removing wt from main data to its own dataset. adding responsive and updating datacard accordingly

README.md

@@ -174,6 +174,103 @@ configs:
     - name: chase_notes
       dtype: string
       description: notes added during data curation and parsing
+    - name: responsive
+      dtype: string
+      description: Per the paper(s), The authors consider a target responsive if Madj > 1.7 and pval < 0.05
+
+- config_name: control_2014
+  description: This stores the WT/background strains "WT-BY4743", "WT-MATA" and "WT-YPD" from Kemmeren 2014
+  dataset_type: annotated_features
+  default: true
+  metadata_fields: ["strain"]
+  data_files:
+  - split: train
+    path: control_2014.parquet
+  dataset_info:
+    features:
+    - name: sample_id
+      dtype: integer
+      description: >-
+        unique identifier for a specific sample.
+        The sample ID identifies a unique regulator.
+    - name: strain
+      dtype: string
+      description: >-
+        The genotype or strain used in the experiment,
+        one of "WT-BY4743", "WT-MATA" and "WT-YPD"
+      role: regulator_identifier
+    - name: regulator_symbol
+      dtype: string
+      description: >-
+        induced transcriptional regulator common name.
+        If no common name exists, then the `regulator_locus_tag` is used.
+      role: regulator_identifier
+    - name: reporterId
+      dtype: string
+      description: probe ID as reported from the original data
+    - name: target_locus_tag
+      dtype: string
+      description: >-
+        The systematic ID of the feature to which the effect/pvalue is assigned.
+        See hf/BrentLab/yeast_genome_resources
+      role: target_identifier
+    - name: target_symbol
+      dtype: string
+      description: >-
+        The common name of the feature to which the effect/pvalue is assigned.
+        If there is no common name, the `target_locus_tag` is used.
+      role: target_identifier
+    - name: M
+      dtype: float64
+      description: log₂ fold change (mutant vs wildtype)
+      role: quantitative_measure
+    - name: A
+      dtype: float64
+      description: >-
+        average log2 intensity of the two channels, a proxy for expression level
+        (This is a guess based on microarray convention -- not specified on holstege site)
+      role: quantitative_measure
+    - name: pval
+      dtype: float64
+      description: significance of the modeled effect (M), from limma
+      role: quantitative_measure
+    - name: variable_in_wt
+      dtype: string
+      description: >-
+        True if the given locus is variable in the WT condition.
+        Recommended to remove these from analysis. False otherwise.
+        See Holstege website for more information
+      role: experimental_condition
+    - name: multiple_probes
+      dtype: string
+      description: >-
+        True if there is more than one probe associated with
+        the same genomic locus. False otherwise
+      role: experimental_condition
+    - name: kemmeren_regulator
+      dtype: string
+      description: >-
+        True if the regulator is one of the regulators studied in the
+        original Kemmeren et al. (2014) global regulator study. False otherwise
+      role: experimental_condition
+    - name: description
+      dtype: string
+      description: >-
+        functional description of the induced regulator
+        from the original paper supplement
+      role: experimental_condition
+    - name: mating_type
+      dtype: string
+      description: mating type of the strain background used in the experiment
+      role: experimental_condition
+    - name: chase_notes
+      dtype: string
+      description: notes added during data curation and parsing
+    - name: responsive
+      dtype: string
+      description: >-
+        Per the paper(s), The authors consider a target responsive
+        if M > 1.7 and pval < 0.05
 ---
 # Kemmeren 2014
 

control_2014.parquet

@@ -0,0 +1,3 @@
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+size 661123

kemmeren_2014.parquet

@@ -1,3 +1,3 @@
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-size 326968372
+oid sha256:dc1d91a81eaf54b93c3062416a7348719e6f172f7fdb36380121ce55a7dbef80
+size 301350946

kemmeren_2014.parquet.md5

@@ -1 +0,0 @@
-94f81f31aa3d65c89b084cdbe4b72901  kemmeren_2014.parquet