Overview of Human Protein

Protein classes - The Human Protein Atlas

• versions:

https://v18.proteinatlas.org/humanproteome/proteinclasses(version of 2018-09-08)
https://v17.proteinatlas.org/humanproteome/proteinclasses
https://v16.proteinatlas.org/humanproteome/proteinclasses
...

Example of protein class(catalog)

$ python query.py -g PIM1
Enzymes
#ENZYME proteins
##Transferases
#Kinases
##CAMK Ser or Thr protein kinases
##MEMSAT-SVM predicted membrane proteins
##SCAMPI predicted membrane proteins
##SPOCTOPUS predicted membrane proteins
Predicted intracellular proteins
Cancer-related genes
#Candidate cancer biomarkers
#COSMIC somatic mutations in cancer genes
##COSMIC Somatic Mutations
##COSMIC Translocations
Mapped to UniProt SWISS-PROT
#UniProt - Evidence at protein level
#########################################################
Cancer-related genes, Enzymes, Predicted intracellular proteins

Example of Gene synonym

$ python query.py -g PKN1 -i "Gene synonym"
Enzymes
#ENZYME proteins
##Transferases
#Kinases
##AGC Ser or Thr protein kinases
##MEMSAT-SVM predicted membrane proteins
##SPOCTOPUS predicted membrane proteins
Predicted intracellular proteins
Mapped to UniProt SWISS-PROT
#UniProt - Evidence at protein level
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
#########################################################
DBK, MGC46204, PAK1, PKN, PRK1, PRKCL1

Install and Run

1. Fetch up-to-date proteinclasses

1.1 Usage

python fetch.py

1.2 What?

• fetch proteinclasses data
• download tsv files into ./tsv

2. Query protein infomation

2.1. make db from tsv files in ./tsv

python query.py --makedb

2.2. query protein classes or other info

python query.py -g PIM1
python query.py -g PIM1 -i "Protein class"
python query.py -g PIM1 -i "Gene synonym"
python query.py -g PIM1 -i ""

item choices:

Gene synonym
Ensembl
Gene description
Chromosome
Position
Protein class
Evidence
Antibody
Reliability (IH)
Reliability (Mouse Brain)
Reliability (IF)
Subcellular location
Prognostic p-value
RNA cancer category
RNA tissue category
RNA TS
RNA TS TPM
TPM max in non-specific
RNA cell line category