615..17200625,-!p9@Grlf1!0.18!1.01!Grlf1;;chr5:53981661..53981672,+!p5@Rbpj!0.18!1.01!Rbpj;;chr7:31206743..31206761,+!p1@Nfkbid!0.18!1.01!Nfkbid;;chr8:87324203..87324206,-!p10@Nfix!0.18!1.01!Nfix;;chr2:115890294..115890334,-!p9@Meis2!0.18!1.01!Meis2;;chr1:74634786..74634804,-!p5@Zfp142!0.18!1.01!Zfp142;;chr2:168780729..168780740,-!p3@LOC100502777,p3@Zfp64!0.18!0.51!Zfp64;;chr2:154395524..154395535,-!p5@E2f1!0.18!0.51!E2f1;;chr1:135557383..135557395,-!p5@Zbed6!0.18!0.51!Zbed6;;chr2:147871627..147871641,-!p1@Foxa2!0.18!0.51!Foxa2;;chr2:156665551..156665562,+!p6@Tgif2!0.18!0.51!Tgif2;;chr2:30700830..30700843,+!p4@Prrx2!0.18!0.51!Prrx2;;chr2:30701003..30701028,+!p6@Prrx2!0.18!0.51!Prrx2;;chr2:32229906..32229942,+!p3@Ciz1!0.18!0.51!Ciz1;;chr19:59533139..59533152,+!p2@Emx2!0.18!0.51!Emx2;;chr1:189432881..189432903,+!p2@Esrrg!0.18!0.51!Esrrg;;chr1:135557400..135557421,-!p4@Zbed6!0.18!0.51!Zbed6;;chr14:52640336..52640341,-!p20@Zfp219!0.18!0.51!Zfp219;;chr12:75002389..75002406,+!p4@Hif1a!0.18!0.51!Hif1a;;chr15:37163041..37163061,+!p5@Grhl2!0.18!0.51!Grhl2;;chr13:40826119..40826131,-!p7@Tfap2a!0.18!0.51!Tfap2a;;chr13:40824310..40824314,-!p6@Tfap2a!0.18!0.51!Tfap2a;;chr14:52640344..52640350,-!p17@Zfp219!0.18!0.51!Zfp219;;chr14:17407671..17407684,-!p7@Rarb!0.18!0.51!Rarb;;chr13:29045308..29045318,-!p10@Sox4!0.18!0.51!Sox4;;chr12:86939997..86940040,+!p4@Jdp2!0.18!0.51!Jdp2;;chr13:55932624..55932641,-!p2@Pitx1!0.18!0.51!Pitx1;;chr12:57714257..57714278,-!p1@Nkx2-9!0.18!0.51!Nkx2-9;;chr15:37163065..37163092,+!p4@Grhl2!0.18!0.51!Grhl2;;chr12:57714288..57714305,-!p2@Nkx2-9!0.18!0.51!Nkx2-9;;chr12:25257265..25257294,+!p2@Grhl1!0.18!0.51!Grhl1;;chr16:18587052..18587063,-!p3@Tbx1!0.18!0.51!Tbx1;;chr16:18588291..18588301,-!p2@Tbx1!0.18!0.51!Tbx1;;chr17:28409136..28409150,+!p3@Ppard!0.18!0.51!Ppard;;chr17:44873235..44873245,-!p17@Runx2!0.18!0.51!Runx2;;chr19:46379320..46379329,+!p9@Nfkb2!0.18!0.51!Nfkb2;;chr19:46380374..46380397,+!p7@Nfkb2!0.18!0.51!Nfkb2;;chr18:3280995..3281013,-!p23@Crem!0.18!0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4617,-!p1@Zkscan3!0.02!16.68!Zkscan3;;chr3:19957802..19957857,+!p1@Hltf!0.02!16.18!Hltf;;chr15:76181777..76181802,+!p2@Maf1!0.02!14.66!Maf1;;chr6:48036529..48036657,-!p1@Zfp746!0.02!13.65!Zfp746;;chr10:80813050..80813114,-!p2@Hmg20b!0.02!9.60!Hmg20b;;chr8:72520015..72520053,-!p2@Gatad2a!0.02!5.56!Gatad2a;;chr3:52072315..52072327,+!p2@Foxo1!0.02!5.06!Foxo1;;chr10:82226833..82226864,-!p3@Nfyb!0.02!4.04!Nfyb;;chr1:172797920..172797931,-!p3@Atf6!0.02!2.02!Atf6;;chr2:38781916..38781974,-!p1@Nr6a1!0.02!2.02!Nr6a1;;chr19:5637475..5637486,+!p6@Rela!0.02!1.52!Rela;;chr13:67182439..67182491,-!p2@Zfp708!0.02!1.52!Zfp708;;chr11:87881818..87881834,+!p4@Vezf1!0.02!1.52!Vezf1;;chrX:35542909..35542927,+!p4@Zbtb33!0.02!1.52!Zbtb33;;chr2:181100194..181100205,+!p5@Zgpat!0.02!1.01!Zgpat;;chr5:104183477..104183548,+!p6@Aff1!0.02!1.01!Aff1;;chr3:30993859..30993870,+!p5@Skil!0.02!0.51!Skil;;chr5:38611621..38611635,-!p2@Zbtb49!0.02!0.51!Zbtb49;;chr16:3872255..3872283,-!p4@Zfp597!0.02!0.51!Zfp597;;chr13:53568104..53568156,-!p1@Msx2!0.02!0.51!Msx2;;chr12:25336286..25336297,+!p2@Klf11!0.02!0.51!Klf11;;chr12:32635051..32635062,-!p2@Hbp1!0.02!0.51!Hbp1;;chr11:99092312..99092333,-!p4@Smarce1!0.02!0.51!Smarce1;;chr11:97524680..97524700,+!p3@Mllt6!0.02!0.51!Mllt6;;chr10:20032267..20032298,+!p1@Bclaf1!0.01!46.00!Bclaf1;;chr10:70700783..70700832,-!p1@Tfam!0.01!34.88!Tfam;;chr13:59924433..59924504,-!p1@Zcchc6!0.01!19.72!Zcchc6;;chr5:108697916..108697943,+!p2@Dr1!0.01!10.11!Dr1;;chr16:17531112..17531164,-!p1@Thap7!0.01!9.10!Thap7;;chr14:31832311..31832343,+!p1@Pbrm1!0.01!8.09!Pbrm1;;chr3:95032091..95032183,-!p1@Mllt11!0.01!7.08!Mllt11;;chr4:43575544..43575565,+!p2@Creb3!0.01!4.55!Creb3;;chr6:131338483..131338494,-!p5@Csda!0.01!4.04!Csda;;chr10:80600749..80600766,+!p2@Zbtb7a!0.01!4.04!Zbtb7a;;chr2:37278526..37278575,-!p2@Rc3h2!0.01!3.03!Rc3h2;;chr11:98636575..98636607,-!p2@Nr1d1!0.01!2.53!Nr1d1;;chr4:87678709..87678726,-!p4@Mllt3!0.01!2.02!Mllt3;;chr14:76903992..76904056,+!p6@Tsc22d1!0.01!1.01!Tsc22d1;;chr14:79915502..79915514,+!p4@Elf1!0.01!0.51!Elf1;;chr12:119540395..119540415,-!p5@Sp4!0.01!0.51!Sp4;;chr13:64254502..64254515,-!p3@Zfp367!0.01!0.51!Zfp367;;chr4:135129538..135129558,-!p1@Grhl3!0.01!0.51!Grhl3;;chr2:70313168..70313184,+!p1@Sp5!0.01!0.51!Sp5;;chr19:28754655..28754673,-!p3@Glis3!0.01!0.51!Glis3;;chr8:109868335..109868338,+!p3@Nfat5!0.01!0.51!Nfat5;;chr7:28516464..28516475,+!p3@Zfp60!0.01!0.51!Zfp60;;chr11:85646469..85646488,+!p5@Tbx2!0.01!0.51!Tbx2;;chr13:58503837..58503885,-!p1@Hnrnpk!0.00!254.28!Hnrnpk;;chr12:81213989..81214006,-!p1@Zfp36l1!0.00!46.51!Zfp36l1;;chr8:77517558..77517597,+!p1@Hmgxb4!0.00!19.21!Hmgxb4;;chr15:81575487..81575561,+!p1@Zc3h7b!0.00!18.70!Zc3h7b;;chr4:102787007..102787050,+!p1@Mier1!0.00!14.15!Mier1;;chr3:52072329..52072346,+!p1@Foxo1!0.00!13.14!Foxo1;;chr6:72849716..72849805,-!p1@Kcmf1!0.00!10.62!Kcmf1;;chr7:105851601..105851647,+!p2@Prkrir!0.00!7.58!Prkrir;;chr8:112229478..112229536,+!p1@Zfp821!0.00!7.08!Zfp821;;chr5:34163023..34163090,+!p2@Whsc1!0.00!5.06!Whsc1;;chr3:8666963..8666978,-!p1@Hey1!0.00!5.06!Hey1;;chr16:17530781..17530882,-!p2@Thap7!0.00!4.55!Thap7;;chr11:99092233..99092273,-!p2@Smarce1!0.00!3.54!Smarce1;;chr4:62626594..62626651,+!p1@Zfp618!0.00!2.53!Zfp618;;chr15:103170533..103170556,-!p1@Zfp385a!0.00!2.53!Zfp385a;;chr1:181733737..181733755,-!p2@Ahctf1!0.00!2.02!Ahctf1;;chr1:181476392..181476407,-!p2@Tfb2m!0.00!1.52!Tfb2m;;chr7:50568466..50568486,-!p2@Zfp715!0.00!1.52!Zfp715;;chr9:63869751..63869767,-!p1@Smad6!0.00!1.52!Smad6;;chr15:50721616..50721632,-!p4@Trps1!0.00!1.52!Trps1;;chr2:31428187..31428198,+!p3@Fubp3!0.00!1.01!Fubp3;;chr17:28487603..28487626,-!p2@Tead3!0.00!1.01!Tead3;;chr16:43619057..43619078,+!p8@Zbtb20!0.00!1.01!Zbtb20;;chr10:80812991..80813004,-!p3@Hmg20b!0.00!1.01!Hmg20b;;chr11:58136860..58136874,-!p2@Zfp672!0.00!1.01!Zfp672;;chr3:89197216..89197258,-!p3@Zbtb7b!0.00!1.01!Zbtb7b;;chr4:135700687..135700719,+!p2@Id3!0.00!0.51!Id3;;
+|ffid_belonging_in_development=CL:0000223,CL:0000377
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 43: @@
 |has_quality=
 |id=FF:13369-143G3
-|is_a=EFO:0002091;;FF:0000103;;FF:0011232
+|is_a=EFO:0002091;;FF:0011232
-|name=Tracheal epithelial cells, differentiation to ciliated epithelial cells, 000hr, biol_rep3
+|is_obsolete=
+|library_id=CNhs13741
+|library_id_phase_based=2:CNhs13741
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;13369
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13369
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep3.CNhs13741.13369-143G3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep3.CNhs13741.13369-143G3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep3.CNhs13741.13369-143G3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep3.CNhs13741.13369-143G3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep3.CNhs13741.13369-143G3.mm9.nobarcode.rdna.fa.gz
+|name=Tracheal epithelial cells, differentiation to ciliated epithelial cells
 |namespace=
 |part_of=
@@ Line 44: / Line 63: @@
 |profile_rnaseq=
 |profile_srnaseq=
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,0.0783045492882655,0,0,0,0,0.219083388336436,0,0,0,0,0.0888439057459905,0,0.111529277850403,0,0,0,0,0,0,0,0,0,0,0,0,0.177687811491981,-0.0781142804834573,0,0.400809590620714,0,0,0,-0.0576114111293375,-0.0872013824988623,0.026364669963044,-0.984211366477826,-0.269868638010351,0.849191662164219,0,0,0,0,0,0,0,0,0,0.303422628732977,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,0,-0.0285458971623357,0.169657854501188,-0.158091042771083,-0.0140823980615935,0,0,-0.145309149361067,0,0,0,-0.138362600626022,-0.0451748623791691,-0.0484328106159402,-0.0788315948399074,0,0,0,0,0,0,-0.0826843900821455,-0.238737695592622,0.221194943758556,0,0,0,0.292510291314521,0
 |rna_box=143
 |rna_catalog_number=
@@ Line 57: / Line 77: @@
 |rna_weight_ug=3.74
 |sample_age=
+|sample_category=time courses
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 75: / Line 96: @@
 |sample_strain=C57BL/6J
 |sample_tissue=
+|time= 000hr
+|timecourse=Tracheal_to_ciliated_epithelium
 |top_motifs=
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13369-143G3;search_select_hide=table117:13369-143G3
 }}

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FF:13369-143G3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:57, 4 June 2020

CNhs13741

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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