manifests/tfbind10_pho4.json

{
  "citation": [
    {
      "text": "Le et al. (2018), Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding.",
      "url": "https://doi.org/10.1073/pnas.1715888115"
    },
    {
      "text": "Fordyce Lab (2018), BET-seq Processed Data.",
      "url": "https://doi.org/10.6084/m9.figshare.5728467.v1"
    },
    {
      "text": "Trabucco et al. (2022), Design-Bench.",
      "url": "https://arxiv.org/abs/2202.08450"
    }
  ],
  "context": [
    {
      "constraints": [
        {
          "kind": "allowed_values",
          "values": [
            1,
            2,
            3,
            4
          ]
        }
      ],
      "description": "Published Pho4 experimental replicate identifier.",
      "name": "replicate_id",
      "required": false
    },
    {
      "constraints": [
        {
          "kind": "range",
          "minimum": 0
        }
      ],
      "description": "Raw read count in the Pho4-bound library.",
      "name": "bound_count",
      "required": false
    },
    {
      "constraints": [
        {
          "kind": "range",
          "minimum": 0
        }
      ],
      "description": "Raw read count in the corresponding input library.",
      "name": "input_count",
      "required": false
    },
    {
      "constraints": [
        {
          "kind": "finite"
        },
        {
          "kind": "range",
          "maximum": 1.0,
          "minimum": 0.0
        }
      ],
      "description": "Published bound_count divided by replicate bound depth.",
      "name": "bound_fraction",
      "required": false
    },
    {
      "constraints": [
        {
          "kind": "finite"
        },
        {
          "kind": "range",
          "maximum": 1.0,
          "minimum": 0.0
        }
      ],
      "description": "Published input_count divided by replicate input depth.",
      "name": "input_fraction",
      "required": false
    }
  ],
  "dataset_id": "design-bench/tfbind10-pho4",
  "default_split": "observations",
  "description": "Published Pho4 BET-seq read-count observations for the complete DNA 10-mer flank space, preserving four experimental replicates.",
  "inputs": [
    {
      "constraints": [
        {
          "kind": "alphabet",
          "symbols": [
            "A",
            "C",
            "G",
            "T"
          ]
        },
        {
          "kind": "length",
          "maximum": 10,
          "minimum": 10
        }
      ],
      "description": "Ten variable DNA nucleotides flanking the fixed CACGTG E-box core. Characters 1 through 5 are immediately upstream of the core and characters 6 through 10 are immediately downstream, in the displayed strand's 5-prime-to-3-prime orientation. The fixed core is excluded from this field; the full assayed site follows the template NNNNNCACGTGNNNNN.",
      "name": "sequence"
    }
  ],
  "knowledge": {
    "basic_helix_loop_helix_and_ebox_recognition": {
      "description": "bHLH domain architecture, dimerization, E-box conventions, and recognition beyond a short motif core.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/basic-helix-loop-helix-and-ebox-recognition.md",
      "title": "Basic Helix\u2013Loop\u2013Helix Proteins and E-box Recognition"
    },
    "binding_affinity_and_thermodynamics": {
      "description": "Equilibrium association and dissociation constants, occupancy, binding Gibbs energy, and kinetic rate constants.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/binding-affinity-and-thermodynamics.md",
      "title": "Binding Affinity and Thermodynamics"
    },
    "binding_energy_topography_by_sequencing": {
      "description": "BET-seq assay principles, bound/input count enrichment, relative binding energy, and measurement limitations.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/binding-energy-topography-by-sequencing.md",
      "title": "Binding Energy Topography by Sequencing"
    },
    "binding_sites_motifs_and_sequence_context": {
      "description": "Binding sites, consensus sequences, PFM/PWM representations, strand orientation, and nucleotide dependencies.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/binding-sites-motifs-and-sequence-context.md",
      "title": "Binding Sites, Motifs, and Sequence Context"
    },
    "dna_structure_and_base_pairing": {
      "description": "DNA strand direction, complementarity, canonical base pairing, grooves, and sequence-dependent duplex structure.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/dna-structure-and-base-pairing.md",
      "title": "DNA Structure and Base Pairing"
    },
    "pho4_and_dna_recognition": {
      "description": "Pho4 bHLH biology, CACGTG recognition, flanking-base contacts, and the distinction between affinity and cellular regulation.",
      "media_type": "text/markdown",
      "path": "knowledge/design-bench/tfbind10_pho4/pho4-and-dna-recognition.md",
      "title": "Pho4 and DNA Recognition"
    },
    "transcription_factor_dna_binding": {
      "description": "Physical modes of DNA recognition and the distinctions among affinity, specificity, occupancy, and regulatory activity.",
      "media_type": "text/markdown",
      "path": "knowledge/shared/transcription-factor-dna-binding.md",
      "title": "Transcription Factor\u2013DNA Binding"
    }
  },
  "license": "cc-by-4.0",
  "schema_version": 1,
  "source": [
    {
      "checksum": "sha256:3f6bc76273b00f5e1fb074b8e181077907eb265f12f443546f6da7db8c90f91e",
      "name": "BET-seq Processed Data",
      "notes": "Figshare DOI 10.6084/m9.figshare.5728467.v1.",
      "url": "https://figshare.com/articles/dataset/BET-seq_Processed_Data/5728467",
      "version": "v1"
    },
    {
      "name": "BET-seq analysis code",
      "revision": "d73e583dc2c0d73539b804f41775d8cb3d42e633",
      "url": "https://github.com/FordyceLab/BET-seq"
    },
    {
      "name": "Design-Bench TFBind10 preprocessing",
      "notes": "Recorded for legacy task provenance; not replayed by this release.",
      "revision": "e52939588421b5433f6f2e9b359cf013c542bd89",
      "url": "https://github.com/brandontrabucco/design-bench/blob/e52939588421b5433f6f2e9b359cf013c542bd89/process/process_raw_tf_bind_10.py"
    }
  ],
  "splits": [
    {
      "attributes": {
        "assay": "BET-seq",
        "protein": "Pho4",
        "replicates": 4,
        "sequence_length": 10,
        "shared_input_library": "replicates 3 and 4",
        "unique_sequences": 1048576
      },
      "description": "All published Pho4 source observations across four replicates.",
      "name": "observations",
      "num_rows": 4160533
    }
  ],
  "targets": [
    {
      "description": "Published per-replicate -RT log(bound_fraction/input_fraction); zero counts are retained as signed infinities.",
      "name": "observed_ddg",
      "unit": "kcal/mol"
    }
  ],
  "version": "1.0.0"
}