This track shows intensities of a microarray spotted with short peptides
derived from the entire proteome of SARS-CoV-2. Sera from 10 COVID-19
patients (early stage) and 12 healthy controls were screened on the
peptide microarray for both IgG and IgM responses.
Note that the infections
here were in the early stage, unlike the other microarray track shown on this genome browser.
Display Conventions and Configuration
Genomic locations of peptides that were spotted on the array are highlighted. Because these peptides
overlap, the tracks default to dense mode and the sequence is shown as labels drawn onto the
rectangles, but only visible on high zoom levels. Put any track into pack mode to fully see all
The color is assigned based on the Z-Score, without any other normalization. Blue with decreasing
intensity is assigned to the values -5 to 0, white is 0, and red colors with increasing intensity
are used for the values 0-3.5, exactly as in the original publication figures.
There are also two wiggle/signal style tracks to summary the information, they
show the sum of Z-scores across all peptides, as one score per nucleotide.
Supplemental files were converted from Excel, rearranged and run through the command line script
bigHeat to create a heatmap-like display, with multiplication factors of 2 for negative values,
0.285 for positive values. For better visibility, colormap seismic from matplotlib was used from 0.1
to 0.9 and the range of values after multiplication were restricted to the limits -1 to 1 to address
outliers. Like all tracks, the exact commands are documented in our
makeDoc text files.
The raw data can be explored interactively with the Table Browser or combined
with other datasets in the Data Integrator tool. For automated analysis,
the genome annotation is stored in a bigBed file that can be downloaded from
the download server.
Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed.
Instructions for downloading this command can be found on our
utilities page. The tool can also be used to obtain features within a given
range without downloading the file, for example:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/pbm/IgG_Z-score-_COVID-19_patients/P52.bb -chrom=NC_045512v2 -start=0 -end=29902 stdout
Please refer to our mailing list archives for questions, or our
Data Access FAQ for more
Hongye Wang, Xian Wu, Xiaomei Zhang, Xin Hou, Te Liang, Dan Wang, Fei Teng, Jiayu Dai, Hu Duan,
Shubin Guo, Yongzhe Li, and Xiaobo Yu
Proteome Microarray for Mapping COVID-19 Antibody Interactions at Amino Acid Resolution.
ACS Central Science. 2020