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Graph Model

Graph

Node Types

  1. Celltype

    • Properties:
      • Name (String): Celltype Name

  2. Study

    • Properties:
      • Source (String): Source of the study (e.g. in-house)

  3. Context

    • Properties:
      • Context (String): Specified context (e.g. 6h-0h, RC12h-12h etc.)

  4. FT (Functional Term)

    • Properties:
      • Term (String): Term of entity (e.g. GO:0007275)
      • Category (String): Category of FT (e.g. Biological Process (Gene Ontology))
      • Name (String): Name of FT (e.g. Multicellular organism development)

  5. MeanCount (Placeholder node)

    • Properties: None

  6. OR (Open Region)

    • Properties:
      • Annotation (String):
      • Feature (String):

  7. Source (Placeholder / Aggregation Node)

    • Properties: None

  8. TF (Transcription Factor) / TG (Target Gene)

    • Properties:
      • ENSEMBL (String): The ENSEMBL ID of the Entity
      • ENTREZID (Integer): The Entez Gene ID
      • SYMBOL (String): Symbol(s) of the Gene
      • Annotation (String): Annotation / More info on the Gene
    • Note: Transcription Factors have both TF and TG labels

Relationships

Source-specific

DE Values DA Values Overview

  1. HAS

    • Between:
      • Celltype -> Source
      • Study -> Source
      • Source -> Context
      • Source -> MeanCount
    • Properties: None

  2. MEANCOUNT

    • Between:
      • MeanCount -> TG
      • MeanCount -> OR
    • Properties:
      • Source (Integer): ID of Source node in DB
      • Value (Float): Mean count value found in experiment

  3. DE

    • Between:
      • Context -> TG
    • Properties:
      • Source (Integer): ID of Source node in DB
      • Value (Float): DE Value found in experiment under specified Context
      • p (Float): p value associated with the DE value

  4. DA

    • Between:
      • Context -> OR
    • Properties:
      • Source (Integer): ID of Source node in DB
      • Value (Float): DA Value found in experiment under specified Context
      • p (Float): p value associated with the DA value

  5. CORRELATION

    • Between:
      • TF -> TG
      • OR -> TG
    • Properties:
      • Source (Integer): ID of Source node in DB
      • Correlation (Float): Correlation Value found in experiment between two entities

Source unspecific

FT-TG FT-FT

  1. LINK

    • Between:
      • TG -> FT
    • Properties: None

  2. OVERLAP

    • Between:
      • FT -> FT
    • Properties:
      • Score (Float): Overlap score as previously computed by Victor (?)

  3. STRING

    • Between:
      • TG -> TG
    • Properties:
      • Score (Integer): STRING Association Score between two Genes

  4. MOTIF

    • Between:
      • TF -> OR
    • Properties:
      • Motif (String): Motif of OR that TF binds to
    • Note: This information is not specific to the experiment

  5. DISTANCE

    • Between:
      • OR -> TG
    • Properties:
      • Distance (Integer): Distance between OR and TG
    • Note: This information is not specific to the experiment

Statistics

Nodes:

Type old new
Terms / (in new DB: FT) 24170 24170
Proteins 22048 0 (to be deprecated)
Target Genes (TG) 0 22792
Transcription Factors (TF, are also TGs) 0 2895
Open Regions (OR) 0 106644
Context/Source/Celltype/Study/MeanCount 0 11
Total 46218 153617

Edges:

Type old new
ASSOCIATION / (in new DB: STRING) 7248179 7215830
CORRELATION (TG, TF) 0 1760676
CORRELATION (TG, OR) 0 81790
DA 0 533220
DE 0 50300
DISTANCE 0 95577
KAPPA 81676 0 (to be deprecated)
LINK 0 1742873
MEANCOUNT (TG) 0 10060
MEANCOUNT (OR) 0 106644
MOTIF 0 5558944
OVERLAP 0 3812328
Total 7329855 20968242

Notes

Since some ENSEMBL Gene IDs are mapped to multiple ENSEMBL Protein IDs (protein isoforms), and duplicate associations between traget genes were removed, the resulting number of STRING edges is smaller than that of the ASSOCIATION edges in the previous database. Additionally, for 66 Proteins in STRING no equivalent ENSEMBL Gene IDs were found.