List of lists-annotated (LOLA): A database for annotation and comparison
of published microarray gene lists
Patrick Cahana,1, Amera M. Ahmada, Harry Burkea, Sidney Fua, Yinglei Laib, Liliana Floreac,
Nachiket Dharkera, Todd Kobrinskia, Prachee Kalea, Timothy A. McCaffreya,*
aThe George Washington University Medical Center, Department of Biochemistry and Molecular Biology, 2300 I Street NW. Ross Hall 541,
Washington, D.C. 20037, United States
bDepartment of Statistics, United States
cDepartment of Computer Sciences and The Catherine Birch McCormick Genomics Center, United States
Received 11 May 2005; received in revised form 7 July 2005; accepted 11 July 2005
Available online 2 September 2005
Received by A.J. van Wijnen
Microarray profiling of RNA expression is a powerful tool that generates large lists of transcripts that are potentially relevant to a disease
or treatment. However, because the lists of changed transcripts are embedded in figures and tables, they are typically inaccessible for search
engines. Due to differences in gene nomenclatures, the lists are difficult to compare between studies. LOLA (Lists of Lists Annotated) is an
internet-based database for comparing gene lists from microarray studies or other genomic-scale methods. It serves as a common platform to
compare and reannotate heterogeneous gene lists from different microarray platforms or different genomic methodologies such as serial
analysis of gene expression (SAGE) or proteomics. LOLA (www.lola.gwu.edu) provides researchers with a means to store, annotate, and
compare gene lists produced from different studies or different analyses of the same study. It is especially useful in identifying potentially
‘‘high interest’’ genes which are reported as significant across multiple studies and species. Its application to the fields of stem cell, cancer,
and aging research is demonstrated by comparing published papers.
D 2005 Elsevier B.V. All rights reserved.
Keywords: Microarray; Transcript profiling; Expression profiling; Bioinformatics; Gene expression; Gene annotation; Aging
Microarray analysis of gene expression is capable of
screening the entire transcriptome of a cell type or organ to
find genes which change in association with a disease or
drug treatment. With the exponential growth in gene
expression data, biologists are faced with the challenge of
extracting useful information from this raw data, and
subsequently developing a coherent storage and retrieval
system for the analysis of processed data. Several powerful
software tools and databases have been built to facilitate the
management and curation of raw microarray data. Among
them are OncoMine (Rhodes et al., 2004), SMD (Gollub et
al., 2003), Longhorn (Killion et al., 2003), Array Express
(Brazma et al., 2003), GEO (Edgar et al., 2002), DAVID
(Dennis et al., 2003), and SOURCE (Diehn et al., 2003).
Some serve as repositories of primary gene expression data
from a specific platform, while others provide functional
annotations of genes or gene lists under study (Table 1).
Despite the availability of these tools for managing raw
data, the published results remain surprisingly inaccessible
for further comparison.
0378-1119/$ - see front matter D 2005 Elsevier B.V. All rights reserved.
Abbreviations: AML, acute myeloid leukemia; ApoD, apolipoprotein
D; ESC, embryonic stem cells; LOLA, list of lists annotated; NPC, neural
progenitor cells; RDBMS, relational database management system; RPC,
retinal progenitor cells; SAGE, serial analysis of gene expression.
* Corresponding author. Tel.: +1 202 994 8919; fax: +1 202 994 8924.
E-mail address: email@example.com (T.A. McCaffrey).
1Current address: Division of Biology and Biomedical Research,
Washington University, St. Louis, MO 63110, USA.
Gene 360 (2005) 78 – 82
Microarray studies typically generate lists of 100–500
transcripts which are changed by a given disease or
treatment. There is no uniform and easily accessible method
of comparing lists of genes thought to be significantly
linked to a specific disease or treatment. Enormous
resources have been invested in microarray screening of
aging, cardiovascular diseases, cancer, and dozens of other
diseases, and yet, the resulting data is not amenable to
electronic access, comparison, or updating of the annota-
tions. The comparison of gene lists, arising from microarray,
serial analysis of gene expression (SAGE), or differential
display, is severely hindered by different platforms and
different gene nomenclatures, and the fact that the resulting
gene lists are inaccessible by conventional PubMed
searches. The results of microarray studies, which identify
potentially important lists of genes, could, and should be
compared in order to:
& Identify genes that are robust across different signal
generation, normalization and analysis methods within
the same microarray study.
& Identify genes that are observed in common between
different, independent studies of the same disease or
& Identify sets of genes that may be modulated in common
between different disease states or drug treatments.
To address these needs, LOLA was developed as a web-
enabled database for comparison and annotation of micro-
array-generated lists of genes from divergent platforms and
LOLA allows users to upload their gene lists in order to
identify genes that are observed in common between their
list and other gene lists. LOLA provides a method to
compare and analyze thousands of genes in multiple lists
simultaneously and provides a uniform measure of gene list
similarity. LOLA circumvents many of the problems
associated with integrating and comparing raw microarray
data produced in different studies by allowing users to
simply compare results of prior analyses (Fig. 1).
Recently, The Tumor Analysis Best Practices Working
Group recommended that Affymetrix microarray analyses
utilize at least two probe set algorithms in order to identify
Comparison of features of microarray databases, PubMed, and LOLA
Stores microarray images
Stores raw data
Ability to process raw data
Stores results (gene lists)
Compares results from different studies
Cross platform comparison of results
Cross species comparison of results
Searchable access to published lists
Fig. 1. Comparing the results of microarray studies from different platforms using LOLA. Different microarray platforms, such as Agilent, Affymetrix, and
spotted arrays can be processed through a variety of different analytical methods, such as SAM, t-tests, or clustering, to produce smaller gene lists that are
thought to be related to a particular disease or drug treatment. Regardless of the platform involved, the resulting lists can be compared for similarity/
dissimilarity using LOLA.
P. Cahan et al. / Gene 360 (2005) 78–82
robustly significant genes (Hoffman et al., 2004). LOLA is
an ideal tool to compare lists produced using various
expression measures. Additionally, LOLA provides links to
Entrez Gene (Wheeler et al., 2004), GeneCards (Rebhan et
al., 1997), NetAffx, and PubMed in one interface. Presently,
LOLA archives data on human, mouse and rat genomes.
2. Construction and content
2.1. Database structure
LOLA employs a three-tier web application architecture.
In tier 1, data is stored in the relational database manage-
ment system (RDBMS) MySQL. The tier 2 application layer
is implemented in PHP (www.php.net), which is executed
via calls from the tier 3 Apache web server running on the
Linux operating system. In addition to requirements for data
consistency and the ability to update easily, the data model
was designed to allow for flexible and efficient gene list
comparisons and searches.
Gene annotations are stored and updated by automati-
cally parsing annotation files produced using BioConduc-
tor’s AnnAffy and MetaData packages (Ihaka and
Gentleman, 1996). Each row of an annotation file contains
an Affymetrix probe set identifier, LocusLink/Gene identi-
fier, the gene name and gene symbol, when known. The
number of genes currently archived in LOLA is illustrated
in Fig. 2.
The concordance between any two gene lists is
calculated as the number of genes in common divided by
the number of genes in both of the lists (the intersection
divided by the union). The significance of this concordance
is evaluated in two different ways. First, the variance of the
concordance is calculated as A(B+C)/(A+B+C)3where
A is the number of common genes, while B and C are the
numbers of unique genes on their respective lists (Burke
and Hoang, in preparation). The variance is used to
compute the 95% confidence interval (CI) by standard
methods. If the CI does not include the value 0, which
indicates no concordance, then the concordance is signifi-
cant, with 95% confidence. Secondly, the P-value of a
given intersection size is the probability of observing an
intersection size that occurs by chance and is larger than
the given one. It is calculated as: Pr( X>c|m1, m2, n1, n2,
s)=~x>cPr( x | m1, m2, n1, n2, s), where c is the number
of genes common to both lists, m1and m2are the sizes of
two lists, n1and n2are the sizes of two arrays, and s is the
total number of probes from which the two arrays were
sampled. Evaluating the statistical significance of the
concordance, however, is limited by a number of potential
biases that could systematically favor the presence of gene
subsets on a list. These biases include the selection bias of
named genes for inclusion on microarrays, and the
abundance of some transcripts, which would favor their
3. Results and discussion
3.1. Data access
LOLA provides a simple interface for viewing, storing,
re-annotating, and comparing gene lists. Users create a new
list by uploading a tab-delimited text file of specified format
or by pasting a gene list into a form on the LOLA site. The
user must select the identifier type that is used to identify
each gene. Currently, LOLA supports both Gene and
Affymetrix probe set identifiers. If a matching gene
identifier is not found, that gene will not be stored in the
database, and the submitter notified. A single gene is
allowed to occur multiple times in the same list although it
will only be used once in comparisons. Reference informa-
tion, such as the PubMed citation, study design, sample
types, analysis method and criteria used in generating the
list, can be saved along with the gene list. After a list is
submitted, LOLA will display the annotated gene list for
confirmation by the user prior to saving the list in the
database. Users can create new folders and move lists
among folders to assist in organization. The list is available
for all users to view and compare after the curator has
Gene list summaries, which include list title, description,
analysis type, and the number of genes, are displayed in a
folder hierarchy. Published gene lists are hyperlinked to
their associated PubMed abstracts. The gene names and
descriptions in a list are viewed by clicking on the list title.
Fig. 2. The number of searchable elements referenced in LOLA. The
number of possible probes encompassed in LOLA is graphed as a function
of the species and probe/gene identifier type.
P. Cahan et al. / Gene 360 (2005) 78–82
Each gene is linked to GeneCards, Entrez Gene and, when
applicable, NetAffx through their Affymetrix probe set ID
(Liu et al., 2003). Fold changes or log ratios appear color-
coded in the gene list display.
Gene lists are compared by selecting their check boxes
and pressing the Fcompare lists_ button. LOLA performs a
pair wise comparison between each of the selected lists and
produces a table that reports the number of genes in
common between the lists, the concordance calculation,
confidence interval, and P-value. The names of the genes in
common are retrieved by clicking on the numerical entry in
the Intersection column. When two lists derive from
different species, a gene is counted as common to both if
its homolog is found in the other list, as reported from
NCBI’s HomoloGene. Users can also compare one list of
interest to all accessible lists by selecting the Fcompare to
3.2. Validation of stem cell microarray papers
Lists from a published paper on stem cells were tested on
LOLA in order to demonstrate its usefulness and validate its
results. Fortunel et al. (Fortunel et al., 2003) carried out
gene expression profiling of three stem cell types: embry-
onic stem cells (ESC), neural progenitor cells (NPC) and
retinal progenitor cells (RPC) with their differentiated
progenies. The intersection of these lists defined a list of
385 Fstemness_ genes expressed by all three stem cells. The
same lists of genes were uploaded into LOLA and
compared. LOLA found the same 385 genes enriched in
all three stem cells as was identified in the original analysis.
LOLA confirmed a significant concordance (95% CI)
between ESC and NPC of 0.19 (T0.014), between NPC
and RPC of 0.29 (T0.016), and between ESC and RPC of
0.28 (T0.016), with all P-values less than 10?200.
3.3. Comparison of cancer microarray studies
It can be quite difficult to compare the results of
microarray studies from different laboratories studying the
same disease. Two recent reports by Bullinger et al.
(Bullinger et al., 2004) and Valk et al. (Valk et al., 2004)
used microarrays to identify genes that may have value in
classifying acute myeloid leukemia (AML). The accompa-
nying Perspectives (Lui and Karuturi, 2004) and Editorial
(Grimwade and Haferlach, 2004) emphasized a robust
similarity in the findings of the 2 studies, but did not specify
the number of similar genes that were identified. Comparing
the 133 genes identified by Bullinger (122 found in LOLA)
and the 182 genes identified by Valk, LOLA identified only
9 genes (Table 2) that were in common (concordance=0.040
(+0.026), p=2.66?10?7). While it suggests that the 2
studies did not observe highly similar results (<5%
concordance), the lower end of the 95% confidence interval
falls slightly above 0, indicating a significant concordance,
and the odds of such an overlap occurring randomly are quite
small. In this case, LOLA generates a testable hypothesis that
the 9 genes that are reproducible between the 2 studies may
have greater predictive value than genes that did not
reproduce in both studies.
3.4. Interspecies comparison of microarray analysis of the
One method of evaluating microarray results would be to
determine which genes reproducibly change in different
studies employing a similar design. Aging studies should be
reasonably similar between different species, and so we
conducted an in-depth literature search of microarray studies
involving aging. A total of 25 separate gene lists, from 20
papers, were uploaded into LOLA for comparison. To
illustrate the cross-species function of LOLA, 3 different
microarray studies of brain aging, in 3 different species,
were identified and compared using LOLA. Human post-
mortem frontal cortex specimens from subjects ranging in
age from 26 to 106 were analyzed by Affymetrix GeneChips
to identify genes increased or decreased in subjects over 40
(Lu et al., 2004). Likewise, aging-related genes in rat
hippocampus were identified by microarray analysis (Bla-
lock et al., 2003), as were genes associated with aging of the
neocortex in mice (Prolla, 2002). Using the cross-species
features of LOLA, a 3-way comparison revealed that any 2
lists had significant concordance of 6–8 genes in common
from a total of 134–145 genes per list. However, only 1
gene was common to all 3 lists: apolipoprotein D (ApoD).
ApoD has previously been associated with cellular sen-
escence (Provost et al., 1991) and with aging of the human
brain (Kalman et al., 2000), possibly as a function of the
increased presence of reactive astrocytes in aged brain (del
Valle et al., 2003). Thus, LOLA allows the identification of
genes that change reproducibly in different studies, even
when the studies are in different species.
3.5. Future directions
LOLA’s coverage of gene expression data will continue
to expand as more genomes become available and existing
genome annotations are augmented. An algorithm that will
facilitate comparisons based on Gene Ontologies (GO)
(Ashburner et al., 2000) is under development. In this way,
Genes identified by 2 different studies of acute myeloleucytic leukemia
melanoma associated gene
hypothetical protein FLJ23058
homeo box A4
homeo box B2
homeo box B5
lipocalin 2 (oncogene 24p3)
hypothetical protein from clone 643
pre-B-cell leukemia transcription factor 3 (occurs twice)
P. Cahan et al. / Gene 360 (2005) 78–82
lists that share closely related genes, expressed as detailed Download full-text
GO terms, will still correlate well. TIGR’s microarray
analysis software, MeV (Saeed et al., 2003), has been
adapted in such a way that it can upload new lists directly to
LOLA. There are several other features that are currently
& Sorting lists and genes according to name, symbol, fold
& An option for automatic email notification when a newly
uploaded list meets a threshold similarity to an author’s
& Expanded gene and probe ID associations to allow for
upload and comparison of probes which do not have an
Entrez Gene or Affymetrix ID.
& Improved searching for genes and gene ontologies in
& Downloadable version for local installation.
3.6. Availability and requirements
LOLA is freely available for browsing, uploading of lists,
and comparing publicly available gene lists. Registration is
required to upload gene lists. See: http://www.lola.gwu.edu/.
The source code is available upon request for academic
LOLA stores analyzed microarray gene lists, not raw
data, and measures the concordance among gene lists.
LOLA can be used to answer several types of questions,
including: (1) What genes are changed in all microarray
studies of a particular biological phenomena? (2) What
genes are shared between an investigator’s list and other
analyzed lists, which focus on his area of interest? (3)
Within a microarray experiment, which genes remain
significant across different signal summarization, normal-
ization, and analysis methods? While useful for microarray
data comparison, LOLA is not limited to microarray results,
and is equally capable of comparing results from differential
display, SAGE, or proteomic analyses.
The authors are grateful for the financial support of the
NIH/National Institutes on Aging (AG12712), and The
Catherine Birch McCormick Genomic Center.
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