Things to be aware of:
1. GIF is a palette-based format. That means that you can have up to 256 colors in the image total.
2. GIF transparency is based on exactly one of those colors, and that transparency will be 100%
To get this, translate your image to 8-bits per pixel indexed, which will give you a color map. Choose one color in the palette to be your transparent color, then change that palette entry it to be 100% transparent. Finally, save as GIF.
The problem you will encounter is that in translating to 8bpp, your image will no doubt become dithered, which makes it hard to pick the right color for transparency. This is why programs like PhotoShop, give you a dialog box to let a human pick that color.