Genome Biology 2007, 8:R3
2007Carmona-Saez et al.Volume 8, Issue 1, Article R3
GENECODIS: a web-based tool for finding significant concurrent
annotations in gene lists
Pedro Carmona-Saez*, Monica Chagoyen*†, Francisco Tirado†,
Jose M Carazo* and Alberto Pascual-Montano†
Addresses: *BioComputing Unit, National Center of Biotechnology (CNB-CSIC), C/Darwin 3, Campus Universidad Autónoma de Madrid,
28049 Madrid, Spain. †Computer Architecture Department, Facultad de Ciencias Físicas, Universidad Complutense de Madrid, C/Avenida
Complutense S/N, 28040 Madrid, Spain.
Correspondence: Alberto Pascual-Montano. Email: email@example.com
© 2007 Carmona-Saez et al.; licensee BioMed Central Ltd.
This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which
permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Finding concurrent annotations in gene lists<p>GENECODIS, a web-based tool for finding annotations that frequently co-occur in a set of genes and ranking them by their statistical significance, is presented.</p>
We present GENECODIS, a web-based tool that integrates different sources of information to
search for annotations that frequently co-occur in a set of genes and rank them by statistical
significance. The analysis of concurrent annotations provides significant information for the biologic
interpretation of high-throughput experiments and may outperform the results of standard
methods for the functional analysis of gene lists. GENECODIS is publicly available at http://
High-throughput experimental techniques such as DNA
microarrays or proteomics are allowing researchers to study
biologic systems from a global perspective. In many cases, the
net result of these experiments is a large list of genes or pro-
teins that are potentially interesting for the analyzed system,
for example genes that are differentially expressed among
normal and pathologic tissues. A logical further step in the
analysis workflow is to translate such lists of significant genes
into functional descriptors that help researchers in the proc-
ess of elucidating the biologic meaning of their experimental
Since Khatri and coworkers introduced Onto-Express ,
several methods have been proposed within this context,
aimed at interpreting and extracting biologic knowledge from
large lists of genes or proteins. Most of these applications find
biologic annotations that are significantly enriched in a list of
genes with respect to a reference set, usually the whole
genome or those genes used in a microarray. Using a specific
source of information, for example Gene Ontology (GO) ,
those tools first find all of the GO terms associated with the
set of analyzed genes. The number of appearances of each
term is then determined in the input and reference lists, and
a statistical test - usually the hypergeometric, χ2, bionomial,
or Fisher's exact test - is used to compute p values, which are
subsequently adjusted for multiple testing. The result of this
analysis is a list of single biological annotations from a given
ontology (for instance, GO terms) with their corresponding p
values. Those terms with p values indicating statistical signif-
icance are representative of the analyzed list of genes and can
provide information about the underlying biologic processes.
Good reviews of such methods are available elsewhere [3,4].
Most of the currently available tools, however, are designed to
evaluate single annotations, which means that they provide a
Published: 4 January 2007
Genome Biology 2007, 8:R3 (doi:10.1186/gb-2007-8-1-r3)
Received: 3 July 2006
Revised: 29 September 2006
Accepted: 4 January 2007
The electronic version of this article is the complete one and can be
found online at http://genomebiology.com/2007/8/1/R3
R3.2 Genome Biology 2007, Volume 8, Issue 1, Article R3 Carmona-Saez et al.
Genome Biology 2007, 8:R3
list of annotations with their corresponding p values without
taking into account the potential relationships among them.
Finding relationships among annotations based on co-occur-
rence patterns can extend our understanding of the biologic
events associated with a given experimental system. For
example, a set of differentially expressed genes may be asso-
ciated with the activation of biologic processes that are
restricted to certain cellular organelles. Retrieving such asso-
ciations provides meaningful and additional information for
the interpretation of the experimental results.
In addition, the analysis of single annotations may show lim-
itations in some cases. A simple motivating example of such
limitations can be explained by using a hypothetical case of
GO terms. There are categories such as 'signal transduction'
that, although related to concrete aspects of the cell physiol-
ogy, are associated with genes that are involved in disparate
biologic processes, and therefore they may be annotated
together with other terms such as 'cell proliferation' or 'apop-
tosis'. In this scenario, in a list of genes annotated as 'signal
transduction' and 'cell proliferation', we may find that none of
these terms are significant because a large number of genes in
the genome belonging to each one of these categories are not
included in the analyzed set. On the contrary, the co-occur-
rence of both categories might be significant if most of the
genes simultaneously annotated with both terms are included
in the list. This co-occurrence information reveals that a sig-
nificant proportion of genes in the set are involved in specific
signaling pathways related to cell proliferation. Therefore,
relevant associations might be underestimated if only single
annotations are taken into account.
These observations prompted us to develop GENECODIS, a
web-based tool for finding sets of biological annotations that
frequently appear together and are significant in a set of
genes. It allows the integrated analysis of annotations from
different sources (for example, KEGG pathways, Swiss-Prot
keywords, GO, and InterPro motifs) and generates statistical
rank scores for single annotations and their combinations.
We believe that GENECODIS is an important extension of
existing tools for the functional analysis of gene lists. GENE-
CODIS is publicly available from the application website .
The GENECODIS algorithm
The application that we propose is simple in its concept; it
takes a list of genes as input and determines biological anno-
tations or combinations of annotations that are over-repre-
sented with respect to a reference list. The novelty of this tool
relies in the fact that, before computing the statistical test, it
incorporates a new functionality to extract all combinations
of annotations that appear in at least x genes, with x being a
user-defined threshold (Figure 1 shows an overview of the
Finding sets of terms that frequently appear together
in a list of genes
To extract combinations of gene annotations, GENECODIS
uses a modification to the methodology reported by Car-
mona-Saez and coworkers , which implements the apriori
algorithm to extract associations among gene annotations
and expression patterns.
The apriori algorithm was originally introduced by Agrawal
and coworkers  and has been extensively used to extract
association rules from transaction databases. This algorithm
generates sets of elements that frequently co-occur in a data-
base of transactions. Briefly, the procedure starts by deter-
mining the set of all single annotations ('itemset') that appear
in at least x genes (also known as support threshold) from the
list of interest and establish the frequent k itemsets, where k
= 1. In the second iteration (k = 2), the set of frequent anno-
tations found in the previous step is used to produce the new
set of candidates of size 2 (2-itemset), and the database is
scanned again to explore each gene and counting the fre-
quency of each pair of annotations. However, if the set of
annotations does not satisfy the minimum support constraint
- that is, they do not occur in at least x genes - then they are
not further considered to generate larger itemsets. The proce-
dure continues until no more combinations are possible. At
the end of this search all itemsets that contain the collection
of annotations that co-occur in at least x genes are obtained
(Additional data file 1).
In our previous work  we used the apriori algorithm to
extract association rules among gene annotations and expres-
sion patterns. However, in this work we use it as the initial
step in the methodology included in GENECODIS, namely
the extraction of sets of annotation that frequently co-occur in
a gene list.
It is important to note that increasing the number of different
items (sources of annotation in this case) while decreasing the
minimum support value can significantly multiply the
number of concurrences and thus the computation time.
Additional data file 1 contains a complete study of execution
time and size of the itemsets for different support values in
real datasets. Very extreme scenarios, such as extracting all
possible combinations of terms that appear in at least one
gene (support value of 1), is in many cases a computationally
unfeasible task. For this reason we have provided the applica-
tion with a minimum support value of 3, which is a reasonable
threshold to extract significant biological information from
Once all combinations of annotations that appear in at least x
genes have been extracted, the method counts the occurrence
of each set of annotations in the list of genes and in a refer-
ence list. Note that for each set of concurrent annotations its
frequency is calculated as the number of genes that are
Genome Biology 2007, Volume 8, Issue 1, Article R3 Carmona-Saez et al. R3.3
Genome Biology 2007, 8:R3
simultaneously co-annotated with those terms. By default,
GENECODIS uses as a reference set all genes from the corre-
sponding genome at the NCBI Entrez Gene database , but
users can upload their own reference set (for example, genes
in a chip). Then, a statistical test is applied to identify catego-
ries, and their combinations, that are significantly enriched in
the list of genes. Two statistical tests are implemented in
GENECODIS: the hypergeometric distribution and the χ2 test
of independence. For a detailed description of these methods
in the context of the ontological analysis of gene lists, see the
work of Draghici and coworkers  and the online help for
The p values can then be adjusted for multiple tests using a
simulation-based correction approach [10,11] or the false dis-
covery method proposed by Benjamini and Hochberg .
Overview of the methodology
Overview of the methodology. (a) Annotations from several sources are assigned to genes in the input list. (b) The apriori algorithm is applied to find sets
of annotations that frequently co-occur in the input list. (c) The statistical significance of each annotation or set of concurrent annotations is calculated
based on its frequency in the input and reference sets. The figure illustrates an example in which a list of yeast genes is annotated with Gene Ontology
(GO) terms for 'cellular component' and KEGG pathways. In the output table only the annotations that co-occur in more than five genes are shown.
List of genes
Terms # genes
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Genome Biology 2007, 8:R3
For the simulation-based correction, a gene list of the same
size of the input list is generated by randomly selecting genes
from those used as reference. The frequent itemsets are then
extracted (as described above) from this random list and their
corresponding p values are calculated. This process is
repeated 10,000 times and the corrected p value for each k
itemset is calculated as the fraction of simulations having any
k itemset with a p value as good as or better than the p value
for that k itemset.
Therefore, the result of the analysis performed by GENECO-
DIS consists of a list of annotations or combinations of anno-
tations with their corresponding p values. Annotations
exhibiting p values below a certain threshold can be consid-
ered significantly associated with the list of genes under study
and can be used to discern the biologic mechanisms relevant
to the experimental system.
GENECODIS is a web-based tool that is freely accessible from
the application website . It uses the Entrez Gene database
 as the backbone data structure to link the functional anno-
tations imported from GO together with the correspondences
among gene identifiers (IDs). It allows users to upload gene
lists using different IDs, including, for example, Gene Sym-
bols, Entrez Gene, or Unigene IDs (more information about
the identifiers supported for each organism can be found in
the application website). If duplicated IDs are used in the
input list, then they are treated as unique entries.
For each organism GENECODIS provides analysis of differ-
ent annotations, including the three GO categories (biological
process, cellular component, and molecular function), KEGG
pathways, InterPro Motifs, and Swiss-Prot keywords. GO
annotations for each gene are imported from the NCBI Entrez
Gene database. GENECODIS allows users to select different
levels of the GO hierarchy as well as GO Slim terms .
Information about metabolic pathways is imported from
KEGG database , whereas Swiss-Prot keywords and
InterPro motifs are imported from Swiss-Prot database.
Regarding the supported organisms, GENECODIS currently
works with Arabidopsis thaliana, Bos taurus, Caenorhabdi-
tis elegans, Danio rerio, Drosophila melanogaster, Gallus
gallus, Homo sapiens, Mus musculus, Rattus norvegicus,
pombe. More organisms and annotations will be systemati-
cally added in future versions of the application.
One relative limitation derived from the in-depth search per-
formed is the increase in the computational cost and time as
more annotation categories are analyzed. To tackle this limi-
tation GENECODIS uses an efficient technique to extract fre-
quent itemsets . Additionally, GENECODIS runs on a 16-
processor cluster, which guarantees the simultaneous use of
the tool by multiple users.
GENECODIS at work
We provide two examples showing the analysis performed by
GENECODIS and how the results obtained as combinations
of several biological annotations provide additional informa-
tion that may be useful in the interpretation of high-through-
put experimental data.
To illustrate GENECODIS, we show the results obtained
using data generated by Smith and coworkers . They used
oligonucleotide-based whole genome microarrays to measure
gene expression levels in yeast during growth in oleate (per-
oxisome induction) and growth in glucose (peroxisome
repression conditions). Using different clustering algorithms
they identified 224 yeast genes whose expression patterns
were similar to well known peroxisomal genes.
The list of these 224 genes was re-analyzed using GENECO-
DIS, selecting biological process (BP) and cellular component
(CC) GO Slim annotations. The simultaneous analysis of both
categories provided a global picture of the biological proc-
esses associated with the experimental system linked to cellu-
lar localization information (Figure 2). As was expected, the
most significant category associated with this gene list was
'peroxisome' (CC). Other single categories that were highly
representative were 'generation of precursor metabolites and
energy' (BP), 'carbohydrate metabolism' (BP), and 'lipid
metabolism' (BP), which is consistent with the observation
that the shift to growth in the presence of oleate activates
genes encoding enzymes that are involved in fatty acid degra-
dation, allowing efficient use of the new carbon source .
In addition to these single-category significant annotations,
GENECODIS revealed a new set of associations with a strong
biologic meaning. For example, taking a closer look at the sec-
ond and third categories with the lowest p values, we can see
that a significant set of genes were co-annotated with 'perox-
isome' (CC) and 'lipid metabolism' (BP), and 'peroxisome'
(CC) and 'organelle organization and biosynthesis' (BP),
respectively. These findings allow us to easily identify the set
of peroxisomal genes that are specifically involved in each one
of these two different biological processes. Among the genes
co-annotated as 'peroxisome' (CC) and 'lipid metabolism'
(BP) are the genes involved in the fatty acid β-oxidation path-
way, such as POX1, FAA2, ECI1, FOX2, POT1, and DCI1.
Among genes co-annotated as 'peroxisome' (CC) and
'organelle organization and biosynthesis' (BP) are the PEX
genes, which are involved in peroxisome assembly  and
are required for the increase in the number of these
organelles during growth on oleate .
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Genome Biology 2007, 8:R3
Another interesting set of annotations that show the useful-
ness of the application are those categories related to mito-
chondrial genes. Forty-eight out of 887 yeast genes annotated
as 'mitochondrion' (CC) were present in the list, and therefore
this annotation exhibited a p value of 0.0248 (simulation
corrected p value = 0.2; Additional data file 2). Consequently,
based on the statistical test, this annotation is not considered
significant. Nevertheless, GENECODIS was able to identify a
set of significant co-annotations related to mitochondrial
genes. For example, 6 out of 21 yeast genes that were simulta-
neously annotated with 'mitochondrion' (CC) and 'lipid
metabolism' (BP) were present in the list, and this co-annota-
tion exhibited a p value of 0.000162 (simulation corrected p
value = 0.0086). Among these genes was, for example, the
CRC1 gene, which is a mitochondrial inner membrane carni-
tine transporter that is required for carnitine-dependent
transport of acetyl-coenzyme A from peroxisomes to mito-
chondria. In the same way, the co-annotation of 'mitochon-
drial membrane' (CC) and 'generation of precursor
metabolites and energy' (BP) related to a subset of genes that
are component of the mitochondrial respiratory chain was
found to be significant, with a simulation corrected p value of
Although fatty acid β-oxidation in Saccharomyces cerevisiae
is restricted to peroxisomes, the association of mitochondrion
related categories to this set of genes is highly consistent with
the important role of these organelles in the metabolism of β-
oxidation products. Acetyl-coenzyme A, the final product of
the fatty acid β-oxidation pathway in peroxisomes is trans-
ported to the mitochondria for the final oxidation to CO2 and
H2O . In this way, peroxisomal fatty acid β-oxidation
demands a functional mitochondrial electron transport chain
for energy production, and either functional peroxisomes and
mitochondria are required for growth in the presence of
Screenshot depicting results of the analysis of yeast genes
Screenshot depicting results of the analysis of yeast genes. The 'Annotation/s' column represents the Gene Ontology codes of annotations found in the list.
The '# list' and '# reference' columns represent the number of genes in the input list and reference list for a given annotation, respectively. The 'Genes'
column represents the set of genes in the input list showing a given annotation. The 'Description/s' column represents the textual description of
annotations. CC refers to 'cellular component' and BP to 'biological process' categories. Only annotations with corrected P values ≤ 0.05 are shown. P
values were calculated using the hypergeometric distribution and were corrected using the simulation-based approach.
R3.6 Genome Biology 2007, Volume 8, Issue 1, Article R3 Carmona-Saez et al.
Genome Biology 2007, 8:R3
To provide a second example of the functionality of GENECO-
DIS, we analyzed a set of 85 human genes expressed in testis
reported by Su and coworkers . This dataset was also used
by Zhang and colleagues  to illustrate the performance of
the GOTree Machine (GOTM) software, and therefore it rep-
resents a good test case for our method. Zhang and col-
leagues, using GOTM, reported four main groups of GO
biological process annotations related to the testis gene clus-
ter: categories related to cell proliferation, cell cycle, mitosis,
and meiosis; categories related to testis specific development;
categories related to protein phosphorylation; and categories
related to glycerolipid metabolism.
We used our tool to analyze this set of genes using the GO bio-
logical process categories and InterPro motifs that appear in
at least three genes. The most significant concurrences are
shown in Figure 3. Similar results to those reported by Zhang
and coworkers  were obtained by GENECODIS, except for
the case of categories related to glycerolipid metabolism,
which were not extracted because they were present in only
two genes. In addition, GENECODIS was able to provide new
information for the functional interpretation of this set of
genes. For example, the fifth association revealed that a sig-
nificant set of genes in the analyzed list were co-annotated
with 'protein amino acid phosphorylation' and 'cell cycle' GO
biological process categories and contained protein kinase
motifs. The importance of this observation is the explicit con-
nection between 'protein amino acid phosphorylation' and
'cell cycle' categories.
In order to explain the 'protein phosphorylation' category in
the context of the phenotypic feature of the gene cluster,
Zhang and colleagues  remarked that, 'spermatozoa
undergo a series of changes before and during egg binding to
acquire the ability to fuse with the oocyte. These priming
events are regulated by the activation of compartmentalized
intracellular signaling pathways, which control the phospho-
rylation status of sperm proteins.'
Results provided by GENECODIS complement this finding
and point out that, in this particular case, the 'protein phos-
phorylation' category is mainly related to proteins that are
involved in cell cycle. Indeed, activation and inhibition of
many key regulators of cell cycle are carried out by phospho-
Screenshot depicting results of the analysis of human genes
Screenshot depicting results of the analysis of human genes. GENECODIS results from the analysis of Gene Ontology CC ('cellular component') and
InterPro motifs in the human gene set. Only annotations with corrected P values ≤ 0.05 are shown.
Genome Biology 2007, Volume 8, Issue 1, Article R3 Carmona-Saez et al. R3.7
Genome Biology 2007, 8:R3
This finding can be confirmed by examining the genes that
were co-annotated with both categories: CDC2 (Entrez Gene
ID: 983), aurora kinase A (Entrez Gene ID: 6790), NEK2
(Entrez Gene ID: 4751), BUB1 (Entrez Gene ID: 699), and
BUB1B (Entrez Gene ID: 701). All of these have been associ-
ated with testis tissues and cell proliferation events in previ-
ous studies. For example, the NEK2 gene is predominantly
expressed in spermatocytes and appears to be associated with
meiotic chromosomes in these cells ; expression of the
gene BUB1B in testis decreases with advancing age, and it
may play a role in regulating infertility .
These two examples illustrate the type of information pro-
vided by GENECODIS, which can be useful in helping
researchers to interpret large lists of genes generated by high-
throughput experimental techniques.
High-throughput experimental techniques, such as DNA
microarrays, have opened new ways to study biological sys-
tems from a global perspective. In many cases, these tech-
niques generate huge amounts of data in the form of large
gene or protein lists that share a common property, for exam-
ple genes that are differentially expressed among pathologic
and normal tissues. These data can provide a basis for the
characterization of unknown genes, and at the same time they
are also the basis for elucidating the biological processes asso-
ciated with the experimental system. Methods based on the
ontological analysis of such lists of genes have proved to be
very useful tools for the analysis and interpretation of the
underlying biological mechanisms.
However, most of the current applications for functional pro-
filing essentially use the same general approach and generate
statistical scores for single annotations. They mainly differ on
aspects such as the statistical test used, supported annota-
tions and organisms, the gene identifiers that they are able to
manage, and visualization capabilities. Indeed, a relevant
conclusion of a review of such tools recently reported by
Khatri and Draghici  was that it would be more beneficial
if future applications expand the current approach rather
than providing endless variations of the same idea.
GENECODIS was designed to expand the biological enrich-
ment of annotations by adding the possibility of extracting
not only single enriched categories, but also significant com-
binations of them. To the best of our knowledge there is no
other tool available in the field that integrates information
from different sources in a flexible way for concurrent enrich-
ment studies. A comparison of GENECODIS with related
tools [1,22-25] and an example with test data  is provided
in Additional data file 3. We hope that this tool will help by
complementing available analysis tools for the large genome
Additional data files
The following additional data are available with the online
version of this article. Additional data file 1 contains an illus-
trative example of the GENECODIS algorithm in operation.
Additional data file 2 contains the results obtained by GENE-
CODIS in the analysis of the yeast and human gene sets. Addi-
tional data file 3 provides a description of a comparative
analysis of the results provided by GENECODIS and other
Additional data file 1An illustrative example of the GENECODIS algorithm in operationA file containing an illustrative example of the GENECODIS algo-rithm in operation.Click here for fileAdditional data file 2Results obtained by GENECODIS in the analysis of yeast and human gene setsA file containing the results obtained by GENECODIS in the analy-sis of the yeast and human gene sets. Click here for fileAdditional data file 3Description of a comparative analysis of results provided by GENE-CODIS and other related tools A compressed file containing a description of a comparative analy-sis of the results provided by GENECODIS and other related tools.Click here for file
This work was partially funded by Spanish grants CICYT BFU2004-00217/
BMC, GEN2003-20235-c05-05, CYTED-505PI0058, TIN2005-5619, PR27/
05-13964-BSCH and S-GEN-0166-2006, and a collaborative grant between
the Spanish CSIC and the Canadian NRC (CSIC-050402040003). PCS is
recipient of a grant from Comunidad Autonoma de Madrid (CAM). APM
acknowledges the support of the Spanish Ramón y Cajal program. We
thank Enrique de la Torre and Cesar Vicente for their technical support.
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