In [1]:
from bigraph_viz import plot_bigraph

dpi = '70'
save = True

tx = {
    'transcription': {
        '_type': 'process',
        'inputs': {
            'DNA': ['DNA (mg/ml)'],
        },
        'outputs': {
            'mRNA': ['mRNA (mg/ml)'],
        }
    }
}

stoch_tx = {
    'stochastic transcription': {
        '_type': 'process',
        'inputs': {
            'DNA': ['DNA (counts)'],
        },
        'outputs': {
            'mRNA': ['mRNA (counts)'],
        }
    }
}

tl = {
    'translation': {
        '_type': 'process',
        'inputs': {
            'mRNA': ['mRNA (mg/ml)'],
        },
        'outputs': {
            'protein': ['protein (mg/ml)'],
        }
    }
}

division = {
    'division': {
        '_type': 'process',
        'inputs': {
            'mass': ['mass (mg)'],
        },
        'outputs': {
            'divide': ['..', '..', 'cells'],
        }
    }
}

mass_volume = {
    'mg to fL': {
        '_type': 'process',
        'inputs': {
            'mass': ['mass (mg)'],
            'density': ['density (mg/fL)'],
        },
        'outputs': {
            'volume': ['volume (fL)'],
        }
    },
}

# calculate_mass = {
#     'calculate mass': {
#         '_type': 'process',
#         'inputs': {
#             'counts': ['volume (fL)'],
#             'density': ['density (mg/fL)'],
#         },
#         'outputs': {
#             'mass': ['mass (mg)'],
#         }
#     },
# }

counts_concs = {
    'counts to mg/ml': {
        '_type': 'process',
        'inputs': {
            'counts': ['mRNA (counts)'],
            'volume': ['volume (fL)'],
        },
        'outputs': {
            'mg/ml': ['mRNA (mg/ml)'],
        }
    },
}

multibody = {
    'multibody physics': {
        '_type': 'process',
        'inputs': {
            'cells': ['cells'],
        },
        'outputs': {
            'cells': ['cells'],
        }
    },
}

diffusion = {
    'diffusion': {
        '_type': 'process',
        'inputs': {
            'cells': ['cells'],
            'fields': ['fields'],
            'dimensions': ['dimensions'],
        },
        'outputs': {
            'cells': ['cells'],
            'fields': ['fields'],
            'dimensions': ['dimensions'],
        }
    },
}
In [2]:
tx_composite = {
    **tx,
}

plot_settings= {
    'rankdir': 'RL',
    'node_border_colors': {
        ('DNA (mg/ml)',): 'darkgreen',
        ('mRNA (mg/ml)',): 'darkorange',
        # ('protein',): 'darkslateblue',
    }
}
plot_bigraph(
    tx_composite,
    **plot_settings,
    filename='tx_composite' if save else None,
    dpi=dpi,
    )

Writing out/tx_composite
Out[2]:
bigraph ('DNA (mg/ml)',) DNA (mg/ml) ('transcription',) transcription ('DNA (mg/ml)',)->('transcription',) DNA ('mRNA (mg/ml)',) mRNA (mg/ml) ('mRNA (mg/ml)',)->('transcription',) mRNA
In [3]:
txtl_composite = {
    **tx,
    **tl
}

plot_settings= {
    'rankdir': 'RL',
    'node_border_colors': {
        ('DNA (mg/ml)',): 'darkgreen',
        ('mRNA (mg/ml)',): 'darkorange',
        ('protein (mg/ml)',): 'darkslateblue',
    }
}
plot_bigraph(
    txtl_composite,
    **plot_settings,
    filename='txtl_composite' if save else None,
    dpi=dpi,
    )

Writing out/txtl_composite
Out[3]:
bigraph ('DNA (mg/ml)',) DNA (mg/ml) ('transcription',) transcription ('DNA (mg/ml)',)->('transcription',) DNA ('mRNA (mg/ml)',) mRNA (mg/ml) ('mRNA (mg/ml)',)->('transcription',) mRNA ('translation',) translation ('mRNA (mg/ml)',)->('translation',) mRNA ('protein (mg/ml)',) protein (mg/ml) ('protein (mg/ml)',)->('translation',) protein
In [4]:
stochastic_txtl_composite = {
    **tx,
    **counts_concs,
    **tl,
}

plot_settings= {
    'rankdir': 'TD',
    'node_border_colors': {
        ('DNA (mg/ml)',): 'darkgreen',
        ('mRNA (mg/ml)',): 'darkorange',
        ('mRNA (counts)',): 'darkorange',
        ('protein (mg/ml)',): 'darkslateblue',
    }
}
plot_bigraph(
    stochastic_txtl_composite,
    **plot_settings,
    filename='stochastic_txtl_composite' if save else None,
    dpi=dpi,
    )

Writing out/stochastic_txtl_composite
Out[4]:
bigraph ('volume (fL)',) volume (fL) ('counts to mg/ml',) counts to mg/ml ('volume (fL)',)->('counts to mg/ml',) volume ('mRNA (counts)',) mRNA (counts) ('mRNA (counts)',)->('counts to mg/ml',) counts ('mRNA (mg/ml)',) mRNA (mg/ml) ('mRNA (mg/ml)',)->('counts to mg/ml',) mg/ml ('transcription',) transcription ('mRNA (mg/ml)',)->('transcription',) mRNA ('translation',) translation ('mRNA (mg/ml)',)->('translation',) mRNA ('DNA (mg/ml)',) DNA (mg/ml) ('DNA (mg/ml)',)->('transcription',) DNA ('protein (mg/ml)',) protein (mg/ml) ('protein (mg/ml)',)->('translation',) protein

Nested cell¶

In [5]:
stochastic_txtl_with_division = {
    **stochastic_txtl_composite,
    **division,
    **mass_volume
}

nested_single_cell = {
    'cells': {
        '0': stochastic_txtl_with_division
    },
    **multibody,
    **diffusion
}

plot_settings= {
    'rankdir': 'TD',
    'remove_process_place_edges': True,
}
plot_bigraph(
    nested_single_cell,
    **plot_settings,
    filename='nested_single_cell' if save else None,
    dpi=dpi,
    )

Writing out/nested_single_cell
Out[5]:
bigraph ('fields',) fields ('diffusion',) diffusion ('fields',)->('diffusion',) fields ('dimensions',) dimensions ('dimensions',)->('diffusion',) dimensions ('cells',) cells ('cells', '0') 0 ('cells',)->('cells', '0') ('cells',)->('diffusion',) cells ('cells', '0', 'division') division ('cells',)->('cells', '0', 'division') divide ('multibody physics',) multibody physics ('cells',)->('multibody physics',) cells ('cells', '0', 'mass (mg)') mass (mg) ('cells', '0')->('cells', '0', 'mass (mg)') ('cells', '0', 'density (mg/fL)') density (mg/fL) ('cells', '0')->('cells', '0', 'density (mg/fL)') ('cells', '0', 'volume (fL)') volume (fL) ('cells', '0')->('cells', '0', 'volume (fL)') ('cells', '0', 'mRNA (counts)') mRNA (counts) ('cells', '0')->('cells', '0', 'mRNA (counts)') ('cells', '0', 'mRNA (mg/ml)') mRNA (mg/ml) ('cells', '0')->('cells', '0', 'mRNA (mg/ml)') ('cells', '0', 'DNA (mg/ml)') DNA (mg/ml) ('cells', '0')->('cells', '0', 'DNA (mg/ml)') ('cells', '0', 'protein (mg/ml)') protein (mg/ml) ('cells', '0')->('cells', '0', 'protein (mg/ml)') ('cells', '0', 'mg to fL') mg to fL ('cells', '0', 'counts to mg/ml') counts to mg/ml ('cells', '0', 'transcription') transcription ('cells', '0', 'translation') translation ('cells', '0', 'mass (mg)')->('cells', '0', 'mg to fL') mass ('cells', '0', 'mass (mg)')->('cells', '0', 'division') mass ('cells', '0', 'density (mg/fL)')->('cells', '0', 'mg to fL') density ('cells', '0', 'volume (fL)')->('cells', '0', 'mg to fL') volume ('cells', '0', 'volume (fL)')->('cells', '0', 'counts to mg/ml') volume ('cells', '0', 'mRNA (counts)')->('cells', '0', 'counts to mg/ml') counts ('cells', '0', 'mRNA (mg/ml)')->('cells', '0', 'counts to mg/ml') mg/ml ('cells', '0', 'mRNA (mg/ml)')->('cells', '0', 'transcription') mRNA ('cells', '0', 'mRNA (mg/ml)')->('cells', '0', 'translation') mRNA ('cells', '0', 'DNA (mg/ml)')->('cells', '0', 'transcription') DNA ('cells', '0', 'protein (mg/ml)')->('cells', '0', 'translation') protein
In [6]:
nested_two_cell = {
    'cells': {
        '1': stochastic_txtl_with_division,
        '2': stochastic_txtl_with_division,
    },
    **multibody,
    **diffusion
}

plot_settings= {
    'rankdir': 'TD',
    'remove_process_place_edges': True,
}
plot_bigraph(
    nested_two_cell,
    **plot_settings,
    filename='nested_two_cell' if save else None,
    dpi=dpi,
    )

Writing out/nested_two_cell
Out[6]:
bigraph ('fields',) fields ('diffusion',) diffusion ('fields',)->('diffusion',) fields ('dimensions',) dimensions ('dimensions',)->('diffusion',) dimensions ('cells',) cells ('cells', '1') 1 ('cells',)->('cells', '1') ('cells', '2') 2 ('cells',)->('cells', '2') ('cells',)->('diffusion',) cells ('cells', '1', 'division') division ('cells',)->('cells', '1', 'division') divide ('cells', '2', 'division') division ('cells',)->('cells', '2', 'division') divide ('multibody physics',) multibody physics ('cells',)->('multibody physics',) cells ('cells', '1', 'mass (mg)') mass (mg) ('cells', '1')->('cells', '1', 'mass (mg)') ('cells', '1', 'density (mg/fL)') density (mg/fL) ('cells', '1')->('cells', '1', 'density (mg/fL)') ('cells', '1', 'volume (fL)') volume (fL) ('cells', '1')->('cells', '1', 'volume (fL)') ('cells', '1', 'mRNA (counts)') mRNA (counts) ('cells', '1')->('cells', '1', 'mRNA (counts)') ('cells', '1', 'mRNA (mg/ml)') mRNA (mg/ml) ('cells', '1')->('cells', '1', 'mRNA (mg/ml)') ('cells', '1', 'DNA (mg/ml)') DNA (mg/ml) ('cells', '1')->('cells', '1', 'DNA (mg/ml)') ('cells', '1', 'protein (mg/ml)') protein (mg/ml) ('cells', '1')->('cells', '1', 'protein (mg/ml)') ('cells', '1', 'mg to fL') mg to fL ('cells', '1', 'counts to mg/ml') counts to mg/ml ('cells', '1', 'transcription') transcription ('cells', '1', 'translation') translation ('cells', '1', 'mass (mg)')->('cells', '1', 'mg to fL') mass ('cells', '1', 'mass (mg)')->('cells', '1', 'division') mass ('cells', '1', 'density (mg/fL)')->('cells', '1', 'mg to fL') density ('cells', '1', 'volume (fL)')->('cells', '1', 'mg to fL') volume ('cells', '1', 'volume (fL)')->('cells', '1', 'counts to mg/ml') volume ('cells', '1', 'mRNA (counts)')->('cells', '1', 'counts to mg/ml') counts ('cells', '1', 'mRNA (mg/ml)')->('cells', '1', 'counts to mg/ml') mg/ml ('cells', '1', 'mRNA (mg/ml)')->('cells', '1', 'transcription') mRNA ('cells', '1', 'mRNA (mg/ml)')->('cells', '1', 'translation') mRNA ('cells', '1', 'DNA (mg/ml)')->('cells', '1', 'transcription') DNA ('cells', '1', 'protein (mg/ml)')->('cells', '1', 'translation') protein ('cells', '2', 'mass (mg)') mass (mg) ('cells', '2')->('cells', '2', 'mass (mg)') ('cells', '2', 'density (mg/fL)') density (mg/fL) ('cells', '2')->('cells', '2', 'density (mg/fL)') ('cells', '2', 'volume (fL)') volume (fL) ('cells', '2')->('cells', '2', 'volume (fL)') ('cells', '2', 'mRNA (counts)') mRNA (counts) ('cells', '2')->('cells', '2', 'mRNA (counts)') ('cells', '2', 'mRNA (mg/ml)') mRNA (mg/ml) ('cells', '2')->('cells', '2', 'mRNA (mg/ml)') ('cells', '2', 'DNA (mg/ml)') DNA (mg/ml) ('cells', '2')->('cells', '2', 'DNA (mg/ml)') ('cells', '2', 'protein (mg/ml)') protein (mg/ml) ('cells', '2')->('cells', '2', 'protein (mg/ml)') ('cells', '2', 'mg to fL') mg to fL ('cells', '2', 'counts to mg/ml') counts to mg/ml ('cells', '2', 'transcription') transcription ('cells', '2', 'translation') translation ('cells', '2', 'mass (mg)')->('cells', '2', 'mg to fL') mass ('cells', '2', 'mass (mg)')->('cells', '2', 'division') mass ('cells', '2', 'density (mg/fL)')->('cells', '2', 'mg to fL') density ('cells', '2', 'volume (fL)')->('cells', '2', 'mg to fL') volume ('cells', '2', 'volume (fL)')->('cells', '2', 'counts to mg/ml') volume ('cells', '2', 'mRNA (counts)')->('cells', '2', 'counts to mg/ml') counts ('cells', '2', 'mRNA (mg/ml)')->('cells', '2', 'counts to mg/ml') mg/ml ('cells', '2', 'mRNA (mg/ml)')->('cells', '2', 'transcription') mRNA ('cells', '2', 'mRNA (mg/ml)')->('cells', '2', 'translation') mRNA ('cells', '2', 'DNA (mg/ml)')->('cells', '2', 'transcription') DNA ('cells', '2', 'protein (mg/ml)')->('cells', '2', 'translation') protein

Cell hierarchy¶

In [7]:
music_map = {
    'cell': {
        'cytoplasm': {
            'secretory organelles': {
                'transmembrane transport systems': {
                    'ion transmembrane transport systems': {}}},
            'cytoplasmic organelles': {
                'subgroup of cytoplasmic organelles': {
                    'metabolic organelles': {
                        'subgroup of metabolic organelles': {},
                        'mitochondrion': {}},
                    'ribonucleoprotein complex family': {
                        'RNA processing complex 1': {'RNA splicing complex 1': {}},
                        'ribosome biogenesis community': {
                            'ribosome': {
                                'ribosomal subunit': {
                                    'mitochondirial large ribosomal subunit': {
                                        # 'large ribosomal subunit subcomplex 1': {}
                                    },
                                    'mito-cyto ribosomal cluster': {},
                                    'cotranslational protein targeting to membrane system': {},
                                    'ribosomal complex 5': {},
                                    'ribosomal complex 2': {}}},
                            'nucleic acid binding complex': {}}}}},
            'transcriptional regulation complex family': {
                'transcriptional regulation complexes': {}}},
        'nucleus': {
            'DNA metabolic assembly': {},
            'nuclear lumen': {
                'nucleolus': {
                    'ribonucleprotein complex family': {},
                    'RNA processing complex family': {
                        'RNA processing complex 1': {},
                        'RNA splicing complex family': {}},
                    'splicosomal complex family': {}},
                'nuclear splicing speckle': {}},
            'nuclear body': {},
            'nucleo-plasm 1': {
                'chromosome organization complex family': {
                    'chromatin organization complex family': {
                        'HAT complex family': {
                            'NuA4 HAT complex': {}}}}},
            'nucleo-plasm 2': {
                'chromatin regulation complex': {}},
            'nuclear transcriptional speckle': {
                'negative regulation of RNA biosynthesis process': {}}}}}
music_map1 = music_map
plot_bigraph(music_map1, 
             filename='cell_hierarchy' if save else None,
             dpi=dpi,
             )

Writing out/cell_hierarchy
Out[7]:
bigraph ('cell',) cell ('cell', 'cytoplasm') cytoplasm ('cell',)->('cell', 'cytoplasm') ('cell', 'nucleus') nucleus ('cell',)->('cell', 'nucleus') ('cell', 'cytoplasm', 'secretory organelles') secretory organelles ('cell', 'cytoplasm')->('cell', 'cytoplasm', 'secretory organelles') ('cell', 'cytoplasm', 'cytoplasmic organelles') cytoplasmic organelles ('cell', 'cytoplasm')->('cell', 'cytoplasm', 'cytoplasmic organelles') ('cell', 'cytoplasm', 'transcriptional regulation complex family') transcriptional regulation complex family ('cell', 'cytoplasm')->('cell', 'cytoplasm', 'transcriptional regulation complex family') ('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems') transmembrane transport systems ('cell', 'cytoplasm', 'secretory organelles')->('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems') ('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems', 'ion transmembrane transport systems') ion transmembrane transport systems ('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems')->('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems', 'ion transmembrane transport systems') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles') subgroup of cytoplasmic organelles ('cell', 'cytoplasm', 'cytoplasmic organelles')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles') metabolic organelles ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family') ribonucleoprotein complex family ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', 'subgroup of metabolic organelles') subgroup of metabolic organelles ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', 'subgroup of metabolic organelles') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', 'mitochondrion') mitochondrion ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', 'mitochondrion') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'RNA processing complex 1') RNA processing complex 1 ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'RNA processing complex 1') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community') ribosome biogenesis community ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'RNA processing complex 1', 'RNA splicing complex 1') RNA splicing complex 1 ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'RNA processing complex 1')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'RNA processing complex 1', 'RNA splicing complex 1') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome') ribosome ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'nucleic acid binding complex') nucleic acid binding complex ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'nucleic acid binding complex') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit') ribosomal subunit ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'mitochondirial large ribosomal subunit') mitochondirial large ribosomal subunit ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'mitochondirial large ribosomal subunit') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'mito-cyto ribosomal cluster') mito-cyto ribosomal cluster ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'mito-cyto ribosomal cluster') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'cotranslational protein targeting to membrane system') cotranslational protein targeting to membrane system ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'cotranslational protein targeting to membrane system') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'ribosomal complex 5') ribosomal complex 5 ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'ribosomal complex 5') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'ribosomal complex 2') ribosomal complex 2 ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'ribosomal complex 2') ('cell', 'cytoplasm', 'transcriptional regulation complex family', 'transcriptional regulation complexes') transcriptional regulation complexes ('cell', 'cytoplasm', 'transcriptional regulation complex family')->('cell', 'cytoplasm', 'transcriptional regulation complex family', 'transcriptional regulation complexes') ('cell', 'nucleus', 'DNA metabolic assembly') DNA metabolic assembly ('cell', 'nucleus')->('cell', 'nucleus', 'DNA metabolic assembly') ('cell', 'nucleus', 'nuclear lumen') nuclear lumen ('cell', 'nucleus')->('cell', 'nucleus', 'nuclear lumen') ('cell', 'nucleus', 'nuclear body') nuclear body ('cell', 'nucleus')->('cell', 'nucleus', 'nuclear body') ('cell', 'nucleus', 'nucleo-plasm 1') nucleo-plasm 1 ('cell', 'nucleus')->('cell', 'nucleus', 'nucleo-plasm 1') ('cell', 'nucleus', 'nucleo-plasm 2') nucleo-plasm 2 ('cell', 'nucleus')->('cell', 'nucleus', 'nucleo-plasm 2') ('cell', 'nucleus', 'nuclear transcriptional speckle') nuclear transcriptional speckle ('cell', 'nucleus')->('cell', 'nucleus', 'nuclear transcriptional speckle') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus') nucleolus ('cell', 'nucleus', 'nuclear lumen')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus') ('cell', 'nucleus', 'nuclear lumen', 'nuclear splicing speckle') nuclear splicing speckle ('cell', 'nucleus', 'nuclear lumen')->('cell', 'nucleus', 'nuclear lumen', 'nuclear splicing speckle') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'ribonucleprotein complex family') ribonucleprotein complex family ('cell', 'nucleus', 'nuclear lumen', 'nucleolus')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'ribonucleprotein complex family') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family') RNA processing complex family ('cell', 'nucleus', 'nuclear lumen', 'nucleolus')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'splicosomal complex family') splicosomal complex family ('cell', 'nucleus', 'nuclear lumen', 'nucleolus')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'splicosomal complex family') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family', 'RNA processing complex 1') RNA processing complex 1 ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family', 'RNA processing complex 1') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family', 'RNA splicing complex family') RNA splicing complex family ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family', 'RNA splicing complex family') ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family') chromosome organization complex family ('cell', 'nucleus', 'nucleo-plasm 1')->('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family') ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family') chromatin organization complex family ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family')->('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family') ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family', 'HAT complex family') HAT complex family ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family')->('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family', 'HAT complex family') ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family', 'HAT complex family', 'NuA4 HAT complex') NuA4 HAT complex ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family', 'HAT complex family')->('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family', 'HAT complex family', 'NuA4 HAT complex') ('cell', 'nucleus', 'nucleo-plasm 2', 'chromatin regulation complex') chromatin regulation complex ('cell', 'nucleus', 'nucleo-plasm 2')->('cell', 'nucleus', 'nucleo-plasm 2', 'chromatin regulation complex') ('cell', 'nucleus', 'nuclear transcriptional speckle', 'negative regulation of RNA biosynthesis process') negative regulation of RNA biosynthesis process ('cell', 'nucleus', 'nuclear transcriptional speckle')->('cell', 'nucleus', 'nuclear transcriptional speckle', 'negative regulation of RNA biosynthesis process')

Cell hierarchy with functions¶

In [8]:
import copy

transcription_process = {
    '_type': 'process',
    '_outputs': {
        'RNA processing': 'any',
        'regulation': 'any',
        'nucleic acids': 'any',
        'negative regulation': 'any'
    },
    'outputs': {
        'RNA processing': [
            'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family'],
        'regulation': [
            'cytoplasm', 'transcriptional regulation complex family', 'transcriptional regulation complexes'],
        'nucleic acids': [
            'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 
            'ribonucleoprotein complex family', 'ribosome biogenesis community', 'nucleic acid binding complex'],
        'negative regulation': [
            'nucleus', 'nuclear transcriptional speckle', 'negative regulation of RNA biosynthesis process'],
    }
}

translation_process = {
    '_type': 'process',
    '_outputs': {
        'ribosomes': 'any',
        'membrane': 'any'
    },
    'outputs': {
        'ribosomes': [
            'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome'],
        # 'membrane': ['],
    }
}

metabolism_process = {
    '_type': 'process',
    '_outputs': {
        'organelles': 'any',
        'mitochondrion': 'any',
        'ion transport': 'any',
    },
    'outputs': {
        'organelles': [
            'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', ],
        'mitochondrion': [
            'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', 'mitochondrion'],
        'ion transport': [
            'cytoplasm', 'secretory organelles', 'transmembrane transport systems', 'ion transmembrane transport systems'],
    }
}

cell_cycle_process = {
    '_type': 'process',
    '_outputs': {
        'DNA': 'any',
        'chromosome': 'any',
        'chromatin': 'any',
    },
    'outputs': {        
        'DNA': ['nucleus', 'DNA metabolic assembly'],
        'chromosome': ['nucleus', 'nucleo-plasm 1', 'chromosome organization complex family',],
        'chromatin': ['nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family'],
    }
}

signalling_process = {
    '_type': 'process',
    '_outputs': {
        'transport': 'any',
        'trancript regulation': 'any',
    },
    'outputs': {        
        'transport': [
            'cytoplasm', 'secretory organelles', 'transmembrane transport systems'],
        'trancript regulation': [
            'cytoplasm', 'transcriptional regulation complex family', 'transcriptional regulation complexes'],
    }
}

protein_transport_process = {
    '_type': 'process',
    '_outputs': {
        'transmembrane transport': 'any',
        'secretory': 'any',
        'cotranslation': 'any',
    },
    'outputs': {        
        'transmembrane transport': [
            'cytoplasm', 'secretory organelles', 'transmembrane transport systems'],
        'secretory': [
            'cytoplasm', 'secretory organelles'],
        'cotranslation': [
            'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 
            'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'cotranslational protein targeting to membrane system']
    }
}

rna_processing_process = {
    '_type': 'process',
    '_outputs': {
        'processing complex': 'any',
    },
    'outputs': {        
        'processing complex': [
            'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family'],
    }
}

# compose schema
music_map['cell']['transcription'] = transcription_process
music_map['cell']['translation'] = translation_process
music_map['cell']['metabolism'] = metabolism_process
music_map['cell']['cell cycle'] = cell_cycle_process
music_map['cell']['signalling'] = signalling_process
music_map['cell']['protein transport'] = protein_transport_process
music_map['cell']['RNA processing'] = rna_processing_process

music_map2 = music_map

# plot
plot_settingsx = copy.deepcopy(plot_settings)
plot_settingsx['label_margin'] = '0.02'
plot_settingsx['node_border_colors'] = {
    ('cell', 'translation'): 'blue',
    ('cell', 'transcription'): 'blue',
    ('cell', 'metabolism'): 'blue',
    ('cell', 'cell cycle'): 'blue',
    ('cell', 'signalling'): 'blue',
    ('cell', 'protein transport'): 'blue',
    ('cell', 'RNA processing'): 'blue',
}
plot_settingsx['remove_process_place_edges'] = True
plot_bigraph(music_map2, 
             filename='cell_hierarchy_functions' if save else None,
             **plot_settingsx,
             dpi=dpi,
             )

Writing out/cell_hierarchy_functions
Out[8]:
bigraph ('cell',) cell ('cell', 'cytoplasm') cytoplasm ('cell',)->('cell', 'cytoplasm') ('cell', 'nucleus') nucleus ('cell',)->('cell', 'nucleus') ('cell', 'transcription') transcription ('cell', 'translation') translation ('cell', 'metabolism') metabolism ('cell', 'cell cycle') cell cycle ('cell', 'signalling') signalling ('cell', 'protein transport') protein transport ('cell', 'RNA processing') RNA processing ('cell', 'cytoplasm', 'secretory organelles') secretory organelles ('cell', 'cytoplasm')->('cell', 'cytoplasm', 'secretory organelles') ('cell', 'cytoplasm', 'cytoplasmic organelles') cytoplasmic organelles ('cell', 'cytoplasm')->('cell', 'cytoplasm', 'cytoplasmic organelles') ('cell', 'cytoplasm', 'transcriptional regulation complex family') transcriptional regulation complex family ('cell', 'cytoplasm')->('cell', 'cytoplasm', 'transcriptional regulation complex family') ('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems') transmembrane transport systems ('cell', 'cytoplasm', 'secretory organelles')->('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems') ('cell', 'cytoplasm', 'secretory organelles')->('cell', 'protein transport') secretory ('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems', 'ion transmembrane transport systems') ion transmembrane transport systems ('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems')->('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems', 'ion transmembrane transport systems') ('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems')->('cell', 'signalling') transport ('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems')->('cell', 'protein transport') transmembrane transport ('cell', 'cytoplasm', 'secretory organelles', 'transmembrane transport systems', 'ion transmembrane transport systems')->('cell', 'metabolism') ion transport ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles') subgroup of cytoplasmic organelles ('cell', 'cytoplasm', 'cytoplasmic organelles')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles') metabolic organelles ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family') ribonucleoprotein complex family ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', 'subgroup of metabolic organelles') subgroup of metabolic organelles ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', 'subgroup of metabolic organelles') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', 'mitochondrion') mitochondrion ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', 'mitochondrion') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles')->('cell', 'metabolism') organelles ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'metabolic organelles', 'mitochondrion')->('cell', 'metabolism') mitochondrion ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'RNA processing complex 1') RNA processing complex 1 ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'RNA processing complex 1') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community') ribosome biogenesis community ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'RNA processing complex 1', 'RNA splicing complex 1') RNA splicing complex 1 ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'RNA processing complex 1')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'RNA processing complex 1', 'RNA splicing complex 1') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome') ribosome ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'nucleic acid binding complex') nucleic acid binding complex ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'nucleic acid binding complex') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit') ribosomal subunit ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome')->('cell', 'translation') ribosomes ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'mitochondirial large ribosomal subunit') mitochondirial large ribosomal subunit ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'mitochondirial large ribosomal subunit') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'mito-cyto ribosomal cluster') mito-cyto ribosomal cluster ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'mito-cyto ribosomal cluster') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'cotranslational protein targeting to membrane system') cotranslational protein targeting to membrane system ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'cotranslational protein targeting to membrane system') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'ribosomal complex 5') ribosomal complex 5 ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'ribosomal complex 5') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'ribosomal complex 2') ribosomal complex 2 ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit')->('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'ribosomal complex 2') ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'ribosome', 'ribosomal subunit', 'cotranslational protein targeting to membrane system')->('cell', 'protein transport') cotranslation ('cell', 'cytoplasm', 'cytoplasmic organelles', 'subgroup of cytoplasmic organelles', 'ribonucleoprotein complex family', 'ribosome biogenesis community', 'nucleic acid binding complex')->('cell', 'transcription') nucleic acids ('cell', 'cytoplasm', 'transcriptional regulation complex family', 'transcriptional regulation complexes') transcriptional regulation complexes ('cell', 'cytoplasm', 'transcriptional regulation complex family')->('cell', 'cytoplasm', 'transcriptional regulation complex family', 'transcriptional regulation complexes') ('cell', 'cytoplasm', 'transcriptional regulation complex family', 'transcriptional regulation complexes')->('cell', 'transcription') regulation ('cell', 'cytoplasm', 'transcriptional regulation complex family', 'transcriptional regulation complexes')->('cell', 'signalling') trancript regulation ('cell', 'nucleus', 'DNA metabolic assembly') DNA metabolic assembly ('cell', 'nucleus')->('cell', 'nucleus', 'DNA metabolic assembly') ('cell', 'nucleus', 'nuclear lumen') nuclear lumen ('cell', 'nucleus')->('cell', 'nucleus', 'nuclear lumen') ('cell', 'nucleus', 'nuclear body') nuclear body ('cell', 'nucleus')->('cell', 'nucleus', 'nuclear body') ('cell', 'nucleus', 'nucleo-plasm 1') nucleo-plasm 1 ('cell', 'nucleus')->('cell', 'nucleus', 'nucleo-plasm 1') ('cell', 'nucleus', 'nucleo-plasm 2') nucleo-plasm 2 ('cell', 'nucleus')->('cell', 'nucleus', 'nucleo-plasm 2') ('cell', 'nucleus', 'nuclear transcriptional speckle') nuclear transcriptional speckle ('cell', 'nucleus')->('cell', 'nucleus', 'nuclear transcriptional speckle') ('cell', 'nucleus', 'DNA metabolic assembly')->('cell', 'cell cycle') DNA ('cell', 'nucleus', 'nuclear lumen', 'nucleolus') nucleolus ('cell', 'nucleus', 'nuclear lumen')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus') ('cell', 'nucleus', 'nuclear lumen', 'nuclear splicing speckle') nuclear splicing speckle ('cell', 'nucleus', 'nuclear lumen')->('cell', 'nucleus', 'nuclear lumen', 'nuclear splicing speckle') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'ribonucleprotein complex family') ribonucleprotein complex family ('cell', 'nucleus', 'nuclear lumen', 'nucleolus')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'ribonucleprotein complex family') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family') RNA processing complex family ('cell', 'nucleus', 'nuclear lumen', 'nucleolus')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'splicosomal complex family') splicosomal complex family ('cell', 'nucleus', 'nuclear lumen', 'nucleolus')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'splicosomal complex family') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family', 'RNA processing complex 1') RNA processing complex 1 ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family', 'RNA processing complex 1') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family', 'RNA splicing complex family') RNA splicing complex family ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family')->('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family', 'RNA splicing complex family') ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family')->('cell', 'transcription') RNA processing ('cell', 'nucleus', 'nuclear lumen', 'nucleolus', 'RNA processing complex family')->('cell', 'RNA processing') processing complex ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family') chromosome organization complex family ('cell', 'nucleus', 'nucleo-plasm 1')->('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family') ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family') chromatin organization complex family ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family')->('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family') ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family')->('cell', 'cell cycle') chromosome ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family', 'HAT complex family') HAT complex family ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family')->('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family', 'HAT complex family') ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family')->('cell', 'cell cycle') chromatin ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family', 'HAT complex family', 'NuA4 HAT complex') NuA4 HAT complex ('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family', 'HAT complex family')->('cell', 'nucleus', 'nucleo-plasm 1', 'chromosome organization complex family', 'chromatin organization complex family', 'HAT complex family', 'NuA4 HAT complex') ('cell', 'nucleus', 'nucleo-plasm 2', 'chromatin regulation complex') chromatin regulation complex ('cell', 'nucleus', 'nucleo-plasm 2')->('cell', 'nucleus', 'nucleo-plasm 2', 'chromatin regulation complex') ('cell', 'nucleus', 'nuclear transcriptional speckle', 'negative regulation of RNA biosynthesis process') negative regulation of RNA biosynthesis process ('cell', 'nucleus', 'nuclear transcriptional speckle')->('cell', 'nucleus', 'nuclear transcriptional speckle', 'negative regulation of RNA biosynthesis process') ('cell', 'nucleus', 'nuclear transcriptional speckle', 'negative regulation of RNA biosynthesis process')->('cell', 'transcription') negative regulation ('cell', 'translation', 'm', 'e', 'm', 'b', 'r', 'a', 'n', 'e')_output->('cell', 'translation') membrane