Barley Expression Database
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CONTENTS

Keyword Search
What is the Keyword Search view?
What should I put in the text field as keywords?
How does the system select the displayed data?
Explanation of the columns
Sorting algorithm
Searching technique1: AND operation
Searching technique2: Limitation of species
Searching technique3: NOT operation
Searching tequnique4: Quotation
Searching tequnique5: OR operation
Searching tequnique6: Forward match
Searching tequnique7: Sort by E-value
Searching tequnique8: Sort by Cluster ID

Expression Profile Search
What is the Expression Profile Search view?
Explanation of the columns
Treatments
Searching technique: ADD operation


Keyword Search

What is the Keyword Search view?

Keyword search shows the predicted ORF of the barley clusters, contigs and singlets from our dataset generated from partial sequences of barley complete cDNA library, and functional annotation based on the similarity to known protein entries from public database including keywords submitted by user in their description or their protein IDs.

What should I put in the text field as keywords?

You can put following words or ID as keywords.

This search does not distinguish uppercase from lowercase.

How does the system select the displayed data?

If you put "zinc" into search text field and push the search button, first this system search known protein database (UniProt and RefSeq ) entries including "zinc" in the description or protein ID of the entry. Then the system picks up barley contigs or singlets from our dataset, which have a functional annotation of similarity to the know database entries selected above. Finally, this system sorts the result or sorts and summarizes the result. At the result, barley clusters with annotation related "zinc" are displayed.

Explanation of the columns

Column name explanation

column name explanation
Cluster ID Name of a cluster of barley. If you want to know the definition of the cluster, please see help page for clusterViewer.
Contig ID Name of a contig or a singlet EST ID of barley.
Supported by UniProt or RefSeq Information about an annotated known protein entry against a barley contig consensus sequence or a barley singlet EST sequence. All the annotated entry have amino acid sequence similarity with the barley sequence above E-value < 0.01 when all barley sequences execute blastx against known protein database (UniProt and RefSeq).
Hit order Hit rank in the Blastx result per each contig or singlet. If the displayed protein entry is the best hit of the contig or the singlet, "Top hit" is displayed in this column.
E-value E-value in the Blastx result.
UniProt or RefSeq The annotated known protein ID in UniProt or RefSeq.
Species The source organism of the annotated known protein entry.
Description The description string of the annotated known protein entry.

Sorting algorithm

You can select three sorting algorithm to sort the result records from at the right side of the "Free words" input area.

Sorting algorithm Explanation of sorting algorithm
Hit Score (Default) The result records are sorted by keyword hit score, in which records including keywords more frequently are superior to records including keyword less frequently in their descriptions.
Cluster ID The result records are order by cluster ID and contig ID. Then the records are grouped by contig ID, in which only the best hit annotated entry is displayed as a representative annotation of barley contig or barley singlet whereas some annotated entries are displayed per each contig or singlet when the other two algorithms are selected.
E-value The result records are order by E-value, in which records with higher similarity annotation is superior to records with lower similarity annotation. Therefore, you can preferentially see through only more reliable annotations.

Searching technique1: AND operation

When you put "kinase" as a query word and push search button, this system display "Too Many Hits" as a response, which is returned when the result include over 10,000 records. To limit the searching result, you can add some query words like "histidine kinase". Because this system regard space as an "AND" operator, returned records contain both "histidine" and "kinase".

Searching technique2: Limitation of species

You can also reduce record number to limit search target organism. When you select "______Arabidopsis thaliana (thale cress)" from species select box at the left of the "Free words" input area, all annotation in the returned records came Arabidopsis thaliana. And when you select "______[Triticeae]" from species select box, all annotation in the returned records came from species classified as a higher taxonomic group "Triticeae" including "Triticum aestivum", "Hordeum vulgare", "Triticum turgidum" and etc. Here such phrase in parentheses like "[Triticeae]" means a higher taxonomic group.

Searching technique3: NOT operation

When you want to exclude such records like "putative" or "unknown function", you can add a word you want exclude as like "-putative". Here minus symbol just before a word means "NOT" operator and all result records do not include the word "putative". Note that this system does not regard minus symbol between characters like "C-terminal" as "NOT" operator but regard hyphenation.

Searching tequnique4: Quotation

In case you are interested in "EC 5.5.1.4" but not interested in "EC protein", you can get result include only "EC 5.5.1.4" to quote the query word like "EC 5.5.1.4". When you input unquoted EC as a query, the returned result includes "EC protein" and "plant EC metallothionein-like family" and etc. The double quotation also ensures the order of these quoted words in the result records. When you input "MAP kinase" as a query with quotations, "MAP protein kinase" is not included in the result.

Searching tequnique5: OR operation

In case a word you are interested in have some synonyms like "Oryza sativa" and "rice", you can use "OR" operator and case arc like "( "Oryza sativa" OR rice )". Following figure represent a result of response against a query "( CL10042 OR CL1086 ) ( Oryza OR Zea ) -sativa -mays", in which displayed result only include cluster ID "CL10042" or "CL1082" and annotated entry limit "Oryza" or "Zea". Note that more abundant entry "Oryza sativa" and "Zea mays" are excluded from the result because of the minus operation "-sativa -mays".

Searching tequnique6: Forward match

When you want execute forward search, you can select "Begin With" from match mode select box at the left of the search button. For instance, when you want to search "AdhA" and "AdhC", you set "adh" as a query and select "Begin With" option. However a lot of entries including "adhesion", "adhesin" or "adhaerence" are displayed, you should reset a query "adh -adhe -adhaerence" to exclude not interested words. Note that you can search words composed of prefix plus number like "adh1" and "adh3" with "adh" as a query in "Exact match" mode because this system regards arrayed alphabet and arrayed number as different word.

Searching tequnique7: Sort by E-value

Because keyword search target includes most of all annotated known protein having E-value less than 0.01, displayed known entry do not necessarily represent valid functional annotation of the barley contig or singlet. For instance, when you search "EC 1.1.1.1", you find a result record having its hit order is 130th and its E-value is 1e-20. However, you can not decide whether the displayed functional annotation is valid, because the hit order is low and the E-value is not enough low. In such a case, you can confirm validity by searching a contig ID you are interested in with sorting by "E-value". At the result of contig ID search, all annotated entries of the contig ordered by E-value are displayed. If a description of the best hit annotation is similar to "EC 1.1.1.1" and if E-value of the best hit annotation is enough low, the annotation is valid.

Searching tequnique8: Sort by Cluster ID

When you are interested in a barley cluster and you want to validate annotation of the cluster, you can confirm by searching the cluster ID with sorting by "Cluster ID". At the result of cluster ID search, you can get top hits annotation of each component contigs and singlets of the cluster. If the all annotation is similar to each other, the annotation and the cluster construction must be valid. Note that "no significant hits" on the table means that the singlet have no significant hit against all UniProt and RefSeq entries.

Expression Profile Search

What is the Expression Profile Search view?

Expression profile search shows the results of microarray experiments from 42 different treatments/conditions, and positively/netatively correlated expression profiles among genes.

Explanation of the columns

Column name explanation

column name explanation
Clone ID Clone name of barley FLcDNA.
Condition Conditions that is specified in the expression profile search (Stress/Organ/Time/Fold change).
Fold Relative fold change of gene expression compared with the control.
FLcDNA/Cluster ID/Accession No IDs for a FLcDNA sequence.
Contig ID/Cluster ID Contig ID is a name of a contig or a singlet EST ID of barley. Cluster ID is a name of a cluster of barley for ESTs. If you want to know the definition of the cluster, please see help page for clusterViewer.
RefSeq Top Hit/UniProt Top Hit The best annotated known protein ID in UniProt or RefSeq.

Treatments

Abrreviation Treatment Explanation
ABA Abscisic acid The 4-day-old germinated seedlings were transferred onto two layers of No. 2 filter paper with 4.5ml of 50 microM ABA solution in a 9 cm Petri dish sealed with Parafilm. The dishes were incubated at 24.C for 3 or 6 hours.
Al Hydroponic aluminium The 4-day-old germinated seedlings were transferred onto two layers of No. 2 filter paper with 4.5ml of 100 microM AlCl3 solution in a 9 cm Petri dish sealed with Parafilm. The dishes were incubated at 24.C for 3 or 6 hours.
Cold Cold stress The 4-day-old germinated seedlings were transferred onto two layers of No. 2 filter paper with 4.5 ml of distilled water in a 9 cm Petri dish sealed with Parafilm. The dishes were incubated at 4.C for 3 or 6 hours.
Dry Drought stress The 4-day-old germinated seedlings were transferred onto dry paper towels on a bench and incubated at room temperature, which was approximately 23.C, for 3 or 6 hours.
MetJA Methyl jasmonate treatment The 4-day-old germinated seedlings were transferred onto two layers of No. 2 filter paper with 4.5 ml of 100 microM Methyl jasmonate (MeJA) in a 9 cm Petri dish sealed with Parafilm. The dishes were incubated at 4.C for 3 or 6 hours.
NT Non treatment The 4-day-old germinated seedlings were transferred onto two layers of No. 2 filter paper without any treatments in a 9 cm Petri dish sealed with Parafilm. The dishes were incubated at 23.C, for 3 or 6 hours.
Salt Salt treatment The 4-day-old germinated seedlings were transferred onto two layers of No. 2 filter paper with 4.5 ml of 0.2 M sodium chloride (NaCl) solution in a Petri dish sealed with Parafilm. The dishes were incubated at 24.C for 3 or 6 hours.

Searching technique: ADD operation

To specify expression profiles, combination of conditions were allowed. In case of one of 42 condition (treatment, organ and Time), fold change is used for the threshold. In other case, two or more conditions are combined by "ADD" button.