The version 15 database has been loaded and the appropriate files generated for The Development Site. The difference report is below the fold.
This time there is not a lot of new stuff. Seventy-five property name/value pairs were deleted and 17 new ones were added.
Difference Report for NMPDR 15.
| Statistics for old Sprout | |
|---|---|
| Genomes | 452 |
| Subsystems | 541 |
| Roles | 7706 |
| External function assignments | 10044671 |
| Features | 1946272 |
| Functional Coupling | 1030257 |
| Statistics for new Sprout | |
| Genomes | 452 |
| Subsystems | 541 |
| Roles | 7706 |
| External function assignments | 10044671 |
| Features | 1946272 |
| Functional Coupling | 1030257 |
| Candidates for Campylobacter: one | |
| Campylobacter fetus subsp. fetus 82-40 | 360106.3 |
| Deleted Properties: 75 | |
| Essential Gene Sets Bacterial = potential essential | 51 |
| SP essential merged = essential | 187 |
| SP essential merged = nonessential | 556 |
| SP essential merged = potential essential | 3 |
| SP essential merged = potential essential | 51 |
| SP essential merged = undetermined | 1246 |
| evidence code = icw(1);Alanine biosynthesis | 32 |
| evidence code = icw(1);Flavodoxin | 2 |
| evidence code = icw(1);Galactosylceramide and Sulfatide metabolism | 14 |
| evidence code = icw(1);General Secretion Pathway | 124 |
| evidence code = icw(1);Glycogen metabolism | 683 |
| evidence code = icw(1);uridine kinase cluster 1 | 155 |
| evidence code = idu(10);Alanine biosynthesis | 10 |
| evidence code = idu(10);Biotin biosynthesis | 54 |
| evidence code = idu(10);Galactosylceramide and Sulfatide metabolism | 10 |
| evidence code = idu(10);Methionine Biosynthesis | 10 |
| evidence code = idu(11);Biotin biosynthesis | 30 |
| evidence code = idu(11);Glutathione-regulated potassium-efflux system and associated functions | 11 |
| evidence code = idu(11);Peptidoglycan Biosynthesis | 33 |
| evidence code = idu(11);Threonine degradation | 11 |
| evidence code = idu(12);Biotin biosynthesis | 41 |
| evidence code = idu(13);Biotin biosynthesis | 13 |
| evidence code = idu(13);Glutathione-regulated potassium-efflux system and associated functions | 13 |
| evidence code = idu(14);Glutathione-regulated potassium-efflux system and associated functions | 25 |
| evidence code = idu(16);Glutathione-regulated potassium-efflux system and associated functions | 16 |
| evidence code = idu(17);Biotin biosynthesis | 17 |
| evidence code = idu(18);Peptidoglycan Biosynthesis | 36 |
| evidence code = idu(2);Flavodoxin | 90 |
| evidence code = idu(2);Galactosylceramide and Sulfatide metabolism | 73 |
| evidence code = idu(2);General Secretion Pathway | 11 |
| evidence code = idu(2);Glycogen metabolism | 139 |
| evidence code = idu(2);MT1-MMP Pericellular Network | 6 |
| evidence code = idu(21);Biotin biosynthesis | 16 |
| evidence code = idu(22);Biotin biosynthesis | 18 |
| evidence code = idu(29);Biotin biosynthesis | 26 |
| evidence code = idu(3);Flavodoxin | 11 |
| evidence code = idu(3);Galactosylceramide and Sulfatide metabolism | 24 |
| evidence code = idu(3);General Secretion Pathway | 3 |
| evidence code = idu(3);Glycogen metabolism | 6 |
| evidence code = idu(3);MT1-MMP Pericellular Network | 9 |
| evidence code = idu(32);Biotin biosynthesis | 28 |
| evidence code = idu(34);Biotin biosynthesis | 28 |
| evidence code = idu(4);Flavodoxin | 24 |
| evidence code = idu(4);Galactosylceramide and Sulfatide metabolism | 32 |
| evidence code = idu(4);Glycogen metabolism | 7 |
| evidence code = idu(4);KDO2-Lipid A biosynthesis | 2 |
| evidence code = idu(4);MT1-MMP Pericellular Network | 8 |
| evidence code = idu(4);Proline Synthesis | 17 |
| evidence code = idu(4);carnitine metabolism | 8 |
| evidence code = idu(5);Alanine biosynthesis | 73 |
| evidence code = idu(5);Biotin biosynthesis | 135 |
| evidence code = idu(5);Flavodoxin | 5 |
| evidence code = idu(5);Galactosylceramide and Sulfatide metabolism | 30 |
| evidence code = idu(5);MT1-MMP Pericellular Network | 5 |
| evidence code = idu(5);Proline Synthesis | 4 |
| evidence code = idu(6);Auxin biosynthesis | 6 |
| evidence code = idu(6);Biotin biosynthesis | 118 |
| evidence code = idu(6);Galactosylceramide and Sulfatide metabolism | 6 |
| evidence code = idu(6);Threonine synthesis | 4 |
| evidence code = idu(7);Biotin biosynthesis | 77 |
| evidence code = idu(7);Flavodoxin | 7 |
| evidence code = idu(7);MT1-MMP Pericellular Network | 7 |
| evidence code = idu(7);Peptidoglycan Biosynthesis | 21 |
| evidence code = idu(8);Biotin biosynthesis | 21 |
| evidence code = idu(8);Fe-S cluster assembly | 5 |
| evidence code = idu(8);Glutathione-regulated potassium-efflux system and associated functions | 16 |
| evidence code = idu(8);Peptidoglycan Biosynthesis | 15 |
| evidence code = idu(9);Biotin biosynthesis | 24 |
| evidence code = idu(9);Galactosylceramide and Sulfatide metabolism | 9 |
| evidence code = isu;Flavodoxin | 349 |
| evidence code = isu;Galactosylceramide and Sulfatide metabolism | 121 |
| evidence code = isu;General Secretion Pathway | 144 |
| evidence code = isu;Glycogen metabolism | 964 |
| evidence code = isu;MT1-MMP Pericellular Network | 6 |
| evidence code = isu;uridine kinase cluster 1 | 165 |
| New Properties: 17 | |
| essential = Hutchison CA | 348 |
| evidence code = icw(1);Glyoxylate dicarboxylate metabolism | 902 |
| evidence code = idu(2);Alanine Biosynthesis | 32 |
| evidence code = idu(2);Glyoxylate dicarboxylate metabolism | 317 |
| evidence code = idu(3);Alanine Biosynthesis | 48 |
| evidence code = idu(3);Glyoxylate dicarboxylate metabolism | 155 |
| evidence code = idu(3);Malonate decarboxylase | 10 |
| evidence code = idu(3);carnitine metabolism | 1 |
| evidence code = idu(4);Alanine Biosynthesis | 24 |
| evidence code = idu(4);Glyoxylate dicarboxylate metabolism | 57 |
| evidence code = idu(4);Malonate decarboxylase | 6 |
| evidence code = idu(5);Glyoxylate dicarboxylate metabolism | 15 |
| evidence code = idu(6);Alanine Biosynthesis | 18 |
| evidence code = idu(6);Glyoxylate dicarboxylate metabolism | 6 |
| evidence code = idu(7);Alanine Biosynthesis | 7 |
| evidence code = isu;Alanine Biosynthesis | 121 |
| evidence code = isu;Glyoxylate dicarboxylate metabolism | 1184 |
Comments (1)
One of the new properties (essential = Hutchison CA) is the corrected data set for the essential genes list linked from the M. genitalium bar of the graph. The link presently reads as follows: ../FIG/SearchSkeleton.cgi?propName=MG_essential_Hutchison_2006;subsystem=(all);genome=243273.1;SPROUT=1;Search=Go;propValue=essential, potential_essential;Class=FidSearch;NoForm=1
So my question is how do I rephrase this for the new property; does propName=essential and propValue=Hutchison_CA, or vice-versa?
Posted by leslie | October 10, 2006 12:00 PM
Posted on October 10, 2006 12:00