Because many of the cancer associated expression changes identified to date generally play a role in cancers from different organs, we speculated whether the collection of tumor associated alternative TSSs identified here in the context of CRC could also have relevance to other cancers.
While the deregulation of individual oncogenes and tumour suppressors is an important event in cancer, gene expression changes can also affect large domains of the genome containing multiple genes that exhibit a concordant change in expression in a phenomenon termed long-range epigenetic regulation (LRER) [ 29, 30].
In normal breast tissues and primary breast cancers HDAC1 expression changes were mostly not significant.
Extension of RNA-seq analysis to the entire ETS family revealed a number of cancer-associated expression changes.
Due to its extended lifespan and multiple cancer-associated expression changes, the HMEC system provides a model of partial carcinogenic transformation from normal to pre-malignancy.
In part, TCGA provides detailed information about cancer-dependent gene expression changes, including changes in the expression of transcription-regulating microRNAs.
Thus, it is useful to infer the activity alterations of TFs in cancers from the expression changes of their target genes.
First, our results show that some chromosomes appear to be more active than others (Table 2A), with, for instance, chromosomes 15, 19 and Y being rarely involved in cancer-related gene expression changes compared to chromosomes 4 and 6.
This suggests that the HN profile is not an effect of the tumour, but instead may be a marker of increased breast cancer risk, or a reflection of breast cancer's earliest gene expression changes.
Using genechip technology to study multiple types of cancer simultaneously we can identify whether multiple cancers have similar gene expression changes [ 21].
