FF:1359-25C7

Name:	lung, neonate N25
Species:	Mouse (Mus musculus)
Library ID:	CNhs11119
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information
Sample information strain C57BL/6J tissue lung dev stage 25 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  SAMD00005110 Library accession numbers Library id Method Exp. accession id Run accession id CNhs11119 CAGE DRX009042 DRR009916 Accession ID Mm9 Library id BAM CTSS CNhs11119 DRZ001341 DRZ002724 Accession ID Mm10 Library id BAM CTSS CNhs11119 DRZ012691 DRZ014074

Download raw sequence, BAM & CTSS
Mm9 Fasta BAM CTSS download download donwload Mm10 BAM CTSS download donwload

Relative expression to median (log10)

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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

CNhs11119

MCL coexpression id	Coexpression dpi cluster scores median value
0	0
1	0
10	0.061
100	0
1000	0.125
1001	0.239
1002	--0.0136
1003	0.127
1004	0
1005	0.171
1006	0.202
1007	0.0478
1008	0
1009	0.365
101	--0.0861
1010	0
1011	--0.0314
1012	0.181
1013	0.0727
1014	0.129
1015	--0.182
1016	0.0533
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.156
1023	0
1024	0.589
1025	1.121
1026	0
1027	0
1028	0.0692
1029	0.473
103	0.175
1030	0.407
1031	0.287
1032	0.0642
1033	0
1034	0.228
1035	0.0692
1036	--0.157
1037	0.019
1038	0.508
1039	0.0897
104	0
1040	0.491
1041	0.344

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family 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

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

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JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11119

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.294
MA0003.1	MA0003.1	0.0946
MA0004.1	MA0004.1	0.0747
MA0006.1	MA0006.1	0.0458
MA0007.1	MA0007.1	0.311
MA0009.1	MA0009.1	0.364
MA0014.1	MA0014.1	0.688
MA0017.1	MA0017.1	0.202
MA0018.2	MA0018.2	1.48844e-5
MA0019.1	MA0019.1	0.898
MA0024.1	MA0024.1	7.6534e-4
MA0025.1	MA0025.1	0.791
MA0027.1	MA0027.1	0.665
MA0028.1	MA0028.1	0.0117
MA0029.1	MA0029.1	0.72
MA0030.1	MA0030.1	0.376
MA0031.1	MA0031.1	0.0677
MA0035.2	MA0035.2	0.0876
MA0038.1	MA0038.1	0.668
MA0039.2	MA0039.2	0.00326
MA0040.1	MA0040.1	0.56
MA0041.1	MA0041.1	0.257
MA0042.1	MA0042.1	0.503
MA0043.1	MA0043.1	0.00212
MA0046.1	MA0046.1	1.63639e-9
MA0047.2	MA0047.2	6.40277e-5
MA0048.1	MA0048.1	0.857
MA0050.1	MA0050.1	7.01164e-8
MA0051.1	MA0051.1	1.9027e-4
MA0052.1	MA0052.1	0.0615
MA0055.1	MA0055.1	0.818
MA0057.1	MA0057.1	0.277
MA0058.1	MA0058.1	0.05
MA0059.1	MA0059.1	0.0874
MA0060.1	MA0060.1	8.97089e-10
MA0061.1	MA0061.1	0.0223
MA0062.2	MA0062.2	0.0152
MA0065.2	MA0065.2	0.863
MA0066.1	MA0066.1	0.876
MA0067.1	MA0067.1	0.683
MA0068.1	MA0068.1	0.939
MA0069.1	MA0069.1	0.655
MA0070.1	MA0070.1	0.532
MA0071.1	MA0071.1	0.285
MA0072.1	MA0072.1	0.341
MA0073.1	MA0073.1	0.801
MA0074.1	MA0074.1	0.566
MA0076.1	MA0076.1	0.00459
MA0077.1	MA0077.1	0.0116
MA0078.1	MA0078.1	0.00438
MA0079.2	MA0079.2	0.0609
MA0080.2	MA0080.2	7.75867e-10
MA0081.1	MA0081.1	0.194
MA0083.1	MA0083.1	0.0337
MA0084.1	MA0084.1	0.816
MA0087.1	MA0087.1	0.562
MA0088.1	MA0088.1	0.725
MA0090.1	MA0090.1	0.0891
MA0091.1	MA0091.1	0.623
MA0092.1	MA0092.1	0.484
MA0093.1	MA0093.1	0.0695
MA0099.2	MA0099.2	0.273
MA0100.1	MA0100.1	0.137
MA0101.1	MA0101.1	0.143
MA0102.2	MA0102.2	0.366
MA0103.1	MA0103.1	0.93
MA0104.2	MA0104.2	0.00285
MA0105.1	MA0105.1	0.178
MA0106.1	MA0106.1	0.0223
MA0107.1	MA0107.1	0.00522
MA0108.2	MA0108.2	0.433
MA0111.1	MA0111.1	0.438
MA0112.2	MA0112.2	0.0134
MA0113.1	MA0113.1	0.87
MA0114.1	MA0114.1	0.0345
MA0115.1	MA0115.1	0.0971
MA0116.1	MA0116.1	0.14
MA0117.1	MA0117.1	0.378
MA0119.1	MA0119.1	0.0369
MA0122.1	MA0122.1	0.242
MA0124.1	MA0124.1	0.52
MA0125.1	MA0125.1	0.0519
MA0131.1	MA0131.1	0.22
MA0135.1	MA0135.1	0.263
MA0136.1	MA0136.1	0.0068
MA0137.2	MA0137.2	0.917
MA0138.2	MA0138.2	0.828
MA0139.1	MA0139.1	0.0648
MA0140.1	MA0140.1	0.824
MA0141.1	MA0141.1	0.0694
MA0142.1	MA0142.1	0.869
MA0143.1	MA0143.1	0.287
MA0144.1	MA0144.1	0.345
MA0145.1	MA0145.1	0.00151
MA0146.1	MA0146.1	0.323
MA0147.1	MA0147.1	0.00168
MA0148.1	MA0148.1	1.71498e-4
MA0149.1	MA0149.1	0.65
MA0150.1	MA0150.1	0.37
MA0152.1	MA0152.1	0.213
MA0153.1	MA0153.1	3.11583e-7
MA0154.1	MA0154.1	0.00366
MA0155.1	MA0155.1	0.158
MA0156.1	MA0156.1	0.0013
MA0157.1	MA0157.1	0.0645
MA0159.1	MA0159.1	0.83
MA0160.1	MA0160.1	0.0888
MA0162.1	MA0162.1	0.16
MA0163.1	MA0163.1	0.74
MA0164.1	MA0164.1	0.401
MA0258.1	MA0258.1	0.242
MA0259.1	MA0259.1	0.0108

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 in 169 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: CNhs11119

Novel motif	Logo	P-value
1	1	0.641
10	10	0.815
100	100	0.26
101	101	0.496
102	102	0.588
103	103	0.282
104	104	0.619
105	105	0.439
106	106	9.21095e-4
107	107	0.00577
108	108	0.667
109	109	0.172
11	11	0.859
110	110	0.867
111	111	0.867
112	112	0.201
113	113	0.975
114	114	0.386
115	115	0.535
116	116	0.914
117	117	0.326
118	118	0.812
119	119	0.0804
12	12	0.681
120	120	0.169
121	121	0.638
122	122	0.815
123	123	0.96
124	124	0.579
125	125	0.449
126	126	0.292
127	127	0.223
128	128	0.00447
129	129	0.0879
13	13	0.0147
130	130	0.00761
131	131	0.126
132	132	0.338
133	133	0.463
134	134	0.744
135	135	0.583
136	136	0.337
137	137	0.326
138	138	0.0496
139	139	0.643
14	14	0.29
140	140	0.561
141	141	0.265
142	142	0.315
143	143	0.611
144	144	0.721
145	145	0.168
146	146	0.819
147	147	0.825
148	148	0.306
149	149	0.125
15	15	0.414
150	150	0.145
151	151	0.181
152	152	0.0251
153	153	0.583
154	154	0.321
155	155	0.678
156	156	0.357
157	157	0.975
158	158	0.915
159	159	0.0333
160	160	0.0752
161	161	0.466
162	162	0.403
163	163	0.852
164	164	0.568
165	165	0.766
166	166	0.235
167	167	0.764
168	168	0.945
169	169	0.00869
17	17	0.345
18	18	0.155
19	19	0.036
2	2	0.129
20	20	0.374
21	21	0.617
22	22	0.103
23	23	0.0333
24	24	0.316
25	25	0.324
26	26	0.0626
27	27	0.867
28	28	0.52
29	29	0.511
3	3	0.454
30	30	0.86
31	31	0.884
32	32	0.714
33	33	0.74
34	34	0.421
35	35	0.315
36	36	0.871
37	37	0.0403
38	38	0.199
39	39	0.076
4	4	0.715
40	40	0.61
41	41	0.392
42	42	0.607
43	43	0.135
44	44	0.577
45	45	0.169
46	46	0.687
47	47	0.629
48	48	0.894
49	49	0.261
5	5	0.521
50	50	0.321
51	51	0.659
52	52	0.0668
53	53	0.402
54	54	0.806
55	55	0.895
56	56	0.356
57	57	0.998
58	58	0.586
59	59	0.0478
6	6	0.923
60	60	0.0336
61	61	0.739
62	62	0.803
63	63	0.142
64	64	0.716
65	65	0.201
66	66	0.105
67	67	0.491
68	68	0.632
69	69	0.986
7	7	0.346
70	70	0.437
71	71	0.308
72	72	0.91
73	73	0.145
74	74	0.475
75	75	0.751
76	76	0.718
77	77	0.23
78	78	0.861
79	79	0.616
8	8	0.883
80	80	0.811
81	81	0.858
82	82	0.329
83	83	0.253
84	84	0.279
85	85	0.0422
86	86	0.826
87	87	0.0206
88	88	0.979
89	89	0.343
9	9	0.154
90	90	0.642
91	91	0.167
92	92	0.136
93	93	0.595
94	94	0.864
95	95	0.656
96	96	0.813
97	97	0.847
98	98	0.704
99	99	0.259

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: CNhs11119

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011488 mouse lung- neonate N25 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)
0000309 (mouse neonate N25 sample)
0011488 (mouse lung- neonate N25 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)