Dear Lilian,

You might want to try Biointerpreter
(http://genotypic.co.in/bio_interpreter.html). It can take gene symbols and
provide 15 different biological views like Gene ontologies, pathways, Gene
expression data.

It is available for Human, Mouse, Drosophila, M.tuberculosis, Arabidopsis, Rat
and Rice. We suggest human database for querying bovine gene symbols.

Biointerpreter is provided for users as an annual subscription. It is currently
available on a free, limited time, full-functionality trial access for one
month. Please  reply back to this email/ write to biointerpreter@...
to obtain your trial login.

Best

Kavitha





--- In microarray@yahoogroups.com, Lilian <lijoli@...> wrote:
>
> Hello all!
>
> I have ran an microarray experiment analysis comparing monocytes from blood to
macrophages from endometrium from pregnant cows. I used the bovine agilent chip
4x44K, and my experimental design is showed below. I tried to used the
R-Bioconductor to analyze my data but there is no annotation package for the
bovine agilent array, also I tried the LimmaGUI, but I could not use the
LimmaGui because of my technical replications were read as a biological
replications. So, I used the JMP genomics to analyze my data. My raw data was
previous normalized within array using the LOWESS normalization and in the JMP
I performed the quantile normalization to normalize the data between arrays. I
used the proc ANOVA to do the stats and find the differential regulated genes.
>  PROC ANOVA
> Model: Animal, Replicate, Tissue
> Fixed Effects: Tissue, Replicate, Replicate*Tissue
> Random effects: Animal, Animal*Tissue, Animal*Replicate,
Animal*Tissue*Replicate
>  
> I used the FDR correction fixed at 0.01 the genes were considered
differentially expressed (DE)  had p-value<0.05 and at least 2-fold increased ou
decreased expression.
>  
> I have got around DE 1,200 genes and now I am working on the ontology
analysis. I have a problem because the agilent ID is not read in most of the
softwares for gene ontology and in general I get only 300 genes annotated out of
over 600 genes that I analyze using the DAVID. Do you have any comments on that?
Is that normal not get the ontology analysis for more than a half genes?
>  
> I am really new on microarray analysis and I am working by myself, it has been
a big challenge for me to do it, so I really appreciate any comments that you
might have.
>  
> Thanks in advance
>  
> Lilian Oliveira
>  
> Lilian Oliveira DVM Ms
> Ph.D. Candidate
> Animal Molecular and Cell Biology
> University of Florida
> Phone/Fax: (352) 392-5590/392-5595
>
> Replicate   Tissue      Channel
> 1                1              Blood       Cy3
> 1                1              Endo        CY5
> 2                1              Blood       Cy3
> 2                1              Endo        CY5
> 3                1              Blood       Cy3
> 3                1              Endo        CY5
> 4                1              Blood       Cy3
> 4                1              Endo        CY5
> 1                2              Endo        Cy3
> 1                2              Blood       Cy5
> 2                2              Endo        Cy3
> 2                2              Blood       Cy5
> 3                2              Blood       Cy3
> 3                2              Endo        Cy5
> 4                2              Endo        Cy3
> 4                2              Blood      Cy5
>
>
>
>
>
> [Non-text portions of this message have been removed]
>