RealTime ready Assay Search Tips

 

Can't find what you're looking for on the RealTime ready Configurator?
Use these suggestions to optimize your search:

Organism-Specific Searches
Search by Keyword
Search by Focus Panel
Batch Upload
Search by Pathway
Search Example

In each search category (Search by Keyword, Search by Focus Panel, Search by Pathway, Batch Upload), there are checkboxes that allow you to select specific organisms. All organisms can be selected individually or in combination. The search results will be restricted to the matching filters.

 

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The default setting (search for "KEYWORD" in "All") finds genes with any annotation that matches to the Keyword or Phrase.

The "Search For" Field

• Keyword search is case insensitive.
• The two allowed operators AND/OR need to be in uppercase; otherwise they will be interpreted as keywords.

For example, “chromatin and modifying” will not match to “chromatin modifying enzyme.” You should instead search for “chromatin AND modifying.”

• Keywords can be single words or short sentences/phrases. Keywords separated by a space are interpreted as exact phrases.

For example, "apoptotic AND inducer" will produce one result for ACIN1, the "apoptotic chromatin condensation inducer 1." On the other hand, searching for "apoptotic inducer" will produce no hits because that exact phrase is not contained in the description.

• 'AND' precedes 'OR' in order of operations.

For example, "cullin 1 OR CCND1 AND Cell cycle" will be interpreted as:
i. Find genes containing "cullin 1"
ii. Find genes containing "CCND1 AND Cell cycle"

 

Wildcard Search

A wildcard is a special character (in this case, the asterisk "*") that is used as a placeholder for one or multiple characters, enabling extremely versatile searches. With wildcard search enabled (it is disabled by default), all keywords will be interpreted with a right truncation as in "KEYWO*". All AND/OR combined keywords will also be interpreted as "KEYWO*". Examples:

• MAP*14 matches MAPK14 and MAP3K14
• MAPK*14 matches MAPK14 but not MAP3K14
• MAP*K matches MAPKs, MAP2Ks, MAP3Ks, ...
• MAPK will have the same matches as MAPK*
• MAPK1 OR CCND matches MAPK1* plus CCND*

 

The "Search in" Dropdown Menu

• Use the "Search in" dropdown menu to limit the search results to certain ID or accession number contexts.

For example, searching “2475” in ‘All’ will bring up CST3 (which has the HGNC ID 2475) as well as MTOR (which has the EntrezGene ID 2475). Selecting the correct ID/accession number search context will help narrow the results and speed up the search.

 

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Most of the genes are grouped and categorized in panels or lists covering a certain topic. These predefined lists are valuable entry points for assembling customized plate layouts covering a certain field of interest. The gene lists are mainly literature-based compilations of various public sources (PubMed, GeneOntology, PFAM, Reactome, etc.). The lists are sorted and grouped alphabetically. Individual lists are also grouped into main topics and can therefore be found in several contexts (e.g., NF-kappaB will be listed on its own as well as under "Immune Response" or "Signal Transduction").

 

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An upload file must have one ID per line and a maximum of 384 lines. IDs and accession numbers of various origins may be combined in one file. However, the more restrictive the ID field selection is, the more precise the search results will be.

• Use as few different ID types as possible to get more concise search results.

For example, providing a list of HGNC IDs and applying the filter accordingly will omit any search results where the HGNC ID matches an EntrezGene ID by chance.

 

Sample ID Fields

Accession	Description	Examples
Assay ID	Assay IDs as provided in the configuration portal	100000+
Affymetrix	Affymetrix probe set	202443_x_at,
Agilent	Agilent Probe set IDs	A_23_P200792
CCDS	Consensus CodingSequence	CCDS43905
EMBL / Genbank / DDBJ	Ids provided by one of the three authorities	11275978
Ensembl	Ensembl IDs	ENSG00000134250
Entrez Gene	Entrez Gene UIDs	4853
HAVANA	IDs provided by 'Human And Vertebrate Analysis aNd Annotation' effort	OTTHUMT00000055087
HGNC	'Human Genome Organisation Gene Nomenclature Committee' Names and IDs	NOTCH1
Illumina	Illumina Probe IDs	ILMN_1729161
IPI	International Protein Index	IPI00412982
MIM	Online Mendelian Inheritance in Man	109730
miRBase	miRBase Sequence Ids	MI0000060
NimbleGen	NimbleGen Probe IDs	NM_024408P09940
PDB	Protein Database Ids	1PB5
Refseq	Refseq Nucleotide or Protein IDs	NM_017617
Rfam	Database of RNA Families
UCSC	UCSC IDs	uc003olp
Unigene	Unigene Cluster ID	Hs.495473
UniProt / Swissprot / TrEMBL	UniProt protein ID	B7WP15_HUMAN

 

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The graphical representation of signaling cascades can be used to make gene selections for a certain topic.

• Clicking on a gene symbol will add the gene name/synonym to a name-based search.

Because individual gene names or symbols might be ambiguously used in literature, the search result derived from a pathway-based search is not necessarily a one-to-one representation of the pathway shown. For example, JNK1 might be mapped to its HGNC name (MAPK8), and ERK1/2 might be one of the two MAP kinases (ERK1 or ERK2). The search text box may show an "aliased" search term. For example, the family of Toll Like Receptors from one pathway will be added to the search as "TLRs." The alias is internally expanded to the individual members of the corresponding gene family, and the result table will show all Toll Like Receptors.

 

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Question: "How can I evaluate the expression of p38 kinase in several human tissue samples?"

Without further knowledge, you could start a Keyword search for "p38" in "Gene Name/Alias." Unfortunately, p38 is a rather ambiguous gene name, so this particular search might bring up some puzzling results, such as:

• AHSA1 having p38 as alias
• GRAP2 having P38 as alias
• MAPK1 having p38 as alias
• MAPK14 (the "mitogen-activated protein kinase 14") having p38 as alias

Keep in mind that some identifiers that are in wide use in a specific scientific community might be used completely differently in another research field. In this particular case, the last item in the results list: MAPK14, would be the best choice.

Searching “MAPK14” (the official name for p38 as assigned by the HUGO Gene Nomenclature Committee), would lead to the relevant assays directly. Another option is to start with accession numbers right away. For example, in the p38/MAPK14 example you could use sequence identifiers that link to MAPK14 transcripts from various sources (in this case, restricted to "H. Sapiens")

• ENST00000229795 (Ensembl transcript ID)
• NM_001315 (refseq DNA)
• AB074150 (EMBL ID)
• NP_620581 (Refseq peptide ID)
• A_14_P111428 (Agilent Probe ID)
• 202530_at (Affymetrix probe-set ID)
• 20212154 (Pubmed ID with additional referenced genes by this article)

All these accession numbers are internally mapped to the matching gene p38/MAPK14 and to our assays for that particular gene.

Answer: Order a RealTime ready Assay for MAPK14, Assay ID 105593.

 

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