MECHANISMS OF RESTORATION OF LIVER MASS AFTER
INJURY REVEALED VIA SIMILARITIES AND DIFFERENCES
WITH LIVER EMBRYOGENESIS#
Hasan H. Otu, Kamila Naxerova, Karen Ho, Handan Can, Nicole Nesbitt, Towia, A.
Libermann, Seth J. Karp
#
Running title: Mechanisms of Liver Regeneration
Supplemental Document
Online Materials
Expression.xls: In this data set we show the expression values of all 45,101
genes after the normalization has been performed as discussed in the
manuscript. The results are shown for all 32 samples. Development time course
samples are denoted by 10.5, 11.5 etc. while regeneration time course samples
are denoted 1, 2, etc. corresponding to time points describes in the manuscript.
Replicates are labeled a,b (e.g. 0a and 0b for the normal adult liver samples).
Correlation Matrix.xls: This file shows the Pearson correlation coefficient
between all pairs of samples. The data is arranged in a matrix form. Correlation
coefficients are generated using all genes on thechip.
Development Upregulated.xls: This data set shows the genes that are upregulated in at least one development time point compared to adult liver.
Comparisons are appended one after another where for each comparison signal
values for the samples involved in the comparison are followed by Fold Change
(FC) and Lower Confidence Bound (LCB) of FC values. The column “filtered”
denotes if a given gene is identified as significantly up-regulated (LCB>1.5) in a
particular comparison.
Regeneration Upregulated.xls: This data set shows the genes that are upregulated in at least one regeneration time point compared to adult liver.
Comparisons are appended one after another where for each comparison signal
values for the samples involved in the comparison are followed by Fold Change
(FC) and Lower Confidence Bound (LCB) of FC values. The column “filtered”
denotes if a given gene is identified as significantly up-regulated (LCB>1.5) in a
particular comparison.
Venn.xls: This file has three worksheet: Dev shows 8876 genes that are
uniquely up-regulated in development; Reg shows 1226 genes that are uniquely
up-regulated in regeneration; Dev and Reg shows 885 genes that are upregulated both in development and regeneration. This comparison is shown in
the file Venn.bmp. The organization of data in Venn.xls is similar to the format
used in files Development Upregulated.xls and Regeneration
Upregulated.xls.
Tree Diff.bmp: This file shows hierarchical clustering of all samples using the
10,987 genes shown in the files Venn.xls and Venn.bmp. In other words, this is
clustering of samples using the genes that are up-regulated at least at one time
point during regeneration or development.
EASE Development.xls: This file shows EASE analysis results regarding GO
categories that exist in genes up-regulated at least at one time point during
development. The decription of columns are as follows:
System: GO category (Biological process, Cellular Component, Molecular
Function),
Gene category: The class within each GO category
List hits: Number of genes in the input gene list that belong to the corresponding
“Gene category”.
EASE Score: Level of significance for the overrepresentation of the Gene
category in the input list. Please refer to the manuscript for details. An EASE
score less than 0.05 is considered significant.
Gene identifiers: Entrez Gene identifiers of the unique genes in the input list that
belong to the corresponding “Gene category”.
Affymetrix probesets: Affymetrix probe identifiers used on the chip that belong to
the corresponding “Gene category”. These transcripts are mapped to the Entrez
Gene identifiers shown in the previous cell representing the unique gene list.
The categories that are used in Table 1 of the manuscript are shown with a
yellow background.
EASE Regeneration.xls: This file shows EASE analysis results regarding GO
categories that exist in genes up-regulated at least at one time point during
regeneration. The organization of data is similar to that used in file EASE
Development.xls.
EASE Intersection.xls: This file shows EASE analysis results regarding GO
categories that exist in genes up-regulated at least at one time point during
development and regeneration. The organization of data is similar to that used in
file EASE Development.xls.