|
•Published
Data:
Abstract
Full Manuscript
Figures
•Supplemental
Data:
Supplemental Tables
Database
CAGED Report
Nearest Neighbors
•Raw Data
GEO Database
(enter accession # GSE989 and # GSE990)
•Links:
CHIP
CAGED
Affymetrix
|
Supplemental
Web site for
Expression
Profiling and Identification of Novel Genes Involved in Myogenic
Differentiation
Kinga K. Tomczak, Voichita D. Marinescu, Marco F. Ramoni, Despina Sanoudou, Federica Montanaro, Mei Han, Louis M. Kunkel, Isaac S. Kohane, and Alan H. Beggs
Division of Genetics: Children's Hospital, Children's Hospital
Informatics Program, Harvard Medical School, Boston, MA
Skeletal muscle differentiation is a complex, highly coordinated
process that relies on precise temporal gene expression patterns.
To better understand this cascade of transcriptional events,
we used expression profiling to analyze gene expression in a
12-day time course of differentiating C2C12 myoblasts. Cluster
analysis specific for time- ordered microarray experiments classified
2,895 genes and ESTs with variable expression levels between
proliferating and differentiating cells into 22 clusters with
distinct expression patterns during myogenesis. Expression patterns
for several known and novel genes, were independently confirmed
by quantitative real-time PCR and/or western blotting and immunofluorescence.
MyoD and MEF family members exhibited unique expression kinetics
that were highly coordinated with cell cycle withdrawal regulators.
Among genes with peak expression levels during cell cycle withdrawal
were Vcam1, Itgb3, Itga5, Vcl as well as Ptger4, a gene not
previously associated with the process of myogenesis. One interesting
uncharacterized transcript that is highly induced during myogenesis
encodes several immunoglobulin repeats with sequence similarity
to titin, a large sarcomeric protein. These data sets identify
many additional uncharacterized transcripts that may play important
functions in muscle cell proliferation and differentiation and
provide a baseline for comparison with C2C12 cells expressing
various mutant genes involved in myopathic disorders.
Figure 1: CAGED
1.1 clustering of gene expession patterns during myogenesis
Figure 2: Functional
categorization of genes clustered by CAGED into Groups I-III
Figure 3: Comparison
of Quantitative Real-time PCR (RQ-PCR) and microarray data for
caveolin-3, diabetes-related ankyrin repeats (Darp) and selected
ESTs
Figure 4: Comparison
of GeneChip data with protein levels and localization for selected
genes
Figure 5: Transcriptional
patterns of expression for selected genes involved in myogenesis
Supplemental Data
Supplemental Table 1: List of
Affymetrix probe sets classified into Group I clusters. [Excel,
Html]
Supplemental
Table 2: List of Affymetrix probe sets classified
into Group II clusters [Excel,
Html]
Supplemental
Table 3: List of Affymetrix probe sets classified
into Group III clusters [Excel, Html]
Supplemental
Table 4: List of Affymetrix probe sets classified
into Group IV clusters [Excel,
Html]
Supplemental
Table 5: Nearest Neighbors of Sequence T (168291_f_at)
[Excel,
Html]
- MS Access
2000 database (11MB):
C2C12database.mdb
Contains three tables (MasterTableC2C12, ClusteredProbeSets_ExpressionData,
ClusteredProbeSets_Annotated) and a searchable Form that
displays the combined results for a given probe set in a
one-page view.
- Expression
values:
ClusteredProbeSets_ExpressionData.xls
(Excel)
ClusteredProbeSets_ExpressionData.txt
(Tab-delimited)
- Cluster
annotations:
ClusteredProbeSets_Annotated.xls
(Excel)
ClusteredProbeSets_Annotated.txt
(Tab-delimited)
Details
of the clustering analysis
Results
for 67 selected probe sets (Excel)
Results
for 67 selected probe sets (Html)
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