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 - GenePix 4200A"],"sample_synonyms":["labeling."],"description_synonyms":["Cas1, 猫(cats), Ribonucleic, InChIKey=ISWSIDIOOBJBQZ-UHFFFAOYAI, Carnitine acetylase, Microarray Analytical, Nanoarray, YPD, Nanoarray Analytical Device, number, A4, Gene, Cs-1, baker's yeast, BOUND WATER, CTRCT40, oxidane, “家猫(domestic cat)” EXACT genbank_common_name [], presence, TYPE, “家猫(Felis domesticus)” RELATED synonym [], Saccharomyces italicus, InChIKey=XLYOFNOQVPJJNP-UHFFFAOYAF, UCRBP, agua, HOH, DAGA4, CrAT, YIN-YANG-1, \"Felis silvestris catus\" RELATED synonym [], C6H6O, Nanoarray Analytical, manganese catalase activity, domestic cat, Gm48, HOT, Nanoarray Analytical Devices, Sodium Phenolate, yeast, Gene Products, Phenol, biological_replicate., Analysis, caperase activity, MAM, Microarray Analytical Devices, SCG3, 2210418N07, Non Polyadenylated, bacterial catalase-peroxidase activity, Microchip, RNA Gene Products, lager beer yeast, Oc1ccccc1, Carbolic Acid, Microarray Microchip, DELTA, [H]O[H], ADHFe1, acide carbolique, \"Felis domesticus\" RELATED synonym [], Gene Expressions, InChI=1/C6H6O/c7-6-4-2-1-3-5-6/h1-5, 1.1.99.24, Benzenol, hot, ADH8, yeast extract peptone dextrose, INO80S, Microchips, Saccharomyes cerevisiae, Karbolsaeure, Analytical Device, \"cat\" EXACT common_name [], 家猫(domestic cat), Xcat, eau, Y, Saccharomyces uvarum var. melibiosus, Expressions, ecotype, Analytical Devices, Microarray Analytical Device, Nhs1, Cy5, \"cats\" EXACT common_name [], DELTA1, Non-Polyadenylated RNA, Phenylic acid, haem catalase activity, Candida robusta, LMPY, Catl, Saccharomyces capensis, Carbol, dihydridooxygen, cats, Expression, Delta, dihydrogen oxide, brewer's yeast, CXN, “猫(cats)” EXACT common_name [], Phenic acid, catalase-peroxidase activity, “猫(Felis silvestris catus)” RELATED synonym [], AI315345, RNA, equilase activity, total RNA extract, heme catalase activity, ribose nucleic acid, Microarray, Devices, aqua, ribonucleic acids, SCML1, InChI=1/H2O/h1H2, Hydroxybenzene, RNS, 2.3.1.7, buffer, Carnitine acetyltransferase, Cell, Saccaromyces cerevisiae, AI195249, LGMD2C, A330009E03Rik, strain, Fe-containing alcohol dehydrogenase, acide phenique, Sccharomyces cerevisiae, H2O, count in organism, Device, catalase reaction, DL1, count, NF-E1, yeast nucleic acid, Ribonukleinsaeure, “猫(cat)” EXACT common_name [], Felis domesticus, pentosenucleic acids, cultivar, Ribonucleic acids, Sodium, Gm389, CAT, GAT, Hydrogen Oxide, Data Base, CS1, optidase activity, ACGNAT, Saccharomyces oviformis, ribonucleic acid, Acid, Phenolate, Yeast, Cas-1, \"domestic cat\" EXACT genbank_common_name [], DMDA1, Non Polyadenylated RNA, carbolic acid, hydrogen-peroxide:hydrogen-peroxide oxidoreductase activity, hydrogen hydroxide, Non-Polyadenylated, PhOH, Ribonucleic Acid, cat, NHS, Felis silvestris catus, Alcohol dehydrogenase iron-containing protein 1, acqua, 猫(cat), Sodium Salt, biological replicate, DMDA, Carbolsaeure, Microarray Microchips, Cat01, Phenolate Sodium, SCARMD2, high temperature, 7H, microarray, Wasser, quantitative, [OH2], presence or absence in organism"],"data_synonyms":["scale tissue, C6orf190, Pak3bp, peltate hair, number, A4, IMAGE, EXTR1, Tuberosities, Computer, PAPSS 2, PAPSS 1, TYPE, 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, 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, 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), IMAGE., Radial Tuberosities, Software Applications, SAT, DMDA1, scale, 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, cool-1, SCARMD2, cardinality, quotient, Radial Tuberosity, Adenylylsulfate 3'-phosphotransferase, mKIAA0142, ATP-sulfurylase, Tuberosity, Computer Software Applications"],"name_synonyms":["DAGA4, A4, Cell., DMDA, MAM, DMDA1, SCG3, TYPE, SCARMD2, LGMD2C"],"view_count":["128"],"additional_accession":["GSE24004"]},"is_claimable":true,"name":"Gis2 mutant versus wild-type cells","description":"To measure the relative changes of gene expression upon Gis2p depletion, 50 ml of delta Gis2 cells or the respective wild-type strain BY4741 were grown in YPD at 30 degrees celsius to an OD600 of 0.5- 0.6. Cells were harvested by centrifugation and washed twice with 5ml of bidistilled water (ddH2O). RNA was isolated by hot phenol extraction for microarray analysis. 20 ug of total RNA derived from wild-type and knock-out cells were reverse transcribed in the presence of 5-(3-aminoallyl)-dUTP and natural dNTPs with a mixture of N9 and dT20V primers, and cDNAs were covalently linked to Cy3 and Cy5 NHS-monoesters (GE HealthSciences Cat# RPN5661), respectively, and competitively hybridized onto yeast oligo arrays at 42 degrees celsius for 14 hours in formamide-based hybridization buffer. Microarrays were scanned with an Axonscanner 4200 (Molecular Devices) and analyzed with GenePix Pro 5.1 (Molecular devices) before uploading into Stanford Microarray Database. Biological Replicate","dates":{"publication":"2010-12-22","updated":"2014-05-01"},"accession":"E-GEOD-24004","cross_references":{"TAXONOMY":["4932"]}}