Example #1
0
def ens_genes_for(factor_name, pssm_map):
    return set(
        pssm_map[m]
        for m
        in set(str(m.acc) for m in transfac_factors.matrices_by_factor_name(factor_name))
        if m in pssm_map
    )
Example #2
0
def ens_genes_for(factor_name, pssm_map):
    return set(pssm_map[m] for m in set(
        str(m.acc)
        for m in transfac_factors.matrices_by_factor_name(factor_name))
               if m in pssm_map)
Example #3
0
    'ATF',
    'CREB',
    'Arnt',
    'YY1',
]
"""
The transcription factors in "Genome-Wide In Silico Identification of Transcriptional
Regulators Controlling the Cell Cycle in Human Cells" Elkon et al. Table 3
"""
elkon_tf_ens_genes = dict(
    (tf, ens_genes_for(tf, pssm_map)) for tf in elkon_tfs)
raise
for factor_name in elkon_tfs:
    print factor_name, ':', ','.join(
        set(m.name
            for m in transfac_factors.matrices_by_factor_name(factor_name)))

open('elkon-cell-cycle-small-ensembl.txt',
     'w').write('\n'.join('\n'.join(pssm_map[matrix])
                          for matrix in elkon_tfs_small.values()))
open('elkon-cell-cycle-ensembl.txt',
     'w').write('\n'.join('\n'.join(pssm_map[matrix])
                          for matrix in elkon_tfs.values()))

#translated = S.translate('ensembl', 'H**o sapiens', 'unigene', 'ensembl_gene_id', [ 'Hs.239', 'Hs.715518', 'Hs.181768', 'Hs.427236' ])
#print 'Translated: %s' % ', '.join('->'.join(map(str, x)) for x in translated)


def yield_refs(filename):
    """Yield references in filename"""
    f = open(file)
Example #4
0
    'NF-Y',
    'NRF-1',
    'ETF',
    'ATF',
    'CREB',
    'Arnt',
    'YY1',
]
"""
The transcription factors in "Genome-Wide In Silico Identification of Transcriptional
Regulators Controlling the Cell Cycle in Human Cells" Elkon et al. Table 3
"""
elkon_tf_ens_genes = dict((tf, ens_genes_for(tf, pssm_map)) for tf in elkon_tfs)
raise
for factor_name in elkon_tfs:
    print factor_name, ':', ','.join(set(m.name for m in transfac_factors.matrices_by_factor_name(factor_name)))




open('elkon-cell-cycle-small-ensembl.txt', 'w').write('\n'.join('\n'.join(pssm_map[matrix]) for matrix in elkon_tfs_small.values()))
open('elkon-cell-cycle-ensembl.txt', 'w').write('\n'.join('\n'.join(pssm_map[matrix]) for matrix in elkon_tfs.values()))






#translated = S.translate('ensembl', 'H**o sapiens', 'unigene', 'ensembl_gene_id', [ 'Hs.239', 'Hs.715518', 'Hs.181768', 'Hs.427236' ])
#print 'Translated: %s' % ', '.join('->'.join(map(str, x)) for x in translated)