decoupler.op.progeny

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decoupler.op.progeny#

decoupler.op.progeny(organism='human', top=inf, thr_padj=0.05, license='academic', verbose=False)#

Pathway RespOnsive GENes for activity inference (PROGENy) [SKK+18].

Wrapper to access PROGENy model gene weights. Each pathway is defined with a collection of target genes, each interaction has an associated p-value and weight. The top significant interactions per pathway are returned.

Here is a brief description of each pathway:

  • Androgen: involved in the growth and development of the male reproductive organs

  • EGFR: regulates growth, survival, migration, apoptosis, proliferation, and differentiation in mammalian cells

  • Estrogen: promotes the growth and development of the female reproductive organs

  • Hypoxia: promotes angiogenesis and metabolic reprogramming when O2 levels are low

  • JAK-STAT: involved in immunity, cell division, cell death, and tumor formation

  • MAPK: integrates external signals and promotes cell growth and proliferation

  • NFkB: regulates immune response, cytokine production and cell survival

  • p53: regulates cell cycle, apoptosis, DNA repair and tumor suppression

  • PI3K: promotes growth and proliferation

  • TGFb: involved in development, homeostasis, and repair of most tissues

  • TNFa: mediates haematopoiesis, immune surveillance, tumour regression and protection from infection

  • Trail: induces apoptosis

  • VEGF: mediates angiogenesis, vascular permeability, and cell migration

  • WNT: regulates organ morphogenesis during development and tissue repair

Parameters:

  • organism (str (default: 'human')) – The organism of interest. By default human.

  • top (int | float (default: inf)) – Number of genes per pathway to return. By default all of them.

  • thr_padj (float (default: 0.05)) – Significance threshold to trim interactions.

  • license (str (default: 'academic')) – Which license to use, available options are: academic, commercial, or nonprofit. By default, is set to academic to retrieve all possible interactions. Users are expected to comply with license regulations according to their affiliation.

  • verbose (bool (default: False)) – Whether to display progress messages and additional execution details.

Return type:

DataFrame

Returns:

Dataframe in long format containing target genes for each pathway with their associated weights and p-values.

Example

import decoupler as dc

pg = dc.op.progeny()
pg
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