databaseArrayExpressfile_versions

scores0093additionalomics_typeTranscriptomicssubmitterStanford Microarray DatabaseKaren GuilleminspeciesHomo Sapienssubmitter_keywordsunknown experiment typefull_dataset_linkhttps://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3556submitter_emailarray@genome.stanford.edurepositoryGEOArrayExpressdata_protocolAssay Data Transformation - ID_REF = ID_REF<br>CH1I_MEAN = Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>CH2I_MEAN = Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>CH1B_MEDIAN = The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background<br>CH2B_MEDIAN = The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>CH1D_MEAN = The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel<br>CH2D_MEAN = .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH1I_MEDIAN = Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>CH2I_MEDIAN = Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>CH1B_MEAN = The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background<br>CH2B_MEAN = The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background<br>CH1D_MEDIAN = The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale<br>CH2D_MEDIAN = The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale<br>CH1_PER_SAT = The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale<br>CH2_PER_SAT = The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale<br>CH1I_SD = The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel<br>CH2I_SD = The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH1B_SD = The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background<br>CH2B_SD = The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>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<br>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<br>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<br>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<br>SUM_MEAN = The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale<br>SUM_MEDIAN = The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale<br>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<br>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<br>RAT2_MEDIAN = The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale<br>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<br>PIX_RAT2_MEDIAN = The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale<br>RAT2_SD = The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale<br>TOT_SPIX = The total number of feature pixels.; Type: integer; Scale: linear_scale<br>TOT_BPIX = The total number of background pixels.; Type: integer; Scale: linear_scale<br>REGR = The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale<br>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<br>DIAMETER = The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale<br>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<br>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<br>TOP = Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>BOT = Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>LEFT = Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>RIGHT = Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale<br>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<br>CH2IN_MEAN = Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>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<br>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<br>RAT2N_MEAN = Type: float; Scale: linear_scale<br>CH2IN_MEDIAN = Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale<br>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<br>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<br>RAT2N_MEDIAN = Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale<br>VALUE = 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<br>LOG_RAT2N_MEDIAN = 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
Feature Extraction - VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)description_synonymsD22S750, PLANH2, PLANH1, Solute carrier family 19 member 2, CTAP3, MA387, NAP-2, Effects, Longterm., 上皮的, A4, Beta-TG, CD339, biosynthesis, Yperite, SED1, MFGM, TYPE, Long Term, II, DAGA4, period, MIF, TGB, technical_replicate, 1, MAM, 1'-thiobis(2-chloroethane), SCG3, Effect, MIX, multicellular organismal biosynthetic process, single-organism biosynthetic process, THMD1, L1Ag, Longterm, formation, anabolism, SCYB7, Long-Term, 60B8Ag, Cy5, HsT1201, Lost, bis(2-chloroethyl) sulphide, synthesis, JAGL1, THBGB, h, MRP8, 1-chloro-2-[(2-chloroethyl)sulfanyl]ethane, sample, ThTr-1, HJ1, mustard gas, TC, MFGME8, TC-2, TC-1, LDGF, Long-Term Effect, InChIKey=QKSKPIVNLNLAAV-UHFFFAOYAK, PAI, Long-Term Effects, 60B8AG, sulfur mustard, CXCL7, D22S676, Endothelial plasminogen activator inhibitor, total RNA extract, 1-chloro-2-[(2-chloroethyl)thio]ethane, synthesize, InChI=1/C4H8Cl2S/c5-1-3-7-4-2-6/h1-4H2, MDGF, MFG-E8, Longterm Effect, Serpin E1, CAGE (cap analysis gene expression), PAI-2, PAI-1, CTAPIII, ClCCSCCCl, PAI1, Cell, PBP, LGMD2C, PAI2, TC2, TC1, CAGE, B-TG1, CAGA, bis(2-chloroethyl)sulfane, epithelial, CP-10, Long Term Effects, MIXL, TRMA, Thiamine carrier 1, TCI, Epitheliocyte, epitheliocyte, THTR1, MILD1, technical replicate, THBGB1, TGB1, CGLA, Caga, p8, DMDA1, TC II, Senfgas, AI323541, CFAG, MFGMP-E8, AWS, sample population, CTAP-III, Longterm Effects, B8Ag, O-acetyl GD3 ganglioside synthase, OAcGD3S, DMDA, Milk fat globule-EGF factor 8, P8, TCII, NIF, DEL, Ags, AGS, SCARMD2, ThTr1, C4H8Cl2S, THT1, CFAg, HC, time, AHD, LA-PF4data_synonymsscale tissue, C6orf190, Pak3bp, peltate hair, number, A4, IMAGE, EXTR1, Tuberosities, Computer, PAPSS 2, PAPSS 1, presence, 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, ratio., 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, count in organism, Software Tool, Adenosine-5'-phosphosulfate 3'-phosphotransferase, count, 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, 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, quantitative, Radial Tuberosity, Adenylylsulfate 3'-phosphotransferase, mKIAA0142, ATP-sulfurylase, Tuberosity, presence or absence in organism, Computer Software Applicationsname_synonymsTransitional Epithelial Cell, Transitional, Adenomatous Epithelial Cell, Squamous Cells, Adenomatous Epithelial Cells, Squamous Cell, Epithelial Cell, Glandular Epithelial Cells, Adenomatous, Adenomatous Epithelial, Glandular Epithelial, Squamous, Glandular, Transitional Epithelial, infectivity, Cell, Helicobacter Infections., Helicobacter Pylori Infection, Squamous Epithelial Cells, Cuboidal Glandular Epithelial Cells, Epithelial Cells, Transitional Epithelial Cells, Cells, Pathogenicity, virulence, Columnar Glandular Epithelial Cells, Squamous Epithelial Cell, Squamous Epithelial, Glandular Epithelial Cell, Epithelialview_count9isClaimabletruesearch_count3search_domainspatentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0genome_assembly~0sc-experiments~0taxonomy~1ebiweb_people~0enzymeportal_enzymes~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0imgt-hla~0patentnucleotides~0ensemblroot~0europepmc~1non-coding~0identifiers_registry~0pdbechem~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0human_diseases~0embl~0treefam~0project~1uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0sbo~0lrg~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0metagenomics~0pfam~0varsite~0citation_count0citation_count_scaled0.0reanalysis_count_scaled0.0view_count_scaled0.0027837921435199505download_count_scaled1.1257458065968704E-4download_count5additional_accessionGSE3556is_claimabletruenameCag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection.descriptionTC1: gastric epithelial (AGS) cells infected with wild type H. pylori (G27) and isogenic mutants in cagA and vacA for 0, 0.5, 3, 6, and 12 hours. Total RNA was used to make single stranded Cy5 labelled probe and compared to Cy3 labelled probe from uninfected AGS cells. Hybridizations of G27 (trial 4) and cagA- (trial 3) timecourses were done in parallel. A technical replicate of the G27 time course (trial 5) and hybridization of vacA- (trial 3) time course were done in parallel. The cagA 6 and 12 hour time points were technically replicated (trial 4) (the cagA 6 hour sample of trial 3 was lost). TC2: Biological replication and expansion of TC1, using more isogenic mutants and timepoints. AGS cells were mock infected, infected with G27, and isogenic mutants in cagN, cagA, cagE, and a deletion of the cag PAI for 0. 1, 3, 6, 12, and 24 hours. Probe synthesis and hybridization was done as in TC1. Note: there may have been a sample mix-up with PAI 12, swapping it with G27 or cagN 12. Groups of assays that are related as part of a time series. Computeddatespublication2005-11-03submission2005-11-03updated2011-10-18accessionE-GEOD-3556cross_referencesTAXONOMY9606