Analyzing workflow of prediction of potential risk regions.

<p>It comprises expression data analysis of different human cancers including breast, colorectal, endometrial, gastric, liver, lung, ovarian, pancreatic, prostate, testicular, bladder, intestine neuroendocrine, cervical and renal cancers as well as glioblastoma. This primary analysis followed by extraction of altered genes, count the chromosomal regions of altered genes and prediction of risk regions based on region frequency.</p

Network of common altered variants in different cancers including mir-200c, mir-141, and GAPDH at 12p13.3.

<p>Network was constructed using pathway studio 9 software. Shortest path algorithm was applied to construct network. Network was assembled based on bioinformatics and literature, combined with biological interpretation of the microarray data and enriched Gene Ontology functional groups. Purple: over-regulated entities in most of cancers Blue: down-regulated entities in most of cancers. O-vertex represent TFs, represents positive-regulated, and represents negative-regulated.</p

Common altered mRNAs (including class I and II) extracted from 11 human cancers using digital differential display (DDD), together with the available online microarray.

<p>Abbreviations: PCSR, Potential Cancer-Susceptibility Region; M, Microarray; D, Digital Differential Display.</p><p>Symbols: ↑, over-expression; ↓, down-expression; ✓, risk region.</p

Gene ontology classes.

<p>Percentage of differentially expressed contigs annotated for Biological Process, Cellular Component and Molecular Function GO categories. *indicates a significant estimation at 0.05.</p

Statistics of <i>de</i><i>novo</i> transcriptome assembly and annotation.

<p><i>De novo</i> assembley was performed using Trinity package following the standard manual. Annotation was achieved using BLASTX program. Mapping statistics of reads to the transcriptome assemblies and peach genome are also provided, which was obtained using Bowtie v2 package.</p><p>Abbreviations: HSA, stressed anther of H genotype; HCA, control anther of H genotype; HSO, stressed ovary of H genotype; HCO, control ovary of H genotype.</p

Distribution of differentially expressed genes of almond under frost stress.

<p>Venn diagram indicating the number of differentially expressed contigs under frost in anther and ovary tissues of almond.</p

Basic statistics of RNA-seq reads in almond obtained from Illumina HiSeq-2000.

<p>The qualtiy of reads in Fastq files were analyzed using FastQC software. The reads were subjected to vigorous quality filtering using FastX toolkit before further analysis.</p><p>Abbreviations: HSA, stressed anther of H genotype; HCA, control anther of H genotype; HSO, stressed ovary of H genotype; HCO, control ovary of H genotype.</p

Homology of almond transcriptome to other plant species.

<p>The percent of BLASTX top-hit with different plant species. Maximum homology of almond transcripts were observed with peach (<i>Prunus persica</i>).</p

Distribution of log₂ fold change for differentially expressed genes.

<p>A and B are distribution of log₂ FC in anther and ovary, respectively.</p

The list of primers used for gene expression analysis by quantitative Real Time PCR.

<p>Corresponding annealing temperatures and amplicon sizes are shown for each gene.</p><p>Abbreviations: F, Forward primer; R, Reverse primer.</p