Personal tools

Difference between revisions of "FF:1265-44F5"

From FANTOM5_SSTAR

Jump to: navigation, search
 
Line 1: Line 1:
 
{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005078
 
|DRA_sample_Accession=CAGE@SAMD00005078
|accession_numbers=CAGE;DRX009072;DRR009946;DRZ001371;DRZ002754
+
|accession_numbers=CAGE;DRX009072;DRR009946;DRZ001371;DRZ002754;DRZ012721;DRZ014104
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000007,UBERON:0001894,UBERON:0000479,UBERON:0004121,UBERON:0003296,UBERON:0010133,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0002616,UBERON:0002780,UBERON:0002530,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001890,UBERON:0000949
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000007,UBERON:0001894,UBERON:0000479,UBERON:0004121,UBERON:0003296,UBERON:0010133,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0002616,UBERON:0002780,UBERON:0002530,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001890,UBERON:0000949
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=

Latest revision as of 12:50, 10 August 2017


Name:pituitary gland, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs11039
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuepituitary gland
dev stage17 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005078
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11039 CAGE DRX009072 DRR009946
Accession ID Mm9

Library idBAMCTSS
CNhs11039 DRZ001371 DRZ002754
Accession ID Mm10

Library idBAMCTSS
CNhs11039 DRZ012721 DRZ014104
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11039

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.174
10 0
100 0.0662
1000 --0.0024
1001 0
1002 0.197
1003 0.0914
1004 0.328
1005 0
1006 0.13
1007 0.0213
1008 0
1009 0.0549
101 --0.0628
1010 0
1011 0.016
1012 0.0662
1013 0.069
1014 0.402
1015 0.179
1016 0.236
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0176
1023 0
1024 0.142
1025 0.00503
1026 0
1027 0.213
1028 0
1029 0.105
103 0.473
1030 0
1031 0.492
1032 0.0203
1033 0.124
1034 0
1035 0
1036 0.0313
1037 0
1038 0.00635
1039 --0.0425
104 0
1040 0.106
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



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: CNhs11039

Jaspar motif P-value
MA0002.2 2.98391e-7
MA0003.1 0.177
MA0004.1 0.506
MA0006.1 0.501
MA0007.1 0.543
MA0009.1 0.805
MA0014.1 0.535
MA0017.1 1.98568e-9
MA0018.2 0.044
MA0019.1 0.697
MA0024.1 0.312
MA0025.1 0.454
MA0027.1 0.804
MA0028.1 0.777
MA0029.1 0.967
MA0030.1 0.869
MA0031.1 0.852
MA0035.2 0.0013
MA0038.1 0.183
MA0039.2 0.368
MA0040.1 0.337
MA0041.1 0.37
MA0042.1 0.735
MA0043.1 0.0664
MA0046.1 1.12868e-25
MA0047.2 0.00289
MA0048.1 0.249
MA0050.1 0.0426
MA0051.1 0.0711
MA0052.1 1.50423e-6
MA0055.1 0.781
MA0057.1 0.156
MA0058.1 0.468
MA0059.1 0.178
MA0060.1 1.38505e-4
MA0061.1 0.0287
MA0062.2 0.177
MA0065.2 1.88112e-6
MA0066.1 0.00528
MA0067.1 0.724
MA0068.1 0.0623
MA0069.1 0.163
MA0070.1 0.929
MA0071.1 0.016
MA0072.1 0.0358
MA0073.1 0.713
MA0074.1 0.202
MA0076.1 0.66
MA0077.1 0.524
MA0078.1 0.139
MA0079.2 0.173
MA0080.2 3.30083e-9
MA0081.1 0.192
MA0083.1 0.103
MA0084.1 0.377
MA0087.1 0.859
MA0088.1 0.303
MA0090.1 0.114
MA0091.1 0.918
MA0092.1 0.558
MA0093.1 0.586
MA0099.2 4.26099e-5
MA0100.1 0.51
MA0101.1 0.0547
MA0102.2 0.926
MA0103.1 0.29
MA0104.2 0.465
MA0105.1 0.00188
MA0106.1 0.144
MA0107.1 0.0338
MA0108.2 0.49
MA0111.1 0.781
MA0112.2 2.22011e-7
MA0113.1 0.951
MA0114.1 5.15379e-8
MA0115.1 2.84069e-7
MA0116.1 0.0106
MA0117.1 0.805
MA0119.1 0.0786
MA0122.1 0.999
MA0124.1 0.792
MA0125.1 0.0375
MA0131.1 0.566
MA0135.1 0.569
MA0136.1 2.27311e-8
MA0137.2 0.0713
MA0138.2 0.945
MA0139.1 0.16
MA0140.1 7.87287e-4
MA0141.1 5.36801e-4
MA0142.1 0.8
MA0143.1 0.92
MA0144.1 0.102
MA0145.1 0.218
MA0146.1 0.091
MA0147.1 0.395
MA0148.1 0.00153
MA0149.1 0.00882
MA0150.1 2.83872e-4
MA0152.1 0.498
MA0153.1 4.02288e-22
MA0154.1 0.0125
MA0155.1 0.922
MA0156.1 0.00228
MA0157.1 0.871
MA0159.1 7.62718e-4
MA0160.1 0.00165
MA0162.1 0.298
MA0163.1 1.6014e-4
MA0164.1 0.624
MA0258.1 3.24227e-5
MA0259.1 0.814



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: CNhs11039

Novel motif P-value
1 0.0623
10 0.0638
100 0.748
101 0.585
102 0.992
103 0.149
104 0.522
105 0.593
106 0.0129
107 0.0583
108 0.837
109 0.111
11 0.117
110 0.0641
111 0.0127
112 0.0416
113 0.755
114 0.0572
115 0.664
116 0.379
117 0.013
118 0.415
119 0.0839
12 0.652
120 0.694
121 0.42
122 0.488
123 0.875
124 0.853
125 0.242
126 0.131
127 0.0561
128 0.0265
129 0.144
13 0.00703
130 0.598
131 0.935
132 0.626
133 0.497
134 0.722
135 0.142
136 0.929
137 0.8
138 0.535
139 0.0345
14 0.614
140 0.0185
141 0.623
142 0.288
143 0.85
144 0.636
145 0.113
146 0.447
147 0.999
148 0.584
149 0.441
15 0.0655
150 0.171
151 0.345
152 0.2
153 0.993
154 0.715
155 0.585
156 1.90575e-5
157 0.735
158 0.205
159 0.925
160 0.538
161 0.557
162 0.893
163 0.0825
164 0.0451
165 0.0562
166 0.49
167 0.0991
168 0.657
169 5.16478e-4
17 0.143
18 0.47
19 0.157
2 0.958
20 0.598
21 0.835
22 0.247
23 0.372
24 0.318
25 0.364
26 0.012
27 0.6
28 0.425
29 0.0931
3 0.165
30 0.981
31 0.65
32 0.491
33 0.266
34 0.777
35 0.381
36 0.234
37 0.0525
38 0.469
39 0.634
4 0.363
40 0.354
41 0.055
42 0.425
43 0.0869
44 0.0913
45 0.51
46 0.0738
47 0.26
48 0.0921
49 0.0951
5 0.0551
50 0.844
51 0.507
52 0.26
53 0.973
54 0.441
55 0.283
56 0.545
57 0.435
58 0.318
59 0.081
6 0.725
60 0.0284
61 0.261
62 0.0734
63 0.106
64 0.428
65 0.22
66 0.768
67 0.69
68 0.1
69 0.662
7 0.0625
70 0.0217
71 0.0265
72 0.378
73 0.0789
74 0.47
75 0.0648
76 0.837
77 0.238
78 0.00575
79 0.769
8 0.0445
80 0.183
81 0.489
82 0.174
83 0.293
84 0.212
85 0.0447
86 0.154
87 0.549
88 0.488
89 0.232
9 0.56
90 0.252
91 0.263
92 0.192
93 0.0274
94 0.226
95 0.163
96 0.197
97 0.787
98 0.414
99 0.629



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: CNhs11039


FANTOM5 (FF) ontology


Direct parent terms


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)
0000922 (embryo)
0000955 (brain)
0000007 (pituitary gland)
0001894 (diencephalon)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0003296 (gland of diencephalon)
0010133 (neuroendocrine gland)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001890 (forebrain)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000300 (mouse embryonic day 17 sample)
0011519 (mouse pituitary gland- embryo E17 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:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)