Datasets:

BrentLab
/

hughes_2006

@@ -1,107 +1,104 @@
----
-license: mit
-language:
-- en
-tags:
-- biology
-- genomics
-- yeast
-- transcription-factors
-- gene-expression
-- perturbation-screen
-- overexpression
-- knockout
-- microarray
-- functional-genomics
-pretty_name: "Hughes 2006 Yeast Transcription Factor Perturbation Dataset"
-size_categories:
-- 100K<n<1M
-task_categories:
-- other
-source_datasets:
-- original
-dataset_info:
-  features:
-    - name: regulator_locus_tag
-      dtype: string
-      description: Systematic gene name (ORF identifier) of the perturbed transcription factor
-    - name: regulator_symbol
-      dtype: string
-      description: Standard gene symbol of the perturbed transcription factor
-    - name: target_locus_tag
-      dtype: string
-      description: Systematic gene name (ORF identifier) of the target gene measured
-    - name: target_symbol
-      dtype: string
-      description: Standard gene symbol of the target gene measured
-    - name: dye_plus
-      dtype: float
-      description: Normalized log2 fold change for positive (+) dye orientation
-    - name: dye_minus
-      dtype: float
-      description: Normalized log2 fold change for negative (-) dye orientation
-    - name: mean_norm_log2fc
-      dtype: float
-      description: Average log2 fold change across dye orientations; 0 when orientations have opposite signs, single value when only one orientation available
-configs:
-- config_name: metadata
-  description: Transcription factor metadata including essentiality and QC status
-  default: true
-  data_files:
-  - split: train
-    path: metadata.parquet
-- config_name: overexpression
-  description: Overexpression perturbation normalized log2 fold changes
-  data_files:
-  - split: train
-    path: overexpression.parquet
-- config_name: knockout
-  description: Deletion/knockout perturbation normalized log2 fold changes
-  data_files:
-  - split: train
-    path: knockout.parquet
----
-# Hughes 2006
-This data is parsed from data presented in this paper:
-https://www.pnas.org/doi/10.1073/pnas.0605140103
-The data is made available by the author at:
-https://hugheslab.ccbr.utoronto.ca/supplementary-data/yeastTF/
-and on NCBI with accession GSE5499. However, I used the data provided by the author above.
-Details on my parsing can be found in `scripts/`. The gene features are from
-BrentLab/yeast_genome_resources
-## Data
-`overexpression.parquet` and `knockout.parquet` have the same structure
-| Field                 | Description                                                                                                                                 |
-|-----------------------|---------------------------------------------------------------------------------------------------------------------------------------------|
-| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the perturbed transcription factor                                                                 |
-| `regulator_symbol`    | Standard gene symbol of the perturbed transcription factor                                                                                  |
-| `target_locus_tag`    | Systematic gene name (ORF identifier) of the target gene measured                                                                           |
-| `target_symbol`       | Standard gene symbol of the target gene measured                                                                                            |
-| `dye_plus`            | Normalized log2 fold change for positive (+) dye orientation                                                                                |
-| `dye_minus`           | Normalized log2 fold change for negative (-) dye orientation                                                                                |
-| `mean_norm_log2fc`    | Average log2 fold change across dye orientations; 0 when orientations have opposite signs, single value when only one orientation available |
-`metadata.parquet` contains transcription factor information
-| Field                 | Description                                                                                                             |
-|-----------------------|-------------------------------------------------------------------------------------------------------------------------|
-| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the transcription factor                                                      |
-| `regulator_symbol`    | Standard gene symbol of the transcription factor                                                                       |
-| `found_domain`        | Identified DNA-binding domain(s) or protein family classification                                                      |
-| `sgd_description`     | Functional description from Saccharomyces Genome Database (SGD)                                                       |
-| `essential`           | Boolean indicating whether the gene is essential for viability                                                         |
-| `oe_passed_qc`        | Boolean indicating whether overexpression experiments passed quality control                                           |
-| `del_passed_qc`       | Boolean indicating whether deletion experiments passed quality control                                                 |
-**Dataset Author and Contact**: Chase Mateusiak [@cmatKhan](https://github.com/cmatkhan/)

+---
+license: mit
+language:
+- en
+tags:
+- biology
+- genomics
+- yeast
+- transcription-factors
+- gene-expression
+- perturbation-screen
+- overexpression
+- knockout
+- microarray
+- functional-genomics
+pretty_name: "Hughes 2006 Yeast Transcription Factor Perturbation Dataset"
+size_categories:
+- 100K<n<1M
+task_categories:
+- other
+source_datasets:
+- original
+dataset_info:
+  features:
+    - name: regulator_locus_tag
+      dtype: string
+      description: Systematic gene name (ORF identifier) of the perturbed transcription factor
+    - name: regulator_symbol
+      dtype: string
+      description: Standard gene symbol of the perturbed transcription factor
+    - name: target_locus_tag
+      dtype: string
+      description: Systematic gene name (ORF identifier) of the target gene measured
+    - name: target_symbol
+      dtype: string
+      description: Standard gene symbol of the target gene measured
+    - name: dye_plus
+      dtype: float
+      description: Normalized log2 fold change for positive (+) dye orientation
+    - name: dye_minus
+      dtype: float
+      description: Normalized log2 fold change for negative (-) dye orientation
+    - name: mean_norm_log2fc
+      dtype: float
+      description: Average log2 fold change across dye orientations; 0 when orientations have opposite signs, single value when only one orientation available
+configs:
+- config_name: metadata
+  description: Transcription factor metadata including essentiality and QC status
+  default: true
+  data_files:
+  - split: train
+    path: metadata.parquet
+- config_name: overexpression
+  description: Overexpression perturbation normalized log2 fold changes
+  data_files:
+  - split: train
+    path: overexpression.parquet
+- config_name: knockout
+  description: Deletion/knockout perturbation normalized log2 fold changes
+  data_files:
+  - split: train
+    path: knockout.parquet
+---
+# Hughes 2006
+This data is parsed from data presented in this paper:
+https://www.pnas.org/doi/10.1073/pnas.0605140103
+The data is made [available by the author](https://hugheslab.ccbr.utoronto.ca/supplementary-data/yeastTF/) and on
+NCBI with accession [GSE5499](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5499).
+I used the data provided by the author.
+Details on my parsing can be found in `scripts/`. The gene features are from
+BrentLab/yeast_genome_resources
+## Data
+`overexpression.parquet` and `knockout.parquet` have the same structure
+| Field                 | Description                                                                                                                                 |
+|-----------------------|---------------------------------------------------------------------------------------------------------------------------------------------|
+| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the perturbed transcription factor                                                                 |
+| `regulator_symbol`    | Standard gene symbol of the perturbed transcription factor                                                                                  |
+| `target_locus_tag`    | Systematic gene name (ORF identifier) of the target gene measured                                                                           |
+| `target_symbol`       | Standard gene symbol of the target gene measured                                                                                            |
+| `dye_plus`            | Normalized log2 fold change for positive (+) dye orientation                                                                                |
+| `dye_minus`           | Normalized log2 fold change for negative (-) dye orientation                                                                                |
+| `mean_norm_log2fc`    | Average log2 fold change across dye orientations; 0 when orientations have opposite signs, single value when only one orientation available |
+`metadata.parquet` contains transcription factor information
+| Field                 | Description                                                                                                             |
+|-----------------------|-------------------------------------------------------------------------------------------------------------------------|
+| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the transcription factor                                                      |
+| `regulator_symbol`    | Standard gene symbol of the transcription factor                                                                       |
+| `found_domain`        | Identified DNA-binding domain(s) or protein family classification                                                      |
+| `sgd_description`     | Functional description from Saccharomyces Genome Database (SGD)                                                       |
+| `essential`           | Boolean indicating whether the gene is essential for viability                                                         |
+| `oe_passed_qc`        | Boolean indicating whether overexpression experiments passed quality control                                           |
+| `del_passed_qc`       | Boolean indicating whether deletion experiments passed quality control                                                 |
+**Dataset Author and Contact**: Chase Mateusiak [@cmatKhan](https://github.com/cmatkhan/)