Additional file 2: Figure S2. of Microarray-based identification of genes associated with cancer progression and prognosis in hepatocellular carcinoma

Protein/gene-protein/gene interaction network of the 27 genes that were stably and consistently dysregulated in 386 cases of hepatocellular carcinoma compared with 327 cases of normal liver tissue according to the four independent microarrays retrieved from the Oncomine database. (PDF 306 kb

Additional file 1: Table S1. of Microarray-based identification of genes associated with cancer progression and prognosis in hepatocellular carcinoma

Biological process and cellular component annotation of the 80 genes associated with HCC development and progression by DAVID online tool. (PDF 167 kb

Mapping read information to sense and antisense genes at the five successive stages of symptom development.

<p>Mapping read information to sense and antisense genes at the five successive stages of symptom development.</p

Dynamics of transcription factor accumulation profiles.

<p>(a) Dendrogram of transcription factors. Clustering of 527 transcription factors expressed at significantly different levels at the CK phase, during the transition from the CK to the DP phase, and the DP phase clustered into three lineages (G1, G2, and G3) using the self-organization tree algorithm (SOTA). (b) Distribution of transcription factor family proteins among G1, G2 and G3. (c) Distribution of transcription factor families that are expressed at different levels among the CK, CP, IP, PP and DP phases; of which, CP, IP, PP are the transition stage from CK to DP.</p

GO annotation of DGEs in leaf development in response to <i>B</i>. <i>zeicola</i> infection.

<p>The Y-axis represents the percentage of targeted genes mapped by the GO term and represents the abundance of the GO term. The X-axis expresses the definition of GO terms.</p

Defining the stages of maize leaf development in response to <i>B</i>. <i>zeicola</i> and observation of the successive stages of infection by <i>B</i>. <i>zeicola</i> under a scanning electron microscope.

<p>After inoculation, conidia of <i>B</i>. <i>zeicola</i> germinated, and one or two germ tubes were extruded from the poles of the conidia within 2~6 h. Appressorium-like structures were observed in contact with the maize leaf periderm after 12 h, at which time most of the structures had not yet penetrated into leaf surface cells; thus, this time point represents the contact phase (CP) of the disease development. At 24 h, numerous hyphae had differentiated from the germ tubes and were highly branched, and appressoria had directly penetrated the epidermal cell walls, in most cases by developing a constricted penetration peg. However, the fungus also entered through stomata and the intercellular space. This process was considered the penetration period (PP). At 36 h after inoculation, as observed during penetration, the fungus procured host nutrients and grew numerous mycelia on or underneath infected tissues. At the same time, some peridermal cells were collapsed, and a few infected tissues exhibited water-soaked spots, indicating that the infection had developed to the incubation period (IP). After 48h, more water-soaked spots appeared and more obvious symptoms were observed, and this was identified as the end of incubation period—disease periods (DP). The process of disease period was as follows: extensive mycelia colonized on leaf surface and the fungus appeared to have dissolved the cuticle as well as two suberized layers (arrowheads) that indicated mechanical pressure has occurred during host cell wall (HCW) penetration. At last, obvious necrosis appeared on the infected leaf at 96h after inoculation, Meanwhile, a great of new conidia reproduced on necrotic spots, it might be symptoms period (SP)</p

Numbers of differently expressed genes among the developmental stages of leaves infected with <i>B</i>. <i>zeicola</i> compared with mock-treatment (Fig. 5a); functional categories and genes grouped according to developmental dynamics using the K-Means clustering algorithm (Fig. 5b).

<p>Numbers of differently expressed genes among the developmental stages of leaves infected with <i>B</i>. <i>zeicola</i> compared with mock-treatment (Fig. 5a); functional categories and genes grouped according to developmental dynamics using the K-Means clustering algorithm (Fig. 5b).</p

Determination of SOD, POD, PPO, CAT, and PAL enzyme activity in maize leaves responsive to <i>B</i>. <i>zeicola</i>.

<p>Determination of SOD, POD, PPO, CAT, and PAL enzyme activity in maize leaves responsive to <i>B</i>. <i>zeicola</i>.</p

Digital Gene Expression (DGE) analysis of the Mo17 leaf transcriptome responding to <i>B</i>. <i>zeicola</i> infection.

<p>(a) Distribution of reads among the annotated genomic features of maize. (b) Shared and total reads among the phases of symptom development. (c) Distribution of reads among gene models and relative to transcript abundance. (d) Shared and unique reads among the phases of symptom development.</p

Cluster and parallel plot of transcription factors expressed at significantly different levels in the five successive stages of infection.

<p>(a) Clusters of transcription factors expressed at significantly different levels in the five successive stages of infection. (b) Parallel plot of transcription factors expressed at significantly different levels in the five successive stages of infection.</p