FF:683-20E5: Difference between revisions

Latest revision as of 19:19, 4 June 2020

Name:	lung, neonate N06
Species:	Mouse (Mus musculus)
Library ID:	CNhs11212
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	lung
dev stage	6 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		SAMD00005933

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11212		CAGE		DRX009038		DRR009912

Accession ID Mm9

Library id		BAM		CTSS
CNhs11212		DRZ001337		DRZ002720

Accession ID Mm10

Library id		BAM		CTSS
CNhs11212		DRZ012687		DRZ014070

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

CNhs11212

0	0
1	0
10	0
100	0
1000	0.0318
1001	0.145
1002	-0.0623
1003	0.15
1004	0
1005	0.173
1006	0.0636
1007	0.147
1008	0.0636
1009	0.428
101	-0.0207
1010	0
1011	-0.0142
1012	0.0636
1013	-0.0195
1014	0.0831
1015	-0.012
1016	0.205
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.00561
1022	0.0999
1023	0
1024	0.594
1025	1.285
1026	0
1027	0
1028	0
1029	0.487
103	0.187
1030	0.0636
1031	0.568
1032	0.0549
1033	0
1034	0.168
1035	0
1036	-0.0446
1037	0
1038	0.567
1039	-0.049
104	0
1040	0.531
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: CNhs11212

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.319
MA0003.1	MA0003.1	0.1
MA0004.1	MA0004.1	0.0135
MA0006.1	MA0006.1	0.0349
MA0007.1	MA0007.1	0.0535
MA0009.1	MA0009.1	0.954
MA0014.1	MA0014.1	0.933
MA0017.1	MA0017.1	4.11734e-5
MA0018.2	MA0018.2	0.00367
MA0019.1	MA0019.1	0.562
MA0024.1	MA0024.1	0.43
MA0025.1	MA0025.1	0.866
MA0027.1	MA0027.1	0.422
MA0028.1	MA0028.1	0.00136
MA0029.1	MA0029.1	0.9
MA0030.1	MA0030.1	0.0159
MA0031.1	MA0031.1	0.0245
MA0035.2	MA0035.2	0.107
MA0038.1	MA0038.1	0.893
MA0039.2	MA0039.2	0.026
MA0040.1	MA0040.1	0.471
MA0041.1	MA0041.1	0.311
MA0042.1	MA0042.1	0.487
MA0043.1	MA0043.1	0.359
MA0046.1	MA0046.1	1.07895e-9
MA0047.2	MA0047.2	1.32094e-5
MA0048.1	MA0048.1	0.756
MA0050.1	MA0050.1	0.0368
MA0051.1	MA0051.1	0.12
MA0052.1	MA0052.1	0.0914
MA0055.1	MA0055.1	0.607
MA0057.1	MA0057.1	0.755
MA0058.1	MA0058.1	0.00161
MA0059.1	MA0059.1	4.31961e-5
MA0060.1	MA0060.1	0.00787
MA0061.1	MA0061.1	0.702
MA0062.2	MA0062.2	0.00184
MA0065.2	MA0065.2	0.00135
MA0066.1	MA0066.1	0.0362
MA0067.1	MA0067.1	0.497
MA0068.1	MA0068.1	0.755
MA0069.1	MA0069.1	0.757
MA0070.1	MA0070.1	0.909
MA0071.1	MA0071.1	0.00317
MA0072.1	MA0072.1	0.0436
MA0073.1	MA0073.1	0.669
MA0074.1	MA0074.1	0.273
MA0076.1	MA0076.1	8.7368e-4
MA0077.1	MA0077.1	0.342
MA0078.1	MA0078.1	0.00816
MA0079.2	MA0079.2	0.065
MA0080.2	MA0080.2	2.35562e-4
MA0081.1	MA0081.1	0.281
MA0083.1	MA0083.1	2.88279e-6
MA0084.1	MA0084.1	0.741
MA0087.1	MA0087.1	0.546
MA0088.1	MA0088.1	0.284
MA0090.1	MA0090.1	0.0129
MA0091.1	MA0091.1	0.477
MA0092.1	MA0092.1	0.746
MA0093.1	MA0093.1	0.00993
MA0099.2	MA0099.2	0.0535
MA0100.1	MA0100.1	0.493
MA0101.1	MA0101.1	0.477
MA0102.2	MA0102.2	0.451
MA0103.1	MA0103.1	0.0122
MA0104.2	MA0104.2	6.0077e-5
MA0105.1	MA0105.1	0.0343
MA0106.1	MA0106.1	0.146
MA0107.1	MA0107.1	0.0334
MA0108.2	MA0108.2	0.831
MA0111.1	MA0111.1	0.913
MA0112.2	MA0112.2	0.0744
MA0113.1	MA0113.1	0.613
MA0114.1	MA0114.1	7.53432e-7
MA0115.1	MA0115.1	0.00506
MA0116.1	MA0116.1	0.0328
MA0117.1	MA0117.1	0.207
MA0119.1	MA0119.1	0.378
MA0122.1	MA0122.1	0.172
MA0124.1	MA0124.1	0.144
MA0125.1	MA0125.1	0.325
MA0131.1	MA0131.1	0.512
MA0135.1	MA0135.1	0.801
MA0136.1	MA0136.1	0.476
MA0137.2	MA0137.2	0.579
MA0138.2	MA0138.2	0.132
MA0139.1	MA0139.1	0.9
MA0140.1	MA0140.1	0.344
MA0141.1	MA0141.1	4.52091e-7
MA0142.1	MA0142.1	0.341
MA0143.1	MA0143.1	0.951
MA0144.1	MA0144.1	0.649
MA0145.1	MA0145.1	0.00304
MA0146.1	MA0146.1	0.928
MA0147.1	MA0147.1	3.5889e-6
MA0148.1	MA0148.1	1.07242e-4
MA0149.1	MA0149.1	0.65
MA0150.1	MA0150.1	0.00202
MA0152.1	MA0152.1	0.667
MA0153.1	MA0153.1	1.05985e-5
MA0154.1	MA0154.1	0.625
MA0155.1	MA0155.1	0.301
MA0156.1	MA0156.1	0.0428
MA0157.1	MA0157.1	0.0365
MA0159.1	MA0159.1	5.84476e-4
MA0160.1	MA0160.1	1.31606e-4
MA0162.1	MA0162.1	0.506
MA0163.1	MA0163.1	0.00225
MA0164.1	MA0164.1	0.312
MA0258.1	MA0258.1	0.0112
MA0259.1	MA0259.1	0.0233

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: CNhs11212

Novel motif	Logo	P-value
1	1	0.244
10	10	0.0844
100	100	0.191
101	101	0.553
102	102	0.731
103	103	0.502
104	104	0.696
105	105	0.884
106	106	0.0892
107	107	0.00666
108	108	0.659
109	109	0.155
11	11	0.0952
110	110	0.231
111	111	0.0658
112	112	0.614
113	113	0.873
114	114	0.0883
115	115	0.411
116	116	0.399
117	117	0.0103
118	118	0.346
119	119	0.862
12	12	0.46
120	120	0.0954
121	121	0.231
122	122	0.81
123	123	0.65
124	124	0.352
125	125	0.531
126	126	0.861
127	127	0.633
128	128	0.0997
129	129	0.58
13	13	0.449
130	130	0.012
131	131	0.0359
132	132	0.808
133	133	0.628
134	134	0.508
135	135	0.302
136	136	0.981
137	137	0.244
138	138	0.149
139	139	0.184
14	14	0.807
140	140	0.464
141	141	0.822
142	142	0.696
143	143	0.393
144	144	0.712
145	145	0.88
146	146	0.921
147	147	0.46
148	148	0.821
149	149	0.264
15	15	0.513
150	150	0.365
151	151	0.844
152	152	0.122
153	153	0.766
154	154	0.489
155	155	0.705
156	156	0.00113
157	157	0.868
158	158	0.832
159	159	0.0353
160	160	0.258
161	161	0.592
162	162	0.333
163	163	0.84
164	164	0.727
165	165	0.367
166	166	0.153
167	167	0.354
168	168	0.973
169	169	0.305
17	17	0.463
18	18	0.00535
19	19	0.152
2	2	0.162
20	20	0.189
21	21	0.924
22	22	0.402
23	23	0.221
24	24	0.725
25	25	0.177
26	26	0.619
27	27	0.715
28	28	0.769
29	29	0.0569
3	3	0.235
30	30	0.568
31	31	0.422
32	32	0.121
33	33	0.593
34	34	0.495
35	35	0.00563
36	36	0.369
37	37	0.958
38	38	0.563
39	39	0.183
4	4	0.78
40	40	0.988
41	41	0.331
42	42	0.625
43	43	0.706
44	44	0.0272
45	45	0.256
46	46	0.388
47	47	0.301
48	48	0.225
49	49	0.244
5	5	0.653
50	50	0.405
51	51	0.893
52	52	0.12
53	53	0.362
54	54	0.943
55	55	0.827
56	56	0.745
57	57	0.308
58	58	0.741
59	59	0.54
6	6	0.746
60	60	0.199
61	61	0.692
62	62	0.278
63	63	0.967
64	64	0.113
65	65	0.859
66	66	0.181
67	67	0.887
68	68	0.174
69	69	0.532
7	7	0.84
70	70	0.0257
71	71	0.178
72	72	0.258
73	73	0.628
74	74	0.945
75	75	0.0201
76	76	0.5
77	77	0.564
78	78	0.155
79	79	0.772
8	8	0.0642
80	80	0.658
81	81	0.14
82	82	0.403
83	83	0.823
84	84	0.494
85	85	0.886
86	86	0.761
87	87	0.0083
88	88	0.609
89	89	0.674
9	9	0.336
90	90	0.0126
91	91	0.662
92	92	0.52
93	93	0.472
94	94	0.344
95	95	0.351
96	96	0.328
97	97	0.696
98	98	0.582
99	99	0.353

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: CNhs11212

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011402 mouse lung- neonate N06 sample

part_of relathionship
UBERON:0000170 pair of lungs

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)
0002048 (lung)
0002100 (trunk)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0005177 (trunk region element)
0000117 (respiratory tube)
0000171 (respiration organ)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000312 (mouse neonate N6 sample)
0011402 (mouse lung- neonate N06 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:0001041 (foregut)
UBERON:0008947 (respiratory primordium)
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:0002048,UBERON:0002100,UBERON:0000483,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000077,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000025,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005153,UBERON:0005911,UBERON:0004921,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0009569,UBERON:0005291,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0003104,UBERON:0000464,UBERON:0001048,UBERON:0000925,UBERON:0005181,UBERON:0006598,UBERON:0004185,UBERON:0005157,UBERON:0002532,UBERON:0001555,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0007026,UBERON:0001041,UBERON:0002224,UBERON:0000915,UBERON:0009142,UBERON:0008947,UBERON:0003258,UBERON:0005597,UBERON:0006595,UBERON:0006603,UBERON:0000118
+|DRA_sample_Accession=CAGE@SAMD00005933
+|accession_numbers=CAGE;DRX009038;DRR009912;DRZ001337;DRZ002720;DRZ012687;DRZ014070
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002048,UBERON:0002100,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0000464,UBERON:0005181,UBERON:0010317,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0002224,UBERON:0000915
 |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:0000312,FF:0011402
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:85699862..85699920,+!p1@Tbx4!2.09!120.75!Tbx4;;chr10:22539932..22539956,-!p1@Tcf21!2.04!279.01!Tcf21;;chr8:123608252..123608268,+!p1@Foxf1a!1.90!114.92!Foxf1a;;chr5:77543897..77543911,-!p2@Hopx!1.74!101.52!Hopx;;chr12:37835141..37835194,+!p1@Meox2!1.70!147.70!Meox2;;chr2:180069370..180069409,-!p1@Gata5!1.70!57.69!Gata5;;chr12:57636034..57636087,-!p1@Nkx2-1!1.63!42.09!Nkx2-1;;chr12:37835120..37835133,+!p2@Meox2!1.59!54.23!Meox2;;chr13:31717548..31717596,+!p1@Foxf2!1.55!66.05!Foxf2;;chr2:103264213..103264233,+!p1@Elf5!1.49!30.11!Elf5;;chr5:98609885..98609900,+!p1@Prdm8!1.47!28.22!Prdm8;;chr11:85646303..85646329,+!p1@Tbx2!1.37!144.71!Tbx2;;chr12:57636178..57636194,-!p2@Nkx2-1!1.34!20.97!Nkx2-1;;chr12:37835203..37835218,+!p3@Meox2!1.25!20.02!Meox2;;chr13:72766250..72766273,+!p1@Irx2!1.21!23.33!Irx2;;chr17:87153462..87153473,+!p3@Epas1!1.20!56.12!Epas1;;chr12:57636220..57636236,-!p3@Nkx2-1!1.20!14.82!Nkx2-1;;chr17:87153028..87153049,+!p2@Epas1!1.18!283.11!Epas1;;chr6:52154386..52154407,-!p2@Hoxa5!1.18!17.81!Hoxa5;;chr12:37835248..37835260,+!p4@Meox2!1.18!14.19!Meox2;;chr6:52154414..52154462,-!p1@Hoxa5!1.17!19.07!Hoxa5;;chr14:64562503..64562524,+!p1@Sox7!1.16!78.03!Sox7;;chr13:72766279..72766296,+!p2@Irx2!1.16!20.18!Irx2;;chr12:57636240..57636256,-!p4@Nkx2-1!1.15!13.08!Nkx2-1;;chr13:72101161..72101177,-!p2@Irx1!1.14!17.66!Irx1;;chr11:85703483..85703508,+!p2@Tbx4!1.14!12.77!Tbx4;;chr2:147871627..147871641,-!p1@Foxa2!1.11!11.98!Foxa2;;chr11:85646263..85646278,+!p2@Tbx2!1.10!29.79!Tbx2;;chr11:85646341..85646352,+!p3@Tbx2!1.10!23.17!Tbx2;;chr17:87153240..87153254,+!p1@Epas1!1.08!215.17!Epas1;;chr12:58646974..58647003,-!p1@Foxa1!1.08!14.66!Foxa1;;chr11:116196664..116196679,-!p1@Foxj1!1.06!16.08!Foxj1;;chr13:31717597..31717613,+!p2@Foxf2!1.06!10.56!Foxf2;;chr17:87153440..87153451,+!p4@Epas1!1.05!21.28!Epas1;;chr1:4483679..4483695,-!p1@Sox17!1.02!45.40!Sox17;;chr18:53623836..53623839,+!p1@Prdm6!1.02!11.03!Prdm6;;chr12:57637732..57637777,-!p5@Nkx2-1!1.01!9.30!Nkx2-1;;chr11:85646469..85646488,+!p5@Tbx2!1.00!13.71!Tbx2;;chr6:99216488..99216534,-!p2@Foxp1!0.98!24.59!Foxp1;;chr1:186556323..186556370,-!p2@Hlx!0.96!22.86!Hlx;;chr8:94325814..94325839,-!p2@Irx3!0.96!17.50!Irx3;;chr5:120120667..120120685,+!p3@Tbx3!0.96!15.76!Tbx3;;chr9:96159147..96159204,+!p2@Tfdp2!0.96!15.45!Tfdp2;;chr1:4486481..4486501,-!p2@Sox17!0.96!12.30!Sox17;;chr1:4486453..4486470,-!p3@Sox17!0.96!10.56!Sox17;;chr5:120285144..120285160,+!p1@Tbx5!0.96!8.20!Tbx5;;chr11:96164821..96164865,+!p1@Hoxb5!0.96!8.04!Hoxb5;;chr11:85646427..85646451,+!p4@Tbx2!0.94!13.87!Tbx2;;chr5:77543935..77543947,-!p4@Hopx!0.94!7.72!Hopx;;chr16:95680889..95680991,-!p1@Erg!0.93!63.53!Erg;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.93!13.24!Hoxb2;;chr11:85699562..85699575,+!p6@Tbx4!0.93!7.57!Tbx4;;chr11:85703335..85703350,+!p4@Tbx4!0.93!7.57!Tbx4;;chr11:83664365..83664383,+!p1@Hnf1b!0.93!7.57!Hnf1b;;chr6:88148650..88148669,+!p1@Gata2!0.92!63.05!Gata2;;chr12:36219645..36219730,-!p1@Ahr!0.91!72.99!Ahr;;chr18:52775562..52775650,+!p1@Zfp474!0.91!7.09!Zfp474;;chr10:92773591..92773623,-!p1@Elk3!0.89!159.21!Elk3;;chr16:14705925..14705951,+!p1@Snai2!0.89!49.81!Snai2;;chr2:103143336..103143367,-!p1@Ehf!0.89!11.35!Ehf;;chr17:87153519..87153533,+!p5@Epas1!0.89!10.09!Epas1;;chr3:30408674..30408716,-!p2@Mecom!0.88!11.19!Mecom;;chr16:14705961..14705978,+!p2@Snai2!0.87!31.21!Snai2;;chr4:148275237..148275311,+!p2@Casz1!0.87!28.06!Casz1;;chr8:94881733..94881790,+!p1@Irx5!0.87!12.93!Irx5;;chr12:37835219..37835230,+!p5@Meox2!0.87!6.46!Meox2;;chr6:14851287..14851342,+!p1@Foxp2!0.86!21.75!Foxp2;;chr13:72101178..72101203,-!p1@Irx1!0.86!10.09!Irx1;;chr9:24578720..24578735,-!p1@Tbx20!0.86!6.31!Tbx20;;chr3:30408603..30408668,-!p1@Mecom!0.85!14.66!Mecom;;chr5:77544170..77544181,-!p6@Hopx!0.85!6.15!Hopx;;chr1:4486505..4486527,-!p5@Sox17!0.84!8.04!Sox17;;chr2:181406327..181406350,-!p1@Sox18!0.83!194.52!Sox18;;chr14:98568971..98569025,-!p1@Dach1!0.83!48.08!Dach1;;chr17:87153505..87153516,+!p6@Epas1!0.83!8.20!Epas1;;chr13:72101141..72101158,-!p3@Irx1!0.83!7.41!Irx1;;chr5:120285161..120285176,+!p2@Tbx5!0.83!5.83!Tbx5;;chr6:52114821..52114828,-!p1@Hoxa2!0.81!8.51!Hoxa2;;chr13:99954640..99954681,+!p1@Zfp366!0.80!20.65!Zfp366;;chr8:94325321..94325366,-!p1@Irx3!0.80!13.56!Irx3;;chr4:82151274..82151290,-!p3@Nfib!0.79!90.80!Nfib;;chr4:122911086..122911112,+!p1@Heyl!0.79!65.26!Heyl;;chr4:135840573..135840601,+!p1@Zfp46!0.79!44.61!Zfp46;;chr11:96180045..96180059,+!p1@Hoxb4!0.79!7.41!Hoxb4;;chr8:94325486..94325510,-!p4@Irx3!0.79!6.94!Irx3;;chr6:128250380..128250442,-!p2@Tead4!0.79!6.78!Tead4;;chr2:167363692..167363710,+!p1@Snai1!0.78!67.63!Snai1;;chr12:39506873..39506913,+!p1@Etv1!0.78!56.43!Etv1;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.78!6.78!Hoxb2;;chr11:96213264..96213282,+!p@chr11:96213264..96213282,+!0.78!6.46!Hoxb2;;chr10:67599319..67599360,-!p2@Arid5b!0.77!59.11!Arid5b;;chr4:119406389..119406411,+!p1@Hivep3!0.77!26.48!Hivep3;;chr5:120121446..120121461,+!p2@Tbx3!0.77!17.50!Tbx3;;chr2:180069423..180069434,-!p2@Gata5!0.77!4.89!Gata5;;chr13:31717614..31717628,+!p3@Foxf2!0.76!4.73!Foxf2;;chr2:44968737..44968758,-!p2@Zeb2!0.75!29.16!Zeb2;;chr10:126778916..126778974,-!p1@Gli1!0.75!11.03!Gli1;;chr2:147871948..147871977,-!p3@Foxa2!0.75!4.57!Foxa2;;chr11:52096804..52096896,-!p1@Tcf7!0.74!40.83!Tcf7;;chr6:144730427..144730508,-!p1@Sox5!0.74!30.27!Sox5;;chr19:26681672..26681716,+!p5@Smarca2!0.74!20.81!Smarca2;;chr6:52141694..52141715,-!p1@Hoxa4!0.74!5.83!Hoxa4;;chr18:11052642..11052659,+!p1@Gata6!0.73!24.75!Gata6;;chr2:77357622..77357704,-!p1@Zfp385b!0.73!12.93!Zfp385b;;chr12:39507680..39507715,+!p2@Etv1!0.73!9.14!Etv1;;chr6:128250471..128250519,-!p1@Tead4!0.72!8.99!Tead4;;chr3:8666963..8666978,-!p1@Hey1!0.71!29.64!Hey1;;chr14:22807107..22807119,-!p2@Zfp503!0.71!20.33!Zfp503;;chr1:4486530..4486557,-!p4@Sox17!0.71!5.52!Sox17;;chr2:103264245..103264268,+!p2@Elf5!0.71!4.10!Elf5;;chr16:22439681..22439698,-!p1@Etv5!0.70!79.13!Etv5;;chr11:18918917..18918944,-!p1@Meis1!0.70!58.96!Meis1;;chr14:98568761..98568814,-!p2@Dach1!0.70!30.74!Dach1;;chr5:120121020..120121049,+!p1@Tbx3!0.70!27.59!Tbx3;;chr18:55147667..55147746,-!p2@Zfp608!0.70!20.49!Zfp608;;chr2:44968721..44968734,-!p6@Zeb2!0.70!16.71!Zeb2;;chr4:82151653..82151706,-!p2@Nfib!0.69!124.69!Nfib;;chr14:22807083..22807104,-!p1@Zfp503!0.69!77.24!Zfp503;;chr4:119406412..119406439,+!p2@Hivep3!0.69!8.35!Hivep3;;chr2:164228702..164228719,+!p1@Rbpjl!0.69!3.94!Rbpjl;;chr11:96180069..96180089,+!p3@Hoxb4!0.69!3.94!Hoxb4;;chr16:22439654..22439676,-!p2@Etv5!0.68!25.38!Etv5;;chr4:119486912..119486954,+!p3@Hivep3!0.68!7.09!Hivep3;;chr11:70043257..70043263,-!p1@Bcl6b!0.68!7.09!Bcl6b;;chr2:120365588..120365602,-!p2@Zfp106!0.68!6.78!Zfp106;;chr8:94325847..94325869,-!p3@Irx3!0.68!6.46!Irx3;;chr9:63869890..63869908,-!p6@Smad6!0.68!5.20!Smad6;;chr8:74842952..74842970,+!p1@Klf2!0.67!288.31!Klf2;;chr4:82151178..82151262,-!p1@Nfib!0.67!173.56!Nfib;;chr9:32503590..32503680,+!p1@Ets1!0.67!154.64!Ets1;;chr11:16908650..16908690,-!p1@Plek!0.67!25.69!Plek;;chr4:13670571..13670625,+!p1@Runx1t1!0.67!11.19!Runx1t1;;chr15:81633165..81633188,+!p2@Tef!0.66!33.73!Tef;;chr6:52163319..52163342,-!p1@Hoxa3!0.66!5.52!Hoxa3;;chr11:52096066..52096081,-!p2@Tcf7!0.66!4.57!Tcf7;;chr5:77524250..77524300,-!p1@Hopx!0.65!82.13!Hopx;;chr4:97444012..97444045,+!p4@Nfia!0.65!30.11!Nfia;;chr14:65568469..65568511,-!p2@Hmbox1!0.65!12.93!Hmbox1;;chr4:148178559..148178603,+!p1@Casz1!0.65!11.19!Casz1;;chr18:11052606..11052633,+!p4@Gata6!0.65!9.77!Gata6;;chr4:135840623..135840632,+!p5@Zfp46!0.65!4.89!Zfp46;;chr12:57637882..57637924,-!p6@Nkx2-1!0.65!3.47!Nkx2-1;;chr11:96164905..96164919,+!p2@Hoxb5!0.65!3.47!Hoxb5;;chr11:18918959..18918976,-!p2@Meis1!0.64!52.97!Meis1;;chr17:34730333..34730362,+!p2@Pbx2!0.64!15.13!Pbx2;;chr1:186556410..186556424,-!p1@Hlx!0.64!11.98!Hlx;;chr10:92773708..92773734,-!p3@Elk3!0.64!7.41!Elk3;;chr7:38554763..38554780,-!p1@Zfp536!0.64!6.62!Zfp536;;chr6:98978245..98978289,-!p1@Foxp1!0.63!57.06!Foxp1;;chr2:91034924..91034946,-!p2@Nr1h3!0.63!4.26!Nr1h3;;chr17:37139472..37139514,+!p1@Zfp57!0.62!25.22!Zfp57;;chr1:137155026..137155042,-!p1@Elf3!0.62!21.75!Elf3;;chr9:63869802..63869815,-!p3@Smad6!0.62!6.94!Smad6;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!0.62!6.62!Zbtb38;;chr10:67599361..67599372,-!p5@Arid5b!0.62!5.36!Arid5b;;chr4:13670626..13670657,+!p5@Runx1t1!0.62!5.20!Runx1t1;;chr8:24780125..24780143,+!p1@Zmat4!0.62!4.89!Zmat4;;chr8:94325779..94325791,-!p7@Irx3!0.62!3.15!Irx3;;chr12:57637649..57637665,-!p8@Nkx2-1!0.62!3.15!Nkx2-1;;chrX:109714331..109714347,+!p1@Zfp711!0.61!14.82!Zfp711;;chr8:87225670..87225697,+!p2@Lyl1!0.61!10.25!Lyl1;;chr9:96653072..96653154,-!p1@Zbtb38!0.61!9.30!Zbtb38;;chr1:186556375..186556404,-!p3@Hlx!0.61!6.15!Hlx;;chr15:40486754..40486771,+!p2@Zfpm2!0.61!5.83!Zfpm2;;chr2:44968512..44968530,-!p1@Zeb2!0.60!80.08!Zeb2;;chr7:119822957..119822980,+!p2@Tead1!0.60!17.18!Tead1;;chr14:98569030..98569059,-!p3@Dach1!0.60!17.02!Dach1;;chr2:152758901..152758925,-!p1@Foxs1!0.60!15.76!Foxs1;;chr4:82151622..82151643,-!p4@Nfib!0.60!14.34!Nfib;;chr6:14851440..14851497,+!p2@Foxp2!0.60!8.35!Foxp2;;chr1:135320989..135321043,-!p1@Sox13!0.59!38.62!Sox13;;chr1:64167550..64167618,-!p4@Klf7!0.59!9.14!Klf7;;chr17:13897299..13897342,+!p3@Mllt4!0.59!7.72!Mllt4;;chr4:13670499..13670526,+!p2@Runx1t1!0.59!7.25!Runx1t1;;chr6:14851250..14851277,+!p4@Foxp2!0.59!3.94!Foxp2;;chr9:71743854..71743909,-!p1@Tcf12!0.58!26.96!Tcf12;;chr16:92697560..92697592,-!p2@Runx1!0.58!21.28!Runx1;;chr14:98568822..98568837,-!p5@Dach1!0.58!4.57!Dach1;;chr12:57637700..57637717,-!p9@Nkx2-1!0.58!2.84!Nkx2-1;;chr4:55545337..55545357,-!p1@Klf4!0.57!50.13!Klf4;;chr16:42907676..42907797,+!p1@Zbtb20!0.57!43.98!Zbtb20;;chr6:99470943..99471024,-!p3@Foxp1!0.57!31.84!Foxp1;;chr4:32325688..32325777,+!p1@Bach2!0.57!29.48!Bach2;;chr2:44968775..44968795,-!p4@Zeb2!0.57!15.45!Zeb2;;chr15:37162796..37162828,+!p1@Grhl2!0.57!5.04!Grhl2;;chr11:18918434..18918489,-!p3@Meis1!0.57!4.73!Meis1;;chr1:38721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+|ffid_belonging_in_development=UBERON:0001041,UBERON:0008947,UBERON:0002532,UBERON:0006595,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011402
 |is_obsolete=
+|library_id=CNhs11212
+|library_id_phase_based=2:CNhs11212
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;683
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;683
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N06.CNhs11212.683-20E5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N06.CNhs11212.683-20E5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N06.CNhs11212.683-20E5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N06.CNhs11212.683-20E5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N06.CNhs11212.683-20E5.mm9.nobarcode.rdna.fa.gz
 |name=lung, neonate N06
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11212,LSID747,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.180162674477644,0.00441915368226149,0,0,0.0635717028550276,0.0912933562119048,0.381557018630184,0,0.0840874319614935,0,0.0635717028550276,0.0838356235264453,0.0592700975535658,0,0,0,0,0,0.131038018141813,0,0,0,0,0,0.119015009568782,0,0,0,0,0,0,0,0.323570708258241,0,0,0,0,0.0466910467754399,0.0419772447030022,0.0533765669254691,-0.149878805328279,0.231908176619661,-0.0575370272031789,0,0,0,0,0,0,0,0,0,0,0.0635717028550276,0,0.256925821460947,0,0,0,0,0,0,0.0317858514275138,0,0,0.0635717028550276,0.133300194113134,0.173543354101309,-0.158091042771083,0.0495655540977867,0,0.0901662631710354,0.0635717028550276,0,0,0,0.0697981242055283,0.0155323482391531,-0.159118501453083,0.133500015967265,0,0,0,0,0.0317858514275138,0,-0.142671721075526,-0.210569851608748,-0.0374320999146443,0,0,0,0,0
 |rna_box=20
 |rna_catalog_number=
@@ Line 56: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=20E5
+|rna_tube_id=2.00E+06
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 79: / Line 97: @@
 |top_motifs=HBP1_HMGB_SSRP1_UBTF:2.28259605904;NKX2-1,4:2.02834041762;NKX3-1:1.94965829989;FOX{I1,J2}:1.86230008656;BPTF:1.76611547068;EP300:1.74952164672;FOXO1,3,4:1.74244875111;IKZF1:1.72791812712;FOX{D1,D2}:1.67022922341;EBF1:1.57570340885;TOPORS:1.56148719388;XCPE1{core}:1.46130176094;IKZF2:1.44267737128;TEAD1:1.42979409478;FOXN1:1.42165669168;ZNF238:1.30104878089;TLX1..3_NFIC{dimer}:1.2551578297;TFCP2:1.25032876304;ZNF384:1.24476195472;SOX5:1.2384871305;NFATC1..3:1.22814866627;T:1.19897106014;SP1:1.18756214079;FOXP1:1.09635087876;MYBL2:1.03799008976;NKX6-1,2:0.998087653776;ETS1,2:0.994115870861;NFIX:0.957151640355;SRF:0.933136702136;IRF1,2:0.926226374202;SPIB:0.917803498019;TFAP4:0.879378364033;TLX2:0.839990243656;GLI1..3:0.831245239287;TFDP1:0.827691061829;MAZ:0.806226373612;SOX2:0.793524137885;NKX2-2,8:0.792038473507;GTF2A1,2:0.779272789773;TFAP2B:0.764548206063;RXR{A,B,G}:0.733432475962;PATZ1:0.717498094801;TGIF1:0.700608863124;FOXQ1:0.671223881047;TEF:0.670047867164;RFX2..5_RFXANK_RFXAP:0.668941686183;PAX5:0.639178301403;HIC1:0.612318024198;GFI1:0.586138189963;TFAP2{A,C}:0.56040637674;GTF2I:0.534175934633;ZIC1..3:0.531982949368;STAT2,4,6:0.512311090032;ELF1,2,4:0.501800477168;SPZ1:0.501356883117;SPI1:0.49957924071;GZF1:0.493538060561;RREB1:0.485254579711;STAT1,3:0.423043129932;RBPJ:0.404488059134;PRDM1:0.403760284237;MTF1:0.395629329782;MEF2{A,B,C,D}:0.394161970935;GATA4:0.393576805518;ALX4:0.36104950074;GATA6:0.354142336717;E2F1..5:0.314831801973;ESR1:0.292138497396;FOXA2:0.267843149794;PITX1..3:0.26359574063;FOXD3:0.244110312222;MZF1:0.240026796328;HAND1,2:0.239457848442;CRX:0.233429389666;STAT5{A,B}:0.222146776087;DBP:0.216129631719;NKX2-3_NKX2-5:0.214586762715;POU5F1:0.207852725316;ZFP161:0.207796813614;GCM1,2:0.207774743043;EGR1..3:0.206765862108;SOX{8,9,10}:0.174154703518;NFE2L1:0.172467705675;ZNF148:0.161052490363;PAX4:0.158781268556;HMGA1,2:0.144139648145;MYFfamily:0.116943774204;ZBTB16:0.115243875529;BACH2:0.109718875181;RFX1:0.102700386282;LEF1_TCF7_TCF7L1,2:0.100923122661;GFI1B:0.098334726878;TBX4,5:0.0860167765006;NR1H4:0.0739042548925;SMAD1..7,9:0.0634701898533;CEBPA,B_DDIT3:0.0545335203442;RXRA_VDR{dimer}:0.0489604049941;MED-1{core}:0.0449119445212;TBP:0.0390508640487;IRF7:0.0274566540424;NFKB1_REL_RELA:0.0150435006733;NFIL3:0.0141859517345;JUN:-0.0114268913493;SNAI1..3:-0.0168809999847;KLF4:-0.0390506734974;RUNX1..3:-0.048867902471;POU3F1..4:-0.073583181211;ALX1:-0.0758067098129;DMAP1_NCOR{1,2}_SMARC:-0.0838003487731;FOS_FOS{B,L1}_JUN{B,D}:-0.135966011582;MTE{core}:-0.150137436232;ATF2:-0.151878995513;BREu{core}:-0.155068463391;FOSL2:-0.159009089055;ZEB1:-0.16237618662;CUX2:-0.186446215558;FOX{F1,F2,J1}:-0.193165711627;NFE2L2:-0.207103477356;HIF1A:-0.220449532435;ZNF423:-0.223099749683;POU2F1..3:-0.232976422785;NKX3-2:-0.247830677717;PAX1,9:-0.268182369611;HMX1:-0.290916514152;NR3C1:-0.305017489661;SOX17:-0.314917103966;PRRX1,2:-0.331067915295;TP53:-0.337064648313;MYB:-0.339927192958;NHLH1,2:-0.346432876324;FOXP3:-0.355801518933;HNF1A:-0.357995164236;CDC5L:-0.379207545661;REST:-0.379859401289;AR:-0.385472285621;ZBTB6:-0.416307277476;HNF4A_NR2F1,2:-0.42734249703;EVI1:-0.430479506252;NANOG{mouse}:-0.440966393933;CDX1,2,4:-0.450600366661;ADNP_IRX_SIX_ZHX:-0.473165883892;FOXL1:-0.505938903866;NR6A1:-0.50798927696;NANOG:-0.513228309403;HLF:-0.529984833183;POU6F1:-0.560186150593;AIRE:-0.565401957903;PBX1:-0.586475472179;LMO2:-0.633526089441;TAL1_TCF{3,4,12}:-0.639327950428;NRF1:-0.639360324895;AHR_ARNT_ARNT2:-0.666842671116;MAFB:-0.66970565385;bHLH_family:-0.671407718887;ONECUT1,2:-0.682312549343;PDX1:-0.687805611248;PAX6:-0.721746327864;ATF4:-0.724133649587;POU1F1:-0.731013306565;SREBF1,2:-0.733314338039;HOX{A5,B5}:-0.745345790237;ELK1,4_GABP{A,B1}:-0.751990137241;CREB1:-0.761834510196;FOXM1:-0.771951674348;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.777571427608;PPARG:-0.780783722624;EN1,2:-0.798093268757;MYOD1:-0.802369109296;UFEwm:-0.814603582474;LHX3,4:-0.822439158648;NFY{A,B,C}:-0.832126630832;ATF5_CREB3:-0.836086052182;NFE2:-0.885497279827;ZNF143:-0.89591954837;HOX{A4,D4}:-0.897232267808;VSX1,2:-0.921223806559;ATF6:-0.980590790909;ARID5B:-0.99619116903;PAX2:-1.07765335429;RORA:-1.11265429498;HOXA9_MEIS1:-1.18285986346;HSF1,2:-1.19730914338;ESRRA:-1.25876257123;OCT4_SOX2{dimer}:-1.4326327448;NR5A1,2:-1.43787812148;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.45312247212;PAX8:-1.64447971664;HES1:-1.67043537188;YY1:-1.87298217242
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:683-20E5;search_select_hide=table117:683-20E5
 }}

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FF:683-20E5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:19, 4 June 2020

CNhs11212

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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