System and process of determining a biological pathway based on a treatment of a biological specimen
Provided herein is a system and method for analyzing microarray data (transcriptome profiles), metabolite data (metabolome profiles), protein level data (proteome profiles), or any combination thereof to determine the biochemical pathways affected by a treatment. The system and method can be used to generate biochemical pathway information for any organism for which metabolic profile data can be obtained. The system and method may allow users to query the pathways generated and to filter the results of queries based on the -omic profile data, pathways involving molecules of interest, notions of biochemical importance, milestone molecules, and other factors. The system and method may also be suitable for discovery of regulatory sequences in genes. In an exemplary use, the system and method can be utilized to identify three genes involved in “de novo” ammonia “biosynthesis” that are induced by light, and was able to identify a putative cis-element, GWTTGTGG, that is likely involved in the regulation of those genes.
1. A computer-readable medium having stored thereon computer-executable instructions for determining a biological pathway based on a treatment of a biological specimen, wherein, when the instructions are executed by a processor, the following procedures are performed, the procedures comprising:
obtaining at least one profile generated from a treated biological specimen;
determining whether the at least one profile contains information that matches with information associated with a reference biological pathway; and
generating the reference biological pathway using a user-selectable criterion and based on the matched information;
wherein the reference biological pathway comprises biological reactions obtained from a reference database having a plurality of records,
wherein each of the records comprises a biological reaction containing a plurality of molecules,
wherein the user-selectable criterion comprises an importance factor assigned to one or more products of the biological reactions located in the records of the reference database, and
wherein the plurality of molecules are selected from among substrates and products.
2. The computer-readable medium of claim 1 , wherein the reference biological pathway is generated using a transitive closure matrix.
3. The computer-readable medium of claim 1 , wherein each of the records comprises at least one product and at least one substrate associated with the biological reaction.
4. The computer-readable medium of claim 3 , wherein each of the records further comprises information based on at least one of an enzyme or free energy associated with the biological reaction.
5. The computer-readable medium of claim 3 , wherein the reference biological pathway is generated by:
(a) identifying at least one molecule;
(b) searching the records of the reference database for information concerning the at least one molecule;
(c) identifying which of the records has information concerning the at least one molecule;
(d) identifying further molecules associated with the identified one or more records of (c);
(e) searching the reference database to identify further biological reactions using the further molecules identified in (d);
(f) linking the biological reaction of the identified records of (c) with the further biological reactions of (e) based on a common molecule to build a reference biological pathway, wherein the linking substep includes defining the product of the biological reaction as a substrate for a subsequently linked biological reaction; and
(g) repeating (b) to (f) until every record in the reference database is searched.
6. The computer-readable medium of claim 1 , wherein the importance factor determines whether the identified biological reaction associated with the product is to be eliminated from the reference biological pathway.
7. The computer-readable medium of claim 5 , further comprising searching a second reference database comprising a plurality of records, wherein each of the records contains information relating to a transporter biological reaction, and wherein each of the records comprises a transporter protein, a molecule and an organelle.
8. The computer-readable medium of claim 7 , wherein each of the records is assigned a unique identifying number.
9. The computer-readable medium of claim 7 , wherein the at least one molecule is assigned further unique identifying numbers, wherein one of the further unique identifying numbers corresponds to the at least one molecule at an external position and another one of the further unique identifying numbers corresponds to the at least one molecule at an internal position.
10. The computer-readable medium of claim 7 , wherein each of the records further comprises information associated with a directionality of the transporter.
11. The computer-readable medium of claim 1 , wherein each of the records is assigned a unique identifying number.
12. The computer-readable medium of claim 1 , wherein each of the records further comprises information associated with a subcellular localization of one of the product, the substrate, and an enzyme.
13. The computer-readable medium of claim 1 , wherein each of the plurality of molecules has a unique identifying number.
14. The computer-readable medium of claim 1 , wherein the at least one profile is obtained from microarray data generated from the treated biological specimen.
15. The computer-readable medium of claim 13 , wherein the at least one profile is obtained from microarray data generated from the treated biological specimen.
16. The computer-readable medium of claim 15 , wherein the unique identifying number is based on a gene and an identification number.
17. The computer-readable medium of claim 1 , wherein the at least one profile is selectively obtained from a profile containing metabolic information in combination with at least one of a transcriptional profile and a proteomic profile.