WebMOTIFS: Available Gene and Probe Names

This page lists the sets of gene names and microarrays currently supported by WebMOTIFS:

These gene names/names of probes from these arrays can be used to specify input to WebMOTIFS.

Sample gene names for S. cerevisiae: YAL008W, YBR255W, YGR131W

Sample gene names for M. musculus: NM_001001180, NM_001001181, NM_001001182

Sample gene names for H. sapiens: NM_000024, NM_000025, NM_000026

For S. cerevisiae: No transcriptional profiling arrays currently available.

For M. musculus:

Array Name	Sample Probe ID	Sequences Analyzed
Affymetrix GeneChip Murine Genome U47A verions 1 About this array(NCBI GEO site)	96838_at	User can choose sequences from -1000 to +200 or sequences from -2000 to +200 (relative to transcription start)
Affymetrix GeneChip Mouse Genome 430 2.0 Array About this array(NCBI GEO site)	1427138_at	User can choose sequences from -1000 to +200 or sequences from -2000 to +200 (relative to transcription start)

For H. sapiens:

Array Name	Sample Probe ID	Sequences Analyzed
Affymetrix GeneChip Human Genome U133 Array Set A About this array(NCBI GEO site)	212034_s_at	User can choose seuqences from -1000 to +200 or sequences from -2000 to +200 (relative to the transcription start site

For S. cerevisiae:

Array Name	Sample Probe ID	Sequences Analyzed
Yeast6kArray PCR-based array, used in Harbison 2004	iYAL069W	Full intergenic region upstream of probe (sizes range from 60-1500bp, 480bp average)

For M. musculus:

Array Name	Sample Probe ID	Coverage	Sequences Analyzed
M. musculus 13K promoter array PCR-based array, used in Macisaac 2006	Mm1_1_1_1	13,000 features (represented by PCR probes), spanning from 750bp upstream to 250bp downstream of transcription start sites.	Sequence of PCR probe (700-900 bp), with no overlap between probes

For H. sapiens:

Array Name	Sample Probe ID	Coverage	Sequences Analyzed
H. sapiens 13K promoter array PCR-based array, used in Macisaac 2006, more details here.	NM_018933	Promoters of 13,000 human genes (represented by PCR probes), spanning from 700bp upstream to 200bp downstream of transcription start sites	Sequence of PCR probe, plus an additional 250bp on either side (1200-1400bp total), with no overlap between probes.
H. sapiens 19K promoter array PCR-based array, used in Macisaac 2006, more details here.	chr10: 100753935- 100754767	As for about 13k array, plus coverage from -4kb upstream to +2kb downstream for 276 diverse genes, and coverage around 175 microRNA	Sequence of PCR probe, plus an additional 250bp on either side (1200-1500bp total), with no overlap between probes.
Agilent H. sapiens custom 10-array set Oligonucleotide array, see Supplementary information for Boyer et al 2005 for details	chr10: 100015691- 100016191	18,000 human transcription start sites from 8kb upstream to 2kb downstream, with oligonucleotide probes approximately every 280bp	500bp window centered around each probe, with no overlap between probes.