Table of Contents. 1. What is CREP and when to use it?

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1 Table of Contents 1. What is CREP and when to use it? How to login CREP? How to make use of CREP in general? How to query by identifiers? How to query by sequences? What will be displayed in the detail page of a probe set? What is the Chronologer view of a probe set? What is the Chronologer view of multiple probe sets? How to retrieve data? What is CREP and when to use it? CREP (Collection of Rice Expression Profiles) is a database of gene expression profiles which are conducted using the commercial Affymetrix Rice GeneChip microarray. CREP consists of two databases: (1) emule. A dynamic gene expression atlas covering the entire life cycle of multiple rice cultivars. (2) estress. Gene expression profiling of rice responses to biotic and abiotic stress. Thirty-nine tissues of three indica rice genotypes, Minghui 63, Zhenshan 97 and their hybrid Shanyou 63 were collected for analyzing the expression profiles. emule is constructed to meet the demands of querying these expression profiles for single or multiple genes. Two HTML-based search interfaces are introduced: 1) a blast-based query interface enabling the users to find genes using sequence search; 2) an interface named Rice Multi-platform Microarray Search serving as a converting tool allowing users to search their genes using identifiers from different annotation sources or microarray platforms, i.e. TIGR rice gene locus, KOME rice cdna identifier, and identifier for Agilent, NSF and BGI rice microarrays. As the microarray has not been sufficiently annotated by Affymetrix, annotation data from TIGR are integrated. Several tools for displaying the expression profiles have also been developed. An 1

2 interface named Gene Chronologer is used for displaying quantitatively expression profiles of single gene and comparing expression levels of the three genotypes, which would be useful for quantifying heterosis in the transcriptional levels. For comparison of multiple genes, a tool named Multi-genes Chronologer is supported. In addition, several tools are also provided for deeper view of the expression profiles. A tool named Gene Context is used to obtain corresponding genes in the 25 kb context of a certain genome position, this tool would be useful for studying local co-expression in genome segments. Gene Correlator calculates all Pearson correlations by selecting each gene against all genes in the microarray and the corresponding gene pairs with correlation coefficients larger than 0.8 or the biggest 100 and the lowest 100 are listed. Information from other resources, i.e. SNP data from OryzaSNP project and expression profiles from SALK, are supported by multifarious links. You can go straight to the CREP by enter its address: (Fig. 1). Fig How to login CREP? Please login as guest unless you have other account and want to submit or edit your own data (Fig. 2). 2

3 Fig How to make use of CREP in general? There are three panels marked in the home page for different purposes (Fig. 3). 1. Panel listing projects, experiments, microarrays, samples, platforms and experiment parameters stored in the database of CREP. 2. Panel for querying CREP with known identifier terms. 3. Panel for querying CREP with known DNA/RNA or protein sequences. Fig. 3 3

4 4. How to query by identifiers? Clicking Query button in the toolbar of CREP home page can bring you into the query page. There are two tabs in the query page: Quick Query for simply but quickly querying but only accepting identifier of probe set name on the Affymetrix platform (Fig. 4). Submission will display the details of the probe set. Fig. 4 Rice Multi-platform Microarrary Search is adapted from the NSF Rice Oligonucleotide Array Project. The Rice Multi-platform Search page is a tool that allows users the ability to search across five different rice oligo microarray platform types (Affymetrix,Agilent, BGI/Yale, NSF-20K, NSF-45K) to determine which probes from each platform map to a common a gene target. (Fig. 5). We also added an additional useful property: user can now provide PFAM ( accession number to fetch an entire gene family at a time. 4

5 Fig. 5 Rice Multi-platform Microarrary Search can accept multiple identifiers at a time. Multiple identifiers need to be separated by space or comma. Once user submitted their identifiers, the page will flow to Query Results, which shows synonymous identifiers from each platform and the PFAM accession number if the gene has (Fig. 6). Click the hyperlink of any probe set in the column Affymetrix will display the details of the probe set provided by Affymetrix, MSU/TIGR and CREP. Click other identifier will go to corresponding website. See Multi-genes chronologer for advance useful information of this page. 5

6 Fig How to query by sequences? Clicking Blast! button in the toolbar of CREP home page can bring you into the blast page (Fig. 7). Just input your sequences and operate like normal blast procedure. The blast results provided links to probe sets matched with your sequences (Fig. 8). 6

7 Fig. 7 Fig What will be displayed in the detail page of a probe set? 7

8 The CREP Browser page displays the details of a probe set with information from Affymetrix, MSU/TIGR (now version 4, will soon update to version 5 and 6) and our own resources: Description. Description from Affymetrix and links to NCBI or KOME (Fig. 9). Fig. 9 Associated TIGR Gene Locus. The probe sequences were mapped to rice genome and associated to rice genes based on annotations of MSU/TIGR version 4.0 (Fig. 10). Fig. 10 Gene Context (flanking 25kb). Display genes located in the flanking 25 kb of the gene associated with the probe set. See Multi-genes Chronologer for advance useful information (Fig. 11). 8

9 Fig. 11 Gene Ontology Classification. Gene ontology information from MSU/TIGR (Fig. 12). Fig. 12 Probe Info. Display the details of probes which constitute the probe set (Fig. 13). 9

10 Fig. 13 Target Sequence. The sequence used to design the probe set (Fig. 14). Fig. 14 Expression Profiles. Links to the essence of CREP (Fig. 15). Chronologer for displaying expression profiles of a gene. Chronologer (Grouped) for displaying and comparing expression profiles of a gene between the three genotypes. Heterosis View displaying heterotic expression patterns of your gene. Gene Correlator for discovering genes co-expressed with your gene. SALK RiceGE links to SALK, the guy collected many public microarray data. Rice MPSS links to Rice MPSS database. RiceArray Coexpression Database links to RiceArray Coexpression Database. 10

11 Fig. 15 Miscellaneous. You can fetch SNP data near the location of the probe set. The SNP data is provided by OryzaSNP project. Links to putative homologies in rice or Arabidopsis are also provided (Fig. 16). Fig What is the Chronologer view of a probe set? Gene Chronologer is recruited for displaying quantitatively expression profiles of single gene and comparing expression levels of the three genotypes, which would be useful for quantifying heterosis in the transcriptional levels (Fig. 17, Fig. 18). Gene Chronologer can be accessed from the detail page of a probe set. Ungrouped. 11

12 Fig. 17 Grouped. Fig. 18 Tips: click the bar can obtain the details of the replications. 12

13 8. What is the Chronologer view of multiple probe sets? Multi-genes Chronologer is provided for comparisons of expression profiles of multiple genes (Fig. 21). Multi-genes Chronologer can be found at two places. Query Results of Rice Multi-platform Microarrary Search (Fig. 19). Fig. 19 Gene Context in the detail page of a probe set (Fig. 20). Fig

14 Fig How to retrieve data? The expression profiling data of queried genes can be downloaded from Multi-genes Chronologer by clicking csv file in the bottom left of the page (Fig. 21). You can also obtain the profiles for single gene from Gene Chronologer (Fig. 17). 14