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ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
Open accessAbstract
With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have arisen. However, novel tools and strategies are required to accommodate this large volume of genomic information and to facilitate the transfer of predictions generated by comparative sequence alignment to researchers focused on experimental annotation of genome function. Here, we present the ECR Browser, a tool that provides easy and dynamic access to whole genome alignments of human, mouse, rat and fish sequences. This web-based tool (http://ecrbrowser.dcode.org) provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites. The genome alignment portal of the ECR Browser also permits fast and automated alignments of any user-submitted sequence to the genome of choice. The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes.
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“Using the Evolutionarily Conserved Regions browser (35), we found that the miR-146a promoter contains two evolutionarily conserved regions, ECR1 and ECR2.”
From The DNA damage response induces inflammation and senescence by inhibiting autophagy of GATA4. (2015) · cites this paper as [35]
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Basic local alignment search tool
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<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
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Initial sequencing and comparative analysis of the mouse genome
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The UCSC Genome Browser Database
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Epigenetic regulation of the extrinsic oncosuppressor PTX3 gene in inflammation and cancer
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“PTX3 enhancer conservation was investigated with Evolutionary Conserved Regions (ECRs) browser.(49)”
MethodDNA methylation analysis of the mammalian PEG3 imprinted domain
Huang, J. M., & Kim, J. (2009) · Gene · doi:10.1016/j.gene.2009.04.016 · Cited by 55
“To test evolutionary conservation, the sequence of each CpG island was analyzed using BLAST (Altschul et al., 1990) and the ECR browser of the dcode website (http://www.dcode.org/) (Ovcharenko et al., 2004).”
MethodISL1 Directly Regulates FGF10 Transcription during Human Cardiac Outflow Formation
Golzio, C., Havis, E., Daubas, P., Nuel, G., Babarit, C., Münnich, A., Vekemans, M. J. J., Zaffran, S., Lyonnet, S., & Etchevers, H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030677 · Cited by 54
“org) [40], identified two candidate regions conserved among therian mammals (Fig.”
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“Nine of these DMRT CNGs fit the criteria for core evolutionarily conserved regions that are at least 350 bp long and show 77% identity with human sequence [ 47 ] :F( 5′ of DMRT1); K, A, E, Q, and R (within DMRT1 introns); B and C (between DMRT1 and DMRT3); and region V (within DMRT3 introns).”
BackgroundHoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis
Yan, T., Ooi, W. F., Qamra, A., Cheung, A. M. S., Ma, D., Sundaram, G. M., Xu, C., Xing, M., Poon, L.-F., Wang, J., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02601-1 · Cited by 53
Impact of genomics on research in the ratPreprint
Lazar, J., Moreno, C., Jacob, H. J., & Kwitek, A. E. (2005) · Genome Research · doi:10.1101/gr.3744005 · Cited by 53
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“The candidate enhancer region (Rib-Cage Specific Enhancer: RCSE) [chr11, 111,838,889– 111,839,334 (mm10)] was determined as well conserved region among mice, chickens, opossums, and humans, nearby the strongest peak (Ovcharenko et al., 2004) (Figure 1C).”
Gene expression of NMDA receptor subunits in the cerebellum of elderly patients with schizophrenia
Schmitt, A., Koschel, J., Zink, M., Bauer, M., Sommer, C., Frank, J., Treutlein, J., Schulze, T. G., Schneider-Axmann, T., Parlapani, E., et al. (2009) · European Archives of Psychiatry and Clinical Neuroscience · doi:10.1007/s00406-009-0017-1 · Cited by 53
“ECRs are DNA regions that have been mapped to align with other genomes and are conserved with greater than or equal to 70% identity over at least 100 bp [38, 45].”
BackgroundNatsuizaka, M., Naganuma, S., Kagawa, S., Ohashi, S., Ahmadi, A., Subramanian, H. E., Chang, S., Nakagawa, K. J., Ji, X., Liebhaber, S. A., et al. (2012) · The FASEB Journal · doi:10.1096/fj.11-198598 · Cited by 50
“The ECR browser (29), the second algorithm, predicted 99 potential HREs based on the HRE core motif within a 100-kb region spanning a 60-kb 5=-upstream region of the transcription start site for IGFBP3, the entire IGFBP3 gene and its adjacent IGFBP1 located in the 3=-downstream region of IGFBP3 in a head-to-tail orien…”
MethodMAD1 and its life as a MYC antagonist: An update
Lüscher, B. (2011) · European Journal of Cell Biology · doi:10.1016/j.ejcb.2011.07.005 · Cited by 49
The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity
Ritter, D., Li, Q., Kostka, D., Pollard, K. S., Guo, S., & Chuang, J. H. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq128 · Cited by 49
“The second is by identification of large numbers of highly conserved intergenic sequences (Bejerano et al. 2004; Ovcharenko et al. 2004; Visel, Minovitsky, et al. 2007; Engstrom et al. 2008; Persampieri et al. 2008; Stephen, Pheasant et al. 2008; Wang et al. 2008), large fractions of which can act…”
BackgroundThe Orphan Nuclear Receptor Nur77 Is a Determinant of Myofiber Size and Muscle Mass in Mice
Tontonoz, P., Cortez-Toledo, O., Wroblewski, K., Hong, C., Lim, L., Carranza, R., Conneely, O. M., METZGER, D., & Chao, L. C. (2015) · Molecular and Cellular Biology · doi:10.1128/mcb.00715-14 · Cited by 48
“analysis of the genes positively regulated by Nur77 to identify putative Nur77-binding response elements (NBRE) (43).”
BackgroundGene Structure Evolution of the Na+-Ca2+ Exchanger (NCX) Family
On, C., Marshall, C. R., Chen, N., Moyes, C. D., & Tibbits, G. F. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-127 · Cited by 49
“The lizard (Feb.2007) sequences were obtained from the University of California Santa Cruz (UCSC) Genome Browser [45].”
MethodInfluentialCTCF and EGR1 suppress breast cancer cell migration through transcriptional control of Nm23-H1
Wong, K. M., Song, J., & Wong, Y. H. (2021) · Scientific Reports · doi:10.1038/s41598-020-79869-9 · Cited by 48
Schemmer, J., Araúzo-Bravo, M. J., Haas, N., Schäfer, S., Weber, S. N., Becker, A., Eckert, D., Zimmer, A., Nettersheim, D., & Schorle, H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071113 · Cited by 48
Tscherner, A. K., Brown, A. C., Stalker, L., Kao, J., Dufort, I., Sirard, M., & LaMarre, J. (2018) · Scientific Reports · doi:10.1038/s41598-018-29874-w · Cited by 49
Miesfeld, J. B., Ghiasvand, N. M., Marsh-Armstrong, B. P., Marsh‐Armstrong, N., Miller, E. B., Zhang, P., Manna, S. K., Zawadzki, R. J., Brown, N. L., & Glaser, T. M. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2006888117 · Cited by 44
Adaptive variation regulates the expression of the human SGK1 gene in response to stress
Luca, F., Kashyap, S., Southard, C., Zou, M., Witonsky, D., Di Rienzo, A., & Conzen, S. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000489 · Cited by 45
“To identify additional regulatory regions beyond the promoter, we performed a bioinformatics analysis to identify additional GREs [40] and Evolutionary Conserved Regions (ECRs) between human and dog, mouse, or opossum (Figure 1) [41].”
MethodPalles, C., Johnson, N., Coupland, B., Taylor, C., Carvajal, J. J., Holly, J. M. P., Fentiman, I. S., Silva, I. D. S., Ashworth, A., Peto, J., et al. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn034 · Cited by 47
“through the ECR browser ( 31 ) suggests that cross-species conservation around IGF1 extends beyond the 234 kb region that we screened.”
BackgroundRelationship between Delta-like and proneural bHLH genes during chick retinal development
Nelson, B. R., & Reh, T. A. (2008) · Developmental Dynamics · doi:10.1002/dvdy.21550 · Cited by 45
Lymphoid Enhancer Binding Factor 1 Regulates Transcription through Gene Looping
Yun, K., So, J., Jash, A., & Im, S. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0802744 · Cited by 45
“gov/vista) (34, 35) or ECR browser (36).”
The ubiquitin ligase Mindbomb 1 coordinates gastrointestinal secretory cell maturation
Capoccia, B. J., Jin, R. U., Kong, Y., Peek, R. M., Fassan, M., Rugge, M., & Mills, J. C. (2013) · Journal of Clinical Investigation · doi:10.1172/jci65703 · Cited by 46
“The ECR browser (78) was used to analyze the human genomic sequence for MIB1 5 ′ to the transcription start.”
MethodGañán‐Gómez, I., Wei, Y., Yang, H., Pierce, S. A., Bueso-Ramos, C., Călin, G. A., Boyano-Adánez, M. D. C., & Garcia‐Manero, G. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093404 · Cited by 45
“For instance, conserved binding sites for various transcription factors, which could be responsible for the independent transcription of miR125a, exist in the intergenic region between miR-99b and let-7e [68].”
BackgroundFANCD2 associated with sporadic breast cancer risk
Barroso, E. (2006) · Carcinogenesis · doi:10.1093/carcin/bgl062 · Cited by 45
Santos, F. C. D., Peixoto, M. G. C. D., Fonseca, P. A. D. S., Pires, M. D. F. Á., Ventura, R. V., Rosse, I. C., Bruneli, F. Â. T., Machado, M. A., & Carvalho, M. R. S. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169163 · Cited by 45
The Long Non-coding RNA Flatr Anticipates Foxp3 Expression in Regulatory T Cells
Brajic, A., Franckaert, D., Burton, O. T., Bornschein, S., Calvanese, A., Demeyer, S., Cools, J., Dooley, J., Schlenner, S., & Liston, A. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01989 · Cited by 44
Interpreting mammalian evolution using Fugu genome comparisons
Ovcharenko, I., Stubbs, L. J., & Loots, G. G. (2004) · Genomics · doi:10.1016/j.ygeno.2004.07.011 · Cited by 44
“We also applied these newly defined parameters on human–chicken and human–frog whole genome alignments available from the ECR Browser [6].”
MethodInfluentialSelf-citationMedway, C., Combarros, O., Cortina‐Borja, M., Butler, H., Ibrahim‐Verbaas, C. A., de Bruijn, R. F. A. G., Koudstaal, P. J., van Duijn, C. M., Ikram, M. A., Mateo, I., et al. (2013) · European Journal of Human Genetics · doi:10.1038/ejhg.2013.116 · Cited by 43
The role and regulation of friend of GATA-1 (FOG-1) during blood development in the zebrafish
Amigo, J. D., Ackermann, G. E., Cope, J. J., Yu, M., Cooney, J. D., Ma, D.-D., Langer, N. B., Shafizadeh, E., Shaw, G., Horsely, W., et al. (2009) · Blood · doi:10.1182/blood-2008-12-189910 · Cited by 45
Pang, C. J., Lemsaddek, W., Alhashem, Y. N., Bondzi, C., Redmond, L. C., Ah-Son, N., Dumur, C. I., Archer, K. J., Haar, J. L., Lloyd, J. A., et al. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.00104-12 · Cited by 43
“The evolutionarily conserved region (ECR) browser interface was used to navigate through alignments of the human and mouse genes for Myc (56).”
MethodXu, X., Scott, M. M., & Deneris, E. S. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.00456-06 · Cited by 44
“ing ECR browser (43), with sequences 76611222 to 76790069 from human chro-”
BackgroundPost-GWAS Functional Characterization of Susceptibility Variants for Chronic Lymphocytic Leukemia
Sillé, F. C. M., Thomas, R., Smith, M. T., Conde, L., & Skibola, C. F. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029632 · Cited by 42
“Using the ECR browser [21], we found six SNPs in evolutionarily conserved regions (,31.”
MethodGenome-Wide Analysis of Copy Number Variation in Type 1 Diabetes
Grayson, B. L., Smith, M. E., Thomas, J. W., Wang, L., Dexheimer, P. J., Jeffrey, J., Fain, P. R., Nanduri, P., Eisenbarth, G. S., & Aune, T. M. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015393 · Cited by 42
“Two regions, CNP934 and CNP1162, contain at least one segment of DNA longer than 100 bp with more than 70% evolutionarily conserved sequence to mus musculus as determined by the ECR browser, defined as an evolutionarily conserved noncoding sequence[30].”
BackgroundQuiñones, H. I., Savage, T. K., Battiste, J., & Johnson, J. E. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.02.012 · Cited by 43
Molecular Mechanisms Controlling the Migration of Striatal Interneurons
Villar‐Cerviño, V., Kappeler, C., Pereira, S. N., Henkemeyer, M. J., Rago, L., Nieto, M. A., & Marín, Ó. (2015) · Journal of Neuroscience · doi:10.1523/jneurosci.4317-14.2015 · Cited by 45
“In silico analysis of the 5 flanking region of the Mus musculus EphB1 and EphB3 locus (EphB1 accession number NM_173447 and EphB3 accession number NM_010143) was performed using ECR browser (Ovcharenko et al., 2004).”
MethodHong, S., Chung, S., Leung, K. K. A., Hwang, I.-S., Moon, J., & Kim, K. (2013) · Stem Cells and Development · doi:10.1089/scd.2013.0406 · Cited by 41
“In addition, we compared the same mouse and rat TH promoter regions ranging from 10kb upstream ( - 10 kb) of the transcriptional start site using the Lmx1a homeodomain binding motif 5 ¢ -TAAT-3 ¢ [12,43] with ECR browser program [40].”
Zúñiga, A., Laurent, F., López-Rı́os, J., Klasen, C., Matt, N., & Zeller, R. (2012) · BMC Developmental Biology · doi:10.1186/1471-213x-12-23 · Cited by 40
“[54] and the ClustalW2 program [55].”
Pdx1 regulates pancreas tubulogenesis and E-cadherin expression
Marty‐Santos, L., & Cleaver, O. B. (2015) · Development · doi:10.1242/dev.126755 · Cited by 41
“Using the Evolutionary Conservation of Genomes (ECR) browser (Ovcharenko et al., 2004) and performing sequence alignments with consensus Pdx1 binding sequence CATYAS, we identified two conserved predicted binding Fig.”
MethodBrown, E., Rowan, C. R., Strowitzki, M. J., Fagundes, R. R., Faber, K. N., Güntsch, A., Halligan, D. N., Kugler, J., Jones, F., Lee, C. T., et al. (2020) · The FASEB Journal · doi:10.1096/fj.201902103r · Cited by 43
Erythroid Kruppel-like Factor Regulates the G1 Cyclin Dependent Kinase Inhibitor p18INK4c
Tallack, M. R., Keys, J. R., & Perkins, A. C. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.02.109 · Cited by 41
Krueger, K. C., & Deneris, E. S. (2008) · Journal of Neuroscience · doi:10.1523/jneurosci.4349-08.2008 · Cited by 41
“Gene annotation information was derived from NCBI (FEV GenBank accession number NM_017521; Pet-1 GenBank accession number NM_153111) and the ECR browser tools (Ovcharenko et al., 2004).”
MethodTranscriptional regulation of MMP13 by Lef1 in chondrocytes
Yun, K., & Im, S. (2007) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2007.10.121 · Cited by 40
Extended IL10 haplotypes and their association with HIV progression to AIDS
Oleksyk, T. K., Shrestha, S., Truelove, A. L., Goedert, J. J., Donfield, S. M., Phair, J., Mehta, S. H., O’Brien, S. J., & Smith, M. W. (2009) · Genes and Immunity · doi:10.1038/gene.2009.9 · Cited by 40
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“Age in reference year mean (SD) 57 (12) 56 (12) Race or ethnicity White 274 (34) 292 (33) African-American 243 (30) 250 (28) Latina 285 (36) 346 (39) Menopausal status Premenopausal 236 (29) 291 (33) 1.”
Krüger, M., Amort, J., Wilgenbus, P., Helmstädter, J., Grechowa, I., Ebert, J., Tenzer, S., Moergel, M., Witte, I., & Horke, S. (2016) · Oncotarget · doi:10.18632/oncotarget.9013 · Cited by 40
“com); and (c) PON2-regulating TFs were predicted based on binding sites evolutionally conserved between mice and humans through the ECR database [33].”
BackgroundMethodInfluentialMedina, M. A., Andrade, V., Caracci, M. O., Ávila, M. E., Verdugo, D. A., Vargas, M. F., Ugarte, G. D., Reyes, A. E., Opazo, C., & Ferrari, G. V. D. (2018) · Translational Psychiatry · doi:10.1038/s41398-018-0093-y · Cited by 40
Buenaventura, D. F., Tegla, M. G. G., & Emerson, M. M. (2018) · Developmental Biology · doi:10.1016/j.ydbio.2018.06.023 · Cited by 39
“ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.”
MethodHodoğlugil, U., Williamson, D. W., & Mahley, R. W. (2009) · Journal of Lipid Research · doi:10.1194/jlr.p001578 · Cited by 40
Wong, H., Wp, K., Probst-Hensch, N. M., Berg, D. V. D., Yu, M. C., & Ingles, S. A. (2008) · Gut · doi:10.1136/gut.2007.140855 · Cited by 39
YY1 is autoregulated through its own DNA-binding sites
Kim, J. H., Yu, S., & Kim, J. (2009) · BMC Molecular Biology · doi:10.1186/1471-2199-10-85 · Cited by 41
“The cluster of YY1 binding sites in the first intron of YY1 was discovered through the ECR (Evolutionary Conserved Region) browser http://www.dcode.org[ 9 ].”
Microcephaly Thin Corpus Callosum Intellectual Disability Syndrome Caused by Mutated TAF2
Hellman-Aharony, S., Smirin‐Yosef, P., Halevy, A., Pasmanik, M., Yeheskel, A., Har‐Zahav, A., Maya, I., Straussberg, R., Dahary, D., Haviv, A., et al. (2013) · Pediatric Neurology · doi:10.1016/j.pediatrneurol.2013.07.017 · Cited by 35
Interaction between Hhex and SOX13 Modulates Wnt/TCF Activity
Marfil, V., Moya, M., Pierreux, C. E., Castell, J. V., Lemaigre, F. P., Real, F. X., & Bort, R. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.046649 · Cited by 38
Novel computational methods for increasing PCR primer design effectiveness in directed sequencing
Li, K., Brownley, A., Stockwell, T. B., Beeson, K. Y., McIntosh, T. C., Busam, D., Ferriera, S., Murphy, S., & Levy, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-191 · Cited by 38
“The ECRs for the individual species are obtained dynamically from the Dcode ECR Browser website [12,13].”
MethodWoolfe, A., & Elgar, G. (2008) · Advances in genetics · doi:10.1016/s0065-2660(07)00012-0 · Cited by 39
USING DIRECTED INFORMATION TO BUILD BIOLOGICALLY RELEVANT INFLUENCE NETWORKS
Rao, A. U. K., Hero, A. O., States, D. J., & Engel, J. D. (2008) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720008003515 · Cited by 38
“If we are interested in the mechanism of regulation of the Gata3 gene (which is known to be implicated in mammalian nephrogenesis), we examine its promoter region for phylogenetically conserved TFBS (Fig. 2). Such information can be obtained from most genome browsers [ 20 ].”
BackgroundJin, X., Iwasa, S., Okada, K., Mitsumata, M., & Ooi, A. (2003) · PubMed · Cited by 38
Jägle, S., Rönsch, K., Timme, S., Andrlová, H., Bertrand, M., Jäger, M., Proske, A., Schrempp, M., Yousaf, A., Michoel, T., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314523111 · Cited by 40
“To identify cis-regulatory elements involved in EPHB3 regulation, we performed in silico analyses exploiting the fact that evolutionary conserved regions (ECRs) often represent DNA elements with regulatory potential (10).”
BackgroundHarly, C., Kenney, D., Wang, Y., Ding, Y., Zhao, Y., Awasthi, P., & Bhandoola, A. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.00470 · Cited by 36
“Motif analysis was done using the ECR Browser (23).”
MethodHuang, B., Brugger, S. M., & Lyons, K. M. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.108498 · Cited by 37
Identification of Copy Number Variants Defining Genomic Differences among Major Human Groups
Armengol, L., Villatoro, S., González, J. R., Pantano, L., García‐Aragonés, M., Rabionet, R., Cáceres, M., & Estivill, X. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007230 · Cited by 38
“The three remaining CNV regions are completely devoid of coding sequences, but using the Evolutionary Conservation of Genomes Browser [57] we identified conserved segments that might have some potential biological function that has not yet been uncovered (data not shown).”
Langhe, S. D., Meerleer, G. D., Ruyck, K. D., Ost, P., Fonteyne, V., Neve, W. D., & Thierens, H. (2014) · Radiotherapy and Oncology · doi:10.1016/j.radonc.2014.04.005 · Cited by 37
“SNPs in these genes were selected using ECR browser [15].”
MethodO'Brien, V. P., Bokelmann, K., Ramı́rez, J., Jobst, K., Ratain, M. J., Brockmöller, J., & Tzvetkov, M. V. (2013) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1124/jpet.113.206359 · Cited by 37
“ECR Browser was used to identify evolutionary conserved regions in the OCT1 gene locus (Ovcharenko et al., 2004).”
MethodThe dynamics of spleen morphogenesis
Burn, S. F., Boot, M. J., de Angelis, C., Doohan, R., Arqués, C. G., Torres, M., & Hill, R. E. (2008) · Developmental Biology · doi:10.1016/j.ydbio.2008.03.031 · Cited by 37
“The NGRS contains two evolutionary conserved regions (ECRs; detected using the ECRbrowser programme (Ovcharenko et al., 2004)), the distal of which shares high sequence identity with the ~300 bp Xenopus sequence which drives expression in the gut in transgenic mice (Sparrow et al., 2000).”
BackgroundRomero‐Pozuelo, J., Dason, J. S., Atwood, H. L., & Ferrús, A. (2007) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2007.05877.x · Cited by 36
“Genome analyses of different Drosophila species were carried out using the ECR browser webbased tool (Ovcharenko et al., 2004).”
MethodRegulation and Function of miR‐214 in Pulmonary Arterial Hypertension
Stevens, H., Deng, L., Grant, J. S., Pinel, K., Thomas, M. J., Morrell, N. W., MacLean, M. R., Baker, A. H., & Denby, L. (2016) · Pulmonary Circulation · doi:10.1086/685079 · Cited by 36
“4 kb with >60% homology to other mammalian species (ECR Browser).(35) We first carried out in silico analysis of this putative promoter region using MatInspector (Genomatix software suite, http://www .”
BackgroundBhatti, P., Church, D. M., Rutter, J. L., Struewing, J. P., & Sigurdson, A. J. (2006) · American Journal of Epidemiology · doi:10.1093/aje/kwj269 · Cited by 36
Bhatia, S., Gordon, C. T., Foster, R. G., Melin, L., Abadie, V., Baujat, G., Vazquez, M., Amiel, J., Lyonnet, S., van Heyningen, V., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005193 · Cited by 35
“Sequence conservation of disease associated CREs was assessed by multiple sequence alignment and visualised using the VISTA or ECR Browser with the human hg19 sequence as base genome [38, 39].”
MethodExpression of a SOX1 overlapping transcript in neural differentiation and cancer models
Ahmad, A., Strohbuecker, S., Tufarelli, C., & Sottile, V. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2580-3 · Cited by 35
“org/) [33] was used to visualise and analyse Evolutionary Conserved Regions (ECRs) of SOX1OT sequence across different species.”
MethodKorostowski, L., Raval, A., Breuer, G., & Engel, N. (2011) · Epigenetics & Chromatin · doi:10.1186/1756-8935-4-21 · Cited by 35
“org) [15] revealed discrete evolutionarily conserved regions (ECRs) (parameters set to 70% identity with a minimum length of 100 bp) that were contained on restriction fragments that had been tested in the 3C substrates (Figure 3).”
Dcode.org anthology of comparative genomic tools
Loots, G. G., & Ovcharenko, I. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki355 · Cited by 37
“Finally, the ECR Browser tool (13) was created to provide an easy graphical interface to the generated alignments.”
MethodSelf-citationTenney, A. P., Gioia, S. A. D., Webb, B. D., Chan, W. M., de Boer, E., Garnai, S. J., Barry, B. J., Ray, T., Kosicki, M., Robson, C. D., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01424-9 · Cited by 31
Apolipoprotein M Gene (APOM) Polymorphism Modifies Metabolic and Disease Traits in Type 2 Diabetes
Zhou, J.-W., Tsui, S. K., Ng, M. C. Y., Geng, H., Li, S.-K., So, W. Y., Ronald, C. W., Wang, Y., Tao, Q., Chen, Z., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017324 · Cited by 34
“The Evolutionary Conserved Regions Browser [20] and the Ensembl Genome Browser were used to identify sequence conservation.”
MethodFernández, L. P., Milne, R. L., Barroso, E., Cuadros, M., Arias, J. I., Ruibal, Á., Benitez, J. J., & Ribas, G. (2006) · International Journal of Cancer · doi:10.1002/ijc.21847 · Cited by 34
Crumbley, C., Wang, Y., Banerjee, S., & Burris, T. P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033804 · Cited by 34
“2 library) [20], revealing a consensus ROR response element (RORE) ,1.”
BackgroundRuyck, K. D., Sabbe, N., Oberije, C., Vandecasteele, K., Thas, O., Ruysscher, D. D., Lambin, P., van Meerbeeck, J. P., Neve, W. D., & Thierens, H. (2011) · International Journal of Radiation Oncology*Biology*Physics · doi:10.1016/j.ijrobp.2011.03.012 · Cited by 34
Kim, F. A., Sing, A., Kaneko, T., Bieman, M. A., Stallwood, N., Sadl, V. S., & Cordes, S. P. (2005) · Mechanisms of Development · doi:10.1016/j.mod.2005.08.001 · Cited by 34
Gli3 Repressor Controls Cell Fates and Cell Adhesion for Proper Establishment of Neurogenic Niche
Wang, H., Kane, A. W., Lee, C., & Ahn, S. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.07.006 · Cited by 31
Loots, G. G. (2008) · Advances in genetics · doi:10.1016/s0065-2660(07)00010-7 · Cited by 34
“In addition to ready-made pairwise alignments, the ECR Browser also aligns user-provided sequences to available genomes and incorporates any available annotation into the visual display of the generated alignment.”
BackgroundMethodInfluentialSelf-citationCisView: A Browser and Database of cis-regulatory Modules Predicted in the Mouse Genome
Sharov, A. A., Dudekula, D. B., & Ko, M. S. H. (2006) · DNA Research · doi:10.1093/dnares/dsl005 · Cited by 34
Liew, C. F., Groves, C. J., Wiltshire, S., Zeggini, E., Frayling, T. M., Owen, K. R., Walker, M., Hitman, G. A., Lévy, J., O’Rahilly, S., et al. (2004) · Diabetologia · doi:10.1007/s00125-004-1575-4 · Cited by 33
“Homology mapping of mammalian (mouse, rat, human) genome sequence (using ECR browser, http://ecrbrowser.dcode.org, accessed 23 September 2004 [ 38 ]) around the SCD gene reveals several conserved noncoding sequences that are strong candidates for a functional role, and which therefore merit efforts to detect and type…”
BackgroundIdentification of regulatory elements in the Isl1 gene locus
Kappen, C., & Salbaum, J. M. (2009) · The International Journal of Developmental Biology · doi:10.1387/ijdb.082819ck · Cited by 31
“Sequence comparisons to other species were performed using the alignment function of the ECR browser (Ovcharenko et al., 2004).”
MethodHIV-1 Tat protein promotes neuronal dysregulation by inhibiting E2F transcription factor 3 (E2F3)
Santerre, M., Bagashev, A., Gorecki, L., Lysek, K. Z., Wang, Y., Shrestha, J., Carpio‐Cano, F. D., Mukerjee, R., & Sawaya, B. E. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.003744 · Cited by 31
“org/)(6) (65) and Target Scan Human (http://www.”
de Frutos, S., Nitta, C. H., Caldwell, E., Friedman, J. K., & Bosc, L. V. G. (2009) · American Journal of Physiology-Lung Cellular and Molecular Physiology · doi:10.1152/ajplung.00060.2009 · Cited by 32
Large-Scale Evidence for Conservation of NMD Candidature Across Mammals
Morais, D. A. D. L., & Harrison, P. M. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011695 · Cited by 31
“Using the ECR browser [37] to generate an alignment of the RPS13, we could observe a high GC content in the intron 1 (.”
MethodVedantham, V., Evangelista, M., Huang, Y., & Srivastava, D. (2012) · Developmental Biology · doi:10.1016/j.ydbio.2012.10.017 · Cited by 31
“2B) (Ovcharenko et al., 2004).”
Bentley, L., Esapa, C. T., Nesbit, M. A., Head, R. A., Evans, H., Lath, D., Scudamore, C. L., Hough, T., Podrini, C., Hannan, F. M., et al. (2013) · Endocrinology · doi:10.1210/en.2013-1247 · Cited by 31
Regulation of human trophoblast syncytialization by histone demethylase LSD1
Milano-Foster, J., Ray, S. S., Home, P., Ganguly, A., Bhattacharya, B., Bajpai, S., Pal, A., Mason, C., & Paul, S. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.010518 · Cited by 31
“The conserved GATA motifs at human CGA locus were identified via genome alignment in ECR Browser (97) (https://ecrbrowser.dcode.org).7 Sequences of ChIP primers are available on request.”
MethodGenomic approaches to studying human-specific developmental traits
Franchini, L. F., & Pollard, K. S. (2015) · Development · doi:10.1242/dev.120048 · Cited by 29
“In the absence of functionally annotated non-coding sequences, using this signature of negative selection in other species helps to enrich for regulatory elements with constrained function (Ovcharenko et al., 2004; Prabhakar et al., 2006b; Schwartz et al., 2000; Siepel et al., 2005).”
BackgroundKenney, J. W., Poole, R. L., Adoff, M. D., Logue, S. F., & Gould, T. J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039939 · Cited by 30
“Analysis of CREB binding to the jnk1 promoter region Initial in silico analysis of the jnk1 promoter region was performed using the evolutionary conserved region browser and the TransFac database [32,33].”
BackgroundMethodBirk, E., Har‐Zahav, A., Manzini, M. C., Pasmanik, M., Kornreich, L., Walsh, C. A., Noben‐Trauth, K., Albin‐Kaplanski, A., Simon, A. J., Colleaux, L., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.10.005 · Cited by 30
“696 The American Journal of Human Genetics 87, 694–700, Novemb August 2009), and Ensembl (GRCh37, February 2009) genome browsers (Figure 2A).(13) DNA and RNA binding motifs were predicted by the following servers: RNABindR, BindN, PPRint, and MEME.”
Resources and transgenesis techniques for functional genomics in Xenopus
Ogino, H., & Ochi, H. (2009) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2009.01098.x · Cited by 30
“Xenopus genomic resources cited in this article Resource name URL General Xenopus resource site Xenbase (with the link to G-Browse) http://xenbase.org/common/index.do Xenopus tropicalis genome project JGI genome browser http://genome.jgi-psf.org/Xentr4/Xentr4.home.html Ensembl genome browser http://www.ensembl.org/Xen…”
BackgroundInfluentialKeys, J. R., Tallack, M. R., Hodge, D. J., Cridland, S. O., David, R., & Perkins, A. C. (2006) · British Journal of Haematology · doi:10.1111/j.1365-2141.2006.06381.x · Cited by 30
“The evolutionary conserved region (ECR) browser interface (Ovcharenko et al, 2004) (http:// ecrbrowser.dcode.org/) was used to identify conserved regions of sequence homology throughout the AHSP gene across species.”
MethodElf5 regulation in the Trophectoderm
Pearton, D. J., Broadhurst, R. B., Donnison, M. J., & Pfeffer, P. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2011.10.007 · Cited by 30
GATA4/FOG2 transcriptional complex regulates Lhx9 gene expression in murine heart development
Smagulova, F. O., Manuylov, N. L., Leach, L. L., & Tevosian, S. G. (2008) · BMC Developmental Biology · doi:10.1186/1471-213x-8-67 · Cited by 29
“To demonstrate that the repression of the Lhx9 gene requires binding of the GATA4/FOG2 protein complex to the Lhx9 cis-regulatory elements we inspected the Lhx9 genomic locus using ECR (evolutionary conserved region) browser [47] (Additional File 3A).”
MethodLi, X., Florez, S. L., Wang, J., Cao, H., & Amendt, B. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054868 · Cited by 29
Muralidharan, B., Keruzoré, M., Pradhan, S. J., Roy, B., Shetty, A. S., Kinare, V., D’Souza, L., Maheshwari, U., Karmodiya, K., Suresh, A., et al. (2017) · Journal of Neuroscience · doi:10.1523/jneurosci.1535-17.2017 · Cited by 29
“A , B , ECR Browser view of the genomic region spanning 50 kb around the Dmrt5 locus.”
Nylén, C., Aoi, W., Abdelmoez, A. M., Lassiter, D. G., Lundell, L. S., Wallberg‐Henriksson, H., Näslund, E. B., Pillon, N. J., & Krook, A. (2018) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00398.2017 · Cited by 30
Metadata
- Authors
- Ovcharenko, I., Nobrega, M. A., Loots, G. G., & Stubbs, L.
- Affiliations
- Lawrence Livermore National Laboratory (US)
- Corresponding author
- Ovcharenko, I.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-07-01
- Volume
- 32
- Issue
- Web Server
- Pages
- W280-W286
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC441493
- OpenAlex
- W1981101983
- Cited by
- 519
- References
- 32
- Citations by year
- 2026: 6 · 2025: 9 · 2024: 10 · 2023: 8 · 2022: 13 · 2021: 32 · 2020: 23 · 2019: 19 · 2018: 27 · 2017: 21 · 2016: 24 · 2015: 21 · 2014: 23 · 2013: 42 · 2012: 40
- FWCI
- 8.17
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (W-7405, -7405-ENG-48)
- Biological and Environmental Research
- Lawrence Livermore National Laboratory (W-7405-ENG 48, -7405-Eng-48)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Keywords
- vertebrate genomes, gene discovery, gene regulatory elements, transcription factor binding site prediction, genome annotation
- MeSH terms
- Animals, Binding Sites, Computer Graphics, Fishes, Humans, Regulatory Sequences, Nucleic Acid, Software, Transcription Factors, Sequence Alignment, Genome, Sequence Analysis, DNA, Systems Integration, Internet, Genomics, Synteny, Mice, Rats
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