Datasets:
Fix formatting for README.md
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README.md
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@@ -22,14 +22,12 @@ enabling insights into the principles influencing co-expression. Overall, co-exp
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is a powerful tool for uncovering gene function, and decreases the experimental tests
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needed to identify functions for currently under-annotated genes.
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Data for
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TR O'Meara, MJ O'Meara, M Sphere, 2020
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DeORFanizing Candida albicans Genes using Co-Expression
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Code available at
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http://github.com/momeara/CalCEN
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## Files ##
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chromsome_features.tsv
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- Candida albicans
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- primary key: feature_name
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- URL: http://www.candidagenome.org/download/chromosomal_feature_files/C_albicans_SC5314/C_albicans_SC5314_A22_current_chromosomal_feature.tab
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- tab separated table with 13,281 rows
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- foreign keys:
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- feature_name -> chromosome_features.feature_name
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- tab separated table with 6,226 row
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expression_runs.tsv
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- Curated set of RNA-seq runs used in this study
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- Collected from NCBI SRA
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- primary key: run_accession
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- tab separated table with 853 rows
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- gene by RNA-seq run expression levels
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- primary key: gene_id
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- foreign keys:
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- gene_id -> genes.feature_name
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- run_accession -> expression_runs.run_accession
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- The FPKM column represents the per-gene, per-run expression level
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- tab separated table with 8,710,174 rows
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- Co-expression network
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- primary key: feature_name_1
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- foreign keys:
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- feature_name_1 -> genes.feature_name
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- feature_name_2 -> genes.feature_name
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- score represents the scaled rank of the association between genes among
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all gene pairs.
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- score >= .99 is the default threshold for a significant association
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- tab separated table with 38,763,076 rows
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blastp_network.tsv
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- blastp sequence similarity network
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- primary key: feature_name_1
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- foreign keys:
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- feature_name_1 -> genes.feature_name
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- feature_name_2 -> genes.feature_name
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- score representes the scaled rank of the blastp Z-score among
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all significant gene pair associations (i.e. missing -> score = 0).
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- tab separated table with 112,129 rows
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sac_gene.tsv
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- genetic associations between orthologous Sac genes Network
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- primary key: feature_name_1
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- foreign keys:
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- feature_name_1 -> genes.feature_name
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- feature_name_2 -> genes.feature_name
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- score represents the scaled rank of the the spearman correlation between
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between binary genetic association collected from BioGRID between orthologous genes
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from sac (higher is more siginficant)
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- tab separated table with 38,763,076 rows
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sac_gene.tsv
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- physical protein-protein interaction between orthologous Sac genes Network
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- primary key: feature_name_1
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- foreign keys:
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- feature_name_1 -> genes.feature_name
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- feature_name_2 -> genes.feature_name
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- score represents the scaled rank of the the extended binary network
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between binary genetic association collected from BioGRID between orthologous genes
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from sac (higher is more siginficant).
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- tab separated table with 14,671,296 rows and columns
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yeast_net_network.tsv
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- YeastNet between orthologous Sac genes network
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- primary key: feature_name_1
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- foreign keys:
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- feature_name_1 -> genes.feature_name
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- feature_name_2 -> genes.feature_name
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- score is taken directly from the YeastNet network
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- tab separated table with 425,792 rows
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go_annotations.tsv
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- GO annotations from Candida Genome Database collected 12-Jun 2018
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- URL: http://www.candidagenome.org/download/go/gene_association.cgd.gz
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- primary key: feature_name
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- foreign keys:
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- feature_name -> genes.feature_name
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- values exclude NOT annotations and are propagated up the ontological hierarchy
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- tab separated table with 29,159 rows
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gba_summary.tsv
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- Summary of guilt-by-association gene-function prediction
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- primary key: anno_id
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- anno_id in [all, MF, BB, CC]
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- network_id is a set of networks ids separated by '|'
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- auroc_mean
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is a powerful tool for uncovering gene function, and decreases the experimental tests
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needed to identify functions for currently under-annotated genes.
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Reference:
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TR O'Meara, MJ O'Meara, M Sphere, 2020
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DeORFanizing Candida albicans Genes using Co-Expression
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Code available at:
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http://github.com/momeara/CalCEN
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## Files ##
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**chromsome_features.tsv**
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- Candida albicans SC5314 chromosome features collected from Candida Genome Database 12-Jun 2018
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- primary key: `feature_name`
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- URL: [http://www.candidagenome.org/download/chromosomal_feature_files/C_albicans_SC5314/C_albicans_SC5314_A22_current_chromosomal_feature.tab](http://www.candidagenome.org/download/chromosomal_feature_files/C_albicans_SC5314/C_albicans_SC5314_A22_current_chromosomal_feature.tab)
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- tab separated table with `13,281` rows
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```
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Column:
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feature_name <chr> "C1_00010W_A", "C1_00010W_B", "C1_00020C_A", ...
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gene_name <chr> NA, NA, NA, NA, NA, NA, "CTA2", "CTA2", NA, ...
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aliases <chr> "orf19.6115|C1_00010W_B|C1_00010W|orf19.1353 ...
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feature_type <chr> "ORF|Dubious", "ORF", "ORF|Uncharacterized", ...
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chromosome <chr> "Ca22chr1A_C_albicans_SC5314", "Ca22chr1B_C_ ...
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start_coordinate <dbl> 4059, 4059, 4720, 4720, 8908, 8908, 10718, 1 ...
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stop_coordinate <dbl> 4397, 4397, 4409, 4409, 8597, 8597, 11485, 1 ...
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strand <chr> "W", "W", "C", "C", "C", "C", "W", "W", "C", ...
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primary_cgd_id <chr> "CAL0000182519", "CAL0000183273", "CAL000018 ...
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secondary_cgd_id <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "CAL ...
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description <chr> "Dubious open reading frame", "Dubious open ...
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creation_date <date> 2014-06-24, 2014-06-24, 2014-06-24, 2014-06 ...
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sequence_coordinate_date <date> 2014-06-24, 2014-06-24, 2014-06-24, 2014-06 ...
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gene_name_date <date> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ...
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gene_name_is_standard <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ...
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sac_ortholog <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "TUP ...
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feature_class <chr> "ORF", "ORF", "ORF", "ORF", "ORF", "ORF", "O ...
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feature_status <chr> "Dubious", NA, "Uncharacterized", NA, "Uncha ...
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is_alternatively_spliced <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ...
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is_transposable_element <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ...
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rna_type <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ...
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is_blocked_reading_frame <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ...
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```
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**genes.tsv**
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- Curated set of `6226` genes use in this study
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- primary key: `feature_name`
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- foreign keys:
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- `feature_name` -> `chromosome_features.feature_name`
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- tab separated table with `6,226` row
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```
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Column:
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feature_name <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180W_ ...
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```
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**expression_runs.tsv**
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- Curated set of RNA-seq runs used in this study
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- Collected from NCBI SRA
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- primary key: `run_accession`
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- tab separated table with `853` rows
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```
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Column:
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submission_accession <chr> "ERA237292", "ERA237292", "ERA237292", ...
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submission_lab <chr> "ArrayExpress", "ArrayExpress", "ArrayE ...
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updated_date <date> 2016-01-11, 2016-01-11, 2016-01-11, 20 ...
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sradb_updated <dttm> 2018-05-24 18:09:52, 2018-05-24 18:09: ...
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study_accession <chr> "ERP003535", "ERP003535", "ERP003535", ...
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study_alias <chr> "E-MTAB-1720", "E-MTAB-1720", "E-MTAB-1 ...
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study_name <chr> "E-MTAB-1720", "E-MTAB-1720", "E-MTAB-1 ...
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study_title <chr> "Initial stress responses of Candida al ...
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study_type <chr> "Transcriptome Analysis", "Transcriptom ...
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study_abstract <chr> "A study was carried out to characteris ...
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center_project_name <chr> "Initial stress responses of Candida al ...
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study_description <chr> "A study was carried out to characteris ...
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study_attribute <chr> "ArrayExpress: E-MTAB-1720", "ArrayExpr ...
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description <chr> "Protocols: Candida albicans (strain CA ...
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design_description <chr> "Initial stress responses of Candida al ...
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sample_accession <chr> "ERS323180", "ERS323177", "ERS323173", ...
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sample_alias <chr> "E-MTAB-1720:NS B", "E-MTAB-1720:XS+NS ...
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sample_name <chr> "E-MTAB-1720:NS B", "E-MTAB-1720:XS+NS ...
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sample_attribute <chr> "organism: Candida albicans || genotype ...
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taxon_id <dbl> 5476, 5476, 5476, 5476, 5476, 5476, 547 ...
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background_strain <chr> "CAI4", "CAI4", "CAI4", "CAI4", "CAI4", ...
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platform <chr> "ILLUMINA", "ILLUMINA", "ILLUMINA", "IL ...
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platform_parameters <chr> "INSTRUMENT_MODEL: Illumina HiSeq 2000" ...
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instrument_model <chr> "Illumina HiSeq 2000", "Illumina HiSeq ...
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library_name <chr> "NS B", "XS+NS D", "NS D", "XS+NS D", " ...
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library_strategy <chr> "RNA-Seq", "RNA-Seq", "RNA-Seq", "RNA-S ...
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library_source <chr> "TRANSCRIPTOMIC", "TRANSCRIPTOMIC", "TR ...
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library_selection <chr> "cDNA", "cDNA", "cDNA", "cDNA", "cDNA", ...
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library_layout <chr> "SINGLE -", "SINGLE -", "SINGLE -", "SI ...
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library_construction_protocol <chr> "Candida albicans (strain CAI4-CIp10) w ...
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is_paired <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALS ...
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read_spec <chr> "READ_INDEX: 0; READ_CLASS: Application ...
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experiment_accession <chr> "ERX283431", "ERX283301", "ERX283317", ...
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experiment_alias <chr> "E-MTAB-1720:120314_0166_D0814ACXX_3_SA ...
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experiment_name <chr> "E-MTAB-1720:120314_0166_D0814ACXX_3_SA ...
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experiment_title <chr> "Illumina HiSeq 2000 sequencing; Initia ...
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experiment_attribute <chr> "Experimental Factor: compound_1: DPTA ...
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run_accession <chr> "ERR310125", "ERR310018", "ERR309994", ...
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run_alias <chr> "E-MTAB-1720:120314_0166_D0814ACXX_3_SA ...
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run_center <chr> "The GenePool, University of Edinburgh" ...
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spots <dbl> 1879764, 6330342, 5750605, 7088156, 649 ...
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bases <dbl> 95867964, 322847442, 293280855, 3614959 ...
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sra_fname <chr> "/nfs/ex7/work/momeara/ca_coexp/sra_806 ...
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year_collected <dbl> 2018, 2018, 2018, 2018, 2018, 2018, 201 ...
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```
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**estimated_expression.tsv**
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- gene by RNA-seq run expression levels
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- primary key: `gene_id`, `run_accession`
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- foreign keys:
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- `gene_id` -> `genes.feature_name`
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- `run_accession` -> `expression_runs.run_accession`
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- The FPKM column represents the per-gene, per-run expression level
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- tab separated table with `8,710,174` rows
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```
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Column:
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gene_id <chr> "C1_00010W_A", "C1_00020C_A", "C1_00030C_A", "C1_000 ...
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transcript_ids <chr> "C1_00010W_A", "C1_00020C_A", "C1_00030C_A", "C1_000 ...
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length <dbl> 339, 312, 312, 768, 348, 1539, 1089, 852, 522, 729, ...
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effective_length <dbl> 290, 263, 263, 719, 299, 1490, 1040, 803, 473, 680, ...
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expected_count <dbl> 24.00, 2149.00, 355.01, 3219.94, 56.00, 8003.00, 696 ...
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TPM <dbl> 3.38, 333.77, 55.14, 182.93, 7.65, 219.40, 273.72, 4 ...
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FPKM <dbl> 4.36, 430.27, 71.08, 235.82, 9.86, 282.83, 352.86, 5 ...
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run_accession <chr> "ERR1143627", "ERR1143627", "ERR1143627", "ERR114362 ...
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study_accession <chr> "ERP013259", "ERP013259", "ERP013259", "ERP013259", ...
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is_paired <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FAL ...
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```
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**CalCEN_network.tsv**
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- Co-expression network
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- primary key: `feature_name_1`, `feature_name_2`
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- foreign keys:
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- `feature_name_1` -> `genes.feature_name`
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- `feature_name_2` -> `genes.feature_name`
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- score represents the scaled rank of the association between genes among
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all gene pairs.
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- `score >= .99` is the default threshold for a significant association
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- tab separated table with `38,763,076` rows
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```
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Column:
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| 168 |
+
feature_name_1 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180 ...
|
| 169 |
+
feature_name_2 <chr> "C3_03580C_A", "C3_03580C_A", "C3_03580C_A", "C3_03580 ...
|
| 170 |
+
score <dbl> 1.00000000, 0.75060056, 0.40875062, 0.68047576, 0.3594 ...
|
| 171 |
+
```
|
| 172 |
|
| 173 |
+
**blastp_network.tsv**
|
| 174 |
- blastp sequence similarity network
|
| 175 |
+
- primary key: `feature_name_1`, `feature_name_2`
|
| 176 |
- foreign keys:
|
| 177 |
+
- `feature_name_1` -> `genes.feature_name`
|
| 178 |
+
- `feature_name_2` -> `genes.feature_name`
|
| 179 |
- score representes the scaled rank of the blastp Z-score among
|
| 180 |
+
all significant gene pair associations (i.e. missing -> `score = 0`).
|
| 181 |
+
- tab separated table with `112,129` rows
|
| 182 |
+
```
|
| 183 |
+
Column:
|
| 184 |
+
feature_name_1 <chr> "C3_03580C_A", "C1_08890C_A", "CR_06460W_A", "C3_03600 ...
|
| 185 |
+
feature_name_2 <chr> "C3_03580C_A", "C3_03580C_A", "C3_03580C_A", "C3_03580 ...
|
| 186 |
+
score <dbl> 0.95015957, 0.18948743, 0.27596712, 0.89713733, 0.0849 ...
|
| 187 |
+
```
|
| 188 |
|
| 189 |
+
**sac_gene.tsv**
|
| 190 |
- genetic associations between orthologous Sac genes Network
|
| 191 |
+
- primary key: `feature_name_1`, `feature_name_2`
|
| 192 |
- foreign keys:
|
| 193 |
+
- `feature_name_1` -> `genes.feature_name`
|
| 194 |
+
- `feature_name_2` -> `genes.feature_name`
|
| 195 |
- score represents the scaled rank of the the spearman correlation between
|
| 196 |
between binary genetic association collected from BioGRID between orthologous genes
|
| 197 |
from sac (higher is more siginficant)
|
| 198 |
+
- tab separated table with `38,763,076` rows
|
| 199 |
+
```
|
| 200 |
+
Column:
|
| 201 |
+
feature_name_1 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180 ...
|
| 202 |
+
feature_name_2 <chr> "C3_03580C_A", "C3_03580C_A", "C3_03580C_A", "C3_03580 ...
|
| 203 |
+
score <dbl> 1.00000000, 0.61167254, 0.23926432, 0.40917646, 0.6116 ...
|
| 204 |
+
```
|
| 205 |
|
| 206 |
+
**sac_gene.tsv**
|
| 207 |
- physical protein-protein interaction between orthologous Sac genes Network
|
| 208 |
+
- primary key: `feature_name_1`, `feature_name_2`
|
| 209 |
- foreign keys:
|
| 210 |
+
- `feature_name_1` -> `genes.feature_name`
|
| 211 |
+
- `feature_name_2` -> `genes.feature_name`
|
| 212 |
- score represents the scaled rank of the the extended binary network
|
| 213 |
between binary genetic association collected from BioGRID between orthologous genes
|
| 214 |
from sac (higher is more siginficant).
|
| 215 |
+
- tab separated table with `14,671,296` rows and columns
|
| 216 |
+
```
|
| 217 |
+
Column:
|
| 218 |
+
feature_name_1 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180 ...
|
| 219 |
+
feature_name_2 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C7_02860 ...
|
| 220 |
+
score <dbl> 1.0000000, 1.0000000, 1.0000000, 0.5000000, 0.5000000, ...
|
| 221 |
+
```
|
| 222 |
|
| 223 |
+
**yeast_net_network.tsv**
|
| 224 |
- YeastNet between orthologous Sac genes network
|
| 225 |
+
- primary key: `feature_name_1`, `feature_name_2`
|
| 226 |
- foreign keys:
|
| 227 |
+
- `feature_name_1` -> `genes.feature_name`
|
| 228 |
+
- `feature_name_2` -> `genes.feature_name`
|
| 229 |
- score is taken directly from the YeastNet network
|
| 230 |
+
- tab separated table with `425,792` rows
|
| 231 |
+
```
|
| 232 |
+
Column:
|
| 233 |
+
feature_name_1 <chr> "C1_12750C_A", "C5_05140W_A", "CR_07620W_A", "C7_04040 ...
|
| 234 |
+
feature_name_2 <chr> "C7_02860C_A", "C7_02860C_A", "C7_02860C_A", "C7_02860 ...
|
| 235 |
+
score <dbl> 2.300967, 2.415099, 2.300967, 2.309640, 2.337247, 2.22 ...
|
| 236 |
+
```
|
| 237 |
|
| 238 |
+
**go_annotations.tsv**
|
| 239 |
- GO annotations from Candida Genome Database collected 12-Jun 2018
|
| 240 |
+
- URL: [http://www.candidagenome.org/download/go/gene_association.cgd.gz](http://www.candidagenome.org/download/go/gene_association.cgd.gz)
|
| 241 |
+
- primary key: `feature_name`, `go_id`
|
| 242 |
- foreign keys:
|
| 243 |
+
- `feature_name` -> `genes.feature_name`
|
| 244 |
- values exclude NOT annotations and are propagated up the ontological hierarchy
|
| 245 |
+
- tab separated table with `29,159` rows
|
| 246 |
+
```
|
| 247 |
+
Column:
|
| 248 |
+
feature_name <chr> "C1_00100C_A", "C1_00640C_A", "C1_02660C_A", "C1_03540C_ ...
|
| 249 |
+
go_id <chr> "GO.0000002", "GO.0000002", "GO.0000002", "GO.0000002", ...
|
| 250 |
+
```
|
| 251 |
|
| 252 |
+
**gba_summary.tsv**
|
| 253 |
- Summary of guilt-by-association gene-function prediction
|
| 254 |
+
- primary key: `anno_id`, `network_id`
|
| 255 |
+
- `anno_id` in [all, MF, BB, CC]
|
| 256 |
+
- `network_id` is a set of networks ids separated by '|'
|
| 257 |
+
- `auroc_mean` is the mean area under the ROC curve summarized over 10-fold cross validation and `auroc_std` is the standard deviation
|
| 258 |
+
- `degree_null_auroc_mean` is the degree null predictor scores and `degree_null_auroc_std` is the standard deviation
|
| 259 |
+
- tab separated table with `125` rows
|
| 260 |
+
```
|
| 261 |
+
Column:
|
| 262 |
+
anno_id <chr> "all", "all", "all", "all", "all", "all", "all ...
|
| 263 |
+
network_id <chr> "CalCEN", "BlastP", "SacPhys", "SacGene", "Yea ...
|
| 264 |
+
auroc_mean <dbl> 0.7522911, 0.6880802, 0.7713754, 0.7525273, 0. ...
|
| 265 |
+
auroc_std <dbl> 0.08311475, 0.11720483, 0.17135738, 0.12416886 ...
|
| 266 |
+
degree_null_auroc_mean <dbl> 0.5111914, 0.5473948, 0.5996210, 0.5926223, 0. ...
|
| 267 |
+
degree_null_auroc_std <dbl> 0.1069059, 0.1418470, 0.1340942, 0.1316009, 0. ...
|
| 268 |
+
```
|