Difference between revisions of "FF:482-18D3"

Revision as of 14:50, 16 October 2013

Name:	intestine, embryo E17
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	C57BL/6J
tissue	intestine
dev stage	17 days embryo
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		DRS008857

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
{{{library_id}}}		{{{accession_numbers}}}

Accession ID Mm9

Library id		BAM		CTSS
{{{library_id}}}

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

CNhs10582

MCL coexpression id	Coexpression dpi cluster scores median value
0	0
1	0
10	0
100	0
1000	0.0501
1001	0
1002	0.243
1003	--0.038
1004	0
1005	0.194
1006	--0.0554
1007	--0.0136
1008	0.0872
1009	--0.00584
101	--0.00728
1010	0
1011	--0.0758
1012	0
1013	0.0458
1014	0.16
1015	--0.0332
1016	--0.0214
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	--0.0631
1023	0
1024	--0.00267
1025	0.822
1026	0
1027	0
1028	0
1029	0.332
103	0.0825
1030	0
1031	0.267
1032	0.115
1033	0
1034	0
1035	0
1036	--0.00419
1037	0
1038	0.0039
1039	--0.189
104	0
1040	--0.0454
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: CNhs10582

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.751
MA0003.1	MA0003.1	0.234
MA0004.1	MA0004.1	0.118
MA0006.1	MA0006.1	0.0783
MA0007.1	MA0007.1	0.386
MA0009.1	MA0009.1	0.913
MA0014.1	MA0014.1	0.895
MA0017.1	MA0017.1	5.44395e-35
MA0018.2	MA0018.2	4.04319e-4
MA0019.1	MA0019.1	0.191
MA0024.1	MA0024.1	0.837
MA0025.1	MA0025.1	0.0371
MA0027.1	MA0027.1	0.267
MA0028.1	MA0028.1	0.258
MA0029.1	MA0029.1	0.963
MA0030.1	MA0030.1	0.738
MA0031.1	MA0031.1	0.985
MA0035.2	MA0035.2	1.3355e-7
MA0038.1	MA0038.1	0.297
MA0039.2	MA0039.2	9.50032e-4
MA0040.1	MA0040.1	0.384
MA0041.1	MA0041.1	0.987
MA0042.1	MA0042.1	0.862
MA0043.1	MA0043.1	0.0114
MA0046.1	MA0046.1	1.20518e-94
MA0047.2	MA0047.2	0.00308
MA0048.1	MA0048.1	0.409
MA0050.1	MA0050.1	0.818
MA0051.1	MA0051.1	0.596
MA0052.1	MA0052.1	7.09562e-4
MA0055.1	MA0055.1	0.529
MA0057.1	MA0057.1	0.293
MA0058.1	MA0058.1	0.0107
MA0059.1	MA0059.1	0.782
MA0060.1	MA0060.1	0.00821
MA0061.1	MA0061.1	0.776
MA0062.2	MA0062.2	0.239
MA0065.2	MA0065.2	1.21566e-8
MA0066.1	MA0066.1	0.401
MA0067.1	MA0067.1	0.219
MA0068.1	MA0068.1	0.102
MA0069.1	MA0069.1	0.0553
MA0070.1	MA0070.1	0.354
MA0071.1	MA0071.1	0.801
MA0072.1	MA0072.1	0.614
MA0073.1	MA0073.1	0.958
MA0074.1	MA0074.1	0.0303
MA0076.1	MA0076.1	0.152
MA0077.1	MA0077.1	0.938
MA0078.1	MA0078.1	0.395
MA0079.2	MA0079.2	0.494
MA0080.2	MA0080.2	0.0586
MA0081.1	MA0081.1	0.0497
MA0083.1	MA0083.1	0.0269
MA0084.1	MA0084.1	0.768
MA0087.1	MA0087.1	0.777
MA0088.1	MA0088.1	0.365
MA0090.1	MA0090.1	0.364
MA0091.1	MA0091.1	0.342
MA0092.1	MA0092.1	0.355
MA0093.1	MA0093.1	0.0618
MA0099.2	MA0099.2	0.517
MA0100.1	MA0100.1	0.00519
MA0101.1	MA0101.1	0.545
MA0102.2	MA0102.2	0.287
MA0103.1	MA0103.1	1.8157e-5
MA0104.2	MA0104.2	0.496
MA0105.1	MA0105.1	0.703
MA0106.1	MA0106.1	0.581
MA0107.1	MA0107.1	0.397
MA0108.2	MA0108.2	0.155
MA0111.1	MA0111.1	0.218
MA0112.2	MA0112.2	0.00822
MA0113.1	MA0113.1	0.927
MA0114.1	MA0114.1	1.74528e-44
MA0115.1	MA0115.1	9.13058e-8
MA0116.1	MA0116.1	0.28
MA0117.1	MA0117.1	0.215
MA0119.1	MA0119.1	0.206
MA0122.1	MA0122.1	0.704
MA0124.1	MA0124.1	0.316
MA0125.1	MA0125.1	0.504
MA0131.1	MA0131.1	0.994
MA0135.1	MA0135.1	0.0163
MA0136.1	MA0136.1	0.252
MA0137.2	MA0137.2	0.588
MA0138.2	MA0138.2	0.754
MA0139.1	MA0139.1	0.0153
MA0140.1	MA0140.1	0.0242
MA0141.1	MA0141.1	0.00417
MA0142.1	MA0142.1	0.0471
MA0143.1	MA0143.1	0.165
MA0144.1	MA0144.1	0.0717
MA0145.1	MA0145.1	0.0888
MA0146.1	MA0146.1	0.153
MA0147.1	MA0147.1	0.192
MA0148.1	MA0148.1	3.47321e-4
MA0149.1	MA0149.1	0.243
MA0150.1	MA0150.1	0.191
MA0152.1	MA0152.1	0.855
MA0153.1	MA0153.1	4.47003e-60
MA0154.1	MA0154.1	0.077
MA0155.1	MA0155.1	0.042
MA0156.1	MA0156.1	0.069
MA0157.1	MA0157.1	0.667
MA0159.1	MA0159.1	0.0553
MA0160.1	MA0160.1	0.0298
MA0162.1	MA0162.1	0.196
MA0163.1	MA0163.1	0.0293
MA0164.1	MA0164.1	0.565
MA0258.1	MA0258.1	0.238
MA0259.1	MA0259.1	0.391

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: CNhs10582

Novel motif	Logo	P-value
1	1	0.714
10	10	0.457
100	100	0.363
101	101	0.906
102	102	0.228
103	103	0.643
104	104	0.976
105	105	0.381
106	106	0.0748
107	107	0.151
108	108	0.93
109	109	0.297
11	11	0.609
110	110	0.434
111	111	0.612
112	112	0.0438
113	113	0.186
114	114	0.864
115	115	0.906
116	116	0.483
117	117	0.913
118	118	0.53
119	119	0.897
12	12	0.543
120	120	0.645
121	121	0.702
122	122	0.638
123	123	0.0156
124	124	0.162
125	125	0.908
126	126	0.0344
127	127	0.908
128	128	0.44
129	129	0.933
13	13	4.97818e-5
130	130	0.481
131	131	0.344
132	132	0.459
133	133	0.53
134	134	0.402
135	135	0.311
136	136	0.223
137	137	0.815
138	138	0.0538
139	139	0.227
14	14	0.948
140	140	0.255
141	141	0.221
142	142	0.295
143	143	0.0769
144	144	0.191
145	145	0.208
146	146	0.0564
147	147	0.438
148	148	0.0733
149	149	0.101
15	15	0.761
150	150	0.276
151	151	0.972
152	152	0.0685
153	153	0.13
154	154	0.257
155	155	0.837
156	156	0.914
157	157	0.636
158	158	0.828
159	159	0.0636
160	160	0.0505
161	161	0.495
162	162	0.629
163	163	0.364
164	164	0.586
165	165	0.592
166	166	0.621
167	167	0.662
168	168	0.229
169	169	0.115
17	17	0.334
18	18	0.0511
19	19	0.0281
2	2	0.181
20	20	0.618
21	21	0.94
22	22	0.227
23	23	0.725
24	24	0.443
25	25	0.975
26	26	0.0253
27	27	0.587
28	28	0.579
29	29	0.621
3	3	0.657
30	30	0.273
31	31	0.988
32	32	0.307
33	33	0.299
34	34	0.31
35	35	0.436
36	36	0.849
37	37	0.23
38	38	0.63
39	39	0.244
4	4	0.306
40	40	0.0994
41	41	0.348
42	42	0.782
43	43	0.502
44	44	0.567
45	45	0.0778
46	46	0.702
47	47	0.807
48	48	0.687
49	49	0.811
5	5	0.662
50	50	0.351
51	51	0.874
52	52	0.0195
53	53	0.664
54	54	0.754
55	55	0.0547
56	56	0.497
57	57	0.122
58	58	0.729
59	59	0.362
6	6	0.962
60	60	0.0728
61	61	0.409
62	62	0.541
63	63	0.604
64	64	0.719
65	65	0.502
66	66	0.86
67	67	0.0663
68	68	0.584
69	69	0.582
7	7	0.0659
70	70	0.664
71	71	0.113
72	72	0.446
73	73	0.419
74	74	0.818
75	75	0.504
76	76	0.473
77	77	0.0201
78	78	0.113
79	79	0.562
8	8	0.734
80	80	0.377
81	81	0.629
82	82	0.795
83	83	0.356
84	84	0.498
85	85	0.382
86	86	0.472
87	87	0.895
88	88	0.553
89	89	0.209
9	9	0.722
90	90	0.785
91	91	0.333
92	92	0.612
93	93	0.618
94	94	0.0714
95	95	0.657
96	96	0.384
97	97	0.343
98	98	0.958
99	99	0.0718

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: CNhs10582

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011370 mouse intestine- embryo E17 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)
0000922 (embryo)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal 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)
0011370 (mouse intestine- 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:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

{{{1}}} Accession numbers

Method		Sample accession id
{{{2}}}

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
{{{4}}}		{{{3}}}

Accession ID

Library id		BAM		CTSS
{{{4}}}

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@DRS008857
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000160,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001555,UBERON:0005409
 |ancestors_in_cell_lineage_facet=
@@ Line 41: / Line 42: @@
 |is_a=EFO:0002091;;FF:0011370
 |is_obsolete=
+|library_ids=CNhs10582
 |name=intestine, embryo E17
 |namespace=FANTOM5
@@ Line 83: / Line 85: @@
 |top_motifs=HNF4A_NR2F1,2:1.96046446143;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.86739970724;HNF1A:1.47459817942;ESRRA:1.35045284726;PDX1:1.34846376521;SREBF1,2:1.26301938913;ATF6:1.22953251441;MYBL2:1.19862521038;ZNF423:1.16658418045;GZF1:1.14911292266;SNAI1..3:1.11398221191;GFI1:1.01390172308;XCPE1{core}:0.970665290228;CDX1,2,4:0.969006126412;NFIX:0.848353883456;SRF:0.836311267054;TOPORS:0.814722545511;FOXM1:0.778624921923;NR6A1:0.768804757802;TLX1..3_NFIC{dimer}:0.709102019086;ZEB1:0.692651071621;ZNF238:0.648293583632;NFY{A,B,C}:0.643668556089;TLX2:0.630030114458;ZNF148:0.622008862701;DMAP1_NCOR{1,2}_SMARC:0.608735237602;RXRA_VDR{dimer}:0.598481696126;MAZ:0.589445285175;NANOG:0.588816232337;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.506211679936;LEF1_TCF7_TCF7L1,2:0.479054037113;SP1:0.468811087164;ADNP_IRX_SIX_ZHX:0.455378949257;TBX4,5:0.41331335929;GATA6:0.412602417501;HIF1A:0.401985887264;NKX2-1,4:0.386889813362;RBPJ:0.383087832058;TFAP4:0.321880583731;ESR1:0.317546287609;GTF2I:0.272502512501;STAT1,3:0.268281529642;FOXA2:0.267360033739;PAX6:0.251541906221;ETS1,2:0.247047437155;PRRX1,2:0.245591831414;CUX2:0.233802128066;TEAD1:0.21933208804;GTF2A1,2:0.189963300659;TFCP2:0.184183389343;POU6F1:0.182311772723;EVI1:0.180727445412;TBP:0.174808537039;RXR{A,B,G}:0.174782715985;NKX3-1:0.162381335193;E2F1..5:0.155618717714;EP300:0.154614456446;RREB1:0.143594937698;VSX1,2:0.140086564525;HMGA1,2:0.139074685909;PAX2:0.138405570828;LMO2:0.137702392733;FOXQ1:0.135212603323;FOX{D1,D2}:0.135192905063;IKZF2:0.131975396581;GFI1B:0.112916051029;ELF1,2,4:0.111550530463;AR:0.097364026128;NANOG{mouse}:0.0938187295026;ARID5B:0.0728760642143;FOX{I1,J2}:0.0675340508524;HIC1:0.0402351237973;PATZ1:0.0360972666796;T:0.0301704811793;REST:0.0179577082468;CDC5L:0.0129818391004;TP53:0.00995925039542;IKZF1:0.00837630522564;FOXN1:0.00671964651892;STAT2,4,6:0.00122982500114;TFDP1:-0.00466891306488;FOSL2:-0.0066354710463;IRF1,2:-0.0169028431502;NR1H4:-0.0210201262121;NKX3-2:-0.0263179758678;ALX4:-0.0267580685482;HMX1:-0.0323824900445;MYOD1:-0.0342810312293;DBP:-0.0383149730198;ZNF143:-0.0553571461912;ZNF384:-0.0594445163762;ONECUT1,2:-0.0752371587519;EBF1:-0.10435079662;GLI1..3:-0.109371477655;POU1F1:-0.109709435631;LHX3,4:-0.116962582496;SMAD1..7,9:-0.131075785324;HBP1_HMGB_SSRP1_UBTF:-0.139392079489;NR5A1,2:-0.144350324503;NFKB1_REL_RELA:-0.150299074051;SPIB:-0.156593014511;PAX8:-0.16427308949;PBX1:-0.170951877816;PAX1,9:-0.173276928011;FOS_FOS{B,L1}_JUN{B,D}:-0.180766975356;SOX17:-0.190031412281;BREu{core}:-0.201158929341;ELK1,4_GABP{A,B1}:-0.202074366642;SPZ1:-0.212915263601;PPARG:-0.215974918016;FOX{F1,F2,J1}:-0.218121359535;bHLH_family:-0.22723227301;AIRE:-0.228857893354;ZBTB6:-0.235438214357;MZF1:-0.240007751605;MED-1{core}:-0.254208466867;FOXP1:-0.258791717206;GCM1,2:-0.268982358311;SPI1:-0.293166677466;IRF7:-0.294526583509;ATF2:-0.295570401257;AHR_ARNT_ARNT2:-0.297578235486;HAND1,2:-0.300575140447;POU3F1..4:-0.306437942823;KLF4:-0.313565484926;MYFfamily:-0.323949478106;OCT4_SOX2{dimer}:-0.349550185386;BPTF:-0.360659834303;GATA4:-0.373919610433;HES1:-0.377608716162;ATF5_CREB3:-0.379377032861;TFAP2B:-0.388401008593;SOX5:-0.391891791623;NKX2-3_NKX2-5:-0.392777813743;ZIC1..3:-0.397072186327;FOXL1:-0.398999932185;MYB:-0.403870570353;SOX2:-0.411081502378;SOX{8,9,10}:-0.413208082893;MTF1:-0.421743486959;NRF1:-0.432398554212;HLF:-0.432399213773;RUNX1..3:-0.434225965247;PRDM1:-0.445070196783;PAX4:-0.452345928962;YY1:-0.467987813741;ZFP161:-0.474845554097;JUN:-0.47720063329;STAT5{A,B}:-0.477958412434;FOXD3:-0.479276233961;RFX1:-0.483442223027;CREB1:-0.507778418116;EN1,2:-0.511506250298;POU2F1..3:-0.512019362757;FOXO1,3,4:-0.525153034161;EGR1..3:-0.53444419991;CEBPA,B_DDIT3:-0.542707978342;ZBTB16:-0.572885017979;TFAP2{A,C}:-0.573214122038;TGIF1:-0.574459783734;NHLH1,2:-0.610327926076;MEF2{A,B,C,D}:-0.611126852218;RORA:-0.626041860439;MTE{core}:-0.637069522816;PAX5:-0.646667947254;TEF:-0.672143439255;CRX:-0.673258727914;PITX1..3:-0.698616749528;NKX2-2,8:-0.705869836918;MAFB:-0.741917384962;UFEwm:-0.756810073934;NFE2:-0.7662788409;NFE2L2:-0.766655566304;NKX6-1,2:-0.769190894485;HOXA9_MEIS1:-0.787385087508;BACH2:-0.787512182853;TAL1_TCF{3,4,12}:-0.795377919054;ATF4:-0.815400009139;NR3C1:-0.858846200494;NFATC1..3:-0.865463773529;HSF1,2:-0.902124309072;RFX2..5_RFXANK_RFXAP:-0.937910247808;POU5F1:-0.944341569092;HOX{A5,B5}:-0.97125195644;FOXP3:-1.08912162224;NFE2L1:-1.15024304607;NFIL3:-1.43763966688;ALX1:-1.45218749499;HOX{A4,D4}:-1.65678469178
 |xref=
+}} {{DRAAccessionNumbers
+|DRA_sample_Accession=CAGE@DRS008857
+|accession_numbers=DRX008994;DRR009868;DRZ001293;DRZ002676;CAGE
+|library_id=CNhs10582
 }}

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Revision as of 14:50, 16 October 2013

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