Hi Madhu, please give us more details. What kind of transfection is the "second" one?

If you silence Timp-1, how are your cells? What is your objective?

There are so many factors that can be playing a role.  Have you confirmed that your plasmid contains your gene of interest?  Are you running a transfection efficiency control to ensure the plasmid is even getting in (something like an empty vector that contains a locus for GFP)?  What cells are you using?  They may not be a good candidate for Lipofectamine transfection.  What about serum?  What media are you using?  Time is also a factor: have you done an experiment where you look at alterations in gene expression over time to determine if you are missing the peak upregulation?  More information can help us help you troubleshoot.