rna_quantification

Units for expression level. FPKM - number of Fragments Per Kilobase of feature length per Million reads FPKM is calculated by dividing the fragment count per feature by the total number of reads in millions (FPM - Fragments Per Million). FPM is then divided by feature length in kilobases to obtain FPKM. TPM - Transcripts per kilobase Per Million reads TPM is calculated by first dividing the fragment/read count by feature length in kilobases (RPK - Reads Per Kilobase). The count of all RPKs in the sample are then divided by a million to generate a ‘per million’ scaling value. For each feature RPK divided by the ‘per million’ scaling factor generated TPM.
enum ExpressionUnit
Symbols:EXPRESSION_UNIT_UNSPECIFIED|FPKM|TPM
  • EXPRESSION_UNIT_UNSPECIFIED:
  • FPKM:
  • TPM:
message RnaQuantificationSet
Fields:
  • id (string) – The RNA quantification set ID.
  • dataset_id (string) – The ID of the dataset this RNA Quantification set belongs to.
  • name (string) – The RNA quantification set name.
  • attributes (Attributes) – A map of additional information about the Quantification Set.

A collection of associated RNAQuantifications. Typically this will be all the Quantifications of samples from an experiment. For example, a time course experiment would be described by a RnaQuantificationSet with the individual RNASeq experiments of the time point being represented as the member RnaQuantifications.

message RnaQuantification
Fields:
  • id (string) – The unique ID assigned to the results of running the described programs on the specified reads and assignment to the listed annotation.
  • name (string) – Name
  • biosample_id (string) – Biosample ID
  • description (string) – Description
  • read_group_ids (string) – ID(s) of the ReadGroup(s) providing the reads for the analysis.
  • programs (list of Program) – Programs can be used to track the provenance of how read data was quantified.
  • feature_set_ids (string) – List of annotation sets used.
  • rna_quantification_set_id (string) – ID of the containing RnaQuantificationSet.
  • attributes (Attributes) – A map of additional information about the Quantification.

Top level identifying information

message ExpressionLevel
Fields:
  • id (string) – Expression ID
  • name (string) – Name
  • rna_quantification_id (string) – The associated RnaQuantification
  • raw_read_count (float) – The number of reads mapped to this feature.
  • expression (float) – Numerical expression value.
  • is_normalized (boolean) – True if the expression value is a normalized value.
  • units (ExpressionUnit) – The units of the expression value if one is given.
  • score (float) – Weighted score for the expression value.
  • conf_interval_low (float) – Lower bound of the confidence interval on the expression value.
  • conf_interval_high (float) – Upper bound of the confidence interval on the expression value.
  • attributes (Attributes) – A map of additional information about the Expression Level.

The actual numerical quantification for each feature.