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Annotations S. cerevisiae (yeast) - ORF (i.e. YNR023W) S. cerevisiae (yeast) - UniprotAC (i.e. P53628) H. sapiens (human) - UniprotAC (i.e. M0R2A7) H. sapiens (human) - ENSEMLB protein (i.e. ENSP00000414321) M. musculus (mouse) - Uniprot AC (i.e. Q60860) M. musculus (mouse) - STRING (i.e. 10090.ENSMUSP00000000003) C. elegans (caeel) - Uniprot AC (i.e. Q95YA4) C. elegans (caeel) - STRING (i.e. 6239.B0310.5) D. melanogaster (drome) - Uniprot AC (i.e. Q8IR73) E. coli (ecoli) - Uniprot AC (i.e. P0AG51) E. coli (ecoli) - STRING (i.e. 511145.b0155) D. rerio (danre) - STRING (i.e. 7227.FBpp0070248)

Scales Aggregation - Pawar, J. Mol. Biol. 2005, 350:379–392 Aggregation - Conchillo-Sole, BMC Bioinformatics 2007, 8:65 Aggregation low - Tartaglia, J Mol Biol 2008, 380(2):425-36 Aggregation med - Tartaglia, J Mol Biol 2008, 380(2):425-36 Aggregation high - Tartaglia, J Mol Biol 2008, 380(2):425-36 Aggregation low - Ferdandez-Escamilla, Nat. Biotechnol. 2004, 22(10):1302-6 Aggregation med - Ferdandez-Escamilla, Nat. Biotechnol. 2004, 22(10):1302-6 Aggregation high - Ferdandez-Escamilla, Nat. Biotechnol. 2004, 22(10):1302-6 Aggregation - Tartaglia, J. Mol. Biol. 2010, 402:919–928 Aggregation - Tartaglia, Protein Science 2005, 14:2735-2740 Alpha-helix, Deleage-Roux, Protein Engineering 1987, 1:289-294 Normalized frequency of alpha-helix, Chou-Fasman, Adv. Enzym. 1978, 47:45-148 Normalized frequency of alpha-helix, with weights, Levitt, Biochemistry 1978, 17:4277-4285 Normalized frequency of alpha-helix, unweighted Levitt, Biochemistry 1978, 17:4277-4285 Normalized frequency of alpha-helix, Burgess et al, Isr.J.Chem. 1974, 12:239-286 Normalized frequency of middle helix, Crawford et al., Proc. Natl. Acad. Sci. USA 1973, 70:538-542 Average relative probability of helix, Kanehisa-Tsong, Biopolymers 1980, 19:1617-1628 Normalized frequency of alpha-helix in all-alpha class, Palau et al., Int. J. Peptide Protein Res. 1981, 19:394-401 Relative frequency in alpha-helix, Prabhakaran, Biochem. J. 1990, 269:691-696 Information measure for alpha-helix, Robson-Suzuki, J. Mol. Biol. 1976, 107:327-356 Normalized frequency of beta-sheet, Chou-Fasman, Adv. Enzymol. 1978, 47:45-148 Normalized frequency of beta-sheet, Crawford et al, Proc. Natl. Acad. Sci. USA 1973, 70:538-542 Average relative probability of beta-sheet, Kanehisa-Tsong, Biopolymers 1980, 19:1617-1628 Average relative probability of inner beta-sheet, Kanehisa-Tsong, Biopolymers 1980, 19:1617-1628 Normalized frequency of beta-sheet, with weights, Levitt, Biochemistry 1978, 17:4277-4285 Normalized frequency of beta-sheet, unweighted, Levitt, Biochemistry 1978, 17:4277-4285 Normalized frequency of beta-sheet in all-beta class, Palau et al., Int. J. Peptide Protein Res. 1981, 19:394-401 Relative frequency in beta-sheet, Prabhakaran, Biochem. J. 1990, 269:691-696 Information measure for pleated-sheet, Robson-Suzuki, J. Mol. Biol. 1976, 107:327-356 Beta-sheet, Deleage-Roux, Protein Engineering 1987, 1:289-294 Membrane-buried preference parameters, Argos et al., Eur. J. Biochem. 1982, 128:565-575 Average volume of buried residue, Chothia, Nature 1975, 254:304-308 Proportion of residues 95% buried, Chothia, J. Mol. Biol. 1976, 105:1-14 Proportion of residues 100% buried, Chothia, J. Mol. Biol. 1976, 105:1-14 Percentage of buried residues, Janin et al., J. Mol. Biol. 1978, 125:357-386 Ratio of buried and accessible molar fractions, Janin, Nature 1979, 277:491-492 Energy transfer from out to in(95%buried), Radzicka-Wolfenden, Biochemistry 1988, 27:1664-1670 Mean area buried on transfer, Rose et al., Science 1985, 229:834-838 Propensity to be buried inside, Wertz-Scheraga, Macromolecules 1978, 11:9-15 Mean volumes of residues buried in protein interiors, Harpaz et al., Structure 1994, 2:641-649 The Chou-Fasman parameter of the coil conformation, Charton-Charton, J. Theor. Biol. 1983, 111:447-450 Normalized relative frequency of coil, Isogai et al., Biopolymers 1980, 19:1183-1210 Normalized frequency of coil, Nagano, J. Mol. Biol. 1973, 75:401-420 Normalized frequency of coil, Tanaka-Scheraga, Macromolecules 1977, 10:9-20 TOP-IDB, Dunker AK, Protein Pept Lett. 2008; 15(9): 956–963 B-Value / Dunker AK, Protein Pept Lett. 2008; 15(9): 956–963 DisProt, Dunker AK, Protein Pept Lett. 2008; 15(9): 956–963 Average flexibility indices, Bhaskaran-Ponnuswamy, Int. J. Peptide Protein Res. 1988, 32:241-255 UnfoldOverFold, Dunker AK, Protein Pept Lett. 2008; 15(9): 956–963 Coil, Deleage-Roux, Protein Engineering 1987, 1:289-294 Hydrophobicity, Eisenberg et al, J. Mol. Biol. 1984, 179:125-142 Hydrophobicity, Kyte & Doolittle, J. Mol. Biol. 1982, 157:105-132 Hydrophobicity, Sweet et al., J. Mol. Biol. 1983, 171:479-488 Hydrophobicity, Roseman, J. Mol. Biol. 1988, 200:513-522 Hydrophobicity, Bull & Breese, Arch. Biochem. Biophys. 1974, 161:665-670 Hydrophobicity, Janin, Nature 1979, 277:491-492 Hydrophobicity, Abraham & Leo, Proteins: Structure; Function and Genetics 1987, 2:130-152 Hydrophobicity, Black, Anal. Biochem. 1991, 193:72-82 Hydrophobicity, Rao & Argos, Biochim. Biophys. Acta 1986, 869:197-214 Hydrophobicity, Fauchere et al., Eur. J. Med. Chem. 1983, 18:369-375 Membrane-buried preference parameters, Argos et al., Eur. J. Biochem. 1982, 128:565-575 AA composition of membrane proteins, Nakashima et al., Proteins 1990, 8:173-178 Normalized composition of membrane proteins, Nakashima et al., Proteins 1990, 8:173-178 Transmembrane regions of non-mt-proteins, Nakashima et al., Proteins 1990, 8:173-178 Transmembrane regions of mt-proteins, Nakashima et al., Proteins 1990, 8:173-178 Turn propensity scale for transmembrane helices, Monne et al., J. Mol. Biol. 1999, 288:141-145 Averaged turn propensities in a transmembrane helix, Monne et al., J. Mol. Biol. 1999, 293:807-814 Composition of amino acids in membrane proteins (percent), Cedano et al., J. Mol. Biol. 1997, 266:594-600 Knowledge-based membrane-propensity scale from 1D_Helix in MPtopo databases, Punta-Maritan, Proteins 2003, 50:114-121 Knowledge-based membrane-propensity scale from 3D_Helix in MPtopo databases, Punta-Maritan, Proteins 2003, 50:114-121 Nucleic Acid Binding - _interface_close-1, Terribilini et al., RNA 2006, 12:1450-1462 Nucleic Acid Binding - classicalRBD, Castello et al., Cell 2011, 149:1393-1406 Nucleic Acid Binding - HB, Nucleic Acids Res. 2011, 39:D277–D282 Nucleic Acid Binding - HOH, Nucleic Acids Res. 2011, 39:D277–D282 Nucleic Acid Binding - interface, Nucleic Acids Res. 2011, 39:D277–D282 Nucleic Acid Binding - interface_center, Terribilini et al., RNA 2006, 12:1450-1462 Nucleic Acid Binding - interface_close+1, Terribilini et al., RNA 2006, 12:1450-1462 Nucleic Acid Binding - mRNAinteractome, Castello et al., Cell 2011, 149:1393-1406 Nucleic Acid Binding - nonclassicalRBD, Castello et al., Cell 2011, 149:1393-1406 Nucleic Acid Binding - unknownRBD, Castello et al., Cell 2011, 149:1393-1406

Normalisation No normalisation between 0 and 1

Expression scale natural logarithm linear

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