--- license: mit language: - en tags: - biology - genomics - yeast - transcription-factors - gene-expression - binding - chec - perturbation - rnaseq - nascent rnaseq pretty_name: "Mahendrawada 2025 ChEC-seq and Nascent RNA-seq data" size_categories: - 100K- unique identifier for a specific sample, which uniquely identifies one of the 178 TFs. Across datasets in this repo, the a given sample_id identifies the same regulator. - name: regulator_locus_tag dtype: string description: Systematic gene name (ORF identifier) of the transcription factor - name: regulator_symbol dtype: string description: Standard gene symbol of the transcription factor - name: target_locus_tag dtype: string description: Systematic gene name (ORF identifier) of the target gene - name: target_symbol dtype: string description: Standard gene symbol of the target gene - name: peak_score dtype: float64 description: ChEC signal around peak center (sum of ChEC signal from -150 to +150 bp from peak summit) normalized to Drosophila spike-in control - name: processing_method dtype: string description: Method used for peak calling and quantification (original authors) - config_name: chec_genome_map_meta description: Sample-level metadata for ChEC-seq experiments including regulator information, experimental conditions, and replicate structure dataset_type: metadata applies_to: ["chec_mahendrawada_m2025_af_replicates", "chec_genome_map"] data_files: - split: train path: chec_genome_map_meta.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA (Sequence Read Archive) accession identifier for this biological replicate role: sample_id - name: mahendrawada_symbol dtype: string description: Transcription factor symbol as reported in Mahendrawada et al. 2025 - name: replicate dtype: string description: Biological replicate identifier. One of A,B,C. All have 3 replicates - name: condition dtype: class_label: names: [ "standard", "SM", "WT", "WT_SM", "admut", "admut_SM", "cAD", "cAD_SM", "dbdmut", "dbdmut_SM", "nAD", "nAD_SM", "ncAD", "ncAD_SM", "30", "37", "galactose", "raffinose"] description: Experimental condition for this sample role: experimental_condition - name: regulator_locus_tag dtype: string description: Systematic gene name (ORF identifier) of the depleted transcription factor role: regulator_identifier - name: regulator_symbol dtype: string description: Standard gene symbol of the depleted transcription factor role: regulator_identifier - name: sample_id dtype: int description: Unique identifier combining regulator, condition, and replicates (used in combined datasets) - config_name: chec_genome_map description: >- ChEC-seq data reprocessed in the Brent Lab. See scripts/ for more details. These are bed format, therefore intervals are 0-based, half open, eg chrI:0-10 in a bed format would be chr:1-10 in IGV which is 1-indexed, closed interval dataset_type: genome_map data_files: - split: train path: chec_genome_map/sra_accession=*/*.parquet dataset_info: partitioning: enabled: true partition_by: ["sra_accession"] features: - name: sra_accession dtype: string description: SRA accession identifier used for partitioning (links to chec_genome_map_meta) role: sample_id - name: chr dtype: string description: Chromosome identifier (e.g., chrI, chrII, chrXVI) - name: start dtype: int description: Feature start position (0-based half open) - name: end dtype: int description: Feature end position (0-based, half open) - name: name dtype: string description: This stores the character `.`, one of the accepted characters for NA in bed6 - name: score dtype: int description: The depth of 5 prime read ends at this location role: quantitative_measure - name: strand dtype: string description: Strand orientation of the mapped fragment from which the 5 prime end originates (+ or -) - config_name: chec_genome_map_control_meta description: Sample-level metadata for ChEC free MNase experiments dataset_type: metadata applies_to: ["chec_genome_map_control"] data_files: - split: train path: chec_genome_map_control_meta.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA (Sequence Read Archive) accession identifier for this biological replicate - name: replicate dtype: string description: Biological replicate identifier. One of A,B,C. All have 3 replicates - name: notes dtype: string description: Additional notes or experimental details for this sample - config_name: chec_genome_map_control description: ChEC free MNase genome-wide signal tracks partitioned by SRA accession, providing position-level chromatin accessibility data dataset_type: genome_map data_files: - split: train path: chec_genome_map_control/sra_accession=*/*.parquet dataset_info: partitioning: enabled: true partition_by: ["sra_accession"] features: - name: sra_accession dtype: string description: SRA accession identifier used for partitioning (links to chec_genome_map_control_meta) role: sample_id - name: chr dtype: string description: Chromosome identifier (e.g., chrI, chrII, chrXVI) - name: start dtype: int description: Feature start position (0-based half open) - name: end dtype: int description: Feature end position (0-based, half open) - name: name dtype: string description: This stores the character `.`, one of the accepted characters for NA in bed6 - name: score dtype: int description: The depth of 5 prime read ends at this location role: quantitative_measure - name: strand dtype: string description: Strand orientation of the mapped fragment from which the 5 prime end originates (+ or -) - config_name: chec_mahendrawada_m2025_af_replicates description: ChEC-seq annotated features at biological replicate level with binding peaks and statistical significance metrics dataset_type: annotated_features data_files: - split: train path: chec_mahendrawada_m2025_af_replicates.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA (Sequence Read Archive) accession identifier for this biological replicate role: sample_id - name: target_locus_tag dtype: string description: Systematic gene identifier for the target gene role: target_identifier - name: target_symbol dtype: string description: Standard gene symbol for the target gene role: target_identifier - name: seqnames dtype: string description: Chromosome identifier (e.g., chrI, chrII) - name: start dtype: int64 description: Peak start position (0-based coordinate) - name: end dtype: int64 description: Peak end position (0-based, exclusive) - name: width dtype: int64 description: Width of the peak in base pairs - name: strand dtype: string description: Strand orientation (+ or -) - name: enrichment dtype: float64 description: Enrichment score for the binding peak role: quantitative_measure - name: poisson_pval dtype: float64 description: P-value from Poisson distribution test for peak significance role: quantitative_measure - name: log_poisson_pval dtype: float64 description: Log-transformed Poisson p-value role: quantitative_measure - name: hypergeometric_pval dtype: float64 description: P-value from hypergeometric distribution test for peak significance role: quantitative_measure - name: log_hypergeometric_pval dtype: float64 description: Log-transformed hypergeometric p-value role: quantitative_measure - name: poisson_qval dtype: float64 description: FDR-adjusted q-value from Poisson test (multiple testing correction) role: quantitative_measure - name: hypergeometric_qval dtype: float64 description: FDR-adjusted q-value from hypergeometric test (multiple testing correction) role: quantitative_measure - config_name: chec_mahendrawada_m2025_af_combined_meta description: Sample-level metadata for combined ChEC-seq experiments with regulator information and experimental conditions dataset_type: metadata applies_to: ["chec_mahendrawada_m2025_af_combined"] data_files: - split: train path: chec_mahendrawada_m2025_af_combined_meta.parquet dataset_info: features: - name: sample_id dtype: string description: Unique identifier combining regulator, condition, and replicates - name: regulator_locus_tag dtype: string description: Systematic gene name (ORF identifier) of the depleted transcription factor role: regulator_identifier - name: regulator_symbol dtype: string description: Standard gene symbol of the depleted transcription factor role: regulator_identifier - name: mahendrawada_symbol dtype: string description: Transcription factor symbol as reported in Mahendrawada et al. 2025 - name: condition dtype: class_label: names: [ "standard", "SM", "WT", "WT_SM", "admut", "admut_SM", "cAD", "cAD_SM", "dbdmut", "dbdmut_SM", "nAD", "nAD_SM", "ncAD", "ncAD_SM", "30", "37", "galactose", "raffinose"] description: Experimental condition for this sample role: experimental_condition - config_name: chec_mahendrawada_m2025_af_combined description: >- Brent Lab reprocessed data from Mahendrawada 2025. See scripts/ for more details. dataset_type: annotated_features data_files: - split: train path: chec_mahendrawada_m2025_af_combined.parquet dataset_info: features: - name: sample_id dtype: string description: >- Unique identifier for a specific regulator/condition. These are made up of the replicates marked as `combine == TRUE` in the replicate level metadata - name: target_locus_tag dtype: string description: Systematic gene identifier for the target gene role: target_identifier - name: target_symbol dtype: string description: Standard gene symbol for the target gene role: target_identifier - name: seqnames dtype: string description: Chromosome identifier (e.g., chrI, chrII) - name: start dtype: int64 description: Peak start position (1-based) - name: end dtype: int64 description: Peak end position (1-based, inclusive) - name: width dtype: int64 description: Width of the peak in base pairs - name: strand dtype: string description: Strand orientation (+ or -) - name: enrichment dtype: float64 description: Enrichment of experiment vs background role: quantitative_measure - name: poisson_pval dtype: float64 description: P-value from Poisson distribution test for peak significance role: quantitative_measure - name: log_poisson_pval dtype: float64 description: Log-transformed Poisson p-value role: quantitative_measure - name: hypergeometric_pval dtype: float64 description: P-value from hypergeometric distribution test for peak significance role: quantitative_measure - name: log_hypergeometric_pval dtype: float64 description: Log-transformed hypergeometric p-value role: quantitative_measure - name: poisson_qval dtype: float64 description: FDR-adjusted q-value from Poisson test (multiple testing correction) role: quantitative_measure - name: hypergeometric_qval dtype: float64 description: FDR-adjusted q-value from hypergeometric test (multiple testing correction) role: quantitative_measure - config_name: rna_seq description: Nascent RNA-seq differential expression data following transcription factor depletion using 4TU metabolic labeling dataset_type: annotated_features metadata_fields: - regulator_locus_tag - regulator_symbol data_files: - split: train path: rnaseq_mahendrawada_2025.parquet dataset_info: features: - name: sample_id dtype: integer description: >- unique identifier for a specific sample, which uniquely identifies one of the 178 TFs. Across datasets in this repo, the a given sample_id identifies the same regulator. - name: db_id dtype: integer description: >- an old unique identifer, for use internally only. Deprecated and will be removed eventually. Do not use in analysis. - name: regulator_locus_tag dtype: string description: Systematic gene name (ORF identifier) of the depleted transcription factor - name: regulator_symbol dtype: string description: Standard gene symbol of the depleted transcription factor - name: target_locus_tag dtype: string description: Systematic gene name (ORF identifier) of the differentially expressed target gene - name: target_symbol dtype: string description: Standard gene symbol of the differentially expressed target gene - name: log2fc dtype: float64 description: Log2 fold change (IAA/DMSO) for significantly affected genes (DESeq2, padj <0.1, FC >= 1.3) - config_name: rnaseq_reprocessed description: Reprocessed nascent RNA-seq differential expression data using DESeq2 without thresholding, comparing IAA-induced TF degradation versus DMSO control dataset_type: annotated_features metadata_fields: - regulator_locus_tag - regulator_symbol - sample_id - env_condition - timepoint data_files: - split: train path: rnaseq_reprocessed.parquet dataset_info: features: - name: sample_id dtype: string description: Composite identifier combining regulator, condition, timepoint, and treatment information from the merged IAA and DMSO sample IDs role: sample_id - name: regulator_locus_tag dtype: string description: Systematic gene identifier for the depleted transcription factor role: regulator_identifier - name: regulator_symbol dtype: string description: Standard gene symbol for the depleted transcription factor role: regulator_identifier - name: env_condition dtype: class_label: names: ["standard_30C", "SM", "galactose", "raffinose", "heat_shock_37C"] description: Environmental growth condition for this experiment role: experimental_condition - name: timepoint dtype: float64 description: Time point in minutes (standard is 30 minutes post-treatment. very few other timepoints) role: experimental_condition - name: target_locus_tag dtype: string description: Systematic gene identifier for the differentially expressed target gene role: target_identifier - name: target_symbol dtype: string description: Standard gene symbol for the differentially expressed target gene role: target_identifier - name: baseMean dtype: float64 description: Mean of normalized counts across all samples (DESeq2 output) role: quantitative_measure - name: log2FoldChange dtype: float64 description: Log2 fold change IAA versus DMSO (DESeq2 output, no thresholding applied) role: quantitative_measure - name: lfcSE dtype: float64 description: Standard error of the log2 fold change estimate (DESeq2 output) role: quantitative_measure - name: stat dtype: float64 description: Wald test statistic (DESeq2 output) role: quantitative_measure - name: pvalue dtype: float64 description: Wald test p-value (DESeq2 output) role: quantitative_measure - name: padj dtype: float64 description: Benjamini-Hochberg adjusted p-value (DESeq2 output) role: quantitative_measure - config_name: degron_counts_meta description: Sample-level metadata for auxin-inducible degron perturbation experiments with HTSeq count statistics dataset_type: metadata applies_to: ["degron_counts"] data_files: - split: train path: degron_counts_meta.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA run accession identifier for this sample role: sample_identifier - name: gsm_accession dtype: string description: GEO sample accession identifier (GSM ID) - name: regulator_locus_tag dtype: string description: Systematic gene identifier for the transcription factor role: regulator_identifier - name: regulator_symbol dtype: string description: Standard gene symbol for the transcription factor role: regulator_identifier - name: degron_treatment dtype: class_label: names: ["DMSO", "IAA"] description: Degron treatment condition (DMSO control or IAA degradation) role: experimental_condition - name: degron_variant dtype: class_label: names: ["mini_N_terminal_IAA7", "full_or_short_IAA7"] description: Type of auxin-inducible degron tag used - name: env_condition dtype: class_label: names: ["standard_30C", "SM", "galactose", "raffinose", "heat_shock_37C"] description: Environmental growth condition role: experimental_condition - name: timepoint dtype: float64 description: Time point for time-series experiments (minutes) - name: replicate dtype: string description: Biological replicate identifier (A, B, or C) - name: no_feature dtype: int64 description: HTSeq count of reads not assigned to any feature - name: ambiguous dtype: int64 description: HTSeq count of reads mapping ambiguously to multiple features - name: too_low_aQual dtype: int64 description: HTSeq count of reads filtered due to low alignment quality - name: alignment_not_unique dtype: int64 description: HTSeq count of reads with non-unique alignments - name: sample_id dtype: string description: Unique sample identifier combining replicates by treatment - config_name: degron_counts description: HTSeq gene-level read counts for auxin-inducible degron perturbation experiments dataset_type: annotated_features data_files: - split: train path: degron_counts.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA run accession identifier linking to sample metadata role: sample_id - name: target_locus_tag dtype: string description: Systematic gene identifier from BrentLab yeast genomic features (compatible with BrentLab yeast collection) role: target_identifier - name: target_symbol dtype: string description: Standard gene symbol from BrentLab yeast genomic features (compatible with BrentLab yeast collection) role: target_identifier - name: orig_locus_tag dtype: string description: Original systematic gene identifier from R64-1-1 genome annotation as reported by Mahendrawada et al. 2025 - name: count dtype: int64 description: HTSeq gene-level read count from R64-1-1 genome annotation role: quantitative_measure - config_name: mnase_fusion_rnaseq_counts_meta description: Sample-level metadata for MNase fusion strain RNA-seq experiments with HTSeq count statistics dataset_type: metadata applies_to: ["mnase_fusion_rnaseq_counts"] data_files: - split: train path: mnase_fusion_rnaseq_counts_meta.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA run accession identifier for this sample role: sample_identifier - name: gsm_accession dtype: string description: GEO sample accession identifier (GSM ID) - name: regulator_locus_tag dtype: string description: Systematic gene identifier for the MNase-tagged transcription factor role: regulator_identifier - name: regulator_symbol dtype: string description: Standard gene symbol for the MNase-tagged transcription factor role: regulator_identifier - name: env_condition dtype: class_label: names: ["standard_30C", "SM", "galactose", "raffinose", "heat_shock_37C"] description: Environmental growth condition role: experimental_condition - name: replicate dtype: string description: Biological replicate identifier (A, B, or C) - name: no_feature dtype: int64 description: HTSeq count of reads not assigned to any feature - name: ambiguous dtype: int64 description: HTSeq count of reads mapping ambiguously to multiple features - name: too_low_aQual dtype: int64 description: HTSeq count of reads filtered due to low alignment quality - name: alignment_not_unique dtype: int64 description: HTSeq count of reads with non-unique alignments - name: sample_id dtype: string description: Unique sample identifier combining replicates by treatment - config_name: mnase_fusion_rnaseq_counts description: HTSeq gene-level read counts for MNase fusion strain RNA-seq experiments dataset_type: annotated_features data_files: - split: train path: mnase_fusion_rnaseq_counts.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA run accession identifier linking to sample metadata role: sample_id - name: target_locus_tag dtype: string description: Systematic gene identifier from BrentLab yeast genomic features (compatible with BrentLab yeast collection) role: target_identifier - name: target_symbol dtype: string description: Standard gene symbol from BrentLab yeast genomic features (compatible with BrentLab yeast collection) role: target_identifier - name: orig_locus_tag dtype: string description: Original systematic gene identifier from R64-1-1 genome annotation as reported by Mahendrawada et al. 2025 - name: count dtype: int64 description: HTSeq gene-level read count from R64-1-1 genome annotation role: quantitative_measure - config_name: wt_baseline_counts_meta description: Sample-level metadata for wild-type baseline RNA-seq experiments with HTSeq count statistics dataset_type: metadata applies_to: ["wt_baseline_counts"] data_files: - split: train path: wt_baseline_counts_meta.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA run accession identifier for this sample role: sample_identifier - name: gsm_accession dtype: string description: GEO sample accession identifier (GSM ID) - name: env_condition dtype: class_label: names: ["standard_30C", "SM", "galactose", "raffinose", "heat_shock_37C"] description: Environmental growth condition role: experimental_condition - name: replicate dtype: string description: Biological replicate identifier (A, B, or C) - name: no_feature dtype: int64 description: HTSeq count of reads not assigned to any feature - name: ambiguous dtype: int64 description: HTSeq count of reads mapping ambiguously to multiple features - name: too_low_aQual dtype: int64 description: HTSeq count of reads filtered due to low alignment quality - name: alignment_not_unique dtype: int64 description: HTSeq count of reads with non-unique alignments - name: sample_id dtype: string description: Unique sample identifier combining replicates by treatment - config_name: wt_baseline_counts description: HTSeq gene-level read counts for wild-type baseline RNA-seq experiments dataset_type: annotated_features data_files: - split: train path: wt_baseline_counts.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA run accession identifier linking to sample metadata role: sample_id - name: target_locus_tag dtype: string description: Systematic gene identifier from BrentLab yeast genomic features (compatible with BrentLab yeast collection) role: target_identifier - name: target_symbol dtype: string description: Standard gene symbol from BrentLab yeast genomic features (compatible with BrentLab yeast collection) role: target_identifier - name: orig_locus_tag dtype: string description: Original systematic gene identifier from R64-1-1 genome annotation as reported by Mahendrawada et al. 2025 - name: count dtype: int64 description: HTSeq gene-level read count from R64-1-1 genome annotation role: quantitative_measure - config_name: wt_degron_control_counts_meta description: Sample-level metadata for wild-type degron control RNA-seq experiments with HTSeq count statistics dataset_type: metadata applies_to: ["wt_degron_control_counts"] data_files: - split: train path: wt_degron_control_counts_meta.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA run accession identifier for this sample role: sample_identifier - name: gsm_accession dtype: string description: GEO sample accession identifier (GSM ID) - name: degron_treatment dtype: class_label: names: ["DMSO", "IAA"] description: Degron treatment condition (DMSO control or IAA degradation) role: experimental_condition - name: replicate dtype: string description: Biological replicate identifier (A, B, or C) - name: no_feature dtype: int64 description: HTSeq count of reads not assigned to any feature - name: ambiguous dtype: int64 description: HTSeq count of reads mapping ambiguously to multiple features - name: too_low_aQual dtype: int64 description: HTSeq count of reads filtered due to low alignment quality - name: alignment_not_unique dtype: int64 description: HTSeq count of reads with non-unique alignments - name: sample_id dtype: string description: Unique sample identifier combining replicates by treatment - config_name: wt_degron_control_counts description: HTSeq gene-level read counts for wild-type degron control RNA-seq experiments dataset_type: annotated_features data_files: - split: train path: wt_degron_control_counts.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA run accession identifier linking to sample metadata role: sample_id - name: target_locus_tag dtype: string description: Systematic gene identifier from BrentLab yeast genomic features (compatible with BrentLab yeast collection) role: target_identifier - name: target_symbol dtype: string description: Standard gene symbol from BrentLab yeast genomic features (compatible with BrentLab yeast collection) role: target_identifier - name: orig_locus_tag dtype: string description: Original systematic gene identifier from R64-1-1 genome annotation as reported by Mahendrawada et al. 2025 - name: count dtype: int64 description: HTSeq gene-level read count from R64-1-1 genome annotation role: quantitative_measure --- # Mahendrawada 2025 This data is taken from the Supplement of [Mahendrawada, L., Warfield, L., Donczew, R. et al. Low overlap of transcription factor DNA binding and regulatory targets. Nature 642, 796–804 (2025). https://doi.org/10.1038/s41586-025-08916-0](https://doi.org/10.1038/s41586-025-08916-0) and [GSE236948](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236948)