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HTAN Proteomics

HTAN supports several proteomics modalities. Modalities supported are growing as new data are generated.

Attributes

WARNING: Manifests provided on this page are for reference only. DO NOT USE THESE MANIFESTS FOR DATA SUBMISSION.

Directions

The interactive tables below are provided to help users understand the HTAN Data Model. The tables allow a user to view, search or download attributes either:

  1. in a specific manifest; or
  2. in all manifests represented on this page.

To view a specific manifest, click on the link in the Manifests tab. The manifest will appear in a new tab on the page. Navigate to the new tab to search for attributes or download the manifest.
To search for attributes among all manifests, navigate to the All Attributes tab and use the search box provided at the top of the tab. All attributes can also be downloaded as a csv file.

Manifest
▲
Description
▲
Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.
Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.
Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.
Attribute
▲
Manifest Name
▲
Description
▲
Required
▲
Conditional If
▲
Data Type
▲
Valid Values
▲
Filename
- RPPA Level 2
- RPPA Level 3
- RPPA Level 4
Name of a file
True
String
File Format
- RPPA Level 2
- RPPA Level 3
- RPPA Level 4
Format of a file (e.g. txt, csv, fastq, bam, etc.)
True
String
- hdf5
- bedgraph
- idx
- idat
- bam
- bai
- excel
- powerpoint
- tif
- tiff
- ome-tiff
- png
- doc
- pdf
- fasta
- fastq
- sam
- vcf
- bcf
- maf
- bed
- chp
- cel
- sif
- tsv
- csv
- txt
- plink
- bigwig
- wiggle
- gct
- bgzip
- zip
- seg
- html
- mov
- hyperlink
- svs
- md
- flagstat
- gtf
- raw
- msf
- rmd
- bed narrowpeak
- bed broadpeak
- bed gappedpeak
- avi
- pzfx
- fig
- xml
- tar
- r script
- abf
- bpm
- dat
- jpg
- locs
- sentrix descriptor file
- python script
- sav
- gzip
- sdf
- rdata
- hic
- ab1
- 7z
- gff3
- json
- sqlite
- svg
- sra
- recal
- tranches
- mtx
- tagalign
- dup
- dicom
- czi
- mex
- cloupe
- am
- cell am
- mpg
- m
- mzml
- scn
- dcc
- rcc
- pkc
- sf
- bedpe
HTAN Participant ID
- RPPA Level 2
- RPPA Level 3
- RPPA Level 4
HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy )
True
String
HTAN Parent Biospecimen ID
- RPPA Level 2
- RPPA Level 3
- RPPA Level 4
HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated
True
- Is lowest level is "Yes - Is lowest level"
String
HTAN Parent Data File ID
- RPPA Level 2
- RPPA Level 3
- RPPA Level 4
HTAN Data File Identifier indicating the file(s) from which these files were derived
True
String
HTAN Data File ID
- RPPA Level 2
- RPPA Level 3
- RPPA Level 4
Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)
True
String
HTAN RPPA Antibody Table
- RPPA Level 2
A table containing antibody level metadata for RPPA
True
String
Assay Type
- RPPA Level 2
- RPPA Level 3
- RPPA Level 4
The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)
True
String
Software and Version
- RPPA Level 2
- RPPA Level 3
Name of software used to generate expression values. String
True
- Pseudo Alignment Used is "Yes - Pseudo Alignment Used"
String
Normalization Method
- RPPA Level 2
- RPPA Level 3
Description of Normalization Process
False
String
Batch Correction Method
- RPPA Level 3
- RPPA Level 4
Method that was used to batch correct Level 3 data
False
String
HTAN RPPA Antibody Table ID
- RPPA Level 2
HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.
True
String
Ab Name Reported on Dataset
- RPPA Level 2
The antibody name.
True
String
GENCODE Gene Symbol Target
- RPPA Level 2
The comma separated list of gene symbols targeted by the antibody.
True
String
UNIPROT Protein ID Target
- RPPA Level 2
The comma separated list of UNIPROT IDs targeted by the antibody.
True
String
Phosphoprotein Flag
- RPPA Level 2
A flag the denotes if an antibody targets a phosphoprotein.
True
String
- true
- false
Vendor
- RPPA Level 2
Vendor
False
String
Catalog Number
- RPPA Level 2
Catalog Number
False
String
Internal Ab ID
- RPPA Level 2
Internal lab ID for an antibody.
True
String
Species
- RPPA Level 2
Host animal.
True
String
- mouse
- rabbit
- goat
RPPA Dilution
- RPPA Level 2
The dilution ratio.
False
String
Phospho Site
- RPPA Level 2
The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)
False
String
RPPA Validation Status
- RPPA Level 2
Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)
False
String
- valid
- use with caution
- under evaluation
- used for qc
Clone
- RPPA Level 2
Clone
False
String
Clonality
- RPPA Level 2
The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
False
String
- clonal
- non-clonal
Antibody Notes
- RPPA Level 2
Notes on antibodies replacements and antibody recognition observations.
False
String