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Created February 1, 2014 05:15
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Fnr direct target comparison to Myers et al.
Raw
gistfile1.txt
{
"metadata": {
"name": ""
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "code",
"collapsed": false,
"input": [
"from trnlib.omeORM import *\n",
"from pandas import *\n",
"\n",
"from numpy import array\n",
"from sqlalchemy import func\n",
"\n",
"from IPython.core.display import HTML\n",
"\n",
"ome = Session()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 1
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"category_1_fnr_paper = [['pyrD','b0945'],\\\n",
" ['ynfEFGH-dmsD','b1587'],\\\n",
" ['pykA','b1854'],\\\n",
" ['nikABCDE','b3746'],\\\n",
" ['focA-pflB','b0904'],\\\n",
" ['yfiD','b2579'],\\\n",
" ['dmsABC','b0894'],\\\n",
" ['narGHJI','b1224'],\\\n",
" ['ydfZ','b1541'],\\\n",
" ['ynjE','b1757'],\\\n",
" ['nirBDC-cysG','b3365'],\\\n",
" ['nrfABCDEFG','b4070'],\\\n",
" ['caiF','b0034'],\\\n",
" ['narK','b1223'],\\\n",
" ['bssR','b0836'],\\\n",
" ['ydhYVWXUT','b1674'],\\\n",
" ['fnrS','b4699'],\\\n",
" ['frdABCD','b4154'],\\\n",
" ['pitA','b3493'],\\\n",
" ['ydjXYZ-ynjABCD','b1750'],\\\n",
" ['hcp-hcr','b0873'],\\\n",
" ['ackA-pta','b2296'],\\\n",
" ['dcuB-fumB','b4123'],\\\n",
" ['ynfK','b1593'],\\\n",
" ['yfcC','b2298'],\\\n",
" ['yhbUV','b3158'],\\\n",
" ['yhcC','b3211'],\\\n",
" ['yhiD','b3508'],\\\n",
" ['yjiML','b4335'],\\\n",
" ['yjjI','b4380'],\\\n",
" ['dcuC','b0621'],\\\n",
" ['pepE','b4021']]\n",
"\n",
"category_2_fnr_paper = [['fnr','b1334'],\\\n",
" ['can','b0126'],\\\n",
" ['hisLGDC','b2018'],\\\n",
" ['ndh','b1109'],\\\n",
" ['fbaB','b2097'],\\\n",
" ['yccA','b0970'],\\\n",
" ['ygjG','b3073'],\\\n",
" ['rmf','b0953'],\\\n",
" ['lysC','b4024'],\\\n",
" ['yecR','b1904'],\\\n",
" ['iraP','b0382'],\\\n",
" ['msrB','b1778'],\\\n",
" ['nrdAB','b2234'],\\\n",
" ['gadE','b3512'],\\\n",
" ['hdeD','b3511'],\\\n",
" ['pdhR-aceEF-lpdA','b0113'],\\\n",
" ['cydAB','b0733'],\\\n",
" ['hdeAB-yhiD','b3510'],\\\n",
" ['ompW','b1256'],\\\n",
" ['ompC','b2215'],\\\n",
" ['hycABCDEFGHI','b2725']]\n",
"\n",
"\n",
"category_3_fnr_paper = [['moaA','b0781'],\\\n",
" ['pepT','b1127'],\\\n",
" ['fdnG','b1474'],\\\n",
" ['napF','b2208'],\\\n",
" ['upp','b2494'],\\\n",
" ['feoA','b3408'],\\\n",
" ['katG','b3942'],\\\n",
" ['cadC','b4133'],\\\n",
" ['nrdD','b4238']]\n",
"\n",
"category_4_fnr_paper = [['ompA','b0957'],\\\n",
" ['ptsG','b1101'],\\\n",
" ['uxaB','b1521'],\\\n",
" ['ptsH','b2415'],\\\n",
" ['guaB','b2508'],\\\n",
" ['fadH','b3081'],\\\n",
" ['uxaC','b3092'],\\\n",
" ['dusB','b3260'],\\\n",
" ['ppiA','b3363'],\\\n",
" ['gntT','b3415'],\\\n",
" ['aspA','b4139']]"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 82
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"category_1_2_discrepancies = {\n",
" 'fnrS': 'significant peak but sRNA not reliably measured on microarray',\\\n",
" 'ydjXYZ-ynjABCD': 'significant peak, diff exp NO3, not measured anaerobically',\\\n",
" 'hcp-hcr': 'significant peak, diff exp NO3, not measured anaerobically',\\\n",
" 'dcuB-fumB': 'weak, insignificant peak, diff expressed',\\\n",
" 'yfcC': 'significant peak, diff exp NO3, not measured anaerobically',\\\n",
" 'yjiML': 'weak, insignificant peak, diff expressed NO3',\\\n",
" 'yjjI': 'weak, insignificant peak, diff expressed',\\\n",
" 'dcuC': 'weak, insignificant peak, diff expressed',\\\n",
" 'pepE': 'no signal, diff expressed',\\\n",
" 'can': 'no signal, diff expressed',\\\n",
" 'hisLGDC': 'no signal, diff expressed',\\\n",
" 'fbaB': 'weak, insignificant peak, diff expressed',\\\n",
" 'yccA': 'weak, insignificant peak, diff expressed',\\\n",
" 'ygjG': 'no signal, diff expressed',\\\n",
" 'lysC': 'weak, insignificant peak, diff expressed',\\\n",
" 'yecR': 'weak, insignificant peak',\\\n",
" 'ompC': 'significant peak, diff exp NO3',\\\n",
" 'hycABCDEFGHI': 'one significant replicate, diff expressed'\n",
" }\n",
" \n",
" \n",
" "
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 73
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"category_1_2_mapping_errors = {\n",
" 'yhcC': 'significant peak, arcB is second gene in operon and is diff expressed',\\\n",
" 'yhiD': 'peak calling error, is now a peak and diff expressed',\\\n",
" 'ndh': 'processing error, definite peak and diff expressed',\\\n",
" 'rmf': 'peak calling error, is now a peak and diff expressed',\\\n",
" 'gadE': 'peak calling error, is now a peak and diff expressed',\\\n",
" 'hdeD': 'peak calling error, is now a peak and diff expressed',\\\n",
" 'hdeAB-yhiD': 'peak calling error, is now a peak and diff expressed, also a repeat'\n",
" }\n",
" \n",
" \n",
" "
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 75
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"len(category_1_fnr_paper+category_2_fnr_paper)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 78,
"text": [
"53"
]
}
],
"prompt_number": 78
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"18/53."
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 80,
"text": [
"0.33962264150943394"
]
}
],
"prompt_number": 80
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"len(category_1_2_discrepancies)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 79,
"text": [
"18"
]
}
],
"prompt_number": 79
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"aa = AllAnalysis\n",
"ome.query(aa).filter(and_(or_(aa.target1 == 'delta-fnr', aa.target2 == 'delta-fnr'),\\\n",
" or_(aa.target1 == 'wt', aa.target2 == 'wt'), aa.fdr < 1, aa.gene_name.ilike('hycC%'),\\\n",
" or_(and_(aa.eacceptor1 == 'anaerobic', aa.eacceptor2 == 'anaerobic'),\\\n",
" and_(aa.eacceptor1 == 'NO3', aa.eacceptor2 == 'NO3'),\\\n",
" and_(aa.eacceptor1 == 'O2', aa.eacceptor2 == 'O2')))).all()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 72,
"text": [
"[AllAnalysis (fdr: 0.039146, fold change 2.121667): for Gene: hycC (b2723) Strain: wt-->delta-fnr on Condition: C:glucose, N:NH4Cl, e:anaerobic,\n",
" AllAnalysis (fdr: 0.000343, fold change -4.206667): for Gene: hycC (b2723) Strain: wt-->delta-fnr on Condition: C:glucose, N:NH4Cl, e:NO3]"
]
}
],
"prompt_number": 72
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"ome.query(cpge).filter(and_(cpge.target=='Fnr', cpge.gene_name.ilike('gadE%'))).all()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 63,
"text": [
"[]"
]
}
],
"prompt_number": 63
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cpge = ChipPeakGeneExpression\n",
"for gene,bnum in category_1_fnr_paper+category_2_fnr_paper:\n",
" if gene in category_1_2_discrepancies.keys() or gene in category_1_2_mapping_errors.keys(): continue\n",
" if not ome.query(cpge).filter(and_(cpge.target=='Fnr', cpge.eacceptor=='anaerobic', cpge.bnum==bnum)).all():\n",
" print gene"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 77
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cat_6 = read_table('Fnr_category_6.txt', index_col='bnum')"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 5
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"HTML(cat_6.to_html())"
],
"language": "python",
"metadata": {},
"outputs": [
{
"html": [
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>gene</th>\n",
" <th>regulation</th>\n",
" <th>DE_current</th>\n",
" <th>DE_previous</th>\n",
" <th>DE_RNAseq</th>\n",
" </tr>\n",
" <tr>\n",
" <th>bnum</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>b0929</th>\n",
" <td> ompF</td>\n",
" <td> Activated</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1073</th>\n",
" <td> flgBCDEFGHIJ</td>\n",
" <td> Activated</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2957</th>\n",
" <td> ansB</td>\n",
" <td> Activated</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3409</th>\n",
" <td> feoB</td>\n",
" <td> Activated</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3947</th>\n",
" <td> ptsA-fsaB-gldA</td>\n",
" <td> Activated</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4115</th>\n",
" <td> adiC</td>\n",
" <td> Activated</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0031</th>\n",
" <td> dapB</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0118</th>\n",
" <td> acnB</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0123</th>\n",
" <td> cueO</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0419</th>\n",
" <td> yajO</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0432</th>\n",
" <td> cyoABCDE</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0450</th>\n",
" <td> glnK-amtB</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0655</th>\n",
" <td> gltIJKL-sroC</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0720</th>\n",
" <td> gltA</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0721</th>\n",
" <td> sdhCDAB-sucABCD</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0735</th>\n",
" <td> ybgE</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0755</th>\n",
" <td> gpmA</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0802</th>\n",
" <td> ybiJ</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0812</th>\n",
" <td> dps</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0854</th>\n",
" <td> potFGHI</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0887</th>\n",
" <td> cydDC</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b0897</th>\n",
" <td> ycaC</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1014</th>\n",
" <td> putA</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1040</th>\n",
" <td> csgDEFG</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1064</th>\n",
" <td> grxB</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1188</th>\n",
" <td> ycgB</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1189</th>\n",
" <td> dadAX</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1216</th>\n",
" <td> chaA</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1276</th>\n",
" <td> acnA</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1283</th>\n",
" <td> osmB</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1469</th>\n",
" <td> narU</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1478</th>\n",
" <td> adhP</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1482</th>\n",
" <td> osmC</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1612</th>\n",
" <td> fumA</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1656</th>\n",
" <td> sodB</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1732</th>\n",
" <td> katE</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1777</th>\n",
" <td> yeaC</td>\n",
" <td> Repressed</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1783</th>\n",
" <td> yeaGH</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1841</th>\n",
" <td> yobA-yebZY</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1897</th>\n",
" <td> otsBA</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1905</th>\n",
" <td> ftnA</td>\n",
" <td> Repressed</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1967</th>\n",
" <td> hchA</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b1988</th>\n",
" <td> nac</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2000</th>\n",
" <td> flu</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2001</th>\n",
" <td> yeeRSTUVW</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2080</th>\n",
" <td> yegP</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2133</th>\n",
" <td> dld</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2153</th>\n",
" <td> folE-yeiB</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2209</th>\n",
" <td> eco</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2234</th>\n",
" <td> nrdAB-yfaE</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2236</th>\n",
" <td> yfaE</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2252</th>\n",
" <td> ais</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2266</th>\n",
" <td> elaB</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2303</th>\n",
" <td> folX-yfcH</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2310</th>\n",
" <td> argT-hisJQMP</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2464</th>\n",
" <td> talA-tktB</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2552</th>\n",
" <td> hmp</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2665</th>\n",
" <td> ygaU</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2672</th>\n",
" <td> ygaM</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2741</th>\n",
" <td> rpoS</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b2936</th>\n",
" <td> yggG</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3097</th>\n",
" <td> yqjCDEK</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3160</th>\n",
" <td> yhbW</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3236</th>\n",
" <td> mdh</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3528</th>\n",
" <td> dctA</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3615</th>\n",
" <td> yibD</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3830</th>\n",
" <td> ysgA</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b3995</th>\n",
" <td> rsd</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4014</th>\n",
" <td> aceBAK</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" <td> +</td>\n",
" </tr>\n",
" <tr>\n",
" <th>b4376</th>\n",
" <td> osmY</td>\n",
" <td> Repressed</td>\n",
" <td> +</td>\n",
" <td> -</td>\n",
" <td> +</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>"
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