Andrew Forney Week 7

Author: Andrew Forney

Assignment: Individual Journal 7

Biological Vocabulary

 * 1) Alternative splicing: the mechanism by which a given gene may be expressed into different mRNA molecules, and then into different types of proteins. (http://www.beelib.com/bee/jsp/us/resultPage.jsp)
 * 2) Exons: The region of a gene that contains the code for producing protein. Each exon codes for a specific portion of the complete protein. Exons are separated by introns, long regions of DNA that have no apparent function. (http://www.medterms.com/script/main/art.asp?articlekey=3353)
 * 3) Gene expression: The translation of information encoded in a gene into protein or RNA. Expressed genes include genes that are transcribed into messenger RNA (mRNA) and then translated into protein, as well as genes that are transcribed into types of RNA such as transfer RNA (tRNA) and ribosomal RNA (rRNA) that are not translated into protein. Gene expression is a highly specific process in which a gene is switched on at a certain time and "speaks out." (http://www.medterms.com/script/main/art.asp?articlekey=3564)
 * 4) RNA interference: The introduction of double-stranded RNA into a cell to inhibit the expression of a gene. Also known as RNA silencing, inhibitory RNA, and RNA inactivation. (http://www.medterms.com/script/main/art.asp?articlekey=20611)
 * 5) Biological assays: determination of the active power of a drug sample by comparing its effects on a live animal or an isolated organ preparation with those of a reference standard. (http://medical-dictionary.thefreedictionary.com/Biological+assay)
 * 6) Polymorphisms: A variation in the DNA that is too common to be due merely to new mutation. A polymorphism must have a frequency of at least 1% in the population. (http://www.medterms.com/script/main/art.asp?articlekey=4992)
 * 7) Genomic amplifications: A cellular process characterized by the production of multiple copies of a particular gene or genes to amplify the phenotype that the gene confers on the cell. Drug resistance in cancer cells is linked to amplification of the gene that prevents absorption of the chemotherapeutic agent by the cell. (http://www.thefreedictionary.com/gene+amplification)
 * 8) Homology: similarity in sequence of a protein or nucleic acid between organisms of the same or different species. (Mac Dictionary)
 * 9) Proteomic: of, or relating to, the study of proteins, or the complete set of proteins produced by a species, using the technologies of large-scale protein separation and identification. (http://www.medterms.com/script/main/art.asp?articlekey=16299)
 * 10) Monoamine receptors: membrane-bound receptors that are coupled to G-proteins. Upon stimulation by agonists, they initiate a cascade of intracellular events that guide biochemical reactions of the cell. (http://www.ncbi.nlm.nih.gov/pubmed/10603576)

Outline: Salomonis et al. (2007) -- GenMAPP 2

 * 1) The purpose of GenMAPP 2, and its predecessor, is to improve the communicative and expressive power behind microarray data analysis in order to better empower and connect the scientific community
 * 2) *	GenMAPP stands for “Gene Map Annotator and Pathway Profiler”
 * 3) *	GenMAPP allows for pathway-based analysis of microarray data
 * 4) 	GenMAPP is a response to biologist needs for clearer representation of genomic data
 * 5) *	Difficulties linking gene-level info to specific higher-level processes
 * 6) *	GenMAPP provides pathway-level information in an attempt to bridge the gap between the micro- and the macro-analysis
 * 7) *	In order to better serve the community, GenMAPP is free, open-source, and client-side software
 * 8) 	Programmed in visual basic, binding GenMAPP to Windows platforms, but allows for several key components
 * 9) *	Records experimental data, gene databases, and pathways separately
 * 10) *	Distributed pathways are reviewed by the GenMAPP staff
 * 11) 	GenMAPP 2 improves upon its predecessor in a variety of manners, addressing those most in demand by the community of biologists
 * 12) *	Major shortcoming of GenMAPP 1: limited species and gene expansion
 * 13) *#	GenMAPP 2 provides a new database schema to provide unlimited species support and genomic expansion
 * 14) *#	New additions to database including OMIM, GO, and PDB to provide better primary source connection
 * 15) *#	Semi-autonomous database population using established database record tables such as from Uniprot and Ensembl
 * 16) *#	Allows for custom gene database definition
 * 17) *	GenMAPP 1 did not allow for easy viewing of time-influenced changes at the genomic level; GenMAPP 2 improves upon this
 * 18) *#	New version allows multiple defined color schemes to be viewed at the same time for swift juxtaposition
 * 19) *#	Extends to easy viewing of RNA transcription and exon portions, allowing multi color scheme views all in one window
 * 20) *	MAPPed data made more portable to reach a wider audience by sporting a variety of new web-ready exports
 * 21) *#	Exported maps retain their interactive nature, capable of linking to their respective components after compilation
 * 22) *#	The level of responsiveness imbued in these exports is a unique feature of GenMAPP (unavailable in its peers’ features)
 * 23) *#	Color schemes can be customized for export and visualization is highly malleable to maximize readability for a wider audience
 * 24) *	GenMAPP provides potent drawing utilities to link pathways in an individual-oriented focus for community curation
 * 25) *#	Customizable layouts allows inter- and intra-linking of map entries for a truly expressive form of communication
 * 26) *#	Already several efforts at community projects, including efforts at Johns Hopkins, the University of Bioinformatics, and even LMU!
 * 27) *	New support for homology maps that can serve as starting points for further mappings
 * 28) *#	“Conversion” function in GenMAPP 2 adds homology information via communication between other databases and a specific map without altering the content of the map
 * 29) *#	Allows for abstraction from the “top down”—human to new species—because human records are the most complete
 * 30) *#	Figure 1: juxtaposes human and dog signaling pathway homologized from preexisting human record
 * 31) *#	Table 1: Illustrates the limitations of the homologizing powers of GenMAPP based on comparisons with different species
 * 32) *# Figure 2: Corroborates the previously acknowledged limitation by displaying the Conversion function’s success rate across species
 * 33) *	Challenge to extend existing pathways in an efficient manner while faced with the slower pace of pathway creation and curation
 * 34) *#	New pathway extension includes additional genes into the preexisting pool to improve pathway coverage about 25%
 * 35) *#	Gene ID’s extracted for one instance and are used as uniform ID’s to query a multitude of other databases
 * 36) *# Figure 3: Illustrates the overlap between GenMAPP data and Gene Ontology and the subsequent benefits of inter-database extraction
 * 37) *# Figure 4: Emphasizes the power in coexpression network extension by showing this tool in action in GenMAPP (items in sidebar)
 * 38) 	The powerful data visualization afforded by GenMAPP 2 can be grasped by several illustrative examples displaying some features unique to this software
 * 39) * Figure 6: Displays power of multi-color denotation as well as multiple data types and data sets all on one screen for easier analysis
 * 40) * Figure 5: Illustrates the potential of color-coated time-course analysis of genomic effects from certain stimuli
 * 41) *	One experiment was used to show the potential examination of whole-genome exon array data
 * 42) *#	Unique to GenMAPP 2 is the viewing of identifiers to a related gene based on colored prioritization to provide a novel visual for analysis
 * 43) *#	This strategy allows for clear representation of what tissues in which some genes are most significantly expressed
 * 44) *	Another experiment compared gene expression and proteomic data of mRNA and protein levels in yeast when exposed to changes in carbon source
 * 45) *#	Physically concurrent coloring bands are used to clearly illustrate the time-effect data using GenMAPP’s color visualization
 * 46) *#	Side-by-side comparisons of this nature are unique to GenMAPP and have very malleable implications as far as analysis is concerned
 * 47) *	A third example illustrates the streamline combination of genomic, phenotypic, and structural information of polymorphisms
 * 48) *#	This feature grants a broad, predictive view of how various polymorphisms, and their proteomic distributions, can have an effect on greater biological systems
 * 49) *#	Using this paradigm, GenMAPP adopts customizable displays to access multiple gene regulations at once
 * 50) 	The future directions of GenMAPP development are primarily threefold:
 * 51) *	Focus on cross-platform adaption of the software
 * 52) *	Create dynamically updated gene databases to further automation
 * 53) *	Continue development of tools to quickly analyze high-throughput data
 * 54) 	Main result: GenMAPP 2 provides powerful tools to visually interpret complex microarray data and pathway changes across a plethora of organisms, and then to share these results in the most efficient manner available

Individual Assignment in Word Format
Allows for portable viewing and proof that the outline meets the specifications

[[Media:BIOL_367_Assignment_-_GenMAPP_2_Information.docx|BIOL 367 Assignment - Individual Journal 7]]

Group Presentation in PowerPoint (2007) Format
[[Media:BIOL_367_Presentation_-_GenMAPP_2.pptx|BIOL 367 Presentation - GenMAPP 2]]