Datasets:

maomlab
/

CalCEN

+---
+license: mit
+task_categories:
+- tabular-regression
+tags:
+- biology
+pretty_name: Candida albicans Co-Expression Network
+size_categories:
+- 10M<n<100M
+---
+# CalCEN: A Co-Expression Network for *Candida albicans*
+Elucidating gene function is a major goal in biology, especially among non-model organisms.
+However, doing so is complicated by the fact that molecular conservation does not always
+mirror functional conservation, and that complex relationships among genes are responsible
+for encoding pathways and higher-order biological processes. Co-expression, a promising
+approach for predicting gene function, relies on the general principle that genes with
+similar expression patterns across multiple conditions will likely be involved in the
+same biological process. For *Candida albicans*, a prevalent human fungal pathogen, we
+leveraged a large amount of publicly available transcriptomic data to generate a C. albicans
+Co-Expression Network (CalCEN), recapitulating known protein networks, predicting gene function, and
+enabling insights into the principles influencing co-expression. Overall, co-expression
+is a powerful tool for uncovering gene function, and decreases the experimental tests
+needed to identify functions for currently under-annotated genes.
+Data for
+    TR O'Meara, MJ O'Meara, M Sphere, 2020
+    DeORFanizing Candida albicans Genes using Co-Expression
+Code available at
+http://github.com/momeara/CalCEN
+*Candida albicans* Co-Expression Network (CalCEN) version 1.0.0
+## Files ##
+chromsome_features.tsv
+  - Candida albicans SC5314chromsome features collected from Candida Genome Database 12-Jun 2018
+  - primary key: feature_name
+  - URL: http://www.candidagenome.org/download/chromosomal_feature_files/C_albicans_SC5314/C_albicans_SC5314_A22_current_chromosomal_feature.tab
+  - tab separated table with 13,281 rows and columns
+      - feature_name             <chr> "C1_00010W_A", "C1_00010W_B", "C1_00020C_A", ...
+      - gene_name                <chr> NA, NA, NA, NA, NA, NA, "CTA2", "CTA2", NA,  ...
+      - aliases                  <chr> "orf19.6115|C1_00010W_B|C1_00010W|orf19.1353 ...
+      - feature_type             <chr> "ORF|Dubious", "ORF", "ORF|Uncharacterized", ...
+      - chromosome               <chr> "Ca22chr1A_C_albicans_SC5314", "Ca22chr1B_C_ ...
+      - start_coordinate         <dbl> 4059, 4059, 4720, 4720, 8908, 8908, 10718, 1 ...
+      - stop_coordinate          <dbl> 4397, 4397, 4409, 4409, 8597, 8597, 11485, 1 ...
+      - strand                   <chr> "W", "W", "C", "C", "C", "C", "W", "W", "C", ...
+      - primary_cgd_id           <chr> "CAL0000182519", "CAL0000183273", "CAL000018 ...
+      - secondary_cgd_id         <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "CAL ...
+      - description              <chr> "Dubious open reading frame", "Dubious open  ...
+      - creation_date            <date> 2014-06-24, 2014-06-24, 2014-06-24, 2014-06 ...
+      - sequence_coordinate_date <date> 2014-06-24, 2014-06-24, 2014-06-24, 2014-06 ...
+      - gene_name_date           <date> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ...
+      - gene_name_is_standard    <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ...
+      - sac_ortholog             <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "TUP ...
+      - feature_class            <chr> "ORF", "ORF", "ORF", "ORF", "ORF", "ORF", "O ...
+      - feature_status           <chr> "Dubious", NA, "Uncharacterized", NA, "Uncha ...
+      - is_alternatively_spliced <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ...
+      - is_transposable_element  <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ...
+      - rna_type                 <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,  ...
+      - is_blocked_reading_frame <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ...
+genes.tsv
+  - Curated set of 6226 genes use in this study
+  - primary key: feature_name
+  - foreign keys:
+      - feature_name -> chromosome_features.feature_name
+  - tab separated table with 6,226 row and columns
+      - feature_name <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180W_ ...
+expression_runs.tsv
+  - Curated set of RNA-seq runs used in this study
+  - Collected from NCBI SRA
+  - primary key: run_accession
+  - tab separated table with 853 rows and columns
+      - submission_accession          <chr> "ERA237292", "ERA237292", "ERA237292",  ...
+      - submission_lab                <chr> "ArrayExpress", "ArrayExpress", "ArrayE ...
+      - updated_date                  <date> 2016-01-11, 2016-01-11, 2016-01-11, 20 ...
+      - sradb_updated                 <dttm> 2018-05-24 18:09:52, 2018-05-24 18:09: ...
+      - study_accession               <chr> "ERP003535", "ERP003535", "ERP003535",  ...
+      - study_alias                   <chr> "E-MTAB-1720", "E-MTAB-1720", "E-MTAB-1 ...
+      - study_name                    <chr> "E-MTAB-1720", "E-MTAB-1720", "E-MTAB-1 ...
+      - study_title                   <chr> "Initial stress responses of Candida al ...
+      - study_type                    <chr> "Transcriptome Analysis", "Transcriptom ...
+      - study_abstract                <chr> "A study was carried out to characteris ...
+      - center_project_name           <chr> "Initial stress responses of Candida al ...
+      - study_description             <chr> "A study was carried out to characteris ...
+      - study_attribute               <chr> "ArrayExpress: E-MTAB-1720", "ArrayExpr ...
+      - description                   <chr> "Protocols: Candida albicans (strain CA ...
+      - design_description            <chr> "Initial stress responses of Candida al ...
+      - sample_accession              <chr> "ERS323180", "ERS323177", "ERS323173",  ...
+      - sample_alias                  <chr> "E-MTAB-1720:NS B", "E-MTAB-1720:XS+NS  ...
+      - sample_name                   <chr> "E-MTAB-1720:NS B", "E-MTAB-1720:XS+NS  ...
+      - sample_attribute              <chr> "organism: Candida albicans || genotype ...
+      - taxon_id                      <dbl> 5476, 5476, 5476, 5476, 5476, 5476, 547 ...
+      - background_strain             <chr> "CAI4", "CAI4", "CAI4", "CAI4", "CAI4", ...
+      - platform                      <chr> "ILLUMINA", "ILLUMINA", "ILLUMINA", "IL ...
+      - platform_parameters           <chr> "INSTRUMENT_MODEL: Illumina HiSeq 2000" ...
+      - instrument_model              <chr> "Illumina HiSeq 2000", "Illumina HiSeq  ...
+      - library_name                  <chr> "NS B", "XS+NS D", "NS D", "XS+NS D", " ...
+      - library_strategy              <chr> "RNA-Seq", "RNA-Seq", "RNA-Seq", "RNA-S ...
+      - library_source                <chr> "TRANSCRIPTOMIC", "TRANSCRIPTOMIC", "TR ...
+      - library_selection             <chr> "cDNA", "cDNA", "cDNA", "cDNA", "cDNA", ...
+      - library_layout                <chr> "SINGLE -", "SINGLE -", "SINGLE -", "SI ...
+      - library_construction_protocol <chr> "Candida albicans (strain CAI4-CIp10) w ...
+      - is_paired                     <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALS ...
+      - read_spec                     <chr> "READ_INDEX: 0; READ_CLASS: Application ...
+      - experiment_accession          <chr> "ERX283431", "ERX283301", "ERX283317",  ...
+      - experiment_alias              <chr> "E-MTAB-1720:120314_0166_D0814ACXX_3_SA ...
+      - experiment_name               <chr> "E-MTAB-1720:120314_0166_D0814ACXX_3_SA ...
+      - experiment_title              <chr> "Illumina HiSeq 2000 sequencing; Initia ...
+      - experiment_attribute          <chr> "Experimental Factor: compound_1: DPTA  ...
+      - run_accession                 <chr> "ERR310125", "ERR310018", "ERR309994",  ...
+      - run_alias                     <chr> "E-MTAB-1720:120314_0166_D0814ACXX_3_SA ...
+      - run_center                    <chr> "The GenePool, University of Edinburgh" ...
+      - spots                         <dbl> 1879764, 6330342, 5750605, 7088156, 649 ...
+      - bases                         <dbl> 95867964, 322847442, 293280855, 3614959 ...
+      - sra_fname                     <chr> "/nfs/ex7/work/momeara/ca_coexp/sra_806 ...
+      - year_collected                <dbl> 2018, 2018, 2018, 2018, 2018, 2018, 201 ...
+estimated_expression.tsv
+  - gene by RNA-seq run expression levels
+  - primary key: gene_id, run_accession
+  - foreign keys:
+      - gene_id -> genes.feature_name
+      - run_accession -> expression_runs.run_accession
+  - The FPKM column represents the per-gene, per-run expression level
+  - tab separated table with 8,710,174 rows and columns
+      - gene_id          <chr> "C1_00010W_A", "C1_00020C_A", "C1_00030C_A", "C1_000 ...
+      - transcript_ids   <chr> "C1_00010W_A", "C1_00020C_A", "C1_00030C_A", "C1_000 ...
+      - length           <dbl> 339, 312, 312, 768, 348, 1539, 1089, 852, 522, 729,  ...
+      - effective_length <dbl> 290, 263, 263, 719, 299, 1490, 1040, 803, 473, 680,  ...
+      - expected_count   <dbl> 24.00, 2149.00, 355.01, 3219.94, 56.00, 8003.00, 696 ...
+      - TPM              <dbl> 3.38, 333.77, 55.14, 182.93, 7.65, 219.40, 273.72, 4 ...
+      - FPKM             <dbl> 4.36, 430.27, 71.08, 235.82, 9.86, 282.83, 352.86, 5 ...
+      - run_accession    <chr> "ERR1143627", "ERR1143627", "ERR1143627", "ERR114362 ...
+      - study_accession  <chr> "ERP013259", "ERP013259", "ERP013259", "ERP013259",  ...
+      - is_paired        <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FAL ...
+CalCEN_network.tsv
+  - Co-expression network
+  - primary key: feature_name_1, feature_name_2
+  - foreign keys:
+      - feature_name_1 -> genes.feature_name
+      - feature_name_2 -> genes.feature_name
+  - score represents the scaled rank of the association between genes among
+    all gene pairs.
+  - score >= .99 is the default threshold for a significant association
+  - tab separated table with 38,763,076 rows and columns
+      - feature_name_1 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180 ...
+      - feature_name_2 <chr> "C3_03580C_A", "C3_03580C_A", "C3_03580C_A", "C3_03580 ...
+      - score          <dbl> 1.00000000, 0.75060056, 0.40875062, 0.68047576, 0.3594 ...
+blastp_network.tsv
+  - blastp sequence similarity network
+  - primary key: feature_name_1, feature_name_2
+  - foreign keys:
+      - feature_name_1 -> genes.feature_name
+      - feature_name_2 -> genes.feature_name
+  - score representes the scaled rank of the blastp Z-score among
+    all significant gene pair associations (i.e. missing -> score = 0).
+  - tab separated table with 112,129 rows and columns:
+      - feature_name_1 <chr> "C3_03580C_A", "C1_08890C_A", "CR_06460W_A", "C3_03600 ...
+      - feature_name_2 <chr> "C3_03580C_A", "C3_03580C_A", "C3_03580C_A", "C3_03580 ...
+      - score          <dbl> 0.95015957, 0.18948743, 0.27596712, 0.89713733, 0.0849 ...
+sac_gene.tsv
+  - genetic associations between orthologous Sac genes Network
+  - primary key: feature_name_1, feature_name_2
+  - foreign keys:
+      - feature_name_1 -> genes.feature_name
+      - feature_name_2 -> genes.feature_name
+  - score represents the scaled rank of the the spearman correlation between
+    between binary genetic association collected from BioGRID between orthologous genes
+    from sac (higher is more siginficant)
+  - tab separated table with 38,763,076 rows and columns
+      - feature_name_1 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180 ...
+      - feature_name_2 <chr> "C3_03580C_A", "C3_03580C_A", "C3_03580C_A", "C3_03580 ...
+      - score          <dbl> 1.00000000, 0.61167254, 0.23926432, 0.40917646, 0.6116 ...
+sac_gene.tsv
+  - physical protein-protein interaction between orthologous Sac genes Network
+  - primary key: feature_name_1, feature_name_2
+  - foreign keys:
+      - feature_name_1 -> genes.feature_name
+      - feature_name_2 -> genes.feature_name
+  - score represents the scaled rank of the the extended binary network
+    between binary genetic association collected from BioGRID between orthologous genes
+    from sac (higher is more siginficant).
+  - tab separated table with 14,671,296 rows and columns
+      - feature_name_1 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180 ...
+      - feature_name_2 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C7_02860 ...
+      - score          <dbl> 1.0000000, 1.0000000, 1.0000000, 0.5000000, 0.5000000, ...
+yeast_net_network.tsv
+  - YeastNet between orthologous Sac genes network
+  - primary key: feature_name_1, feature_name_2
+  - foreign keys:
+      - feature_name_1 -> genes.feature_name
+      - feature_name_2 -> genes.feature_name
+  - score is taken directly from the YeastNet network
+  - tab separated table with 425,792 rows and columns
+      - feature_name_1 <chr> "C1_12750C_A", "C5_05140W_A", "CR_07620W_A", "C7_04040 ...
+      - feature_name_2 <chr> "C7_02860C_A", "C7_02860C_A", "C7_02860C_A", "C7_02860 ...
+      - score          <dbl> 2.300967, 2.415099, 2.300967, 2.309640, 2.337247, 2.22 ...
+go_annotations.tsv
+  - GO annotations from Candida Genome Database collected 12-Jun 2018
+  - URL: http://www.candidagenome.org/download/go/gene_association.cgd.gz
+  - primary key: feature_name, go_id
+  - foreign keys:
+      - feature_name -> genes.feature_name
+  - values exclude NOT annotations and are propagated up the ontological hierarchy
+  - tab separated table with 29,159 rows and columns
+      - feature_name <chr> "C1_00100C_A", "C1_00640C_A", "C1_02660C_A", "C1_03540C_ ...
+      - go_id        <chr> "GO.0000002", "GO.0000002", "GO.0000002", "GO.0000002",  ...
+gba_summary.tsv
+  - Summary of guilt-by-association gene-function prediction
+  - primary key: anno_id, network_id
+  - anno_id in [all, MF, BB, CC]
+  - network_id is a set of networks ids separated by '|'
+  - auroc_mean auroc_std is the area under the ROC curve summarized
+    over 10 fold cross validation
+  - degree_null_auroc_mean, degree_null_auroc_std is the degree null predictor scores
+  - tab separated table with 125 rows with columns
+      - anno_id                <chr> "all", "all", "all", "all", "all", "all", "all ...
+      - network_id             <chr> "CalCEN", "BlastP", "SacPhys", "SacGene", "Yea ...
+      - auroc_mean             <dbl> 0.7522911, 0.6880802, 0.7713754, 0.7525273, 0. ...
+      - auroc_std              <dbl> 0.08311475, 0.11720483, 0.17135738, 0.12416886 ...
+      - degree_null_auroc_mean <dbl> 0.5111914, 0.5473948, 0.5996210, 0.5926223, 0. ...
+      - degree_null_auroc_std  <dbl> 0.1069059, 0.1418470, 0.1340942, 0.1316009, 0. ...