Source code for sfa.data.steinway_2015

# -*- coding: utf-8 -*-

"""
[Reference]
[1] Steinway et al.
    Combinatorial interventions inhibit TGFβ-driven epithelial-to-mesenchymal
    transition and support hybrid cellular phenotypes.
    Npj Systems Biology and Applications (2015)  1(1), 15014.


[2] Steinway, S. N. et al.
    Network modeling of TGFβ signaling in hepatocellular carcinoma
    epithelial-to-mesenchymal transition reveals joint sonic hedgehog
    and Wnt pathway activation.
    Cancer Research (2014) 74(21), 5963–77.

[Information]
The topology of network is curated from reference [1].

"""

import os

import pandas as pd

import sfa
import sfa.base


[docs]def create_data(): return SteinwayData()
[docs]class SteinwayData(sfa.base.Data): def __init__(self): self._abbr = "steinway_2015" self._name = "Steinway et al. Npj Syst Biol Appl (2015) 1(1), 15014" inputs = {} inputs['TGFβ'] = 1.0 dpath = os.path.dirname(__file__) fpath_network = os.path.join(dpath, 'network.sif') A, n2i, dg = sfa.read_sif(fpath_network, as_nx=True) self._A = A self._n2i = n2i self._i2n = {idx: name for name, idx in n2i.items()} self._dg = dg self._inputs = inputs # The following members are not defined due to the lack of data. self._df_conds = None self._df_exp = None self._df_ptb = None self._has_link_perturb = False self._names_ptb = None self._iadj_to_idf = None
# end of def __init__ # end of def class