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| { | |
| "metadata": { | |
| "name": "" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "from trnlib.omeORM import *\n", | |
| "from sqlalchemy import func\n", | |
| "from IPython.core import display\n", | |
| "from IPython.core.display import HTML\n", | |
| "from numpy import random, average\n", | |
| "from pandas import *\n", | |
| "\n", | |
| "import pymongo\n", | |
| "import simplejson as json\n", | |
| "import math\n", | |
| "import os\n", | |
| "\n", | |
| "\n", | |
| "ome = Session()\n", | |
| "connection = pymongo.Connection()\n", | |
| "\n", | |
| "db_gff = connection.gff_database\n", | |
| "gff_data = db_gff.gff_data\n", | |
| "\n", | |
| "anaerobic = ome.query(Condition).filter_by(carbon_source='glucose',eacceptor='anaerobic').first()\n", | |
| "nitrate = ome.query(Condition).filter_by(carbon_source='glucose',eacceptor='NO3').first()\n", | |
| "\n", | |
| "def html_table(matrix):\n", | |
| " table = '<table border=\"1\">\\n'\n", | |
| " for row in matrix:\n", | |
| " table += '<tr>'\n", | |
| " for entry in row: table += '<td>'+str(entry)+'</td>'\n", | |
| " table += '</tr>'\n", | |
| " table += '</table>'\n", | |
| " return HTML(table)" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 1 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "def get_chip_data(target = 'ArcA', carbon_source = 'glucose', nitrogen_source = 'NH4Cl', eacceptor = 'anaerobic', replicates = [1,2,3],\\\n", | |
| " leftpos = 0, rightpos = 200, strand = ['+','-'], value = 0.0):\n", | |
| " condition = ome.query(Condition).filter(and_(Condition.carbon_source == carbon_source, Condition.nitrogen_source == nitrogen_source,\\\n", | |
| " Condition.eacceptor == eacceptor)).first()\n", | |
| " gff_exp_wids = [x[0] for x in ome.query(GFFExperiment.wid).filter(and_(GFFExperiment.target == target, GFFExperiment.condition == condition,\\\n", | |
| " GFFExperiment.replicate.in_(replicates))).all()]\n", | |
| " probes = []\n", | |
| " for probe in gff_data.find({\"$and\": \n", | |
| " [{\"leftpos\" : {\"$gte\": leftpos}}, \n", | |
| " {\"rightpos\": {\"$lte\": rightpos}}, \n", | |
| " {\"strand\": {\"$in\" : strand}},\n", | |
| " {\"value\": {\"$gte\": value}},\n", | |
| " {\"experiment_wid\": {\"$in\" : gff_exp_wids}}\n", | |
| " ]}): \n", | |
| " probes.append(probe)\n", | |
| " return probes\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "def nimblegen_AUC(signals):\n", | |
| " AUC = 0\n", | |
| " a = signals.pop(0)\n", | |
| " b = signals.pop(0)\n", | |
| " if a < b: AUC = (a+b)-a/2\n", | |
| " elif a > b: AUC = (a+b)-b/2\n", | |
| " elif a == b: AUC = (a+b)-a/2\n", | |
| " a = b\n", | |
| " sumval = 0\n", | |
| " for b in signals:\n", | |
| " sumval+=b\t\n", | |
| " if a < b:\n", | |
| " AUC += b-a/2\n", | |
| " elif a > b:\n", | |
| " AUC += b/2\n", | |
| " else:\n", | |
| " AUC += b-a/2\n", | |
| " a = b\n", | |
| " return AUC\n" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 2 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "cpge = ChipPeakGeneExpression\n", | |
| "data = {}\n", | |
| "data2 = {}\n", | |
| "for target,eacceptor in [('ArcA','anaerobic'),('ArcA','NO3'),('Fnr','anaerobic'),('Fnr','NO3')]:\n", | |
| " for x in ome.query(cpge).filter(and_(cpge.target == target, cpge.eacceptor == eacceptor)).all():\n", | |
| " #ChIP_value = nimblegen_AUC([y['value'] for y in get_chip_data(target = x.target, eacceptor = x.eacceptor, \n", | |
| " # leftpos = x.leftpos, rightpos = x.rightpos)])\n", | |
| " ChIP_value = 1.\n", | |
| " if x.target1 != 'wt': inv = -1.0\n", | |
| " else: inv = 1\n", | |
| " try: \n", | |
| " \n", | |
| " if x.fdr < .05: data[x.gene_name][(target+' '+eacceptor)] = x.fold_change*inv\n", | |
| " data2[x.gene_name][(target+' '+eacceptor)] = ChIP_value\n", | |
| " except:\n", | |
| " try: data[x.gene_name]\n", | |
| " except: \n", | |
| " data[x.gene_name] = {'ArcA anaerobic':0.1,'ArcA NO3':0.1,'Fnr anaerobic':0.1,'Fnr NO3':0.1}\n", | |
| " data2[x.gene_name] = {'ArcA anaerobic':0.1,'ArcA NO3':0.1,'Fnr anaerobic':0.1,'Fnr NO3':0.1}\n", | |
| " if x.fdr < .05: data[x.gene_name][target+' '+eacceptor] = x.fold_change*inv\n", | |
| " data2[x.gene_name][(target+' '+eacceptor)] = ChIP_value\n", | |
| " \n", | |
| " \n", | |
| "data_frame = DataFrame(data)\n", | |
| "data_frame2 = DataFrame(data2)" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 3 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "def write_heatmap_json(genes, name):\n", | |
| " \n", | |
| " name_map = {}\n", | |
| " for gene_name in genes:\n", | |
| " x = ome.query(TU.name).filter(TU.genes.contains(ome.query(Gene).filter_by(name=gene_name).first())).first()[0]\n", | |
| " if x == '': x = gene_name\n", | |
| " name_map[gene_name] = x\n", | |
| " \n", | |
| " data_json = json.dumps({\"genes\":[{\"name\": name_map[gene_name] , \"data\": list(data_frame[gene_name].values), \n", | |
| " \"data2\": list(data_frame2[gene_name].values)}\n", | |
| " for gene_name in genes],\n", | |
| " \"headers\":[{\"name\" : \"ArcA anaerobic\"},{\"name\" : \"ArcA NO3\"},{\"name\" : \"Fnr anaerobic\"},{\"name\" : \"Fnr NO3\"}]})\n", | |
| "\n", | |
| " try: os.remove(name+'.json')\n", | |
| " except: None\n", | |
| " open(name+'.json','w').write(data_json)\n", | |
| " \n", | |
| " \n", | |
| "data_frame = data_frame.reindex_axis(Index(['ArcA anaerobic', 'ArcA NO3', 'Fnr anaerobic', 'Fnr NO3'], dtype=object), axis=0)\n", | |
| "data_frame2 = data_frame2.reindex_axis(Index(['ArcA anaerobic', 'ArcA NO3', 'Fnr anaerobic', 'Fnr NO3'], dtype=object), axis=0)\n", | |
| "\n", | |
| "write_heatmap_json(flatten_to_genes(catabolism_tu),'catabolism')\n", | |
| "write_heatmap_json(flatten_to_genes(anabolism_tu),'anabolism')\n", | |
| "write_heatmap_json(flatten_to_genes(chemiosmosis_tu),'chemiosmosis')\n" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "%%timeit\n", | |
| "nimblegen_AUC([x['value'] for x in get_chip_data(leftpos=449500,rightpos=452000,replicates=[1,2,3],strand=['+','-'])])/6" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "1 loops, best of 3: 713 ms per loop\n" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 29 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "def flatten_to_genes(category):\n", | |
| " genes = []\n", | |
| " for x in category: \n", | |
| " for y in category[x]:\n", | |
| " try: \n", | |
| " for z in category[x][y]: genes.append(z)\n", | |
| " except:\n", | |
| " genes.append(y)\n", | |
| " return genes\n", | |
| " " | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 4 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "genes = flatten_to_genes(catabolism_tu)\n", | |
| "name_map = {}\n", | |
| "for gene_name in genes:\n", | |
| " x = ome.query(TU.name).filter(TU.genes.contains(ome.query(Gene).filter_by(name=gene_name).first())).first()[0]\n", | |
| " if x == '': x = gene_name\n", | |
| " name_map[gene_name] = x\n", | |
| "name_map" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "ename": "NameError", | |
| "evalue": "name 'catabolism_tu' is not defined", | |
| "output_type": "pyerr", | |
| "traceback": [ | |
| "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", | |
| "\u001b[0;32m<ipython-input-5-b706e81067c2>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mgenes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mflatten_to_genes\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcatabolism_tu\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2\u001b[0m \u001b[0mname_map\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mgene_name\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mgenes\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0mx\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mome\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mquery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mTU\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfilter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mTU\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgenes\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcontains\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mome\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mquery\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mGene\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfilter_by\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mgene_name\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfirst\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfirst\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mx\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mx\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgene_name\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", | |
| "\u001b[0;31mNameError\u001b[0m: name 'catabolism_tu' is not defined" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 5 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "catabolism = {\n", | |
| " \"transport\": {\n", | |
| " \"carbohydrate\": ['mglA','mglB','mglC','ugpB','ugpA','ugpE','ugpC','kgtP','dcuA','focA',\n", | |
| " 'uraA','ptsG','lldP','exuT'],\n", | |
| " \"amino_acid\": ['metQ','metI','metN','aroP','dppA','dppB','dppB','dppC','dppD','dppF',\n", | |
| " 'oppA','oppB','oppC','oppD','oppF','sstT','hisJ','hisQ',\n", | |
| " 'hisM','hisP','potF','potG','potH','potI','potA','potB','potC','potD',\n", | |
| " 'argT','cycA','putP','tyrP','gabP'],\n", | |
| " \"nucleotides\": ['nupC'],\n", | |
| " \"lipids\": ['fadL']\n", | |
| " },\n", | |
| " \"recycling\": {\n", | |
| " \"carbohydrate\": ['envC','mltA','pldA','ugpQ','arnA','manA','paaK','mhpC','mhpF'],\n", | |
| " \"amino_acid\": ['clpA','clpS','rnpA','pepN','pepQ','ybiS','yhbU','ygjG','gcvA','gcvB',\n", | |
| " 'glpG','pepT','astC','astD','astE'],\n", | |
| " \"lipids\": ['fadI','fadJ','fadD','fadE','fadB','fadA','fadH'],\n", | |
| " \"nucleotides\": ['xseA','csrB']\n", | |
| " },\n", | |
| " \"glycolysis\": ['fsaA','dhaK','dhaL','dhaM','gapA','gpmM','eno','pykA','aceE','aceF',\n", | |
| " 'adhE','lpd','acs'],\n", | |
| " \"TCA\": ['gltA','acnB','icd','sucA','sucB','sucC','sucD','sdhA',\n", | |
| " 'sdhB','sdhC','sdhD','frdA','frdB','frdC','frdD','fumA',\n", | |
| " 'fumB','mdh','glcD','glcB','glcG','aldA'],\n", | |
| " \"accessory\": ['thiE','thiF','thiG','thiH','thiS'],\n", | |
| " \"regulators\": {\n", | |
| " \"carbohydrate\": ['lldR','aer','mhpR','caiF','puuR','pdhR','glcC']\n", | |
| " }\n", | |
| " }" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "anabolism = {\n", | |
| " \"macromolecular_synthesis\": ['nrdA','nrdB','ndk','nudE','nudJ','upp','nrdD','nrdG','ung',\n", | |
| " 'dbpA','rimP','rplY','rpsU','ddlA'],\n", | |
| " \"biosynthesis\": {\n", | |
| " \"nucleotides\": ['sthA','pntA','pntB','pncB','purA','guaA','guaB','ravA',\n", | |
| " 'viaA','katG','pyrD','purM','purN'],\n", | |
| " \"amino_acids\": ['carA','carB','thiC','thrA','thrB','thrC','gabD','gabT',\n", | |
| " 'speA','puuA','puuD','putA','mhpD','mhpE','glpE','gltB',\n", | |
| " 'gltD','gltF','argG'],\n", | |
| " \"lipids\": ['acpP','tpx']\n", | |
| " },\n", | |
| " \"regulators\": ['bssR','rcsB','rcsD','uspA','uspB','uspF','rho','nusA','infA','infB','rutR']\n", | |
| " }\n", | |
| " " | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "chemiosmosis = {\n", | |
| " \"ETC\": {\n", | |
| " \"dehydrogenases\": ['fdnH','fdnI','fdoG','fdoH','fdoI','hybC','hybO','glpD',\n", | |
| " 'hybA','hybB','hybD','hybE','hybF','hybG','nuoA','nuoB',\n", | |
| " 'nuoC','nuoE','nuoF','nuoG','nuoH','nuoI','nuoJ','nuoK',\n", | |
| " 'nuoL','nuoM','nuoN','ndh','lldD','mdh','sdhA','sdhB','sdhC','sdhD'],\n", | |
| " \"oxidoreductases\": ['lhgO','mqo','frdA','frdB','frdC','frdD','dmsA','dmsB','dmsC',\n", | |
| " 'ynfE','ynfF','ynfG','ynfH','nirB','nirD','nirC','nrfA',\n", | |
| " 'nrfB','nrfC','nrfD','nrfF','narG','narH','narI','cyoA','cyoB',\n", | |
| " 'cyoC','cyoD','cyoE','cydA','cydB','hcr'],\n", | |
| " \"accessory\": ['dmsD','ynjE','moaA','moaB','moaC','moaD','moaE','fhuF',\n", | |
| " 'nikA','nikB','nikC','nikD','nikE','hcp','dsbB','msrB','glpE']\n", | |
| " },\n", | |
| " \"fermentation\": ['pflB','yfiD','pta','ackA','adhE','focA'],\n", | |
| " \"ion_pumps\": ['hemG','feoA','feoB','feoC','dcuA','dcuB','osmY','cydD','cydC',\n", | |
| " 'ompC','ompW','pitA','kdpC','narK','narJ','cirA','gsiA',\n", | |
| " 'gsiB','gsiC','gsiD','mntH'],\n", | |
| " \"motility\": ['flhC','flhD'],\n", | |
| " \"regulators\": ['gadX','gadW','nikR','rstA','rstB','narX','narL','glpR']\n", | |
| " }\n", | |
| " \n", | |
| " " | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "ome.query(Gene.info).filter_by(name='yghB').all()" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "output_type": "pyout", | |
| "prompt_number": 52, | |
| "text": [ | |
| "[(u'conserved inner membrane protein')]" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 52 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "b = [x.bnum+'\\t'+x.gene_name for x in ome.query(cpge).join(Gene, Gene.bnum == cpge.bnum).filter(Gene.info.ilike('%membrane%')).filter(and_(cpge.target.in_(['ArcA','Fnr']), cpge.fdr < .05)).filter(not_(cpge.gene_name.in_(a))).order_by(cpge.gene_name).all()]" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 60 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "for x in b: print x" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "stream": "stdout", | |
| "text": [ | |
| "b1445\tydcX\n", | |
| "b1750\tydjX\n", | |
| "b1752\tydjZ\n", | |
| "b1929\tyedE\n", | |
| "b2295\tyfbV\n", | |
| "b2298\tyfcC\n", | |
| "b3009\tyghB\n", | |
| "b3485\tyhhJ\n", | |
| "b3964\tyijD\n", | |
| "b4068\tyjcH\n", | |
| "b4068\tyjcH\n", | |
| "b4176\tyjeT\n", | |
| "b1332\tynaJ\n", | |
| "b3002\tyqhA\n" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 61 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "a = flatten_to_genes(catabolism)+flatten_to_genes(anabolism)+flatten_to_genes(chemiosmosis)\n", | |
| "cpge = ChipPeakGeneExpression\n", | |
| "ome.query(cpge).filter(and_(cpge.target.in_(['ArcA','Fnr']), cpge.fdr < .05)).filter(not_(cpge.gene_name.in_(a))).order_by(cpge.gene_name).all()" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "metadata": {}, | |
| "output_type": "pyout", | |
| "prompt_number": 9, | |
| "text": [ | |
| "[ChipPeakGeneExpression: Fnr (activator) for Gene: arcA (b4401) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.58, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: arcA (b4401) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change -5.15, fdr=3.04e-08),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: arcA (b4401) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 11.27, fdr=1.35e-07),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: argR (b3237) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.42, fdr=4.33e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: betI (b0313) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 1.39, fdr=2.03e-04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: caiA (b0039) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.39, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: csiD (b2659) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -2.32, fdr=1.26e-04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: cspA (b3556) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.48, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: cysG (b3368) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.47, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: dnaG (b3066) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.39, fdr=5.33e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: fabD (b1092) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.19, fdr=8.42e-04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: fabF (b1095) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.43, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: fabG (b1093) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.12, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: fnr (b1334) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 10.95, fdr=2.35e-06),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: fnr (b1334) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 3.32, fdr=1.88e-05),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: folE (b2153) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.48, fdr=3.40e-04),\n", | |
| " ChipPeakGeneExpression: Fnr (repressor) for Gene: groL (b4143) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change -0.45, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: hsdM (b4349) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.34, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: hsdR (b4350) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 5.08, fdr=7.97e-04),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: hsdS (b4348) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.50, fdr=7.83e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (repressor) for Gene: iraP (b0382) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change -2.32, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: ispH (b0029) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.35, fdr=2.95e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: leuD (b0071) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.21, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: leuL (b0075) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.76, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: macA (b0878) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.59, fdr=7.29e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: mcbA (b0806) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.68, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: metV (b2816) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 0.80, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: metW (b2815) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 0.86, fdr=2.87e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: metZ (b2814) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 0.78, fdr=5.61e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: micF (b4439) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.64, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: mutM (b3635) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.63, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: phoH (b1020) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 4.48, fdr=9.38e-08),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: pnp (b3164) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.24, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: pnp (b3164) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.12, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: pnp (b3164) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.12, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: psrD (b4418) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.39, fdr=8.82e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: rbfA (b3167) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.32, fdr=6.93e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: rbfA (b3167) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.11, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: recF (b3700) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.46, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: recF (b3700) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.64, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: ribF (b0025) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.12, fdr=8.16e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: rplU (b3186) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.23, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: rpmA (b3185) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.45, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: rpmB (b3637) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.21, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: rpmG (b3636) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.37, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: rpmH (b3703) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.24, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: rpmH (b3703) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.15, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: rpsO (b3165) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.36, fdr=0.05),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: rpsO (b3165) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.36, fdr=0.05),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: rpsT (b0023) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.52, fdr=0.01),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: secG (b3175) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.46, fdr=7.54e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: secG (b3175) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.56, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: suhB (b2533) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.44, fdr=0.01),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: thrL (b0001) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 1.12, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: truB (b3166) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.65, fdr=4.29e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: uxaC (b3092) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.75, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: xthA (b1749) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.28, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: ybfA/EG11521 (b0699) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 2.00, fdr=5.20e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: ybfA/EG11521 (b0699) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change -0.85, fdr=6.61e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: ybhK/G6402 (b0780) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.74, fdr=3.21e-04),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: ybiU/G6424 (b0821) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -1.84, fdr=4.21e-04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: ybjX/G6460 (b0877) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 1.03, fdr=4.82e-04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: yceD/EG11119 (b1088) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.24, fdr=0.01),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ydcX/G6756 (b1445) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.75, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ydfZ/G6815 (b1541) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 12.27, fdr=2.55e-10),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ydfZ/G6815 (b1541) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 10.15, fdr=1.16e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: ydgC/G6863 (b1607) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -1.54, fdr=1.71e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ydhW/G6900 (b1672) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 0.97, fdr=0.05),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ydhY/G6902 (b1674) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 1.42, fdr=4.14e-04),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ydjX/G6945 (b1750) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 4.50, fdr=2.10e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ydjY/G6946 (b1751) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 5.56, fdr=7.03e-04),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ydjZ/G6947 (b1752) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 4.43, fdr=6.84e-06),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yeaD/G6966 (b1780) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 1.40, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yeaD/G6966 (b1780) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 1.19, fdr=4.80e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yecH/G7036 (b1906) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 5.85, fdr=1.47e-05),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yecH/G7036 (b1906) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 4.39, fdr=2.35e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (repressor) for Gene: yedE/EG11660 (b1929) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change -1.12, fdr=4.91e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yeiG/EG12026 (b2154) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.34, fdr=4.68e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yejG/EG12042 (b2181) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 6.12, fdr=2.05e-09),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yejG/EG12042 (b2181) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -4.00, fdr=3.62e-04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: yfbM/G7179 (b2272) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.72, fdr=0.01),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yfbV/G7189 (b2295) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 0.65, fdr=1.37e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yfcC/G7190 (b2298) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 2.85, fdr=1.29e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yfcZ/G7214 (b2343) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 1.02, fdr=6.26e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yfcZ/G7214 (b2343) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 1.89, fdr=4.46e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (repressor) for Gene: yffL/G7273 (b2443) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.95, fdr=0.01),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yffS/G7280 (b2450) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.32, fdr=3.95e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (repressor) for Gene: yffS/G7280 (b2450) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change -0.32, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: yfiF/EG11786 (b2581) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change -0.26, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: Fnr (repressor) for Gene: yghA/EG11292 (b3003) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.95, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yghB/EG11824 (b3009) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 1.12, fdr=8.67e-04),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: ygjD/EG11171 (b3064) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.31, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yhbS/G7650 (b3156) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 1.13, fdr=3.50e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yhbS/G7650 (b3156) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 0.41, fdr=0.01),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yhbT/G7651 (b3157) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 2.02, fdr=7.04e-07),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yhbT/G7651 (b3157) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.47, fdr=0.01),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yhbV/G7653 (b3159) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 6.60, fdr=2.11e-05),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: yhgE/G7745 (b3402) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.73, fdr=1.53e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: yhhJ/EG11767 (b3485) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.36, fdr=0.05),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yhjE/EG12249 (b3523) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 3.75, fdr=4.63e-05),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yhjE/EG12249 (b3523) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -1.92, fdr=2.22e-04),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yiaG/EG12624 (b3555) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.32, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yibN/EG12295 (b3611) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 0.75, fdr=1.01e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yieE/EG11722 (b3712) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.40, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yigI/EG11467 (b3820) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 5.06, fdr=2.67e-12),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yigZ/EG11484 (b3848) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.41, fdr=1.46e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: yijD/EG11395 (b3964) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.48, fdr=4.27e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yjcH/EG11943 (b4068) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -4.58, fdr=5.88e-04),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yjcH/EG11943 (b4068) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 3.12, fdr=7.31e-05),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yjeT/G7844 (b4176) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.67, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yjiR/G7936 (b4340) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -1.88, fdr=1.42e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: ynaJ/G6668 (b1332) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 4.05, fdr=6.36e-06),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yncD/G6762 (b1451) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -2.16, fdr=1.06e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (repressor) for Gene: yncE/G6763 (b1452) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -4.65, fdr=1.43e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ynfK/G6851 (b1593) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 3.91, fdr=1.22e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ynfK/G6851 (b1593) on Condition: C:glucose, N:NH4Cl, e:anaerobic (fold change 5.05, fdr=2.09e-06),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ynjA/G6948 (b1753) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 1.97, fdr=1.30e-03),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ynjB/G6949 (b1754) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 2.14, fdr=9.41e-04),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ynjC/G6950 (b1755) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 3.02, fdr=2.29e-04),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: ynjD/G6951 (b1756) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 2.26, fdr=2.11e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: ypdA/G7243 (b2380) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.66, fdr=6.12e-03),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: ypdB/G7244 (b2381) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.45, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: ypdC/G7245 (b2382) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.39, fdr=0.02),\n", | |
| " ChipPeakGeneExpression: ArcA (activator) for Gene: yqcA/G7448 (b2790) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.36, fdr=0.04),\n", | |
| " ChipPeakGeneExpression: Fnr (activator) for Gene: yqgC/G7522 (b2940) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change 0.47, fdr=0.03),\n", | |
| " ChipPeakGeneExpression: Fnr (repressor) for Gene: yqhA/G7559 (b3002) on Condition: C:glucose, N:NH4Cl, e:NO3 (fold change -0.36, fdr=0.02)]" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 9 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "catabolism_tu = {\n", | |
| " \"transport\": {\n", | |
| " \"carbohydrate\": ['mglB','ugpE','kgtP','lldP','exuT','focA','uraA','ptsG','dcuA'],\n", | |
| " \"amino_acid\": ['potB','metN','aroP','dppD','oppF','sstT','hisJ','potF','argT',\n", | |
| " 'cycA','putP','gabP','tyrP'],\n", | |
| " \"nucleotides\": ['nupC'],\n", | |
| " \"lipids\": ['fadL']\n", | |
| " },\n", | |
| " \"recycling\": {\n", | |
| " \"carbohydrate\": ['envC','mltA','pldA','ugpQ','mhpF','arnA'],\n", | |
| " \"amino_acid\": ['clpA','ygjG','pepN','pepQ','ybiS','yhbU','rnpA','gcvA','gcvB',\n", | |
| " 'astC',],\n", | |
| " \"lipids\": ['fadJ','fadD','fadE','fadB','fadH']\n", | |
| " },\n", | |
| " \"glycolysis\": ['dhaK','gapA','gpmM','pykA','aceE',\n", | |
| " 'adhE','lpd','acs'],\n", | |
| " \"TCA\": ['gltA','acnB','icd','sucD','sdhC','frdD','fumA','mdh','glcD','aldA'],\n", | |
| " \"accessory\": ['thiE'],\n", | |
| " \"regulators\": {\n", | |
| " \"carbohydrate\": ['aer','lldR','mhpR','glcC','puuR','pdhR','caiF']\n", | |
| " }\n", | |
| " }" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 9 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "anabolism_tu = {\n", | |
| " \"macromolecular_synthesis\": ['ndk','nudE','nrdA','nrdD','upp','ung','dbpA','rimP','rplY','rpsU','ddlA'],\n", | |
| " \"biosynthesis\": {\n", | |
| " \"nucleotides\": ['sthA','pntB','pncB','purA','purN','guaB','ravA','katG','pyrD'],\n", | |
| " \"amino_acids\": ['carA','thiC','gabT','puuD','putA','mhpD','thrA','gltB','argG','speA'],\n", | |
| " \"lipids\": ['tpx']\n", | |
| " \n", | |
| " },\n", | |
| " \"regulators\": ['uspA','uspB','bssR','uspF','rcsD','rho','nusA','infA','infB']\n", | |
| " }\n", | |
| " " | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 10 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "chemiosmosis_tu = {\n", | |
| " \"ETC\": {\n", | |
| " \"dehydrogenases\": ['fdnI','fdoG','hybO','nuoH','lldD','mdh','sdhC'],\n", | |
| " \"oxidoreductases\": ['lhgO','mqo','frdD','dmsA','ynfE','nirD','nrfB','narH','cyoA','cydA','hcr'],\n", | |
| " \"accessory\": ['msrB','glpE','fhuF','ynjE','moaD','nikB','hcp','dsbB']\n", | |
| " },\n", | |
| " \"fermentation\": ['pflB','yfiD','pta','ackA','adhE','focA'],\n", | |
| " \"ion_pumps\": ['hemG','dcuB','cydD','ompC','kdpC','pitA','narK','narJ',\n", | |
| " 'osmY','cirA','feoB','mntH','gsiD'],\n", | |
| " \"motility\": ['flhD'],\n", | |
| " \"regulators\": ['gadW','glpR','narL','nikR','rstA']\n", | |
| " }\n", | |
| " \n", | |
| " \n", | |
| " " | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 11 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "['fdnH','fdnI','fdoG','fdoH','fdoI','hybC','hybO',\n", | |
| " 'hybA','hybB','nuoA','nuoB','nuoC','nuoD','nuoE','nuoF',\n", | |
| " 'nuoG','nuoH','nuoI','nuoJ','nuoK','nuoL','nuoM','nuoN',\n", | |
| " 'ndh','lldD','mdh','sdhA','sdhB','sdhC','sdhD'],\n", | |
| "\n", | |
| "['hemG','feoA','feoB','dcuA','dcuB','osmY','cydD','cydC',\n", | |
| " 'ompC','ompW','pitA','kdpC','kdpD','kdpE']," | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "avg_peak_width = average([x[0] for x in ome.query(ChipPeakGene.rightpos-ChipPeakGene.leftpos).\n", | |
| " group_by(ChipPeakGene.leftpos, ChipPeakGene.rightpos).all()])\n", | |
| "width_aucs = []\n", | |
| "for y in [[x-(avg_peak_width/2),x+(avg_peak_width/2)] for x in random.randint(0,4.6e6,1000)]:\n", | |
| " width_aucs.append(nimblegen_AUC([z['value'] for z in get_chip_data(leftpos=y[0],rightpos=y[1])])/6)" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [], | |
| "prompt_number": 20 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "len(chem_genes+cat_genes+ana_genes)" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "output_type": "pyout", | |
| "prompt_number": 36, | |
| "text": [ | |
| "192" | |
| ] | |
| } | |
| ], | |
| "prompt_number": 36 | |
| }, | |
| { | |
| "cell_type": "code", | |
| "collapsed": false, | |
| "input": [ | |
| "a = flatten_to_genes(catabolism)+flatten_to_genes(anabolism)+flatten_to_genes(chemiosmosis)\n", | |
| "unknown = ['yncD','yncE','rpmA','yciC','yciB','yecH','ypdC','ypdB','yfaL','eno','yjjY',\n", | |
| " 'yhjE','ynjB','ynjA','mutM','pck','rpmG','plsX','rpmF','ypdA','gmhB','yibN',\n", | |
| " 'ynjC','yejG','yfiF','ynjD','ybfA','yceI','mcbA','yqcC','yffL','yffS','ydcX',\n", | |
| " 'ileS','ychE','fkpB','rbbA','yrfF','ybiT','ydgH','rmf','phnJ','metV','metW',\n", | |
| " 'nohB','yddG','aqpZ','yhjE','yfbM','ydjY','ydjZ','ydjX','yceD','yfcC','yfcZ',\n", | |
| " 'yfbV','fsaA','yhgE','yieE','ygjD','yjcH','ssrA','yhiL','slyA','yjeH','yffR',\n", | |
| " 'yghB','ynaJ','ybiU','rplU','ydgC','yeaD','yhiI','paaH','yhiL','phoH','ydhY',\n", | |
| " 'yhiN','metK','yccA','trmJ','yijD','rpoD','uspC','yfdZ','rimO','lpcA','metZ',\n", | |
| " 'yqgB','ybjX','yhbS','yhbT','ybjD','yhbV','yiaG','yjiR','ynfK','ybhK','yqhA',\n", | |
| " 'yghA','ydhI','yqgC','yhhJ','yqcA','yjeT','yigI','ydhY','yedE','csiD']\n", | |
| "redox_exotic = ['yieF']\n", | |
| "unexpressed = ['rhoL','pyrG','avtA','lspA','rhlB','ydhJ','trkH','rnpB','anmK','phnD','phnO',\n", | |
| " 'leuL','leuA','leuB','leuC','leuD','ydcY','rluE','paaJ','ubiC','iaaA','caiB',\n", | |
| " 'kup','asd','fabR','truC','trxA','rutG','fabH','dnaA','dnaN']\n", | |
| "unrelated = ['hsdM']\n", | |
| "contamination = ['fabD','fabG','psrD']\n", | |
| "print data_frame.index\n", | |
| "table = []\n", | |
| "for x in set(data_frame.columns).difference(set(a+unknown+redox_exotic+unexpressed+unrelated+contamination)): \n", | |
| " gene = ome.query(Gene).filter_by(name=x).first()\n", | |
| " table.append((gene._repr_html_(),data_frame[x].values,gene.info))\n", | |
| "html_table(table)\n" | |
| ], | |
| "language": "python", | |
| "metadata": {}, | |
| "outputs": [] | |
| } | |
| ], | |
| "metadata": {} | |
| } | |
| ] | |
| } |
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