Budding yeast genes (Example Dataset 2.1) and fission yeast (Schizosaccharomyces pombe) genes (Example Dataset 2.2) arising from lineage-specific duplication events after the divergence of budding and fission yeasts.
A previous ZIKV outbreak in Brazil was associated with a marked increase in the number of infants born with microcephaly (Mlakar, et al., 2016). Although it is known that ZIKV can be transmitted from mother to child (Mysorekar and Diamond, 2016), it was unclear whether ZIKV directly causes microcephaly (Mlakar, et al., 2016; Pacheco, et al., 2016; Rasmussen, et al., 2016). This gene set was defined based on differentially expressed genes that were identified by Tang, et al. (2016) between Zika virus-infected (ZIKV) and mock-infected human embryonic cortical neural progenitor cells (hNPCs). Following an analysis of this gene set by modPhEA (Example 1.1), several human phenotypes were enriched, including those related to cranial development (e.g., “Abnormality of skull size“ [HP:0000240, FDR-corrected P < 10-13], “Abnormality of the calvaria“ [HP:0002683, FDR-corrected P < 10-3], etc.) and brain development (e.g., “Abnormality of brain morphology“ [HP:0012443, FDR-corrected P < 10-16], “Microcephaly“ [HP:0000252, FDR-corrected P < 10-3], etc.). Consistent with these findings based on human phenotypes, an analysis of mouse phenotypes (Example 1.2) also showed enriched phenotypes of “abnormal cranium size“ (MP:0010031, FDR-corrected P = 0.014), “abnormal brain development“ (MP:0000913, FDR-corrected P < 10-2), etc. These results suggest a molecular basis and a direct contribution of ZIKV infection to microcephaly.
It should be noted that phenotypes
related to abnormal limb development were also identified in both analyses
based on human phenotypes (e.g., “Abnormal appendicular skeleton morphology“
[HP:0011844, FDR-corrected P < 10-2]) and mouse phenotypes
(e.g., “Abnormal limb morphology“ [MP:0002109, FDR-corrected P < 10-3]).
Intriguingly, deformed limbs have recently been reported in newborns infected
by ZIKV (van der Linden,
et al., 2016). Thus,
unexpected phenotypes reported by modPhEA may be clinically important.
Example Datasets 2: Budding yeast genes (Example Dataset
2.1) and fission yeast (Schizosaccharomyces pombe) genes (Example
Dataset 2.2) arising from lineage-specific duplication events after the
divergence of budding and fission yeasts.
[ precomputed result 2.1 / result 2.2 ]
Gene duplication has been proposed to
be an important mechanism underlying organismal adaptation (Ohno, 1970; Zhang, 2003), including that of yeasts (Qian and Zhang, 2014). Based on orthology information
annotated by Ensembl Fungi v29 (http://fungi.ensembl.org), a list of paralogs
in the budding yeast genome and a list of paralogs in the fission yeast genome
that arose after the latest common ancestor of these two yeast species were
obtained. Enriched analyses of these two lists of genes (paralogs), defined as
Example Datasets 2.1 and 2.2, respectively, were conducted based on the budding
yeast phenotypes. Budding yeast can thrive under strictly anaerobic conditions,
while fission yeast cannot (Heslot,
et al., 1970). Correspondingly,
the enriched phenotypic term, “anaerobic metabolism (APO:0000210, FDR-corrected
P = 0.003)“, was identified for duplicated genes in the budding yeast
lineage (Example Datasets 2.1). In addition, the enriched term, “resistance to
chemicals“ (APO:0000087, FDR-corrected P < 10-5), that was
identified in this gene set may be related to the more advanced metabolic
capacity of budding yeast in fermentation, during which yeast cells are exposed
to various stresses. The analysis of genes duplicated in the fission yeast
lineage (Example Dataset 2.2) identified two enriched terms, “spore wall formation“
(APO:0000043, FDR-corrected P = 0.033) and “interaction with
host/environment“ (APO:0000287, FDR-corrected P = 0.028). These two
phenotypes are consistent with a lineage-specific adaptation of fission yeast
that includes the survival of fission yeast as spores in the gut of insect
vectors (Coluccio, et
Example Dataset 3: zebrafish orthologs showing reduced
expression in eyes of cave-dwelling Sinocyclocheilus species
[ precomputed result 3 ]
Normal eyes characterize the surface-dwelling Sinocyclocheilus (Cypriniformes: Cyprinidae) teleost fish species (S. angustiporus), while the cave-dwelling Sinocyclocheilus species (S. anophthalmus) has small eyes that are buried deeply within adipose tissue that is covered with skin. To understand the molecular basis of these differences, whole-eye transcriptomes for both S. angustiporus and S. anophthalmus were profiled (Meng, et al., 2013). Genes with an RNA-seq signal that was decreased by > 50% in the eyes of S. anophthalmus compared with the eyes of S. anophthalmus were identified and defined as this gene set. When an enrichment analysis of zebrafish phenotypes was performed with modPhEA, “eye photoreceptor cell“ (ZFA:0009154, FDR-corrected P = 0.027) and “retinal cone cell“ (ZFA:0009262, FDR-corrected P = 0.028) were identified. These two phenotypic terms are consistent with the reduced retinal cell density and photoreceptor cell height that histologically characterize S. anophthalmus eyes according to Meng, et al. (2013).
In addition to the above two terms,
this gene set of reduced mRNA expression is enriched in phenotypes manifested
in “epiphysis“ (ZFA:0000019, FDR-corrected P = 0.05), a circadian clock pace
maker that contains photoreceptor cells. Interestingly, a recent study
comparing genomes of three Sinocyclocheilus species found that Skp1-Cul1-Fbxl3
(SCF) protein complex, the most relevant in clock mechanism in mammals, has
been degenerated in S. anophthalmus (Yang, et al., 2016). In the future, it will be
interesting to examine if S. anophthalmus lacks circadian rhythms.
Example Dataset 4:C. elegans genes expressed in gonads
[ precomputed result 4 ]
The transcriptomes and proteomes of
fruit fly and nematode were simultaneously compared in a previous study, and
the results suggest that the evolution of the transcriptome is largely neutral (Schrimpf, et al., 2009). That is, protein expression appears
to be largely controlled at the level of protein translation, and mRNA
expression signals do not necessarily predict gene functions. When an
enrichment analysis was performed for genes expressed in an isolated gonad of C.
elegans as determined by RNA-seq (Ortiz, et al., 2014), many phenotypes were identified, including: gonad morphology
(e.g., “gonad morphology variant“ [WBPhenotype:0001355, FDR-corrected P <
10-54]) and fertility (e.g., “fertility reduced“
[WBPhenotype:0001384], FDR-corrected P < 10-88).
Therefore, in contrast with the neutral model of transcriptome evolution that
has been proposed (Khaitovich,
et al., 2004; Schrimpf, et al., 2009), our results from modPhEA indicate that mRNA expression
levels strongly influence functions of the tissue in which the genes are
Example Dataset 5: Genes that are highly expressed after
a blood-meal by malaria vector mosquito.
[ precomputed result 5 ]
Blood-feeding behavior is an important
characteristic of mosquitos. To elucidate the genetic components associated
with the hematophagy of these animals, microarray data for the malaria mosquito
(Anopheles gambiae) (Marinotti,
et al., 2005) were
downloaded. The top 20% of the mosquito genes that exhibited the greatest
increases in gene expression after a blood meal were defined. The remaining 80%
of the A. gambiae genes were used as background data for
performing an enrichment analysis of fruit fly phenotypes. Consistent with our
current understanding that mosquito hematophagy is required for oocyte
development, the results indicated that enrichment of this gene set included
several reproduction-related phenotypes (e.g., “female sterile“ [FBcv:0000366,
FDR-corrected P < 10-8]) and cell cycle-related phenotypes
(e.g., “cell cycle defective“ [FBcv:0000671, FDR-corrected P < 10-6]).
This example dataset and its results have been presented and discussed in our
previous study (Weng and
Example Dataset 6: Highly expressed human genes in
vascular smooth muscle cells of patients with giant cell arteritis (GCA).
[ precomputed result 6 ]
Human diseases can be characterized by phenotypic abnormalities described with human phenotype ontology (HPO) terms. For example, GCA has been described by Groza, et al. (2015) with the human phenotypic terms, vasculitis (HP:0002633), granulomatosis (HP:0002955), amaurosis fugax (HP:0100576), facial palsy (HP: 0010628), renal amyloidosis (HP: 0001917), dysphagia (HP: 0002015), trismus (HP: 0000211), and encephalopathy (HP: 0001298). Accordingly, we customized a phenotype, “giant cell arteritis (GCA)“, by combining the above seven HPO terms. The gene set provided in this example contains genes with a processed expression signal > 8 in at least one of the vascular smooth muscle cell samples analyzed from GCA patients (downloaded from GSE63425 of NCBI GEO). The analysis conducted by modPhEA showed that this gene set is enriched with the customized term, “giant cell arteritis (GCA)“ (P < 10-3).
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