README.md

---
license: mit
task_categories:
- tabular-regression
tags:
- biology
pretty_name: Candida albicans Co-Expression Network
size_categories:
- 10M<n<100M
dataset_info:
- config_name: CalCEN_network
  features:
  - name: feature_name_1
    dtype: string
  - name: feature_name_2
    dtype: string
  - name: score
    dtype: float64
  splits:
  - name: train
    num_bytes: 1472498808
    num_examples: 38763076
  download_size: 633855931
  dataset_size: 1472498808
- config_name: blastp_network
  features:
  - name: feature_name_1
    dtype: string
  - name: feature_name_2
    dtype: string
  - name: score
    dtype: float64
  splits:
  - name: train
    num_bytes: 4260374
    num_examples: 112129
  download_size: 1122972
  dataset_size: 4260374
- config_name: estimated_expression
  features:
  - name: gene_id
    dtype: string
  - name: transcript_ids
    dtype: string
  - name: length
    dtype: float64
  - name: effective_length
    dtype: float64
  - name: expected_count
    dtype: float64
  - name: TPM
    dtype: float64
  - name: FPKM
    dtype: float64
  - name: run_accession
    dtype: string
  - name: study_accession
    dtype: string
  - name: is_paired
    dtype: bool
  splits:
  - name: train
    num_bytes: 843354652
    num_examples: 8710174
  download_size: 305230791
  dataset_size: 843354652
- config_name: sac_gene_network
  features:
  - name: feature_name_1
    dtype: string
  - name: feature_name_2
    dtype: string
  - name: score
    dtype: float64
  splits:
  - name: train
    num_bytes: 1472498808
    num_examples: 38763076
  download_size: 452519443
  dataset_size: 1472498808
- config_name: sac_phys_network
  features:
  - name: feature_name_1
    dtype: string
  - name: feature_name_2
    dtype: string
  - name: score
    dtype: float64
  splits:
  - name: train
    num_bytes: 557509168
    num_examples: 14671296
  download_size: 105496144
  dataset_size: 557509168
- config_name: top_coexp_hits
  features:
  - name: feature_name_1
    dtype: string
  - name: feature_name_2
    dtype: string
  - name: gene_name_1
    dtype: string
  - name: gene_name_2
    dtype: string
  - name: description_1
    dtype: string
  - name: description_2
    dtype: string
  - name: feature_status_1
    dtype: string
  - name: feature_status_2
    dtype: string
  - name: coexp_score
    dtype: float64
  - name: blastp_score
    dtype: float64
  - name: sac_gene_score
    dtype: float64
  - name: sac_phys_score
    dtype: float64
  - name: yeast_net_score
    dtype: float64
  splits:
  - name: train
    num_bytes: 125718471
    num_examples: 311300
  download_size: 24731924
  dataset_size: 125718471
- config_name: yeast_net_network
  features:
  - name: feature_name_1
    dtype: string
  - name: feature_name_2
    dtype: string
  - name: score
    dtype: float64
  splits:
  - name: train
    num_bytes: 16180096
    num_examples: 425792
  download_size: 6316147
  dataset_size: 16180096
configs:
- config_name: CalCEN_network
  data_files:
  - split: train
    path: CalCEN_network/data/train-*
- 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-*
- config_name: sac_gene_network
  data_files:
  - split: train
    path: sac_gene_network/data/train-*
- config_name: sac_phys_network
  data_files:
  - split: train
    path: sac_phys_network/data/train-*
- config_name: top_coexp_hits
  data_files:
  - split: train
    path: top_coexp_hits/data/train-*
- config_name: yeast_net_network
  data_files:
  - split: train
    path: yeast_net_network/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. ...
```