Difference between revisions of "FF:11711-123C1"

Revision as of 13:30, 27 June 2012

Name:	Mouse Cardiac Myocytes, donor1
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	NA
tissue	heart
dev stage	NA
sex	NA
age	NA
cell type	cardiac muscle cell
cell line	NA
company	Sciencell/3H
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

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

CNhs12355

MCL coexpression id	Coexpression dpi cluster scores median value
0	0
1	0
10	0
100	0
1000	0.0639
1001	--0.00986
1002	0.425
1003	0.14
1004	0
1005	0
1006	--0.302
1007	--0.201
1008	0
1009	0.56
101	--0.0743
1010	0
1011	--0.198
1012	0
1013	0.0555
1014	0.00488
1015	--0.0304
1016	0.106
1017	0
1018	0
1019	0
102	0
1020	0.18
1021	0.0994
1022	--0.0704
1023	0
1024	--0.14
1025	0
1026	0
1027	0
1028	0.0994
1029	--0.12
103	0.549
1030	0
1031	0.732
1032	0.0785
1033	--0.0752
1034	0
1035	0
1036	--0.0803
1037	0
1038	-5.64625e-4
1039	--0.154
104	0
1040	0.526
1041	0

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 no result for this sample

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 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: CNhs12355

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.314
MA0003.1	MA0003.1	0.305
MA0004.1	MA0004.1	0.863
MA0006.1	MA0006.1	0.203
MA0007.1	MA0007.1	0.00826
MA0009.1	MA0009.1	0.735
MA0014.1	MA0014.1	0.392
MA0017.1	MA0017.1	0.00911
MA0018.2	MA0018.2	0.0607
MA0019.1	MA0019.1	0.458
MA0024.1	MA0024.1	0.00165
MA0025.1	MA0025.1	0.727
MA0027.1	MA0027.1	0.187
MA0028.1	MA0028.1	0.11
MA0029.1	MA0029.1	0.806
MA0030.1	MA0030.1	0.209
MA0031.1	MA0031.1	0.43
MA0035.2	MA0035.2	0.0121
MA0038.1	MA0038.1	0.1
MA0039.2	MA0039.2	0.115
MA0040.1	MA0040.1	0.0315
MA0041.1	MA0041.1	0.473
MA0042.1	MA0042.1	0.686
MA0043.1	MA0043.1	0.54
MA0046.1	MA0046.1	3.88064e-9
MA0047.2	MA0047.2	0.0084
MA0048.1	MA0048.1	0.0733
MA0050.1	MA0050.1	0.0038
MA0051.1	MA0051.1	0.125
MA0052.1	MA0052.1	0.27
MA0055.1	MA0055.1	0.0107
MA0057.1	MA0057.1	0.0583
MA0058.1	MA0058.1	0.648
MA0059.1	MA0059.1	0.64
MA0060.1	MA0060.1	1.52606e-10
MA0061.1	MA0061.1	0.131
MA0062.2	MA0062.2	0.0877
MA0065.2	MA0065.2	0.807
MA0066.1	MA0066.1	0.492
MA0067.1	MA0067.1	0.841
MA0068.1	MA0068.1	0.0423
MA0069.1	MA0069.1	0.238
MA0070.1	MA0070.1	0.626
MA0071.1	MA0071.1	0.569
MA0072.1	MA0072.1	0.923
MA0073.1	MA0073.1	0.332
MA0074.1	MA0074.1	0.503
MA0076.1	MA0076.1	0.571
MA0077.1	MA0077.1	0.846
MA0078.1	MA0078.1	0.496
MA0079.2	MA0079.2	0.00735
MA0080.2	MA0080.2	0.289
MA0081.1	MA0081.1	0.708
MA0083.1	MA0083.1	1.65715e-4
MA0084.1	MA0084.1	0.545
MA0087.1	MA0087.1	0.712
MA0088.1	MA0088.1	0.516
MA0090.1	MA0090.1	2.72667e-4
MA0091.1	MA0091.1	0.0523
MA0092.1	MA0092.1	0.164
MA0093.1	MA0093.1	0.812
MA0099.2	MA0099.2	5.91583e-9
MA0100.1	MA0100.1	0.985
MA0101.1	MA0101.1	0.0114
MA0102.2	MA0102.2	0.646
MA0103.1	MA0103.1	6.49974e-7
MA0104.2	MA0104.2	0.239
MA0105.1	MA0105.1	0.405
MA0106.1	MA0106.1	4.17265e-4
MA0107.1	MA0107.1	0.0249
MA0108.2	MA0108.2	0.0793
MA0111.1	MA0111.1	0.927
MA0112.2	MA0112.2	0.0181
MA0113.1	MA0113.1	0.0218
MA0114.1	MA0114.1	0.02
MA0115.1	MA0115.1	0.0909
MA0116.1	MA0116.1	0.776
MA0117.1	MA0117.1	0.238
MA0119.1	MA0119.1	0.171
MA0122.1	MA0122.1	0.745
MA0124.1	MA0124.1	0.253
MA0125.1	MA0125.1	0.0292
MA0131.1	MA0131.1	0.559
MA0135.1	MA0135.1	0.343
MA0136.1	MA0136.1	0.35
MA0137.2	MA0137.2	0.299
MA0138.2	MA0138.2	0.00114
MA0139.1	MA0139.1	0.432
MA0140.1	MA0140.1	0.0253
MA0141.1	MA0141.1	0.287
MA0142.1	MA0142.1	0.012
MA0143.1	MA0143.1	0.709
MA0144.1	MA0144.1	0.0091
MA0145.1	MA0145.1	0.0534
MA0146.1	MA0146.1	0.0195
MA0147.1	MA0147.1	0.263
MA0148.1	MA0148.1	0.0864
MA0149.1	MA0149.1	0.966
MA0150.1	MA0150.1	0.00453
MA0152.1	MA0152.1	0.827
MA0153.1	MA0153.1	3.88925e-8
MA0154.1	MA0154.1	0.0423
MA0155.1	MA0155.1	0.915
MA0156.1	MA0156.1	0.0268
MA0157.1	MA0157.1	0.386
MA0159.1	MA0159.1	0.171
MA0160.1	MA0160.1	0.269
MA0162.1	MA0162.1	0.195
MA0163.1	MA0163.1	0.174
MA0164.1	MA0164.1	0.706
MA0258.1	MA0258.1	0.565
MA0259.1	MA0259.1	0.983

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: CNhs12355

Novel motif	Logo	P-value
1	1	0.879
10	10	0.222
100	100	0.478
101	101	0.395
102	102	0.128
103	103	0.817
104	104	0.233
105	105	0.402
106	106	0.0116
107	107	0.369
108	108	0.564
109	109	0.0228
11	11	0.474
110	110	0.199
111	111	0.856
112	112	0.94
113	113	0.471
114	114	0.282
115	115	0.957
116	116	0.0829
117	117	0.0643
118	118	0.886
119	119	0.679
12	12	0.912
120	120	0.402
121	121	0.353
122	122	0.0654
123	123	0.795
124	124	0.494
125	125	0.118
126	126	0.119
127	127	0.0399
128	128	0.0261
129	129	0.241
13	13	0.0737
130	130	0.991
131	131	0.0884
132	132	0.188
133	133	0.201
134	134	0.82
135	135	0.756
136	136	0.033
137	137	0.718
138	138	0.904
139	139	0.817
14	14	0.334
140	140	0.507
141	141	0.318
142	142	0.826
143	143	0.0755
144	144	0.217
145	145	0.237
146	146	0.717
147	147	0.315
148	148	0.983
149	149	0.00557
15	15	0.128
150	150	0.041
151	151	0.612
152	152	0.00866
153	153	0.744
154	154	0.768
155	155	0.186
156	156	0.997
157	157	0.451
158	158	0.698
159	159	0.0776
160	160	0.924
161	161	0.471
162	162	0.392
163	163	0.436
164	164	0.296
165	165	0.37
166	166	0.761
167	167	0.539
168	168	0.709
169	169	0.0198
17	17	0.32
18	18	0.36
19	19	0.0392
2	2	0.383
20	20	0.221
21	21	0.14
22	22	0.139
23	23	0.324
24	24	0.0677
25	25	0.154
26	26	0.0479
27	27	0.287
28	28	0.61
29	29	0.0278
3	3	0.377
30	30	0.36
31	31	0.807
32	32	0.154
33	33	0.95
34	34	0.957
35	35	0.255
36	36	0.556
37	37	0.0312
38	38	0.423
39	39	0.164
4	4	0.323
40	40	0.684
41	41	0.992
42	42	0.543
43	43	0.0674
44	44	0.337
45	45	0.931
46	46	0.657
47	47	0.722
48	48	0.942
49	49	0.92
5	5	0.933
50	50	0.11
51	51	0.696
52	52	0.528
53	53	0.735
54	54	0.546
55	55	0.987
56	56	0.819
57	57	0.796
58	58	0.534
59	59	0.0171
6	6	0.429
60	60	0.465
61	61	0.362
62	62	0.954
63	63	0.352
64	64	0.37
65	65	0.224
66	66	0.796
67	67	0.81
68	68	0.145
69	69	0.984
7	7	0.957
70	70	0.0158
71	71	0.2
72	72	0.771
73	73	0.0016
74	74	0.464
75	75	0.161
76	76	0.667
77	77	0.0415
78	78	0.023
79	79	0.223
8	8	0.623
80	80	0.0224
81	81	0.819
82	82	0.987
83	83	0.629
84	84	0.854
85	85	0.145
86	86	0.572
87	87	0.00877
88	88	0.297
89	89	0.78
9	9	0.774
90	90	0.881
91	91	0.523
92	92	0.0978
93	93	0.575
94	94	0.796
95	95	0.00142
96	96	0.203
97	97	0.264
98	98	0.406
99	99	0.898

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: CNhs12355

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000106 mouse cardiac myocyte 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)
0000055 (non-terminally differentiated cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0000034 (stem cell)
0000680 (muscle precursor cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0000393 (electrically responsive cell)
0000183 (contractile cell)
0000187 (muscle cell)
0000211 (electrically active cell)
0000056 (myoblast)
0000255 (eukaryotic cell)
0002494 (cardiocyte)
0000737 (striated muscle cell)
0000222 (mesodermal cell)
0000746 (cardiac muscle cell)
0000355 (multi-potent skeletal muscle stem cell)
0000513 (cardiac muscle myoblast)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0007100 (primary circulatory organ)
0001134 (skeletal muscle tissue)
0000948 (heart)
0002100 (trunk)
0000483 (epithelium)
0000926 (mesoderm)
0000479 (tissue)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0003914 (epithelial tube)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0003103 (compound organ)
0005291 (embryonic tissue)
0002036 (striated muscle tissue)
0002385 (muscle tissue)
0000486 (multilaminar epithelium)
0003104 (mesenchyme)
0005256 (trunk mesenchyme)
0001048 (primordium)
0006598 (presumptive structure)
0001015 (musculature)
0002532 (epiblast (generic))
0002329 (somite)
0002204 (musculoskeletal system)
0004535 (cardiovascular system)
0000383 (musculature of body)
0005498 (primitive heart tube)
0003077 (paraxial mesoderm)
0004290 (dermomyotome)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0001009 (circulatory system)
0004140 (primary heart field)
0009881 (anterior lateral plate mesoderm)
0006603 (presumptive mesoderm)
0004141 (heart tube)
0003082 (myotome)
0004872 (splanchnic layer of lateral plate mesoderm)
0003084 (heart primordium)
0003059 (presomitic mesoderm)
0007282 (presumptive segmental plate)
0009618 (trunk paraxial mesoderm)
0007285 (presumptive paraxial mesoderm)
0007005 (cardiac mesoderm)
0004139 (cardiogenic plate)
0004291 (heart rudiment)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data
NA

@@ Line 36: / Line 36: @@
 |has_quality=
 |id=FF:11711-123C1
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000106
+|is_a=EFO:0002091;;FF:0000106
+|is_obsolete=
 |name=Mouse Cardiac Myocytes, donor1
 |namespace=FANTOM5
@@ Line 76: / Line 77: @@
 |sample_tissue=heart
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+|xref=
 }}

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Revision as of 13:30, 27 June 2012

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	Mozilla Cavendish Theme based on Cavendish style by Gabriel Wicke modified by DaSch for the Web Community Wiki github Projectpage – Report Bug – Skin-Version: 2.3.5