FF:1387-42A2: Difference between revisions

Revision as of 10:38, 28 November 2014

Name:	epididymis and seminiferous tubule, neonate N30
Species:	Mouse (Mus musculus)
Library ID:	CNhs11199
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	C57BL/6J
tissue	epididymis and seminiferous tubule
dev stage	30 days neonate
sex	male
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		SAMD00005890

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11199		CAGE		DRX008952		DRR009826

Accession ID Mm9

Library id		BAM		CTSS
CNhs11199		DRZ001251		DRZ002634

Download raw sequence, BAM & CTSS

Mm9

BAM	CTSS
[{{{mm9bam}}} download]	[{{{mm9ctss}}} donwload]

Mm10

BAM	CTSS
[{{{mm10bam}}} download]	[{{{mm10ctss}}} 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

CNhs11199

0	0
1	0
10	0
100	0
1000	0.337
1001	0.209
1002	0.0242
1003	-0.00968
1004	0.0509
1005	0.229
1006	0.275
1007	0.0472
1008	0
1009	0.269
101	-0.0484
1010	0
1011	0.024
1012	0.0509
1013	0.11
1014	0
1015	-0.145
1016	-0.107
1017	0
1018	0.0637
1019	0.0509
102	0
1020	0
1021	0.138
1022	0.244
1023	0.0509
1024	0.12
1025	0
1026	0.516
1027	0.0509
1028	0.0509
1029	0.124
103	1.021
1030	0.21
1031	0.0357
1032	0.0318
1033	0.0342
1034	0.124
1035	0.0187
1036	0.00302
1037	0.0509
1038	-0.0447
1039	0.0332
104	0
1040	0.0783
1041	0.708

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: CNhs11199

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	1.52627e-7
MA0003.1	MA0003.1	0.00872
MA0004.1	MA0004.1	0.218
MA0006.1	MA0006.1	0.0905
MA0007.1	MA0007.1	0.0272
MA0009.1	MA0009.1	0.785
MA0014.1	MA0014.1	0.705
MA0017.1	MA0017.1	0.806
MA0018.2	MA0018.2	1.45093e-5
MA0019.1	MA0019.1	0.0579
MA0024.1	MA0024.1	0.898
MA0025.1	MA0025.1	0.297
MA0027.1	MA0027.1	0.41
MA0028.1	MA0028.1	0.0467
MA0029.1	MA0029.1	0.492
MA0030.1	MA0030.1	0.621
MA0031.1	MA0031.1	0.591
MA0035.2	MA0035.2	0.0352
MA0038.1	MA0038.1	0.656
MA0039.2	MA0039.2	0.0401
MA0040.1	MA0040.1	0.0854
MA0041.1	MA0041.1	0.354
MA0042.1	MA0042.1	0.529
MA0043.1	MA0043.1	1.73304e-5
MA0046.1	MA0046.1	0.0021
MA0047.2	MA0047.2	0.865
MA0048.1	MA0048.1	0.459
MA0050.1	MA0050.1	5.56981e-4
MA0051.1	MA0051.1	0.0027
MA0052.1	MA0052.1	4.41334e-12
MA0055.1	MA0055.1	0.442
MA0057.1	MA0057.1	0.321
MA0058.1	MA0058.1	0.167
MA0059.1	MA0059.1	0.179
MA0060.1	MA0060.1	0.676
MA0061.1	MA0061.1	0.215
MA0062.2	MA0062.2	0.0301
MA0065.2	MA0065.2	0.24
MA0066.1	MA0066.1	0.662
MA0067.1	MA0067.1	0.403
MA0068.1	MA0068.1	0.00875
MA0069.1	MA0069.1	0.671
MA0070.1	MA0070.1	0.811
MA0071.1	MA0071.1	0.982
MA0072.1	MA0072.1	0.0629
MA0073.1	MA0073.1	0.836
MA0074.1	MA0074.1	0.935
MA0076.1	MA0076.1	0.0205
MA0077.1	MA0077.1	0.162
MA0078.1	MA0078.1	0.0251
MA0079.2	MA0079.2	0.972
MA0080.2	MA0080.2	3.23998e-10
MA0081.1	MA0081.1	0.141
MA0083.1	MA0083.1	6.89132e-4
MA0084.1	MA0084.1	0.863
MA0087.1	MA0087.1	0.61
MA0088.1	MA0088.1	0.883
MA0090.1	MA0090.1	0.784
MA0091.1	MA0091.1	0.241
MA0092.1	MA0092.1	0.46
MA0093.1	MA0093.1	0.197
MA0099.2	MA0099.2	0.817
MA0100.1	MA0100.1	0.814
MA0101.1	MA0101.1	0.847
MA0102.2	MA0102.2	0.137
MA0103.1	MA0103.1	0.871
MA0104.2	MA0104.2	0.0952
MA0105.1	MA0105.1	0.11
MA0106.1	MA0106.1	0.494
MA0107.1	MA0107.1	0.735
MA0108.2	MA0108.2	0.031
MA0111.1	MA0111.1	0.763
MA0112.2	MA0112.2	5.6601e-5
MA0113.1	MA0113.1	0.00825
MA0114.1	MA0114.1	0.187
MA0115.1	MA0115.1	0.0233
MA0116.1	MA0116.1	0.0469
MA0117.1	MA0117.1	0.856
MA0119.1	MA0119.1	0.0468
MA0122.1	MA0122.1	0.411
MA0124.1	MA0124.1	0.867
MA0125.1	MA0125.1	0.054
MA0131.1	MA0131.1	0.607
MA0135.1	MA0135.1	0.922
MA0136.1	MA0136.1	3.10583e-6
MA0137.2	MA0137.2	0.0467
MA0138.2	MA0138.2	0.94
MA0139.1	MA0139.1	0.34
MA0140.1	MA0140.1	2.30253e-11
MA0141.1	MA0141.1	0.9
MA0142.1	MA0142.1	0.696
MA0143.1	MA0143.1	0.371
MA0144.1	MA0144.1	0.903
MA0145.1	MA0145.1	0.0615
MA0146.1	MA0146.1	0.251
MA0147.1	MA0147.1	0.106
MA0148.1	MA0148.1	0.966
MA0149.1	MA0149.1	0.566
MA0150.1	MA0150.1	0.281
MA0152.1	MA0152.1	0.98
MA0153.1	MA0153.1	9.72368e-4
MA0154.1	MA0154.1	0.00355
MA0155.1	MA0155.1	0.304
MA0156.1	MA0156.1	2.62969e-4
MA0157.1	MA0157.1	0.494
MA0159.1	MA0159.1	0.312
MA0160.1	MA0160.1	0.859
MA0162.1	MA0162.1	0.519
MA0163.1	MA0163.1	0.00294
MA0164.1	MA0164.1	0.287
MA0258.1	MA0258.1	0.0068
MA0259.1	MA0259.1	0.0533

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: CNhs11199

Novel motif	Logo	P-value
1	1	0.537
10	10	0.589
100	100	0.982
101	101	0.84
102	102	0.827
103	103	0.334
104	104	0.295
105	105	0.425
106	106	0.0078
107	107	0.063
108	108	0.414
109	109	0.133
11	11	0.487
110	110	0.303
111	111	0.682
112	112	0.108
113	113	0.432
114	114	0.799
115	115	0.738
116	116	0.363
117	117	0.691
118	118	0.75
119	119	0.0686
12	12	0.353
120	120	0.557
121	121	0.421
122	122	0.348
123	123	0.515
124	124	0.138
125	125	0.238
126	126	0.561
127	127	0.76
128	128	0.0229
129	129	0.559
13	13	0.00665
130	130	0.0508
131	131	0.584
132	132	0.974
133	133	0.356
134	134	0.236
135	135	0.3
136	136	0.63
137	137	0.0274
138	138	0.441
139	139	0.879
14	14	0.332
140	140	0.511
141	141	0.825
142	142	0.108
143	143	0.155
144	144	0.38
145	145	0.197
146	146	0.307
147	147	0.88
148	148	0.109
149	149	0.00677
15	15	0.038
150	150	0.409
151	151	0.146
152	152	0.0733
153	153	0.69
154	154	0.826
155	155	0.965
156	156	0.0213
157	157	0.184
158	158	0.922
159	159	0.581
160	160	0.288
161	161	0.509
162	162	0.618
163	163	0.323
164	164	0.266
165	165	0.00137
166	166	0.0881
167	167	0.0874
168	168	0.169
169	169	9.79221e-4
17	17	0.236
18	18	0.543
19	19	0.0132
2	2	0.13
20	20	0.64
21	21	0.0739
22	22	0.139
23	23	0.159
24	24	0.0626
25	25	0.776
26	26	0.0152
27	27	0.439
28	28	0.671
29	29	0.427
3	3	0.242
30	30	0.521
31	31	0.536
32	32	0.00282
33	33	0.974
34	34	0.164
35	35	0.502
36	36	0.457
37	37	0.0763
38	38	0.409
39	39	0.0873
4	4	0.594
40	40	0.143
41	41	0.079
42	42	0.568
43	43	0.238
44	44	0.492
45	45	0.23
46	46	0.263
47	47	0.477
48	48	0.625
49	49	0.477
5	5	0.213
50	50	0.219
51	51	0.468
52	52	0.119
53	53	0.125
54	54	0.489
55	55	0.101
56	56	0.632
57	57	0.672
58	58	0.268
59	59	0.0118
6	6	0.0792
60	60	0.0466
61	61	0.795
62	62	0.151
63	63	0.106
64	64	0.882
65	65	0.292
66	66	0.823
67	67	0.554
68	68	0.987
69	69	0.00625
7	7	0.099
70	70	0.417
71	71	0.0977
72	72	0.649
73	73	0.12
74	74	0.315
75	75	0.455
76	76	0.423
77	77	0.398
78	78	0.0764
79	79	0.825
8	8	0.593
80	80	0.0664
81	81	0.335
82	82	0.188
83	83	0.28
84	84	0.639
85	85	0.0324
86	86	0.446
87	87	0.277
88	88	0.981
89	89	0.471
9	9	0.237
90	90	0.29
91	91	0.0326
92	92	0.326
93	93	0.545
94	94	0.169
95	95	0.259
96	96	0.418
97	97	0.429
98	98	0.523
99	99	0.477

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: CNhs11199

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011471 mouse epididymis and seminiferous tubule- neonate N30 sample

Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship Analyst: Hideya Kawaji link to source data data

UBERON: Anatomy
0000468 (multi-cellular organism)
0000473 (testis)
0000991 (gonad)
0001301 (epididymis)
0001343 (seminiferous tubule of testis)
0000479 (tissue)
0000058 (duct)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0005904 (duct of male reproductive system)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0004175 (internal genitalia)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)
0006947 (male genital duct)
0004054 (internal male genitalia)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011471 (mouse epididymis and seminiferous tubule- neonate N30 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship Analyst: Hideya Kawaji link to source data data
UBERON:0004871 (somatic layer of lateral plate mesoderm)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0007297 (presumptive pronephric mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11199
-|library_id_phase_based=1:CNhs11199
+|library_id_phase_based=2:CNhs11199
 |name=epididymis and seminiferous tubule, neonate N30
 |namespace=FANTOM5
@@ Line 51: / Line 51: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11199,LSID747,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0436855124929327,0.0509235292940968,0.0737106338258954,0,0.137740408373976,0.00075603558037955,0.109575691932061,0,0.0254617646470484,0,0,0.0534011679774342,0.0509235292940968,0,0,0,0.0254617646470484,0,0.0181668308821266,0,0.0254617646470484,0,0,0.0509235292940968,0.210060181764701,0,0,0,0,0,0,0,0.170275364029767,0,0,0,0,0.0179557970775962,0.0588407477925482,-0.025283784632672,0.153258394109673,-0.370351130773767,0.0301299362764574,0,0,0,0.242154123277983,0,0,0,0.0509235292940968,0,0,0.299998574286809,0,0.0717348608105353,0,0,0,0,0.0509235292940968,0.0509235292940968,0.0675515908714646,0,0,0.0509235292940968,0.0128789822039166,0.182796030798038,0.0173128742781772,0.0577392598371827,0,0,0.0292385214405988,0,0.137740408373976,0,0.00188334060087594,-0.0048504391769993,-0.0854602948328802,0.0965723222093523,0.0143359674579554,0,0,0,0,0,-0.00241422514257505,0.158706384620911,-0.001639528943025,0.0509235292940968,0,0,0,0

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FF:1387-42A2: Difference between revisions

From FANTOM5_SSTAR

Revision as of 10:38, 28 November 2014

CNhs11199

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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