-
1
-
-
5044252972
-
Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome
-
Subramanian S, Kumar S. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 2004;168:373-81.
-
(2004)
Genetics
, vol.168
, pp. 373-381
-
-
Subramanian, S.1
Kumar, S.2
-
2
-
-
0033977618
-
Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
-
Duret L, Mouchiroud D. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol 2000;17:68-74.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 68-74
-
-
Duret, L.1
Mouchiroud, D.2
-
3
-
-
77955223565
-
Expression breadth and expression abundance behave differently in correlations with evolutionary rates
-
Park SG, Choi SS. Expression breadth and expression abundance behave differently in correlations with evolutionary rates. BMC Euol Biol 2010;10:241.
-
(2010)
BMC Euol Biol
, vol.10
, pp. 241
-
-
Park, S.G.1
Choi, S.S.2
-
4
-
-
0036613754
-
Clustering of housekeeping genes provides a unified model of gene order in the human genome
-
Lercher MJ, Urrutia AO, Hurst LD. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 2002;31:180-3.
-
(2002)
Nat Genet
, vol.31
, pp. 180-183
-
-
Lercher, M.J.1
Urrutia, A.O.2
Hurst, L.D.3
-
5
-
-
0345411919
-
Isochores and tissue-specificity
-
Vinogradov AE. Isochores and tissue-specificity. Nucleic Acids Res 2003;31:5212-20.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 5212-5220
-
-
Vinogradov, A.E.1
-
6
-
-
0035183199
-
Determinants of CpG islands: Expression in early embryo and isochore structure
-
Ponger L, Duret L, Mouchiroud D. Determinants of CpG islands: expression in early embryo and isochore structure. Genome Res 2001;11:1854-60.
-
(2001)
Genome Res
, vol.11
, pp. 1854-1860
-
-
Ponger, L.1
Duret, L.2
Mouchiroud, D.3
-
7
-
-
12244313858
-
Analysis of high density expressino microarrays with signed-rank call algorithms
-
Liu W, Mei R, Ryder TB, et al. Analysis of high density expressino microarrays with signed-rank call algorithms. Bioinformatics 2002;18:1593-9.
-
(2002)
Bioinformatics
, vol.18
, pp. 1593-1599
-
-
Liu, W.1
Mei, R.2
Ryder, T.B.3
-
8
-
-
84890310834
-
A model based criterion for gene expression calls using RNA-seq data
-
Wagner GP, Kin K, Lynch VJ. A model based criterion for gene expression calls using RNA-seq data. Theory Biosci 2013;132:159-64.
-
(2013)
Theory Biosci
, vol.132
, pp. 159-164
-
-
Wagner, G.P.1
Kin, K.2
Lynch, V.J.3
-
9
-
-
79958724665
-
RNA sequencing reveals two major classes of gene expression levels in metazoan cells
-
Hebenstreit D, Fang M, Gu M, et al. RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol 2011;7:497.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 497
-
-
Hebenstreit, D.1
Fang, M.2
Gu, M.3
-
10
-
-
61449157724
-
A comprehensive functional analysis of tissue specificity of human gene expression
-
Dezso Z, Nikolsky Y, Sviridov E, et al. A comprehensive functional analysis of tissue specificity of human gene expression. BMC Biol 2008;6:49.
-
(2008)
BMC Biol
, vol.6
, pp. 49
-
-
Dezso, Z.1
Nikolsky, Y.2
Sviridov, E.3
-
11
-
-
74549125753
-
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
-
Ramskold D, Wang ET, Burge CB, et al. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 2009;5:e1000598.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Ramskold, D.1
Wang, E.T.2
Burge, C.B.3
-
12
-
-
84903859893
-
Translational selection in human: More pronounced in housekeeping genes
-
Ma L, Cui P, Zhu J, et al. Translational selection in human: more pronounced in housekeeping genes. Biol Direct 2014;9:17.
-
(2014)
Biol Direct
, vol.9
, pp. 17
-
-
Ma, L.1
Cui, P.2
Zhu, J.3
-
14
-
-
20144376345
-
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
-
Yanai I, Benjamin H, Shmoish M, et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 2005;21:650-9.
-
(2005)
Bioinformatics
, vol.21
, pp. 650-659
-
-
Yanai, I.1
Benjamin, H.2
Shmoish, M.3
-
15
-
-
84930665248
-
Evolutionary analysis of the female-specific avian W chromosome
-
Smeds L, Warmuth V, Bolivar P, et al. Evolutionary analysis of the female-specific avian W chromosome. Nat Commun 2015;6:7330.
-
(2015)
Nat Commun
, vol.6
, pp. 7330
-
-
Smeds, L.1
Warmuth, V.2
Bolivar, P.3
-
16
-
-
84864142569
-
Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human
-
Piasecka B, Robinson-Rechavi M, Bergmann S. Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human. Bioinformatics 2012;28:1865-72.
-
(2012)
Bioinformatics
, vol.28
, pp. 1865-1872
-
-
Piasecka, B.1
Robinson-Rechavi, M.2
Bergmann, S.3
-
17
-
-
84886415585
-
Neofunctionalization of young duplicate genes in Drosophila
-
Assis R, Bachtrog D. Neofunctionalization of young duplicate genes in Drosophila. PNAS 2013;110:17409-14.
-
(2013)
PNAS
, vol.110
, pp. 17409-17414
-
-
Assis, R.1
Bachtrog, D.2
-
18
-
-
84893030090
-
Conserved proteins are fragile
-
Assis R, Kondrashov AS. Conserved proteins are fragile. Mol Biol Euol 2014;31:419-24.
-
(2014)
Mol Biol Euol
, vol.31
, pp. 419-424
-
-
Assis, R.1
Kondrashov, A.S.2
-
19
-
-
84932193767
-
Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana
-
Bush SJ, Kover PX, Urrutia AO. Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana. Mol Ecol 2015;24:3093-106.
-
(2015)
Mol Ecol
, vol.24
, pp. 3093-3106
-
-
Bush, S.J.1
Kover, P.X.2
Urrutia, A.O.3
-
20
-
-
84938613240
-
Tissue-specific evolution of protein coding genes in human and mouse
-
Kryuchkova-Mostacci N, Robinson-Rechavi M. Tissue-specific evolution of protein coding genes in human and mouse. PLoS One 2015;10:e0131673.
-
(2015)
PLoS One
, vol.10
-
-
Kryuchkova-Mostacci, N.1
Robinson-Rechavi, M.2
-
21
-
-
33646882591
-
Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution
-
Liao B-Y, Zhang J. Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol 2006;23:1119-28.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1119-1128
-
-
Liao, B.-Y.1
Zhang, J.2
-
22
-
-
33749579409
-
Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins
-
Liao B-Y, Scott NM, Zhang J. Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol Biol Euol 2006;23:2072-80.
-
(2006)
Mol Biol Euol
, vol.23
, pp. 2072-2080
-
-
Liao, B.-Y.1
Scott, N.M.2
Zhang, J.3
-
23
-
-
79952698915
-
Support for multiple classes of local expression cluster in Drosophila melanogaster, but no evidence for gene order conservation
-
Weber CC, Hurst LD. Support for multiple classes of local expression cluster in Drosophila melanogaster, but no evidence for gene order conservation. Genome Biol 2011;12:R23.
-
(2011)
Genome Biol
, vol.12
, pp. R23
-
-
Weber, C.C.1
Hurst, L.D.2
-
24
-
-
84930815144
-
Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans
-
Zhao L, Wit J, Svetec N, et al. Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans. PLOS Genet 2015;11:e1005184.
-
(2015)
PLOS Genet
, vol.11
-
-
Zhao, L.1
Wit, J.2
Svetec, N.3
-
25
-
-
33750217984
-
Computational analysis of tissue-specific combinatorial gene regulation: Predicting interaction between transcription factors in human tissues
-
Yu X, Lin J, Zack DJ, et al. Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res 2006;34:4925-36.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4925-4936
-
-
Yu, X.1
Lin, J.2
Zack, D.J.3
-
26
-
-
46049110099
-
TiGER: A database for tissue-specific gene expression and regulation
-
Liu X, Yu X, Zack DJ, et al. TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics 2008;9:271.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 271
-
-
Liu, X.1
Yu, X.2
Zack, D.J.3
-
27
-
-
84861541065
-
Mechanisms and evolutionary patterns of mammalian and avian dosage compensation
-
Julien P, Brawand D, Soumillon M, et al. Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol 2012;10:e1001328.
-
(2012)
PLoS Biol
, vol.10
-
-
Julien, P.1
Brawand, D.2
Soumillon, M.3
-
28
-
-
84899484057
-
Origins and functional evolution of Y chromosomes across mammals
-
Cortez D, Marin R, Toledo-Flores D, et al. Origins and functional evolution of Y chromosomes across mammals. Nature 2014;508:488-93.
-
(2014)
Nature
, vol.508
, pp. 488-493
-
-
Cortez, D.1
Marin, R.2
Toledo-Flores, D.3
-
29
-
-
84937027093
-
Rapid divergence and diversification of mammalian duplicate gene functions
-
Assis R, Bachtrog D. Rapid divergence and diversification of mammalian duplicate gene functions. BMC Euol Biol 2015;15:138.
-
(2015)
BMC Euol Biol
, vol.15
, pp. 138
-
-
Assis, R.1
Bachtrog, D.2
-
30
-
-
0347766006
-
Elevated rates of protein secretion, evolution, and disease among tissue-specific genes
-
Winter EE, Goodstadt L, Ponting CP. Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. Genome Res 2004;14:54-61.
-
(2004)
Genome Res
, vol.14
, pp. 54-61
-
-
Winter, E.E.1
Goodstadt, L.2
Ponting, C.P.3
-
31
-
-
32044442759
-
Promoter features related to tissue specificity as measured by Shannon entropy
-
Schug J, Schuller W-P, Kappen C, et al. Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol 2005;6:R33.
-
(2005)
Genome Biol
, vol.6
, pp. R33
-
-
Schug, J.1
Schuller, W.-P.2
Kappen, C.3
-
32
-
-
75649084887
-
Modeling tissue-specific structural patterns in human and mouse promoters
-
Vandenbon A, Nakai K. Modeling tissue-specific structural patterns in human and mouse promoters. Nucleic Acids Res 2010;38:17-25.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 17-25
-
-
Vandenbon, A.1
Nakai, K.2
-
33
-
-
77952796368
-
TiSGeD: A database for tissue-specific genes
-
Xiao S-J, Zhang C, Zou Q, et al. TiSGeD: a database for tissue-specific genes. Bioinformatics 2010;26:1273-5.
-
(2010)
Bioinformatics
, vol.26
, pp. 1273-1275
-
-
Xiao, S.-J.1
Zhang, C.2
Zou, Q.3
-
34
-
-
9144244440
-
Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and Tissuelnfo databases
-
Huminiecki L, Lloyd AT, Wolfe KH. Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and Tissuelnfo databases. BMC Genomics 2003;4:31.
-
(2003)
BMC Genomics
, vol.4
, pp. 31
-
-
Huminiecki, L.1
Lloyd, A.T.2
Wolfe, K.H.3
-
35
-
-
84857872964
-
The use of EST expression matrixes for the quality control of gene expression data
-
Milnthorpe AT, Soloviev M. The use of EST expression matrixes for the quality control of gene expression data. PLoS One 2012;7:e32966.
-
(2012)
PLoS One
, vol.7
-
-
Milnthorpe, A.T.1
Soloviev, M.2
-
36
-
-
77952060263
-
Comparison and consolidation of micro-array data sets of human tissue expression
-
Russ J, Futschik ME. Comparison and consolidation of micro-array data sets of human tissue expression. BMC Genomics 2010;11:305.
-
(2010)
BMC Genomics
, vol.11
, pp. 305
-
-
Russ, J.1
Futschik, M.E.2
-
37
-
-
43349097782
-
Characterization of paralogous protein families in rice
-
Lin H, Ouyang S, Egan A, et al. Characterization of paralogous protein families in rice. BMC Plant Biol 2008;8:18.
-
(2008)
BMC Plant Biol
, vol.8
, pp. 18
-
-
Lin, H.1
Ouyang, S.2
Egan, A.3
-
38
-
-
25444465171
-
Global transcriptome analysis of the C57BL/6J mouse testis by SAGE: Evidence for non-random gene order
-
Divina P, Vlcek C, Strnad P, et al. Global transcriptome analysis of the C57BL/6J mouse testis by SAGE: evidence for non-random gene order. BMC Genomics 2005;6:29.
-
(2005)
BMC Genomics
, vol.6
, pp. 29
-
-
Divina, P.1
Vlcek, C.2
Strnad, P.3
-
39
-
-
84865426634
-
The origins of the Gini index: Extracts from Variabilita e Mutabilita (1912) by Corrado Gini
-
Ceriani L, Verme P. The origins of the Gini index: extracts from Variabilita e Mutabilita (1912) by Corrado Gini. J Econ Inequal 2012;10:421-43.
-
(2012)
J Econ Inequal
, vol.10
, pp. 421-443
-
-
Ceriani, L.1
Verme, P.2
-
46
-
-
84893276590
-
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics
-
Fagerberg L, Hallstrom BM, Oksvold P, et al. Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics 2014;13:397-406.
-
(2014)
Mol Cell Proteomics
, vol.13
, pp. 397-406
-
-
Fagerberg, L.1
Hallstrom, B.M.2
Oksvold, P.3
-
47
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
The ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 2011;9:e1001046.
-
(2011)
PLoS Biol
, vol.9
-
-
-
48
-
-
84914125316
-
Comparison of the transcriptional landscapes between human and mouse tissues
-
Lin S, Lin Y, Nery JR, et al. Comparison of the transcriptional landscapes between human and mouse tissues. PNAS 2014;111:17224-9.
-
(2014)
PNAS
, vol.111
, pp. 17224-17229
-
-
Lin, S.1
Lin, Y.2
Nery, J.R.3
-
49
-
-
80054976678
-
The evolutionofgene expression levels in mammalian organs
-
Brawand D, Soumillon M, Necsulea A, et al. The evolutionofgene expression levels in mammalian organs. Nature 2011;478:343-8.
-
(2011)
Nature
, vol.478
, pp. 343-348
-
-
Brawand, D.1
Soumillon, M.2
Necsulea, A.3
-
50
-
-
48249136251
-
Bgee: Integrating and comparing heterogeneous transcriptome data among species
-
Bastian F, Parmentier G, Roux J, et al. Bgee: integrating and comparing heterogeneous transcriptome data among species. Data Integr Life Sci 2008;5109:124-31.
-
(2008)
Data Integr Life Sci
, vol.5109
, pp. 124-131
-
-
Bastian, F.1
Parmentier, G.2
Roux, J.3
-
51
-
-
21444445235
-
Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues
-
Ge X, Yamamoto S, Tsutsumi S, et al. Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues. Genomics 2005;86:127-41.
-
(2005)
Genomics
, vol.86
, pp. 127-141
-
-
Ge, X.1
Yamamoto, S.2
Tsutsumi, S.3
-
52
-
-
46649115515
-
Using ribosomal protein genes as reference: A tale of caution
-
Thorrez L, Van Deun K, Tranchevent LC, et al. Using ribosomal protein genes as reference: a tale of caution. PLoS One 2008;3:e1854.
-
(2008)
PLoS One
, vol.3
-
-
Thorrez, L.1
Van Deun, K.2
Tranchevent, L.C.3
-
53
-
-
39549113189
-
Correcting for sequence biases in present/absent calls
-
Schuster EF, Blanc E, Partridge L, et al. Correcting for sequence biases in present/absent calls. Genome Biol 2007;8:R125.
-
(2007)
Genome Biol
, vol.8
, pp. R125
-
-
Schuster, E.F.1
Blanc, E.2
Partridge, L.3
-
54
-
-
60849139395
-
GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists
-
Eden E, Navon R, Steinfeld I, et al. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 2009;10:48.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 48
-
-
Eden, E.1
Navon, R.2
Steinfeld, I.3
-
55
-
-
79960610118
-
REVIGO summarizes and visualizes long lists of Gene Ontology terms
-
Supek F, Bosnjak M, Skunca N, et al. REVIGO summarizes and visualizes long lists of Gene Ontology terms. PLoS One 2011;6:e21800.
-
(2011)
PLoS One
, vol.6
-
-
Supek, F.1
Bosnjak, M.2
Skunca, N.3
-
56
-
-
84900819430
-
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
-
Rosikiewicz M, Robinson-Rechavi M. IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinformatics 2014;30:1392-9.
-
(2014)
Bioinformatics
, vol.30
, pp. 1392-1399
-
-
Rosikiewicz, M.1
Robinson-Rechavi, M.2
-
57
-
-
84898618335
-
Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells
-
Zhao S, Fung-Leung W-P, Bittner A, et al. Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One 2014;9:e78644.
-
(2014)
PLoS One
, vol.9
-
-
Zhao, S.1
Fung-Leung, W.-P.2
Bittner, A.3
-
58
-
-
84912527013
-
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
-
Wang C, Gong B, Bushel PR, et al. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol 2014;32:926-32.
-
(2014)
Nat Biotechnol
, vol.32
, pp. 926-932
-
-
Wang, C.1
Gong, B.2
Bushel, P.R.3
-
59
-
-
84865505602
-
Measuring and analyzing tissue specificity of human genes and protein complexes
-
Emig D, Kacprowski T, Albrecht M. Measuring and analyzing tissue specificity of human genes and protein complexes. EURASIP J Bioinforma Syst Biol 2011;2011:5.
-
(2011)
EURASIP J Bioinforma Syst Biol
, vol.2011
, pp. 5
-
-
Emig, D.1
Kacprowski, T.2
Albrecht, M.3
-
60
-
-
71549114836
-
A problem with the correlation coefficient as a measure of gene expression divergence
-
Pereira V, Waxman D, Eyre-Walker A. A problem with the correlation coefficient as a measure of gene expression divergence. Genetics 2009;183:1597-600.
-
(2009)
Genetics
, vol.183
, pp. 1597-1600
-
-
Pereira, V.1
Waxman, D.2
Eyre-Walker, A.3
-
61
-
-
84940969958
-
A reanalysis ofmouse ENCODE comparative gene expression data
-
Gilad Y, Mizrahi-Man O. A reanalysis ofmouse ENCODE comparative gene expression data. F1000Research 2015;4:121.
-
(2015)
F1000Research
, vol.4
, pp. 121
-
-
Gilad, Y.1
Mizrahi-Man, O.2
-
62
-
-
84923205692
-
Revisiting tissue specificity of germline cancer predisposing mutations
-
Maris JM, Knudson AG. Revisiting tissue specificity of germline cancer predisposing mutations. Nat Reu Cancer 2015;15:65-6.
-
(2015)
Nat Reu Cancer
, vol.15
, pp. 65-66
-
-
Maris, J.M.1
Knudson, A.G.2
-
63
-
-
84866846551
-
Tissue specificity of genetic regulation of gene expression
-
Göring HHH. Tissue specificity of genetic regulation of gene expression. Nat Genet 2012;44:1077-8.
-
(2012)
Nat Genet
, vol.44
, pp. 1077-1078
-
-
Göring, H.H.H.1
|