introduction

IBM JUMPSSTART is a tool that analyzes Massively Parallel Signature Sequencing (MPSS) data and provides several helpful views of MPSS data and models.

execution

JUMPSSTART is executed from the command line. Upon successful execution it will display a GUI control panel. There are two versions available here as gzip compressed tar files: an OS X executable and a Windows 32-bit executable. The Windows zip file also contains opengl32.dll. This is the standard OpenGL library and JUMPSSTART requires it to run. If you do not already have OpenGL installed on your computer please copy the opengl32.dll to you WINDOWS\System32 folder prior to running JUMPSSTART. We also have a small demo dataset here for download.

loading and selecting data

You can load an MPSS data file by pressing the load button. Upon doing so a GUI data selection panel will appear.

This panel shows the available datasets. You can select any number of the data columns by simply checking the box to the left of the column name.

merging data columns

Often MPSS datasets contain multiple runs of the same stepper batch stored as columns. You can merge these steppers runs by selecting them in the selection panel and pressing the merge selected after providing a name for the resulting merged data column by typing it into the into field right of the button. If you do not provide a name the result of the merge will fall into the void

modeling replicates

If you wish to model replicate data columns you do so first selecting the two replicate columns in two pull-down menus within the modeling commands area, providing a name for the resulting model in the as field, and then pressing the fit button. If you do not provide a result name then JUMPSSTART will display the default model and data views and then allow the model to fall into the void.

saving results

JUMPSSTART allows you to save two types of results, column-wise and pairwise, by pressing the corresponding button in the file commands area. In both cases JUMPSSTART analyzes the data currently selected in the selection panel using the model currently selected in the current model pull-down menu. JUMPSSTART will use the terminal to query a file name and then writes the results as a tab delimited text file.

column-wise results

Saving column-wise results writes a matrix containing a shared signature column followed by four result columns for each selected data column.

    SIGNATURE   name1  atoms    zeros    delta    name2  ...
    signature1  tpm11  atoms11  zeros11  delta11  tpm21  ...
    signature2  tpm12  atoms12  zeros12  delta12  tpm22  ...
    ...         ...    ...      ...      ...      ...    ...
    signatureN  tpm1N  atoms1N  zeros1N  delta1N  tpm2N  ...

pairwise results

Saving column-wise results writes a tab delimited matrix containing a shared signature column followed by pvalue for all pairs of the selected data columns.

    SIGNATURE   name1_vs_name2  name1_vs_name3  ...
    signature1  pvalue1         pvalue1         ...
    signature2  pvalue2         pvalue2         ...
    ...         ...             ...             ...
    signatureN  pvalue3         pvalue2         ...

MPSS data

MPSS data is a tab delimited text file in the following format

    SIGNATURE   name1    name2    ...  nameN
    signature1  count11  count12  ...  count1N
    signature2  count21  count22  ...  count2N
    ...         ...      ...      ...  ...
    signatureN  countN1  countN2  ...  countNN

where name* are any whitespace free strings, signature* are MPSS signatures represented by strings of length 17 containing only the letters from the set [ATCG] and beginning with GATC, and count** are integer beads counts.

MPSS models

G. Stolovitzky, A. Kundaje, G.A. Held, K. Duggar, C. Haudenschild, D. Zhou, T. Vasicek, K. Smith, A. Aderem and J. Roach, Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression, Proc. Natl. Acad. Sci. USA, 102 (5), 1402-1407 (2005). (Pubmed) (PNAS site) (full text) (Supporting Information)

the void

The void in JUMPSSTART is simply an empty space that consumes anything that falls into it.