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|top_motifs=FOXO1,3,4:3.01034917163;FOX{D1,D2}:2.86433199852;FOX{I1,J2}:2.79800830549;FOXN1:2.62885401585;EBF1:2.33736098;TLX2:2.22001709873;IRF1,2:2.13243928931;HBP1_HMGB_SSRP1_UBTF:1.96655731406;ETS1,2:1.83949157054;STAT2,4,6:1.70831318039;EP300:1.69482030589;SPIB:1.65834895896;NFIL3:1.55103911027;BPTF:1.50320335024;NFATC1..3:1.47783745929;XCPE1{core}:1.43204409422;RFX2..5_RFXANK_RFXAP:1.347787049;SP1:1.30646945252;TEAD1:1.23126164988;T:1.22999651315;SPI1:1.17071685805;ELF1,2,4:1.13574740295;ZNF148:1.09743530907;DMAP1_NCOR{1,2}_SMARC:1.07597694188;TLX1..3_NFIC{dimer}:1.05496265159;IRF7:1.01977083977;TBX4,5:0.962352650919;POU2F1..3:0.94663552462;HAND1,2:0.928982845409;BACH2:0.927847490583;ZEB1:0.919061100332;CEBPA,B_DDIT3:0.901301696493;IKZF2:0.895871627603;IKZF1:0.870382525242;TFCP2:0.829771709891;NKX2-1,4:0.820390331124;TOPORS:0.78583606179;SNAI1..3:0.773480615504;SPZ1:0.772914686895;GZF1:0.760425200058;GTF2A1,2:0.735930906225;NFIX:0.726264569069;TFAP4:0.714595854844;MYBL2:0.705645885415;AR:0.674931264953;RUNX1..3:0.663042091602;SMAD1..7,9:0.634188013939;FOXA2:0.633375632411;HMX1:0.601200396825;MTF1:0.580706771617;PRDM1:0.537292889721;RFX1:0.533563268835;NFE2L1:0.498584769289;RXRA_VDR{dimer}:0.497925122138;STAT5{A,B}:0.496923951978;TFAP2B:0.477565319373;FOS_FOS{B,L1}_JUN{B,D}:0.461805651955;NFKB1_REL_RELA:0.444097211379;SRF:0.420437022741;TGIF1:0.415403595623;FOX{F1,F2,J1}:0.386862065486;FOXQ1:0.379824602217;MAZ:0.364694950241;TFAP2{A,C}:0.329184898367;NKX3-1:0.294898295018;ESR1:0.286117325579;GTF2I:0.243494953492;RBPJ:0.238133406495;NFE2L2:0.217639499811;MEF2{A,B,C,D}:0.211408038543;FOSL2:0.202577522405;ZNF384:0.201221869383;GCM1,2:0.186329651708;PAX5:0.174984992497;HIC1:0.168828122544;JUN:0.160203902611;ZNF423:0.156384511668;NR1H4:0.153097470371;SREBF1,2:0.0974005875516;FOXP1:0.0919388415126;POU5F1:0.0829282801425;FOXD3:0.0672692063648;GATA6:0.0590717149424;CRX:0.0551469359862;GLI1..3:0.0246734689712;ATF6:0.0213460544777;MYOD1:0.0107688292444;ZNF238:0.00804727699302;MYFfamily:-0.00763525423161;TP53:-0.0251820569897;PATZ1:-0.0303455370048;RREB1:-0.0490010217856;NKX3-2:-0.0591072028974;NKX2-2,8:-0.0629451890303;STAT1,3:-0.089458702809;HLF:-0.119867570764;EGR1..3:-0.143784726531;RXR{A,B,G}:-0.145977075557;SOX5:-0.146879891606;ALX1:-0.160254677317;GFI1B:-0.168567898149;MED-1{core}:-0.186518291926;ZFP161:-0.199894261148;SOX2:-0.223585981094;TBP:-0.265996718703;NKX2-3_NKX2-5:-0.275655051702;PPARG:-0.283271460844;NHLH1,2:-0.289277151709;HNF4A_NR2F1,2:-0.316029040077;ZBTB6:-0.325521584558;GATA4:-0.325610795531;TFDP1:-0.337965143299;HNF1A:-0.35629021915;ALX4:-0.368509736875;HMGA1,2:-0.374434594474;LMO2:-0.378982091617;ATF2:-0.390573494609;ATF4:-0.39972866542;REST:-0.425577591319;bHLH_family:-0.427800016498;SOX{8,9,10}:-0.475727363945;MYB:-0.484162220575;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.505068971803;ZIC1..3:-0.511770791859;NFE2:-0.520141454363;GFI1:-0.524036598592;MZF1:-0.532606843995;MTE{core}:-0.561592322299;MAFB:-0.572082968288;ZBTB16:-0.598292439119;PITX1..3:-0.604165134955;HOX{A5,B5}:-0.60978155733;PBX1:-0.61993355329;FOXP3:-0.623775484787;CREB1:-0.62884963766;PAX1,9:-0.64486170729;PAX2:-0.651644819225;ADNP_IRX_SIX_ZHX:-0.656776260698;POU6F1:-0.661330724581;ATF5_CREB3:-0.694752580518;KLF4:-0.706655139625;LEF1_TCF7_TCF7L1,2:-0.710600670569;AHR_ARNT_ARNT2:-0.727171042292;PAX6:-0.728679482385;NR3C1:-0.73163262844;BREu{core}:-0.734210884883;NKX6-1,2:-0.74014348901;PAX4:-0.766067850809;DBP:-0.798496583742;AIRE:-0.808541664216;PDX1:-0.820425086861;HSF1,2:-0.8211335047;ELK1,4_GABP{A,B1}:-0.850678462638;SOX17:-0.857592740691;FOXM1:-0.911579399226;E2F1..5:-0.921967803943;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.938293636651;LHX3,4:-0.944353367806;CUX2:-0.991000356925;NANOG:-0.99608628711;ARID5B:-0.996740590354;PRRX1,2:-1.00310116185;TEF:-1.0123867206;NR6A1:-1.03971097175;NRF1:-1.10175637472;ESRRA:-1.10340800501;HIF1A:-1.22149871385;FOXL1:-1.26978360793;VSX1,2:-1.2792486085;CDX1,2,4:-1.35424372138;OCT4_SOX2{dimer}:-1.39583988333;CDC5L:-1.41234812567;UFEwm:-1.45505173211;TAL1_TCF{3,4,12}:-1.47248570397;HOX{A4,D4}:-1.47780908375;NFY{A,B,C}:-1.48968129045;ONECUT1,2:-1.51596331362;NR5A1,2:-1.52500019402;RORA:-1.53529171198;HOXA9_MEIS1:-1.61420615454;EVI1:-1.62877534909;EN1,2:-1.65854085888;POU3F1..4:-1.66958854754;ZNF143:-1.79163831129;PAX8:-1.90292039046;YY1:-2.04062216802;POU1F1:-2.18573110424;HES1:-2.26305901727;NANOG{mouse}:-2.45772797336
 
}}
 
}}

Revision as of 06:19, 15 February 2012


Name:lung, adult, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
dev stageadult
sexmale
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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs10474

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0382
1001 0.171
1002 0.00476
1003 0.192
1004 0
1005 0.245
1006 0.0829
1007 --0.0748
1008 0.0736
1009 0.204
101 --0.0767
1010 0
1011 0
1012 0.0736
1013 0.0666
1014 --0.0115
1015 --0.191
1016 --0.0866
1017 0
1018 0.0324
1019 0
102 0
1020 0
1021 0
1022 0.2
1023 0
1024 0.47
1025 1.04
1026 0
1027 0
1028 0.137
1029 0.206
103 --0.0384
1030 0.24
1031 0.136
1032 0.015
1033 0.0591
1034 0.284
1035 0
1036 --0.0535
1037 0.0736
1038 0.414
1039 0.0266
104 0
1040 0.519
1041 0.24



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: CNhs10474

Jaspar motif P-value
MA0002.2 7.6146e-4
MA0003.1 0.055
MA0004.1 0.232
MA0006.1 0.0677
MA0007.1 0.994
MA0009.1 0.553
MA0014.1 0.452
MA0017.1 0.0815
MA0018.2 0.0194
MA0019.1 0.663
MA0024.1 8.76242e-5
MA0025.1 0.00146
MA0027.1 0.81
MA0028.1 0.04
MA0029.1 0.747
MA0030.1 2.14136e-4
MA0031.1 3.3352e-6
MA0035.2 0.235
MA0038.1 0.748
MA0039.2 5.93835e-4
MA0040.1 0.0578
MA0041.1 0.856
MA0042.1 0.772
MA0043.1 0.629
MA0046.1 1.31541e-5
MA0047.2 5.89002e-10
MA0048.1 0.367
MA0050.1 4.70277e-19
MA0051.1 1.98694e-10
MA0052.1 0.439
MA0055.1 0.574
MA0057.1 0.351
MA0058.1 0.141
MA0059.1 0.00811
MA0060.1 1.48107e-6
MA0061.1 0.0334
MA0062.2 0.685
MA0065.2 0.531
MA0066.1 0.335
MA0067.1 0.829
MA0068.1 0.416
MA0069.1 0.675
MA0070.1 0.985
MA0071.1 0.198
MA0072.1 0.179
MA0073.1 0.843
MA0074.1 0.35
MA0076.1 0.0379
MA0077.1 0.059
MA0078.1 0.0219
MA0079.2 0.00811
MA0080.2 5.2448e-13
MA0081.1 0.0324
MA0083.1 0.159
MA0084.1 0.869
MA0087.1 0.569
MA0088.1 0.902
MA0090.1 0.0749
MA0091.1 0.289
MA0092.1 0.908
MA0093.1 0.229
MA0099.2 0.472
MA0100.1 0.408
MA0101.1 0.0743
MA0102.2 0.0287
MA0103.1 0.369
MA0104.2 0.0132
MA0105.1 0.821
MA0106.1 0.0945
MA0107.1 0.00129
MA0108.2 0.375
MA0111.1 0.712
MA0112.2 0.386
MA0113.1 0.222
MA0114.1 0.0228
MA0115.1 0.193
MA0116.1 0.537
MA0117.1 0.685
MA0119.1 0.0622
MA0122.1 0.108
MA0124.1 0.995
MA0125.1 0.148
MA0131.1 0.219
MA0135.1 0.134
MA0136.1 9.14572e-9
MA0137.2 0.0902
MA0138.2 0.855
MA0139.1 0.0908
MA0140.1 0.408
MA0141.1 0.00511
MA0142.1 0.116
MA0143.1 0.333
MA0144.1 0.0137
MA0145.1 2.07387e-4
MA0146.1 0.223
MA0147.1 0.00367
MA0148.1 1.60559e-8
MA0149.1 0.956
MA0150.1 0.986
MA0152.1 0.681
MA0153.1 1.6839e-5
MA0154.1 0.00892
MA0155.1 0.44
MA0156.1 5.06007e-11
MA0157.1 7.11136e-5
MA0159.1 0.534
MA0160.1 0.115
MA0162.1 0.327
MA0163.1 0.333
MA0164.1 0.217
MA0258.1 0.644
MA0259.1 0.0138



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: CNhs10474

Novel motif P-value
1 0.903
10 0.365
100 0.215
101 0.354
102 0.522
103 0.337
104 0.865
105 0.389
106 0.00252
107 0.0252
108 0.896
109 0.185
11 0.9
110 0.991
111 0.672
112 0.484
113 0.395
114 0.431
115 0.732
116 0.666
117 0.111
118 0.683
119 0.183
12 0.75
120 0.138
121 0.116
122 0.631
123 0.673
124 0.348
125 0.478
126 0.417
127 0.284
128 0.00529
129 0.139
13 0.0421
130 0.0293
131 0.0431
132 0.417
133 0.662
134 0.548
135 0.239
136 0.498
137 0.222
138 0.213
139 0.987
14 0.237
140 0.5
141 0.21
142 0.474
143 0.603
144 0.611
145 0.353
146 0.492
147 0.726
148 0.412
149 0.0484
15 0.13
150 0.206
151 0.0886
152 0.0187
153 0.721
154 0.842
155 0.409
156 0.0184
157 0.656
158 0.922
159 0.0997
160 0.321
161 0.712
162 0.983
163 0.78
164 0.953
165 0.71
166 0.461
167 0.143
168 0.411
169 0.0367
17 0.51
18 0.0531
19 0.105
2 0.0485
20 0.247
21 0.866
22 0.126
23 0.0558
24 0.146
25 0.358
26 0.383
27 0.406
28 0.47
29 0.316
3 0.902
30 0.483
31 0.997
32 0.522
33 0.714
34 0.524
35 0.0934
36 0.887
37 0.0784
38 0.216
39 0.231
4 0.978
40 0.369
41 0.797
42 0.799
43 0.312
44 0.619
45 0.0516
46 0.891
47 0.577
48 0.854
49 0.553
5 0.747
50 0.513
51 0.62
52 0.0534
53 0.216
54 0.71
55 0.599
56 0.334
57 0.365
58 0.584
59 0.0661
6 0.996
60 0.0352
61 0.738
62 0.784
63 0.291
64 0.478
65 0.11
66 0.309
67 0.836
68 0.398
69 0.783
7 0.463
70 0.367
71 0.803
72 0.899
73 0.094
74 0.804
75 0.367
76 0.437
77 0.285
78 0.729
79 0.972
8 0.706
80 0.201
81 0.639
82 0.591
83 0.095
84 0.472
85 0.189
86 0.856
87 0.93
88 0.832
89 0.435
9 0.199
90 0.509
91 0.598
92 0.362
93 0.0724
94 0.306
95 0.654
96 0.439
97 0.626
98 0.401
99 0.408



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: CNhs10474


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
0000310 (breast)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001443 (chest)
0001555 (digestive tract)
0002048 (lung)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0007023 (adult organism)
0007026 (primitive gut)
0008947 (respiratory primordium)
0009142 (entire embryonic mesenchyme)

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