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 = same as UNF_VALUE but with flagged values removed

UNF_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"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Streptococcus pneumoniae normally resides in the human nasopharynx in a nondisease state. In response to unknown triggers this organism can descend to the lower respiratory tract and/or invade the bloodstream. Regulation and activation of virulence genes play essential roles in this process of disease development. Characterization of S. pneumoniae regulatory networks has been a recent area of interest, but despite inroads little is known about regulation of virulence genes in this pathogen. A putative transcriptional regulator in S. pneumoniae, mgrA, which exhibits homology to the virulence gene activator mga of group A streptococcus, was previously identified as a regulator that is required for development of pneumonia in a murine model. In this study we confirmed that mgrA plays a role in both nasopharyngeal carriage and pneumonia. Transcriptional profiling by microarray technology was used to show that mgrA acts as a repressor of the previously characterized rlrA pathogenicity islet. This is manifested phenotypically by a decrease in adherence to epithelial cells in tissue culture since the rlrA pathogenicity islet contains genes mediating adherence."],"study_type":["unknown experiment type"],"species":["Streptococcus pneumoniae"],"pubmed_title":["MgrA, an orthologue of Mga, Acts as a transcriptional repressor of the genes within the rlrA pathogenicity islet in Streptococcus pneumoniae."],"pubmed_authors":["Elizabeth Joyce","Hemsley C, Joyce E, Hava DL, Kawale A, Camilli A"],"view_count":["59"],"additional_accession":[]},"is_claimable":false,"name":"mgrA acts as a repressor of the rlrA pathogenicity islet","description":"Streptococcus pneumoniae normally resides in the human nasopharynx in a non-disease state. In response to yet unknown triggers it can descend to the lower respiratory tract and/or invade the bloodstream. Regulation and activation of virulence genes play essential roles in this process of disease development. A putative transcriptional regulator in S. pneumoniae, MgrA, with homology to a virulence gene activator, mga, of Group A streptococcus (GAS) was previously identified as being required for development of pneumonia in a murine model. In this work we confirm that mgrA is required for both nasopharyngeal carriage and pneumonia. Transcriptional profiling by microarray technology through the growth course of a strain that bears a deletion of mgrA (AC1500) with that of a strain that over expresses Mgra (AC1481) is used to show that MgrA . This is manifested phenotypically by a decrease in adherence to epithelial cells in tissue culture since rlrA pathogenicity islet contains genes mediating adherence. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed","dates":{},"accession":"E-GEOD-3107","cross_references":{"GEO":["GSE3107"],"pubmed":["14594838"]}}