confirmation of real gene status - (Sep/14/2013 )
If you have a predicted gene that do not show expression under the conditions tested. Then is there a way to find out if it is a real gene or not?
No expression does not necessarily mean no exist of the gene. If there is evidence of expression of the gene from other tissues or cells as evident by the existence of ESTs, that strongly suggests it is a real gene.
If you do not get the expression in any of the tissues or condition tested, is there a way to find out if it is a real gene or not? ISo there is a gene predicted, but no expression observed. Can it be proved if the gene is a real gene or just a pseudogene?
I think that is an interesting question. According to HGNC, A gene is defined as: "a DNA segment that contributes to phenotype/function. In the absence of demonstrated function a gene may be characterized by sequence, transcription or homology". If expression is the criterion for a gene to be called a gene, then how much should the expression be, a few copies in a cells or thousands? Apart from protein coding genes (which should have a reasonable sized ORF), now we have thousands of non-coding genes (miRNA, lncRNA, etc.) whose expression is more tissue specific and elusive.
Further, what about genes that are shut off, like those only active during fetal development? They are still in your genome as an adult (and are still genes), but you may not be "using" them.
You can look at expression data in Gene Expression Omnibus or ArrayExpress to see if your gene is appreciably expressed in many other experiments.