CH1I_MEAN = Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale

CH2I_MEAN = Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale

CH1B_MEDIAN = The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background

CH2B_MEDIAN = The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background

CH1D_MEAN = The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel

CH2D_MEAN = .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel

CH1I_MEDIAN = Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale

CH2I_MEDIAN = Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale

CH1B_MEAN = The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background

CH2B_MEAN = The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background

CH1D_MEDIAN = The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale

CH2D_MEDIAN = The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale

CH1_PER_SAT = The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale

CH2_PER_SAT = The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale

CH1I_SD = The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel

CH2I_SD = The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel

CH1B_SD = The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background

CH2B_SD = The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background

PERGTBCH1I_1SD = The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale

PERGTBCH2I_1SD = The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale

PERGTBCH1I_2SD = The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale

PERGTBCH2I_2SD = The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale

SUM_MEAN = The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale

SUM_MEDIAN = The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale

RAT1_MEAN = Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale

RAT2_MEAN = The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale

RAT2_MEDIAN = The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale

PIX_RAT2_MEAN = The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale

PIX_RAT2_MEDIAN = The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale

RAT2_SD = The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale

TOT_SPIX = The total number of feature pixels.; Type: integer; Scale: linear_scale

TOT_BPIX = The total number of background pixels.; Type: integer; Scale: linear_scale

REGR = The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale

CORR = The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale

DIAMETER = The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale

X_COORD = X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale

Y_COORD = Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale

TOP = Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale

BOT = Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale

LEFT = Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale

RIGHT = Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale

FLAG = The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale

CH2IN_MEAN = Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel

CH2BN_MEDIAN = Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background

CH2DN_MEAN = Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel

RAT2N_MEAN = Type: float; Scale: linear_scale

CH2IN_MEDIAN = Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale

CH2DN_MEDIAN = Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale

RAT1N_MEAN = Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale

RAT2N_MEDIAN = Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale

LOG_RAT2N_MEAN = Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2

VALUE = Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2\n Feature Extraction - VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)\n Image Adquisition - Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software."],"pubmed_abstract":["A fundamental, but unanswered question in host-pathogen interactions is the timing, localization and population distribution of virulence gene expression during infection. Here, microarray and in situ single cell expression methods were used to study Vibrio cholerae growth and virulence gene expression during infection of the rabbit ligated ileal loop model of cholera. Genes encoding the toxin-coregulated pilus (TCP) and cholera toxin (CT) were powerfully expressed early in the infectious process in bacteria adjacent to epithelial surfaces. Increased growth was found to co-localize with virulence gene expression. Significant heterogeneity in the expression of tcpA, the repeating subunit of TCP, was observed late in the infectious process. The expression of tcpA, studied in single cells in a homogeneous medium, demonstrated unimodal induction of tcpA after addition of bicarbonate, a chemical inducer of virulence gene expression. Striking bifurcation of the population occurred during entry into stationary phase: one subpopulation continued to express tcpA, whereas the expression declined in the other subpopulation. ctxA, encoding the A subunit of CT, and toxT, encoding the proximal master regulator of virulence gene expression also exhibited the bifurcation phenotype. The bifurcation phenotype was found to be reversible, epigenetic and to persist after removal of bicarbonate, features consistent with bistable switches. The bistable switch requires the positive-feedback circuit controlling ToxT expression and formation of the CRP-cAMP complex during entry into stationary phase. Key features of this bistable switch also were demonstrated in vivo, where striking heterogeneity in tcpA expression was observed in luminal fluid in later stages of the infection. When this fluid was diluted into artificial seawater, bacterial aggregates continued to express tcpA for prolonged periods of time. The bistable control of virulence gene expression points to a mechanism that could generate a subpopulation of V. cholerae that continues to produce TCP and CT in the rice water stools of cholera patients."],"pubmed_title":["A bistable switch and anatomical site control Vibrio cholerae virulence gene expression in the intestine."],"pubmed_authors":["Nielsen Alex T AT, Dolganov Nadia A NA, Rasmussen Thomas T, Otto Glen G, Miller Michael C MC, Felt Stephen A SA, Torreilles Stéphanie S, Schoolnik Gary K GK"],"pubmed_title_synonyms":["Liquidivibrio cholerae, viral infection, body part, Controlling, gut, Bowel, Gene Expressions, reference sample, 成人消化道, 肠(bowel), Gene, Intestine, Kommabacillus, virus process, Subdivision of cardinal body part, 肠(Bowel), Microspira comma, Expressions, intestinal tract, Pacinia cholerae-asiaticae, Vibrio cholera, 肠(intestines), Bacillus cholerae, 肠道, Vibrio cholerae-asiaticae, bowel, Vibrio choleae, intestines., anatomical site, Spirillum cholerae, Pathogenicity, Spirillum cholerae-asiaticae, virulence, Expression, adult alimentary canal, Bacillo virgola del Koch, Entire intestine, organism subdivision, Vibrio comma, Principal body part subdivision, Controlled, Bacillus cholerae-asiaticae"],"data_synonyms":["scale tissue, C6orf190, Pak3bp, peltate hair, instrument configuration, number, A4, IMAGE, EXTR1, Tuberosities, Computer, PAPSS 2, PAPSS 1, TYPE, hardware, DAGA4, Adenylyl-sulfate kinase, SPOT, SSAT-1, Sulfate adenylate transferase, THOC4, Software Engineering, PDZK6, spot, MAM, SCG3, Computer Program, Application, ALY|REF, hYAK3-2, proportion, p85SPR, Pip92, Cool, SK 2, Radial, Ch1, bA325O24.3, Software Application, plant peltate hair, SK 1, Computer Programs and Programming, HardwareType, Sulfate adenylyltransferase, C6orf207, number of, study assay, EXTL1L, APS kinase, Cy5, PDZD6, Computer Software Application, 2.7.1.25, BEF, data processing, Quality Controls, Tools, Axon, scientific observation, CH1, has or lacks parts of type, RED, REF, scale (sensu Metazoa), associated, REGR, PIX, ratio, Sulfurylase kinase 1, DYRK5, Applications Software, measuring, Sulfurylase kinase 2, betaPix, PAPS synthase 2, PAPS synthase 1, 3'-phosphoadenosine-5'-phosphosulfate synthase, Computer Software, ALY, BOTV, GASP, extra or missing physical or functional parts, trait, radius, feature_extraction, CSA2, LGMD2C, Software Tools, Tool, AI317238, Programs, mereological quality, any method, Program, Computer Applications, Software Tool, Adenosine-5'-phosphosulfate 3'-phosphotransferase, KFSDX, p85Cool1, Computer Applications Software, Computer Applications Softwares, bA325O24.4, median, SSAT, background, Softwares, scales, Software, Regressions (Psychology), Radial Tuberosities, Software Applications, SAT, DMDA1, scale, instrument, INT, KFSD, proportionality, TSEPA, Engineering, Control, rate, RPR, arithmetic mean, Quality, SK1, 2.7.7.4, Controls, SK2, REDK, introduction, betaPix-b, betaPix-c, DC21, Computer Programs, data analysis, Applications, DMDA, Applications Softwares, Regression, Rat2, Computer Software Applications., cool-1, SCARMD2, cardinality, quotient, Radial Tuberosity, Adenylylsulfate 3'-phosphotransferase, mKIAA0142, ATP-sulfurylase, Tuberosity, Computer Software Applications"],"name_synonyms":["rabbits, Microarray Analytical, Materials, European rabbit, Nanoarray, 家兔(domestic rabbit), Microarray, Devices, Nanoarray Analytical Device, Gene, rabbit, \"domestic rabbit\" EXACT common_name [], 兔(rabbit), Cistrons, \"European rabbit\" EXACT common_name [], “穴兔(European rabbit)” EXACT common_name [], Device, Nanoarray Analytical, mucus., \"Japanese white rabbit\" EXACT common_name [], Nanoarray Analytical Devices, mucous, “日本大耳白兔(Japanese white rabbit)” EXACT common_name [], mucous layer, Genetic Materials, Analysis, Microarray Analytical Devices, 穴兔(European rabbit), Microchip, Genetic Material, Japanese white rabbit, Microarray Microchip, “家兔(domestic rabbit)” EXACT common_name [], Genetic, Microchips, Analytical Device, Analytical Devices, Microarray Analytical Device, “兔(rabbit)” EXACT genbank_common_name [], domestic rabbit, 日本大耳白兔(Japanese white rabbit), “兔(rabbits)” EXACT common_name [], Microarray Microchips, Material, \"rabbit\" EXACT genbank_common_name [], 兔(rabbits), Cistron, \"Lepus cuniculus\" RELATED misnomer [], extracellular proteinaceous gel, Lepus cuniculus, \"rabbits\" EXACT common_name []"],"pubmed_abstract_synonyms":["projections, Water, Phenylethylbarbiturate, rabbits, Materials, artificial sequence, 家兔(domestic rabbit), Host Pathogen Relations, FALL39, supply, nutrient medium, 上皮的, CCC1(C(=O)NC(=O)NC1=O)c1ccccc1, BOUND WATER, rabbit, fluid, oxidane, Pacinia cholerae-asiaticae, Long Term, InChIKey=XLYOFNOQVPJJNP-UHFFFAOYAF, 10, 11, HOH, 12, Pathogen-Host Interaction, 13, School-Age, 14, 15, 16, 17, Phenylethylbarbituric Acid, Pathogen Host Interactions, Method, \"Japanese white rabbit\" EXACT common_name [], 18)21-7/h2-4, Sea, CAP-18, 3, 6-trione, 4, establishment and maintenance of substrate location, 18)(H2, Effect, Host-Pathogen Relation, C13orf8, multicellular organismal biosynthetic process, 流体, infectious, viral infection, increased, single-organism biosynthetic process, Eubacteria, “家兔(domestic rabbit)” EXACT common_name [], Gene Expressions, reference sample, D1S181E, cAMP, 7-diol 2-oxide, anabolism, Abp, InChIKey=IVOMOUWHDPKRLL-BJEHYBLCDS, HEL-141, ZNF828, AW743261, virus process, procedures, 5-ethyl-5-phenyl-2, Cholera Toxin B Subunit, “兔(rabbit)” EXACT genbank_common_name [], Epigenomic, Waters, Host Pathogen Interactions, 6-7, Vibrio cholera, Vibrio cholerae-asiaticae, Methodological Studies, Vibrio choleae, Prokaryotae, papilla, 6(1H, CT, dihydridooxygen, Cholera Enterotoxin, Procaryotae, 3H, Lepus cuniculus, Nc1ncnc2n(cnc12)[C@@H]1O[C@@H]2COP(O)(=O)O[C@H]2[C@H]1O, dihydrogen oxide, Long-Term Effects, Liquidivibrio cholerae, close to, establishment and maintenance of substance location, Sea Waters, European rabbit, anatomical protrusion, Epididymis luminal protein 141, Choleragen, (2R, infectious diseases and manifestations, CRP4, CRP2, CRP1, lamina, aqua, cAMP 细胞, Longterm Effect, root caused disease or disorder, flanges, late, CAP18, \"domestic rabbit\" EXACT common_name [], Procedure, 2H2, 5'-phosphate, CAMP, single organism localization, H2O, Interaction, Cyclic AMP, epithelial, School Age, shelf, bact-, Pathogenicity, precocious, red rice, CSRP, Genetic Materials, prokaryotes, 体液, 6-, disease by infectious agent, 穴兔(European rabbit), regulator, Genetic Material, Epitheliocyte, Hydrogen Oxide, Populations, Choleras, 16H, Ab1-341, growth pattern, Seawaters, medium, Epigenetic, non-developmental growth, Host-Pathogen, shelves, CHAMP, Relation, 5-Ethyl-5-phenyl-pyrimidine-2, hydrogen hydroxide, 5H)-trione, 7-, Methodological, Methodological Study, projection, 1H2, ridge, 6R, 1H3, early, acqua, Host-Pathogen Interaction, C10H12N5O6P, Phenotypes, 5-ethyl-5-phenylpyrimidine-2, SYNTHETIC CONSTRUCT sequences, fluid - animal, Patient, Material, spine, rice, 兔(rabbits), Adenosine 3', microarray, artificial, Spirillum cholerae-asiaticae, \"Lepus cuniculus\" RELATED misnomer [], Cistron, School-Age Population, root infectious disease, Wasser, Feedbacks, \"rabbits\" EXACT common_name [], Epigenetics, Cholera, adenosine 3', 7R, time, Prokaryota, accessory, establishment and maintenance of cellular component location, Aa1249, Ba2-693, pili, CRAMP, advanced, Cysteine-rich protein 1, Cholera Toxin Protomer B, infectious disorder, Procedures, Effects, lamellae, Enterotoxin CT, Sea Water, (H2, animal fluid, Gene, Kommabacillus, eubacteria, biosynthesis, Cholera Toxin A Subunit, 兔(rabbit), establishment of cell quiescence, PHENYLETHYLMALONYLUREA, ID, process of organ, supernumerary, 11H2, agua, protrusion, (H, lamella, period, Bacillus cholerae, G1/G0 transition, Host-Pathogen Relations, Client., Relations, Cyclic adenylic acid, CYRP, ESP1, establishment and maintenance of position, Studies, body fluid, Abpa27, Phenylethylbarbitursaeure, toxins, Cholera Toxin Protomer A, root disease or disorder, Vibrio comma, Japanese white rabbit, School-Age Populations, infection, study, 4aR, Vibrio cholerae, [H]O[H], pattern, Genetic, Bacteria