---
license: mit
task_categories:
- tabular-regression
tags:
- biology
pretty_name: Candida albicans Co-Expression Network
size_categories:
- 10M<n<100M
dataset_info:
- config_name: blastp_network
  features:
  - name: "feature_name_1\tfeature_name_2\tscore"
    dtype: string
  splits:
  - name: train
    num_bytes: 5196933
    num_examples: 112129
  download_size: 1833517
  dataset_size: 5196933
- config_name: estimated_expression
  features:
  - name: "gene_id\ttranscript_ids\tlength\teffective_length\texpected_count\tTPM\t\
      FPKM\trun_accession\tstudy_accession\tis_paired"
    dtype: string
  splits:
  - name: train
    num_bytes: 675497726
    num_examples: 8710174
  download_size: 265798552
  dataset_size: 675497726
configs:
- config_name: blastp_network
  data_files:
  - split: train
    path: blastp_network/data/train-*
- config_name: estimated_expression
  data_files:
  - split: train
    path: estimated_expression/data/train-*
---
# 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.

Reference:

    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 SC5314 chromosome 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](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
```
    Column:
    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

```
    Column:
    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
```
    Column:
    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
```
    Column:
    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
```
    Column:
    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
```
    Column:
    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
```
    Column:
    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
```
     Column:
     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
```
    Column:
    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](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
```
    Column:
    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` is the mean area under the ROC curve summarized over 10-fold cross validation and `auroc_std` is the standard deviation
  - `degree_null_auroc_mean` is the degree null predictor scores and `degree_null_auroc_std` is the standard deviation
  - tab separated table with `125` rows
```
    Column:
    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. ...
```