Gene Search

This section would show you details of gene annotation and other features of genes of interest.

1. Gene annotation

We collected and integrated those public gene information data from Ensembl Database and NCBI Gene Database. The data from NCBI were downloaded in 2022-08-26. Human genes (based on GRCh38.p13) and mouse genes (based on GRCm39) were from Ensembl v107 database.

The Gene Datasets contains 68,324 Human gene records, 56,748 Mouse gene records and 463,409 transcripts records, which containing the following attributes:

Datasets Attribution and Source (click to hide or show this panel)

Datasets	Attribute	Source
Gene Info	Symbol	Ensembl Database
	Ensembl ID	Ensembl Database
	Description	Ensembl Database
	Gene Type	Ensembl Database
	Organism	Ensembl Database
	Chromosome, Start, End, Strand	Ensembl Database
	Gene Source	Ensembl Database
	Gene Version	Ensembl Database
	Entrez ID	NCBI Gene Database
	Aliases / Gene Synonyms	NCBI Gene Database
	Chromosomal Location	NCBI Gene Database
	Other Designations	NCBI Gene Database
	Identifiers in Other DB	NCBI Gene Database
Transcript	Transcript ID	Ensembl Database
	Name	Ensembl Database
	Length	Ensembl Database
	Type	Ensembl Database
	Transcription Start Sites (TSS)	Ensembl Database
	Refseq mRNA ID	Ensembl Database
	Refseq ncRNA ID	Ensembl Database
	Version	Ensembl Database
	Start - End	Ensembl Database
	Count	Ensembl Database
	Transcript Support Level (TSL)	Ensembl Database

Explanation of gene attributes are as follows:

Attribute	Description
Symbol	Official short-form abbreviation for a particular gene
Entrez ID	Identifier for a gene from the NCBI Entrez database
Description	A descriptive name for this gene, and those words inside the square brackets show the source of this attribution
Gene Type	A gene classification containing protein coding, lncRNA, processed pseudogene, unprocessed pseudogene, miRNA, TEC, snRNA, misc_RNA, snoRNA and so on, which integrated from Ensembl Database
Organism	Organism where the gene came, containing only two species: Homo sapiens and Mus musculus
Gene Synonyms	A comma-delimited set of unofficial symbols and descriptions that have been used for this gene integrated from NCBI Entrez Database
Other Designations	Semicolon-delimited set of some alternate descriptions that have been assigned to a GeneID. '-' indicates none is being reported.
Identifiers in Other DB	Comma-delimited set of identifiers in other databases for this gene. The unit of the set is database:value. Note that HGNC and MGI include 'HGNC' and 'MGI', respectively, in the value part of their identifier. Consequently, this attribution for these databases will appear like: HGNC:HGNC:1100, this would be interpreted as database='HGNC', value='HGNC:1100'. Example for MGI: MGI:MGI:104537. This would be interpreted as database='MGI', value='MGI:104537'
Location	Chromosome and coordinate where a gene locates, which is 0-based start
Chromosome Location	Cytogenetic location
Gene Version	Gene version integrated from Ensembl Database
Gene Source	The annotation source for this gene integrated from Ensembl Database

Explanation of transcript attributes are as follows:

Attribute	Description
Transcript ID	A stable identifier for this transcript from Ensembl
Name	A name for this transcript from Ensembl
Length	Length of this transcript (bp)
Type	A transcript classification containing protein coding, lncRNA, processed pseudogene, unprocessed pseudogene, miRNA, TEC, snRNA, misc_RNA, snoRNA and so on, which is integrated from Ensembl Database
Transcription Start Sites (TSS)	The transcription start sites of this transcript
Refseq mRNA ID	A corresponding ID of this mRNA from NCBI's Reference Sequences (RefSeq) database
Refseq ncRNA ID	A corresponding ID of this non-coding RNA from NCBI's Reference Sequences (RefSeq) database
Version	The version of this trancript from Ensembl
Start - End	The start and end coordinate of this trancript
Count	The expression count
Transcript Support Level (TSL)	The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript. TSL 1: A transcript where all splice junctions are supported by at least one non-suspect mRNA TSL 2: A transcript where the best supporting mRNA is flagged as suspect or the support is from multiple ESTs TSL 3: A transcript where the only support is from a single EST TSL 4: A transcript where the best supporting EST is flagged as suspect TSL 5: A transcript where no single transcript supports the model structure TSL NA: A transcript that was not analysed for TSL

2. Search rules

The search allows users to choose the organism and id type of genes of interest.

Organisms:

Human: genes from Homo sapiens
Mouse: genes from Mus musculus
All: genes from human or mouse

ID type:

Symbol: short-form abbreviation for a particular gene
Ensembl ID: identifier for a gene from the Ensembl (European Bioinformatics Institute and the Wellcome Trust Sanger Institute) database
Entrez ID: identifier for a gene from the NCBI Entrez database

The search mode is case-insensitive, genes that are partially matched will be return with the perfect match comes first.

3. Spatially variable gene

Please see Identification of spatially variable gene for more details.

4. Expression Rank Score

The expression rank score is defined as the percentile of log-transformed CPM (natural logarithm) in each ST section.