Zrusso Week 9

Number of errors detected

 * I detected 772 errors out of 5221 records in the old database from 2009
 * Richard detected 121 errors out of 5221 records while using the new database from 2010
 * I have more errors, which is to be expected from an older database that is not as comprehensive as the newer database which includes data from more sources.

Top 10 Gene Ontology Terms from MAPPFinder

 * For me
 * 1) Localization
 * 2) Cellular Biopolymer Biosynthetic Process
 * 3) Biopolymer Biosynthetic Process
 * 4) Cellular Macromolecule Biosynthetic Process
 * 5) Macromolecule Biosynthetic Process
 * 6) Cellular Macromolecule Metabolic Process
 * 7) Macromolecule Metabolic Process
 * 8) Cell Projection Organization
 * 9) Biopolymer Metabolic Process
 * 10) Transporter Activity


 * For Richard
 * 1) Branched Chain Family Amino Acid Metabolic Process
 * 2) Branched Chain Family Amino Acid Biosynthetic Process
 * 3) IMP Biosynthetic Process
 * 4) IMP Metabolic Process
 * 5) Arginine Metabolic Process
 * 6) Cellular Nitrogen Compound Biosynthetic Process
 * 7) Leucine Biosynthetic Process
 * 8) Leucine Metabolic Process
 * 9) Amine Biosynthetic Process
 * 10) Arginine Biosynthetic Process

Genes Listed in Merrell et al. (2003

 * For Me
 * VC0028 - NOT FOUND
 * VC0941 - NOT FOUND
 * VC0869 - NOT FOUND
 * VC0051 - NOT FOUND
 * VC0647
 * mRNA catabolic process
 * RNA processing
 * cytoplasm
 * RNA binding
 * 3'-5' exoribonuclease activity
 * transferase activity
 * nucleotidyltransferase activity
 * polyribonucleotide nucleotidyltransferase activity
 * VC0468 - NOT FOUND
 * VC2350 - NOT FOUND
 * VCA0583
 * transport
 * outer membrane-bounded periplasmic space
 * transporter activity
 * For Richard
 * VC0028
 * metal ion binding
 * iron-sulfur cluster binding
 * 4 iron, 4 sulfur cluster binding
 * catalytic activity
 * lyase activity
 * dihydroxy-acid dehydratase
 * VC0941
 * pyridoxal phosphate binding
 * catalytic activity
 * glycine hydroxymethyltransferase
 * VC0869
 * nucleotide binding
 * ATP binding
 * catalytic activity
 * ligase activity
 * phosphoribosilformylglycinamidine synthase activity
 * VC0051
 * nucleotide binding
 * ATP binding
 * catalytic activity
 * lyase activity
 * carboxy-lyase activity
 * phosphoribosylaminoimidazole caroxylase activity
 * VC0647
 * nucleotidyltransferase activity
 * polyribonucleotide nucleotidyltransferase activity
 * VC0468
 * metal ion binding
 * nucleotide binding
 * ATP binding
 * catalytic activity
 * ligase activity
 * glutathione synthase activity
 * VC2350
 * catalytic activity
 * lyase activity
 * deoxyribose-phosphate aldolase activity
 * VCA0583
 * outer membrane-bounded periplasmic space

VCA0583

 * I picked VCA0583 as the gene to examine more closely
 * Its acession number ID is Q9KM06
 * After reading the UniProt and Pfam and Gene Ontology websites on this gene, it was clear that all knew that VCA0583 was part of the transport activity in the cell membrane, but none were very clear on what it did exactly. the closest was Pfam which thought it wasn't actually a transporter, merely a binding site for a signalling molecule which precluded a transport of some type.

Data from txt file
The z score is based on an N of 2475 and a R of 219 distinct genes in the GO.
 * From Me
 * 339 probes met the [Avg_LogFC_all] > .25 AND [Pvalue] < .05 criteria.
 * 291 probes meeting the filter linked to a UniProt ID.
 * 184 genes meeting the criterion linked to a GO term.
 * 5221 Probes in this dataset
 * 4449 Probes linked to a UniProt ID.
 * 1990 Genes linked to a GO term.
 * The z score is based on an N of 1990 and a R of 184 distinct genes in the GO.
 * From Richard
 * 339 probes met the [Avg_LogFC_all] > .25 AND [Pvalue] < .05 criteria.
 * 338 probes meeting the filter linked to a UniProt ID.
 * 219 genes meeting the criterion linked to a GO term.
 * 5221 Probes in this dataset
 * 5100 Probes linked to a UniProt ID.
 * 2475 Genes linked to a GO term.

Interpretation of Results

 * cell projection organization - A process carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell like a flagellum or an axon.
 * flagellum organization - A process carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a flagellum.
 * extracellular region - The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane.
 * thiamin pyrophosphate binding - Interacting selectively and non-covalently with thiamin pyrophosphate, the diphosphoric ester of thiamin.
 * magnesium ion binding - Interacting selectively and non-covalently with magnesium ions.
 * branched chain family amino acid metabolic process - The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
 * flagellin-based flagellum basal body, distal rod - The portion of the central rod of the flagellar basal body that is distal to the cell membrane; spans most of the distance between the inner and outer membranes.
 * flagellin-based flagellum basal body, rod - The central portion of the flagellar basal body, which spans the periplasm and threads through the rings.
 * pigment metabolic process - The chemical reactions and pathways involving pigment, any general or particular coloring matter in living organisms like melanin.
 * pigment biosynthetic process - The chemical reactions and pathways resulting in the formation of a pigment, any general or particular coloring matter in living organisms like melanin.
 * hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines - Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amidine, a compound of the form R-C(=NH)-NH2.
 * hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides - Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
 * monocarboxylic acid transmembrane transporter activity - Catalysis of the transfer of monocarboxylic acids from one side of the membrane to the other.
 * monocarboxylic acid transport - The directed movement of monocarboxylic acids into, out of or within a cell, or between cells by means of some agent such as a transporter or pore.
 * vitamin transporter activity - Enables the directed movement of vitamins into, out of or within a cell, or between cells. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
 * cobalamin transporter activity - Enables the directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell.
 * nucleobase metabolic process - The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine.
 * nucleobase biosynthetic process - The chemical reactions and pathways resulting in the formation of a nucleobase, a nitrogenous base that is a constituent of a nucleic acid.
 * purine base metabolic process - The chemical reactions and pathways involving purine bases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
 * purine base biosynthetic process - The chemical reactions and pathways resulting in the formation of purine bases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.

These first two terms, flagellum and cell projection organization deal with the process of creating and disassembling cell projections and specifically the flagellum, which is required for moving a bacterium. Extracellular region component also deals with the region outside the plasma membrane. It is not directly associated with the previous two terms however they all deal with the region directly outside the cell and how the cell interacts with that region. Since I am analyzing the increase data in the pathogenic strain, this means that the pathogenic V. cholerae is more motile then the non-pathogenic strain. Thiamin pyrophosphate binding is the molecular process dealing with the interaction with thiamin pyrophosphate. I am not quite sure how this relates to V. cholerae being pathogenic. Magnesium ion binding is the molecular function relating to the binding to magnesium ion. I am also not sure how this relates to pathogenicity in V. cholerae. Branched chain family amino acid metabolic process is the process encompassing the chemical reactions and pathways involving branched chain amino acids. I am not exactly sure how this relates to pathogenicity but it most likely relates to the creation of certain proteins that require more branched chain amino acids. Flagellin-based flagellum basal body, distal rod is the cellular component of the flagellum distal to cell membrane and spans the space between the inner and outer membrane. This along with the flagellin-based flagellum basal body, rod cellular component both are the parts of the flagellum which move the bacterial cell. While these components are not directly associated with the first three tems, they all deal with cellular parts on the exterior or outside of the cell. The pigment metabolic process and the pigment biosynthetic process both deal with the chemical reactions and pathways resulting in the formation of a pigment, any general or particular coloring matter in living organisms like melanin. I honestly have no clue how pigmentation relates to pathogenicity. Hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines and hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides are both molecular functions that deal with the catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond. These both relate to the creation of amidines or amines for which again like some previous terms relate to the creation of proteins which no doubt are required for pathogenicity that the lab strains do not have. Monocarboxylic acid transmembrane transporter activity and monocarboxylic acid transport both deal with the transfer of monocarboxylic acids from one side of the cell membrane to another. It is likely that the pathogenic strans require either more or different monocarboxylic acids than the non-pathogenic strain. Vitamin transporter activity is the parent to cobalamin transporter activity and both deal with the transport of vitamins across the cell membrane, so the pathogenic strain no doubt needs more vitamins, specifically cobalamin than the non-pathogenic strain. The nucleobase metabolic process, the nucleobase biosynthetic process and the purine biosynthetic and metabolic processes all deal with the chemical reactions and pathways that relate involve nucleobases like purines and pyrimidines, but specifically purines as we can see that purines are also increased in the pathogenic strain.

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