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Class Projects
Future Work and Possible Project
Topic in Gene Regulatory network
Learning from multiple data sources;
Learning causality in Motifs;
Learning GRN with feedback loops;
Learning from multiple data
sources
 We have gene
expression data and
topological ordering
information;
 Incorporating some
other data sources as
prior knowledge for the
learning;
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Transcription factor
binding location data;
…
Example: Partial regulatory network recovered
using expression data and location data.
Learning Causality in Motifs
•They be used to assemble a transcriptional regulatory network.
•Network motifs are the simplest units of network architecture.
Learning GRN with feedback
loops
Learning GRN with feedback loops
(Con’dProtein-Protein Interactions
Future work and Possible Project
Topics in protein interaction
 Learning from multiple data sources;
 Disease related protein-protein interactions;
 Learning from different species;
Learning from Multiple data sources
(a) Gene Neighbor:
identifies protein pair
encoded in close
proximity across multiple
genomes.
(b) Rosetta Stone
(c) Phylogenetic Profile
(d) Gene Clustering:
closely spaced genes, and
assigns a probability P of
observing a particular gap
distance
Disease related protein-protein
interactions;
Disease Related???
-- Query NCBI OMIM
Database
Learning from different species
BioQA related projects
Projects for BioQA
1. Learning
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Given a set of relevant abstracts, what kind of features can
we obtain to enhance our queries?
Given a set of questions from users, how can we identify
keywords from the questions to form queries?
2. Answer Presentation
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Given a relevant abstract/article,
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how can we retrieve the relevant passage with respect to the user’s
question?
how to extract answers?
Projects for BioQA
3. Automatic Extraction
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Extract relations of gene-disease, gene-biological process (also their
corresponding organisms)
Uniquely identify the genes
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A gene symbol can be associated with multiple gene identifiers. Which
gene identifier is the right one?
Can these extraction processes be generalized?
4. Sortal Resolution
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Given an abstract and query, perform sortal resolution (but not on
pronouns)
Example:
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Given the following abstract:
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“In this report, we show that virus infection of cells results in a dramatic
hyperacetylation of histones H3 and H4 that is localized to the IFN-beta
promoter. … Thus, coactivator-mediated localized hyperacetylation of
histones may play a crucial role in inducible gene expression. [PMID:
10024886]
and the query about histones, perform resolution on histones
Results: histones refer to H3, H4.
Projects for BioQA
5. Semantics of Words
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Dealing with the semantics of words to improve the retrieval of answers
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Example: semantic relation between “role” and “play”
6. Gene symbol variants, disambiguate gene symbols, entity recognition
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Generate gene symbol synonyms and variants given a gene symbol in a query
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Example: variants of “CDC28” can be written as “Cdc28”, “Cdc28p”, “cdc-28”
“GSS” is a synonym of “PRNP”, but “GSS” itself is also a gene which is
unrelated to “PRNP”.
Improve on recognition of diseases, biological processes
7. Extension of Ontology
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To capture biological processes and their possible relations to diseases
Examples:
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learning and/or memory can influence Alzheimer’s disease
Degradation of ubiquitin cycle can cause extra long/short half-life of genes
Extra long/short half-life of genes can cause cancer
CBioC Class Projects
Extraction of organism info for each High-priority. Use existing software for
entity in a relationship
extraction, but need to use biological databases
and algorithms for deducing info (not explicit),
and allow users to correct this info.
Example, PMID 16107876.
KALPESH
Image extension - extracts images
& information about images and
allows collaborative curation.
Take PDFs & other structured documents, and
extract images with their captions & references
within the text, then let users polish. Related.
Use ontologies and some automated 2 people. Information entered by users needs to
tools to ensure consistency and
be validated against existing DB & ontologies.
cross-link info
Also, need to tag our data for
cross-reference. Example
Other projects
Build an Ontology
 Build an ontology for a domain for which we
do not have an ontology yet.
 Verify its consistency.
Various kinds of text extraction
systems
 TREC suggested ones
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Which method/protocol is used in which experiment/procedure
Gene – disease – role
Gene – biological process – role
Gene – mutation type – biological impact
Gene – interaction – gene – function – organ
Gene – interaction – gene – disease – organ
 Protein Lounge inspired
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Kinase-phosphatase
transcription factor
peptide antigen
Drug classification in
Pharmacogenetics
Experimental Data available
Drug response on cell lines; gene expression data; gene copy data; mutation
analysis data; RNAi data
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Data from literature
Mutation data (Sanger lab); NCI-60 drug response data; Mutation analysis data;
Pathway data (e.g. BIND); Gene Ontology
Proprietary data
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Where does the drug physically interact? (600 Kinase – IC 50)
Gene expression data of patients after treatments
Goal:
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Given a patient, what kinds of data do we need in order to determine if a drug
should be applicable to that patient or not? How do we develop a classifier using
these kinds of data?
Find gene and protein interaction network (or components) using these data.