Input on Microbe Annotations for Microarrays Requested

[crystal.han]

Hi AWG members @AnimalAWG @MultiOmicsAWG,

We have been processing microarray datasets and came across some bacteria datasets that do not have BioMart support. Normally, we would use BioMart to help us map the probeset-level output data to gene-level annotations. But since this information is not available for bacteria data, we can either:

(1) Omit annotations entirely in the outputs for bacteria datasets
(2) Use annotation data from the manufacturer

For the latter, note that the annotation data may be quite old. For example, Thermo Fisher provides the following annotation files, both created in 2016 (login required for below links):

• E. coli
• P. aeruginosa

We would like your feedback on whether or not these annotations from the manufacturer would still be useful to include in the output data. Alternatively, we are open to any other sources of annotations that you may know of.

Thank you!

[szewczyk]

Generally I think we’d want to provide some annotation even if it is outdated. Thus, unless anyone comes up with a good open source, the manufacturer annotation might be the best you can do.

[crystal.han]

Thank you for your feedback! We will make sure to include the annotations in that case. Our current outputs include the following annotation fields:

‘ENSEMBL’, ‘SYMBOL’, ‘GENENAME’, ‘REFSEQ’, ‘ENTREZID’, ‘STRING_id’, ‘GOSLIM_IDS’

Some of these fields might not be available in the manufacturer annotations, but we will include what is available.

Are there any other fields besides the ones listed above that you would like to see in the output? Here are all the fields provided by ThermoFisher in the bacteria species linked above (note: some fields might not actually be populated):

Probe Set ID	GeneChip Array	Species Scientific Name	Annotation Date	Sequence Type	Sequence Source	Transcript ID(Array Design)	Target Description	Representative Public ID	Archival UniGene Cluster	UniGene ID	Genome Version	Alignments	Gene Title	Gene Symbol	Chromosomal Location	Unigene Cluster Type	Ensembl	Entrez Gene	SwissProt	EC	OMIM	RefSeq Protein ID	RefSeq Transcript ID	FlyBase	AGI	WormBase	MGI Name	RGD Name	SGD accession number	Gene Ontology Biological Process	Gene Ontology Cellular Component	Gene Ontology Molecular Function	Pathway	InterPro	Trans Membrane	QTL	Annotation Description	Annotation Transcript Cluster	Transcript Assignments	Annotation Notes
AFFX-Athal_actin_at	P. aeruginosa Genome Array	Pseudomonas aeruginosa	30-Mar-16	Control sequence	GenBank	AFFX-Athal_actin	U37281 Arabidopsis thaliana actin-2 mRNA	U37281	—	At.23605	—	—	actin 7	ACT7	—	—	—	830841	P53492	—	—	NP_196543	NM_121018	—	—	—	—	—	—	0006007 // glucose catabolic process // inferred from reviewed computational analysis /// 0006094 // gluconeogenesis // inferred from reviewed computational analysis /// 0007010 // cytoskeleton organization // inferred from reviewed computational analysis /// 0007010 // cytoskeleton organization // traceable author statement /// 0009416 // response to light stimulus // inferred from expression pattern /// 0009611 // response to wounding // inferred from expression pattern /// 0009733 // response to auxin // inferred from expression pattern /// 0009845 // seed germination // inferred from mutant phenotype /// 0010053 // root epidermal cell differentiation // inferred from mutant phenotype /// 0010498 // proteasomal protein catabolic process // inferred from reviewed computational analysis /// 0032880 // regulation of protein localization // inferred from reviewed computational analysis /// 0048364 // root development // inferred from mutant phenotype /// 0048767 // root hair elongation // inferred from mutant phenotype /// 0048767 // root hair elongation // inferred from reviewed computational analysis /// 0051301 // cell division // inferred from mutant phenotype	0005618 // cell wall // inferred from direct assay /// 0005730 // nucleolus // inferred from direct assay /// 0005737 // cytoplasm // not recorded /// 0005739 // mitochondrion // inferred from direct assay /// 0005829 // cytosol // inferred from direct assay /// 0005856 // cytoskeleton // inferred from sequence or structural similarity /// 0005886 // plasma membrane // inferred from direct assay /// 0009506 // plasmodesma // inferred from direct assay /// 0009570 // chloroplast stroma // inferred from direct assay /// 0009941 // chloroplast envelope // inferred from direct assay	0000166 // nucleotide binding // inferred from electronic annotation /// 0005200 // structural constituent of cytoskeleton // inferred from sequence or structural similarity /// 0005515 // protein binding // inferred from physical interaction /// 0005524 // ATP binding // inferred from electronic annotation	—	—	—	—	This probe set was annotated using the Design Representative Id based pipeline to a Entrez Gene identifier using 1 transcripts. // false // Design Representative Id // R	U37281	AFFX-Athal_actin // — // unknown // — // — /// U37281 // U37281 Arabidopsis thaliana actin-2 mRNA // gb // — // —	—
AFFX-Athal_GAPDH_at	P. aeruginosa Genome Array	Pseudomonas aeruginosa	30-Mar-16	Control sequence	GenBank	AFFX-Athal_GAPDH	M64116 Arabidopsis thaliana glyceraldehyde 3-phosphate dehydrogenase C subunit (GapC) gene	M64116	—	At.22963	—	—	glyceraldehyde-3-phosphate dehydrogenase C subunit 1	GAPC1	—	—	—	819567	P25858 /// Q41949 /// Q56WW5	—	—	NP_187062	NM_111283	—	—	—	—	—	—	0006006 // glucose metabolic process // inferred from electronic annotation /// 0006007 // glucose catabolic process // inferred from reviewed computational analysis /// 0006094 // gluconeogenesis // inferred from reviewed computational analysis /// 0006094 // gluconeogenesis // traceable author statement /// 0006096 // glycolytic process // inferred from direct assay /// 0006096 // glycolytic process // inferred from electronic annotation /// 0006096 // glycolytic process // inferred from sequence or structural similarity /// 0006096 // glycolytic process // inferred from reviewed computational analysis /// 0006096 // glycolytic process // traceable author statement /// 0006098 // pentose-phosphate shunt // inferred from reviewed computational analysis /// 0006833 // water transport // inferred from reviewed computational analysis /// 0006972 // hyperosmotic response // inferred from reviewed computational analysis /// 0006979 // response to oxidative stress // inferred from direct assay /// 0006979 // response to oxidative stress // inferred from expression pattern /// 0007010 // cytoskeleton organization // inferred from reviewed computational analysis /// 0007030 // Golgi organization // inferred from reviewed computational analysis /// 0009060 // aerobic respiration // inferred from reviewed computational analysis /// 0009266 // response to temperature stimulus // inferred from reviewed computational analysis /// 0009408 // response to heat // inferred from expression pattern /// 0009651 // response to salt stress // inferred from expression pattern /// 0009651 // response to salt stress // inferred from reviewed computational analysis /// 0009744 // response to sucrose // inferred from expression pattern /// 0010154 // fruit development // inferred from mutant phenotype /// 0010498 // proteasomal protein catabolic process // inferred from reviewed computational analysis /// 0034976 // response to endoplasmic reticulum stress // inferred from reviewed computational analysis /// 0042542 // response to hydrogen peroxide // inferred from direct assay /// 0046686 // response to cadmium ion // inferred from expression pattern /// 0046686 // response to cadmium ion // inferred from reviewed computational analysis /// 0048316 // seed development // inferred from mutant phenotype /// 0051775 // response to redox state // inferred from direct assay /// 0055114 // oxidation-reduction process // inferred from electronic annotation	0005634 // nucleus // inferred from direct assay /// 0005737 // cytoplasm // not recorded /// 0005739 // mitochondrion // inferred from direct assay /// 0005740 // mitochondrial envelope // inferred from direct assay /// 0005774 // vacuolar membrane // inferred from direct assay /// 0005794 // Golgi apparatus // inferred from reviewed computational analysis /// 0005829 // cytosol // inferred from direct assay /// 0005829 // cytosol // traceable author statement /// 0005886 // plasma membrane // inferred from direct assay /// 0009507 // chloroplast // inferred from direct assay /// 0016020 // membrane // inferred from direct assay /// 0048046 // apoplast // inferred from direct assay	0003677 // DNA binding // inferred from electronic annotation /// 0004365 // glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity // traceable author statement /// 0005507 // copper ion binding // inferred from direct assay /// 0008886 // glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity // inferred from direct assay /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0016620 // oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor // inferred from electronic annotation /// 0050661 // NADP binding // inferred from electronic annotation /// 0051287 // NAD binding // inferred from electronic annotation	—	—	—	—	This probe set was annotated using the Design Representative Id based pipeline to a UniGene identifier using 1 transcripts. // false // Design Representative Id // R	M64116	AFFX-Athal_GAPDH // — // unknown // — // — /// M64116 // M64116 Arabidopsis thaliana glyceraldehyde 3-phosphate dehydrogenase C subunit (GapC) gene // gb // — // —	—

[crystal.han]

We would appreciate any feedback on this topic by Friday, August 9th. Thank you all!