DIGITtally is currently able to draw from the following sources:
First described in Chintapalli, V. R., Wang, J., and Dow, J. A. T. (2007). Using FlyAtlas to identify better Drosophila models of human disease. Nature Genetics 39: 715-720
The most recent update on this Dataset is described in Robinson, S. W., Herzyk, P., Dow, J. A. T, and Leader, D. P. (2013). FlyAtlas: database of gene expression in the tissues of Drosophila melanogaster. Nucleic Acids Research 41: D744–D750
Insect types in Dataset: Adult, Larval
Insect tissues in Dataset: Brain/CNS, Head, Crop, Midgut, Hindgut, Malpighian tubule, Ovary, Testis, Accessory gland, Fat Body, Thoracicoabdominal ganglion, Carcass, Salivary gland, Virgin spermatheca, Mated spermatheca, Eye, Heart, Trachea
FlyAtlas1 comprises 44 Affymetrix Dros2 expression arrays, each mapping the expression of 18770 transcripts. The dataset thus contains over 822800 separate datapoints.
For this study, wild-type Canton S adult flies were reared at 22C on a 12:12h light regime, on standard Drosophila diet, 1 week after adult emergence. Tissues were dissected out (from equal numbers of male and female 7-day old flies except in the case of gonads) and pooled to make at least 1500 ng mRNA, then amplified and hybridised using the Affymetrix standard protocol. For each tissue, 4 independent biological replicates were obtained. Each array thus corresponds to one biological replicate.
Note that not all tissues have a larval counterpart - only Salivary glands, Midgut, Malpighian tubule, Hindgut, Fat Body, CNS and carcass do.
As FlyAtlas1 is microarray based, readings have not only expression values for each tissue, but also a "Presence" value, which informs on whether the transcipt is detected at all according to Affymetrix's GCOS software. This can be used to infer how consistently a gene is expressed in a given tissue. By default, DIGITtally requires that at least 3/4 samples from a tissue display detectable expression to classify a gene as consistently expressed in that tissue.
The most recent update on this Dataset is described in Krause, S.A., Overend, G., Dow, J. A. T. and Leader, D. P. (2022) FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression atlas. Nucleic Acids Research 50: D1010–D1015
Insect types in Dataset: Male, Female, Larval
Insect tissues in Dataset: Head, Eye, Brain/CNS, Thoracicoabdominal ganglion, Crop, Midgut, Hindgut, Malpighian Tubules, Fat body, Salivary gland, Heart, Trachea, Ovary, Virgin Spermatheca, Mated Spermatheca, Testis, Accessory glands, Carcass, Rectal pad, Garland cells
As in FlyAtlas1, FLyAtlas2 wild-type Canton S adult flies were reared at 22C on a 12:12h light regime, on standard Drosophila diet, 1 week after adult emergence. Tissues were dissected out (from equal numbers of male and female 7-day old flies except in the case of gonads) and pooled to make at least 1500 ng mRNA.
In FlyAtlas2 theuse of RNA-Seq rather than microarray hybridisation removes any ambiguity in the identification of genesand allows analysis of specific RNA transcripts. Approximately 17,500 genes and 34,500 transcripts are represented.
MOST tissues in FlyAtlas2 have three RNAseq replicates within the dataset. However, the following tissues have only two replicates, so please treat these with care: Eye, Thoracicoabdominal ganglion, Crop, Salivary gland and Female Rectal Pad.
By default, FlyAtlas2 uses an FPKM value of 2 as a cutoff for background-level expression. As such, transcripts with an FPKM under 2 are taken as not expressed in the analysed tissue by DIGITtally, and Whole Fly expressions for genes have a minimum value of 2 for the purposes of enrichment analysis.
First described in Li, H. et al., (2022). Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science 375, 991.
Insect types in Dataset: Adult flies ONLY
Insect tissues in Dataset: Antenna, Body wall, Fat body, Gut, Haltere, Head, Heart, Leg, Male reproductive glands, Malpighian tubule, Oenocyte, Ovary, Proboscis and maxpalp, Testis, Trachea, Wing
The result of a huge multi-centre effort, FlyCellAtlas is an enormous dataset of single-nucleus RNA sequencing data from over 580000 nuclei. These nuclei are annotated at both the tissue level (see above) and at the cell type level (over 250 unique cell types represented).
RNA samples were sequenced using either Smart-seq2 or 10x Genomics sequencing technologies - the latter dataset is utilised for DIGITtally as a "Whole Body" dataset is available. Tissues were broadly isolated by dissection except in cases where this was not possible due to localisation throughout the body - fat body, oenocyte, and trachea. In these cases, tissue-specific fluorescence was utilised to enable FACS-based nuclear isolation.
DIGITtally utilises the "Relaxed" FlyCellAtlas dataset due to the reduced stringency on mitochondrial content within analysed cells, meaning cells with high mitochondrial content (such as those within the digestive tract and malpigian tubules) are not excluded. Still, this dataset contains data on cells which have a < 15% mitochondrial content. Nuclei were also removed if they were found to be "poor quality" - ie had fewer than 10,000 uniquely mapped reads.
For our analyses, we utilise the Unique Molecular Identifier-based read counts found in the FlyCellAtlas Whole Body dataset. Following the stategy outlined by the authors of FlyCellAtlas, we use define a cell as expressing a given gene if at least one Unique Molecular Identifier corresponds to the gene.
First described in Citation:Ashburner, M., and Drysdale, R. (1994). FlyBase—The Drosophila genetic database. 120 (7): 2077–2079.
The most recent update on this Dataset is described in Gramates, L. S. et al, (2022). FlyBase: a guided tour of highlighted features. Genetics, Volume 220, Issue 4, April 2022, iyac035
FlyBase is the major repository for Drosophila melanogaster information, with individual pages for each gene within the fly containing a wealth of data from across the field. Indeed, many of the data sources used to build DIGITtally are key parts of the FlyBase gene summary.
As FlyBase contains information from 113177 INDIVIDUAL research papers, along with thousands of notes from direct personal communications, it is the ideal database to use for a directed literature search for for associations between a set of genes and a given set of tissues of interest.
FlyBase also contains a comprehensive list of the mutant phenotypes associated with alleles of each Drosophila gene. As such, we are able to score genes of interest based on whether they are known to affect specific tissue functions.
The most recent update on this Dataset is described in Hu, Y., Comjean, A., Rodiger, J., Liu, Y., Gao, Y., Chung, V., Zirin, J., Perrimon, N., and Mohr, S. E. (2020). FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update. Nucleic Acids Research 49: D908–D915
This Dataset contains information on Multiple model organisms .
Many tools exist to find orthologs of a gene between different species - particularly those species which have well annotated genomes. However, these tools rarely provide the same results, making it difficult for researchers to know which to use. DIOPT seeks to rectify this issue.
DIOPT integrates 17 different orthology finder algorithms for 10 different model organisms. For each gene, the number of orthology algorithms which return a given ortholog are taken as the "DIOPT score", with a higher score representing a more reliable ortholog. By default, DIGITtally only considers orthologs with a "Moderate" or better DIOPT score (3 or greater) as reliably orthologous.
First described in Kriventseva, E. V., Rahman, N., Espinosa, O., and Zdobnov., E. M. (2017). OrthoDB: the hierarchical catalog of eukaryotic orthologs. Nucleic Acids Research 36:D271-D275
The most recent update on this Dataset is described in Zdobnov, E. M., Kuznetsov, D., Tegenfeldt, F., Manni, M., Berkeley, M., and Kriventseva, E. V. (2021) OrthoDB in 2020: evolutionary and functional annotations of orthologs. Nucleic Acids Research 49:D389–D393
This Dataset contains information on Numerous species .
OrthoDB provides a wide, accessible source of Orthology information across a huge swathe of species - indeed, at time of writing, OrthoDB is a world-leader in the number of species for which orthology information is available. This flexibility is vital to supporting the modular approach of DIGITtally to analysing orthologs to genes of interest in other species.
OrthoDB utilises the OrthoLoger algorithm to search for orthologs of a given gene across species. OrthoLoger uses protein sequence homology to define orthologs for each gene, based on proteins available within UniProt. This does, however, mean that some genes which have only a predicted protein structure cannot have orthologs identified by this process.
OrthoDB is not used to generate scores for DIGITtally directly - instead, OrthoDB is used to define orthologs for genes of interest in Anopheles gambiae, Aedes aegypti, and Bombyx mori.
This Dataset contains information on Anopheles gambiae .
Insect types in Dataset: Male, Female
Insect tissues in Dataset: Head, Salivary Gland, Midgut, Malpighian Tubule, Carcass, Testis, Male Accessory Glands, Ovaries
MozAtlas comprises 60 Affymetrix Anopheles expression arrays performed on 5-day-old G3 laboratory strain mosquitoes, mapping the expression of ~16,000 probes - corresponding to almost 80% of known Anopheles genes. For each tissue and gender, an equal quantity of RNA was pooled from three time points (24, 48, 72hrs). In females samples were taken after the blood-meal. For each of four biological replicates, tissues were pooled from a minimum of 10 mosquitoes dissected at each time point
As MozAtlas is microarray based, readings have not only expression values for each tissue, but also a "Presence" value, which informs on whether the transcipt is detected at all according to Affymetrix's GCOS software. This can be used to infer how consistently a gene is expressed in a given tissue. By default, DIGITtally requires that at least 3/4 samples from a tissue display detectable expression to classify a gene as consistently expressed in that tissue.
This Dataset contains information on Anopheles gambiae .
Insect types in Dataset: Male, Female, Larval
Insect tissues in Dataset: Malpighian Tubules ONLY.
Mosquitos of the A. gambiae Keele strain were at 26 °C and 80% humidity with a 12 h day: night cycle. Adult mosquitoes were given access to 5% glucose in 0.05% para-aminobenzoic acid water, and larvae fed with ground TetraMin tropical fish food (Tetra, USA). Adult mosquitoes were offered a human blood-meal through an artificial membrane once per week.
Malpighian tubules from approximately 400 uninfected An. gambiae larvae, sugar-fed adult males, sugar-fed adult females, and females 3 h after a blood feed were dissected. RNA was isolated, and used for a Plasmodium/Anopheles Genome array containing probe sets to approximately 14,900 An. gambiae transcripts
As MozTubules is microarray based, readings have not only expression values for each tissue, but also a "Presence" value, which informs on whether the transcipt is detected at all according to Affymetrix's GCOS software. This can be used to infer how consistently a gene is expressed in a given tissue. By default, DIGITtally requires that at least 3/4 samples from a tissue display detectable expression to classify a gene as consistently expressed in that tissue.
This Dataset contains information on Aedes aegypti .
Insect types in Dataset: Female mosquitos ONLY.
Insect tissues in Dataset: Head, Thorax, Abdomen, Malpighian Tubules, Ovaries, Gut (Generic), Proventriculus, Anterior Midgut, Posterior Midgut, Hindgut
Aegypti-Atlas we uses 5- to 12-day-old female Ae. aegypti mosquitos. Larvae were reared at a density of 200 larvae per 1 liter tray, recieving 720 mg of fish food. Adults were maintained in humidified chambers (RH 75% ± 5%) at 29 °C on a diet of 10% sucrose ad libitum. Females were reared and maintained in approximately equal proportion with males for a minimum of 5 days prior to blood-feeding and/or dissection and were presumed to be mated.
Mosquitos were dissected, then RNA was harvested for RNA-seq analysis using the Illumina Nextseq 500 platform. Three biological replicates were prepared for each tissue.
To keep analysis consistent with other RNA-seq datasets, raw read counts from the Aegypti-Atlas datasets were converted to FPKMs prior to analysis. By default, DIGITtally uses an FPKM value of 2 as a cutoff for background-level expression. As such, transcripts with an FPKM under 2 are taken as not expressed in the analysed tissue by DIGITtally, and Whole Body expressions for genes have a minimum value of 2 for the purposes of enrichment analysis.
First described in Wang, J. et al. (2005). SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Research 33:D399–D402.
The most recent update on this Dataset is described in Lu, F., Wei, Z., Luo, Y., Guo, H., Zhang, G., Xia, Q. and Wang, Y. (2019). SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm. Nucleic Acids Research 48: D749–D755
This Dataset contains information on Bombyx mori .
Insect types in Dataset: Larvae_4thInstar, Larvae_4thMolt, Larvae_5thInstar, Larvae_Wandering, Larvae_PrePupa, Pupa, Moth
Insect tissues in Dataset: Hemolymph, Epidermis, Head, Testis, Ovary, Malpighian Tubule, Trachea, Midgut, Fat Body, Thorax, Antenna, Legs, Wing, Posterior Silk Gland, Middle Silk Gland, Anterior Silk Gland
The SilkDB RNA-seq dataset is robust, with 253 RNA-seq datasets gatheredfrom different tissues and stages of silkworm. RNA-seq analysis used the Illumina NovaSeq 6000, followed by HISAT2 alignment and Ballgown expression analysis. FPKM values from these analyses are used within DIGITtally.
As SilkDB lacks a true "Whole Body" gene expression reading, DIGITtally generates an artificial whole body expression level by averaging expression across all tissues present in each silkworm. This may not be truly representative of the whole body expression of a given gene due to the differences in relative contributions between different tissues at differing life stages, but should provide a reasonable estimate for enrichment calculations.
Please note that not all tissue types have data associated with each silkworm stage. DIGITtally automatically accounts for this by generating working tissue of interest lists for each selected silkworm type, including only those tissues of interest which have data associated. Final scores for Enrichment, Specificity and Expression are thus split in two, with a half-point for passing the threshold in all applicable tissues in ONE silkworm type, and a second for passing the threshold in ALL selected silkworm types.
By default, DIGITtally uses an FPKM value of 2 as a cutoff for background-level expression. As such, transcripts with an FPKM under 2 are taken as not expressed in the analysed tissue by DIGITtally, and Whole Body expressions for genes have a minimum value of 2 for the purposes of enrichment analysis.
DIGITtally currently utilises the following parameters:
Erichment of each gene in tissues of interest compared to the whole fly.
Individual scores are generated for each of the following data sources:
In FlyAtlas1, enrichment in each tissue of interest is calculated over whole fly readings. If this enrichment is over the provided "Enrichment threshold" - default of 2-fold higher than whole body - a point is scored.
In FlyAtlas1, flies are split into Adult or Larval. As such, it is possible to select one of these fly types specifically, in which case only that type will be considered. By default, though, DIGITtally looks at these types independently, with 1/2 of a point for enrichment per fly type in which a gene is enriched over whole body.
It is also possible to define a fly type as obligatory, in which case a lack of enrichment in these flies automatically reduces the score to 0. This allows users to fine-tune how vital each fly type is to their overall score.
Please note that, as FlyAtlas1 is microarray based, readings from tissues of interest with a presence call under the "Presence Threshold" - default of 3/4 samples from a tissue with detectable expression - are taken as inconsistent expression and excluded.
In FlyAtlas2, enrichment in each tissue of interest is calculated over whole fly readings. If this enrichment is over the provided "Enrichment threshold" - default of 2-fold higher than whole body - a point is scored.
In FlyAtlas2, flies are split into Male, Female or Larval. As such, it is possible to select one of these fly types specifically, in which case only that type will be considered. By default, though, DIGITtally looks at these types independently, with 1/3 of a point for enrichment per fly type in which a gene is enriched over whole body.
It is also possible to define a tissue as obligatory, in which case a lack of enrichment in these flies automatically reduces the score to 0. This allows users to fine-tune how vital each fly type is to their overall score.
Please note that, as the background FPKM value for FlyAtlas2 is 2, this is the minimum divisor for tissue-specific reads. This FPKM value can be modified when setting up your DIGITtally search.
As FlyCellAtlas provides counts of which cells express a given gene, Enrichment checks here look at the distribution of expression. If a given gene is significantly more expressed in target cells compared to non target cells, it scores a point for FlyCellAtlas enrichment.
Distributions are compared using a Chi-squared test, with a Bonferroni correction for multiple testing (default base p-value of 0.01, though this can be modified when setting up your DIGITtally search.)
Following the stategy outlined by the authors of FlyCellAtlas, we use define a cell as expressing a given gene if at least one Unique Molecular Identifier corresponds to the gene. This Unique Molecular Identifier level required to define a cell as positive for expression of a gene can be modified when setting up your DIGITtally search.
Whether a gene appears to be specifically expressed or upregulated within the user-defined tissue(s) of interest.
Individual scores are generated for each of the following data sources:
In FlyAtlas1, expression in each tissue of interest is compared to the highest non-target reading. If tissue of interest expression is higher than this non-target reading times the specificity threshold a point is scored. The specificity threshold has a default of 1, so genes which are higher than non-target by ANY margin score a point, though this can be modified during DIGITtally setup.
In FlyAtlas1, flies are split into Adult or Larval. As such, it is possible to select one of these fly types specifically, in which case only that type will be considered. By default, though, DIGITtally looks at these types independently, with 1/2 of a point for specificity per fly type in which a gene is higher in target than non-target tissues.
It is also possible to define a tissue as obligatory, in which case a lack of specificity in these flies automatically reduces the score to 0. This allows users to fine-tune how vital each fly type is to their overall score.
Please note that, as FlyAtlas1 is microarray based, readings from tissues of interest with a presence call under the "Presence Threshold" - default of 3/4 samples from a tissue with detectable expression - are taken as inconsistent expression and excluded.
In FlyAtlas2, expression in each tissue of interest is compared to the highest non-target reading. If tissue of interest expression is higher than this non-target reading times the specificity threshold a point is scored. The specificity threshold has a default of 1, so genes which are higher than non-target by ANY margin score a point, though this can be modified during DIGITtally setup.
In FlyAtlas2, flies are split into Male, Female or Larval. As such, it is possible to select one of these fly types specifically, in which case only that type will be considered. By default, though, DIGITtally looks at these types independently, with 1/3 of a point for enrichment per fly type in which a gene is higher in target than non-target tissues.
It is also possible to define a tissue as obligatory, in which case a lack of enrichment in these flies automatically reduces the score to 0. This allows users to fine-tune how vital each fly type is to their overall score.
Please note that, as the background FPKM value for FlyAtlas2 is 2, any reads under this value will be treated as 0 (no expression). This FPKM value can be modified when setting up your DIGITtally search.
Within FlyCellAtlas, two Specificity measurements can be used. These are handled seperately, for two individual datapoints towards the final DIGITtally.
Non-Target Expression
The total proportion of non-target cells which do not express a given gene. Thus, the lower the number of non-target cells which express a gene, the higher that gene will score for this specificity measure.
Proportion Expressing gene are Target
The total proportion of cells which express a given gene are classified as Target cells. Thus, the higher the number of cells expressing a gene which belong to user-defined target subsets, the higher that gene will score for this specificity measure.
Following the stategy outlined by the authors of FlyCellAtlas, we use define a cell as expressing a given gene if at least one Unique Molecular Identifier corresponds to the gene. This Unique Molecular Identifier level required to define a cell as positive for expression of a gene can be modified when setting up your DIGITtally search.
The extent to which a gene is expressed in all cells defined as cells of interest.
Due to the requirement for cell-level data, only FlyCellAtlas can be used to measure gene ubiquity.
The total proportion of target cells which express a given gene. Thus, the higher the number of target cells which express a gene, the higher that gene will score for this specificity measure.
Following the stategy outlined by the authors of FlyCellAtlas, we use define a cell as expressing a given gene if at least one Unique Molecular Identifier corresponds to the gene. This Unique Molecular Identifier level required to define a cell as positive for expression of a gene can be modified when setting up your DIGITtally search.
Co-expression of genes with a panel of user-submitted genes of interest.
Due to the requirement for cell-level data, only FlyCellAtlas can be used to measure gene
Note that to utilise this scoring metric, the user must supply a list of reference genes. This can be constructed using the "Genelist Builder" utility on the "Other Utilities" page, or manually generated as a line-separated list of FlyBase identifiers, in .txt format.
A maximum limit of 20 reference genes is currently imposed.
The proportion of cells co-expressed with each of reference genes provided. The proportion of cells co-expressed with each reference gene is calculated, all proportions summed, then divided by the number of references to give a score out of 1 for co-expression
That is to say,the co-expression score for each reference gene will be equal to the number of cells expressing both gene of interest and reference gene (nB) over the number of cells expressing the gene of interest only (nI). Individual co-expression scores are summed and then divided by the number of reference genes. Thus, co-expression score can be described by the equation:
( Σ ( nB / nI ) ) / Number of Reference Genes
Following the stategy outlined by the authors of FlyCellAtlas, we use define a cell as expressing a given gene if at least one Unique Molecular Identifier corresponds to the gene. This Unique Molecular Identifier level required to define a cell as positive for expression of a gene can be modified when setting up your DIGITtally search. This threshold will apply to BOTH the gene of interest and the reference gene.
Whether a gene has been demonstrated in the literature to have any role associated with the tissue(s) of interest.
Known Activity only uses FlyBase-driven literature searches.
Within FlyCellAtlas, two Specificity measurements can be used. These are handled seperately, for two individual datapoints towards the final DIGITtally
Association
This scores whether a gene has any data corresponding to EACH annotation of interest, corresponding to one or more tissues of interest, in its FlyBase record. For each such annotation associated with a gene, an association point is scored. The final association score is a sum of these points, over the number of annotations of interest (max 1)
Phenotype
This scores whether a gene has any mutant alleles causing a phenotype in EACH annotation of interest in its FlyBase record. For each such annotation associated with a gene, a phenotype point is scored. The final phenotype score is a sum of these points, over the number of annotations of interest (max 1)
Orthology measures various things. For insect species, orthology scores whether any combination of orthologs to a Drosophila gene of interest are:
Enriched in selected orthologous tissues;
Specifically upregulated/expressed in selected orthologous tissues;
Expressed at all in selected orthologous tissues.
These measures are used to generate a single orthology score per insect species. By default, each of these aspects are equally weighted, though this can be modified when setting up your DIGITtally search.
For Homo sapiens, given differences in body structure, the Orthology score is instead intended simply to link to possible human orthologs and their relevance to current biological issues.
Orthology is scored seperately by species, rather than data source. As such, MozAtlas and MozTubules are combined to produce an Anopheles Gambiae score when both are selected.
DIOPT data is used to generate the Homo sapiens orthology score. In turn,DIOPT uses 16 different checks of orthology. Genes earn a point if they have a human ortholog detected in at least 3 (the DIOPT cutoff for a "moderate" score) of these data sources. This DIOPT score threshold can be modified when setting up your DIGITtally search.
Optionally, DIGITtally can also check whether any human orthologs to a gene are assocaited with a human disease condition (based on the OMIM database). In this case, the final score is then divided by 2 so a final H.sap score out of 1 is always returned.
MozAtlas is one component of the Anopheles gambiae score, along with MozTubules. These can be used individually, or together. If both data sources are used, the final A.gam score will weight these appropriately so that scores are still out of 1.
In MozAtlas data, genes are scored based on whether any combination of their A.gam orthologs are Enriched in tissues orthologous to tissues of interest, specific to these tissues, or expressed in these tissues at all. Final scores are summed, then divided by three to provide an A.gam score out of 1.
In MozAtlas, mosquitos are split into Male or Female. As such, it is possible to select one specific sex, in which case only that sex will be considered. By default, though, DIGITtally looks for genes which act identically in both sexes, and in this case each threshold must be met in BOTH male and female insects for a point to be scored.
MozAtlas is one component of the Anopheles gambiae score, along with MozTubules. These can be used individually, or together. If both data sources are used, the final A.gam score will weight these appropriately so that scores are still out of 1.
In MozTubules data, genes are scored based only on enrichment, which is provided directly by the dataset. Scores are accumulated across the mosquito types to provide a final MozTubule score, then scores are normalised to be equal to ONE TISSUE from MozAtlas by default - though this can be modified when setting up your DIGITtally search.. The final scores are integrated to provide an A.gam score out of 1.
Aegypti-Atlas data is used to generate the Aedes aegypti orthology score. In Aegypti-Atlas, genes are scored based on whether any combination of their A.aeg orthologs are enriched in tissues orthologous to tissues of interest, specific to these tissues, or expressed in these tissues at all. Only one mosquito type (adult female) is present in AegyptiAtlas.
Please note that, as the background FPKM value for Aegypti-Atlas is 2, any reads under this value will be treated as 0 (no expression). This FPKM value can be modified when setting up your DIGITtally search.
SilkDB data is used to generate the Bombyx mori orthology score. In SilkDB, genes are scored based on whether any combination of their B.mor orthologs are enriched in tissues orthologous to tissues of interest, specific to these tissues, or expressed in these tissues at all. In this case, as no whole body reading is provided, a whole body expression level is estimated by averaging expression in all tissues at that life stage.
To manage the vast silkworm life-stage data available in SilkDB, the B.mor score is modified compared to other orthology scores. A single point is scored if the previously described criteria are met in a single B. mori life stage, another if the criteria are met at ALL life stages.
Please note that, as the background FPKM value for Aegypti-Atlas is 2, any reads under this value will be treated as 0 (no expression). This FPKM value can be modified when setting up your DIGITtally search.