TREC 2005 Genomics Track Ad Hoc Retrieval Topics
This file contains the topics for the ad hoc retrieval task of the TREC 2005 Genomics Track.
There are a total of 50 topics, numbered from 100 to 149. The topics all generally follow a
semantic template, with 10 in each of the 5 templates.
Detailed instructions for the documents and submission of results are provided on the track
protocol page. Experimental groups may use any resources (e.g., databases, Web sites, etc.) to
enhance their queries, as well as edit them manually.
1. Information describing standard methods or protocols for doing some sort of experiment or
procedure.
ID
100
101
102
103
104
105
106
107
108
109
Method or protocol
How to “open up” a cell through a process called “electroporation”
Exact reactions that take place when you do glutathione S-transferase (GST) cleavage
during affinity chromatography
Different quantities of different components to use when pouring a gel to make it
more or less porous
Green fluorescent protein (GFP) tagged proteins to do experiments with tagged
proteins
How to do a microsomal budding assay - budding of vesicles from microsomes in
vitro
Purification of rat IgM
Chromatin IP (Immuno Precipitations) to isolate proteins that are bound to DNA in
order to precipitate the proteins out of the DNA
Normalization procedures that are used for microarray data
Methods for identifying in vivo protein-protein interactions in time and space in the
living cell
Standard methods or protocols for fluorogenic 5'-nuclease assay
2. Information describing the role(s) of a gene involved in a disease.
ID
110
111
112
113
114
115
116
117
118
119
Gene(s)
Interferon-beta
PRNP
IDE gene
MMS2
APC (adenomatous polyposis coli)
Nurr-77
Insulin receptor gene
Aapolipoprotein E (ApoE)
Transforming growth factor-beta1 (TGFbeta1)
GSTM1
Disease
Multiple Sclerosis
Mad Cow Disease
Alzheimer's Disease
Cancer
Colon Cancer
Parkinson’s Disease
Cancer
Alzheimer’s Disease
Cerebral Amyloid Angiopathy (CAA)
Breast Cancer
3. Information describing the role of a gene in a specific biological process.
ID
120
121
122
123
Gene
nucleoside diphosphate kinase (NM23)
BARD1
APC (adenomatous polyposis coli)
COP2
124
125
casein kinase II
Nurr-77
126
127
128
P53
alpha7 nicotinic receptor subunit gene
gamma-aminobutyric acid receptors
(GABABRs)
Interferon-beta
129
Biological Process
tumor progression
BRCA1 regulation
actin assembly
transport of CFTR out of the
endoplasmic reticulum
ribosome assembly
preventing auto-immunity by deleting
reactive T-cells before they migrate to
the spleen or the lymph nodes
apoptosis
ethanol metabolism
inhibitory synaptic transmission
viral entry into host cell
4. Information describing interactions (e.g., promote, suppress, inhibit, etc.) between two or
more genes in the function of an organ or in a disease.
ID
130
131
132
133
Genes
BRCA1 regulation of
ubiquitin
L1 and L2 in the HPV11
virus
APC (adenomatous
polyposis coli) and wnt
phospholipase A2 (PLA2)
and SAR1
134
CFTR and Sec61
135
136
138
Bop and Pes
alpha7 nicotinic receptor
gene and ApoE gene
“Insulin-like” GF and
insulin receptor gene
HNF4 and COUP-TF I
139
Ret and GDNF
137
Function of organ
Disease
cancer
role of L2 in the viral
capsid
colon cancer
Endoplasmic reticulum
transport (i.e. vesicle
budding from the ER)
degradation of CFTR
which leads to cystic
fibrosis
cell growth
neurotoxic effects of
ethanol
function in skin
suppression in the function
of the liver
kidney development
5. Information describing one or more mutations of a given gene and its biological impact or
role.
ID
Gene with mutation
Biological impact
140
141
142
143
144
145
146
147
148
149
BRCA1 185delAG
mutation
Huntingtin mutations
Sonic hedgehog mutations
Mutations of NM23
Mutations in metazoan Pes
Mutations of hypocretin
receptor 2
Mutations of presenilin-1
gene
Mutations of alpha7
nAChR gene
Mutation of familial
hemiplegic migraine type
1 (FHM1)
Mutations of the alpha 4GABAA receptor
role in ovarian cancer
role in Huntington’s Disease
role in developmental disorders
impact on tracheal development
effect on cell growth
narcolepsy
biological impact in Alzheimer's disease
biological impact in alcoholism
neuronal Ca2+ influx in hippocampal neurons
impact on behavior