1000Gp3_GF

Gene frequency for a given population, from the 1000 Genomes Project Phase3 via dbNSFP Version 2.7. Phase3 comprises genomic data from twenty-six populations distributed among five super populations.

In the Manage Columns dialog (Using the Manage Columns Dialog), the main category at the top of the tree displays alternative gene frequencies for all populations combined. Below this is a list of super populations, any of which can be expanded to reveal sub-populations.

S¹

1000Gp3_MAF…

Alternative allele frequency for a given population, from the 1000 Genomes Project Phase3 via dbNSFP Version 2.7. Phase3 comprises genomic data from twenty-six populations distributed among five super populations.

In the Manage Columns dialog (Using the Manage Columns Dialog), the main category at the top of the tree displays alternative allele frequencies for all populations combined. Below this is a list of super populations, any of which can be expanded to reveal sub-populations. See the table above for descriptions.

S¹

/[annotation type]

Available GenBank-style annotations vary based on the annotations you have imported. If the data in your project was imported through the Data Import Wizard, any columns you designated as “Description” during import will appear in this list.

Accessible annotations also vary depending on the table from which you accessed the Manage Columns dialog. Each of the tables whose abbreviation appears on the right offers only a subset of all available annotations.

E, G, I

/qseq_name

Unambiguous name assigned by QSeq to avoid duplicate names in a genome. When duplicate names are found, a number is added to disambiguate.

G²⁰, I²⁰

aaAlt

The alternative amino acid. A period is shown if the variant is a splicing site SNP (i.e., 2 base pairs on each end of an intron).

S¹

aaPos

The amino acid position in relation to the protein. A negative one (-1) appears if the variant is a splicing site SNP (i.e., 2 base pairs on each end of an intron).

S¹

aaRef

The reference amino acid. A period is shown if the variant is a splicing site SNP (i.e., 2 base pairs on each end of an intron).

S¹

adjusted P value

The FDR/Benjamini-Hochberg multiple testing correction value, also known as the “Q value.” This column is available if Bioconductor’s DESeq2 was used as the normalization method, and also applies to T tests and F tests when the FDR/Benjamini-Hochberg multiple testing correction is applied (as it is by default).

G²⁵, I²⁵

amino acid change

The change(s) in the protein sequence using the nomenclature and conventions established by the Human Genome Variation Society (HGVS). The cell text ‘p.(=)’ signifies a synonymous change, while an empty cell denotes a non-coding region.

S

aspect

See the GO Annotation File Format 2.0 Guide for a description.

G²

assigned_by

See the GO Annotation File Format 2.0 Guide for a description.

G²

base mean

The mean of normalized counts for that gene across all samples.

G²⁵, I²⁵

binding protein

The binding protein used for the experiment. Binding proteins are assigned to each experiment by you in the Create Binding Proteins step of the Project Setup Wizard.

F³, P³

called seq

The base or sequence of the permutation. This might be a gap ‘-‘ for a deletion, multiple bases for an insertion, or the same as Ref Seq for a non-change. Multiple called bases are shown with dividers, e.g. T|C, A|-, etc. An empty cell denotes no Database of Single Nucleotide Polymorphism (dbSNP) information, while (NC) refers to “no coverage.” This data derives from the SNP Sequence column in the Data Import Wizard.

S

CCDS_id

CCDS ID, from the HUGO Gene Nomenclature Committee (HGNC).

G⁴

chr

Chromosome number, from the HUGO Gene Nomenclature Committee (HGNC).

G⁴

classification

The category and type of permutation (coding, synonymous, frameshift, etc.)

S

clinvar_clnsig

The clinical/pathological significance from the ClinVar database.

•      Benign (2)

•      Likely benign (3)

•      Likely pathogenic (4)

•      Pathogenic (5)

•      Drug response (6)

•      Histocompatibility (7)

S¹

clinvar_rs

The reference SNP (rs) number from the ClinVar database.

S¹

clinvar_trait

The trait identifier (e.g., CUI, HPO, etc.) from the ClinVar database.

S¹

codonpos

The position on the codon (1, 2 or 3).

S¹

combined SNP seq⁶

The raw coalesced/combined SNP sequence as recorded by SeqMan NGen.

S⁵

contig pos

The position on a gapped contig corresponding to this chromosome (for SeqMan and SeqMan NGen data only).

S

cooks

The Cook’s distance for that gene. It is a measure of how much a single sample is influencing the fitted coefficients for that gene. Large values indicate an outlier count.

G²⁵, I²⁵

COSMIC ID

Catalogue of Somatic Mutations in Cancer (COSMIC) ID with hyperlink to the COSMIC entry.

S⁵

date

See the GO Annotation File Format 2.0 Guide for a description.

G²

DB

See the GO Annotation File Format 2.0 Guide for a description.

G²

db:Reference

See the GO Annotation File Format 2.0 Guide for a description.

G²

db_Object _ID⁷

See the GO Annotation File Format 2.0 Guide for a description.

G²

db_Object_Name⁷

See the GO Annotation File Format 2.0 Guide for a description.

G²

db_Object_Symbol⁷

See the GO Annotation File Format 2.0 Guide for a description.

G²

db_Object_Synonym⁷

See the GO Annotation File Format 2.0 Guide for a description.

G²

DB_Object_Type

See the GO Annotation File Format 2.0 Guide for a description.

G²

dbSNP ID

The Database of Single Nucleotide Polymorphism (dbSNP) ID with hyperlink to the dbSNP entry.

S⁵

depth

The depth of coverage for the SNP.

S⁸

detected exons

The number of exons detected in the gene

G⁹

disease_description

Disease(s) the gene causes or with which it is associated, from Uniprot.

G⁴

DNA Change

The change(s) in the DNA sequence using the nomenclature established by the Human Genome Variation Society (HGVS).

S

downstream gene

The name of the nearest downstream gene within 100 kilobases of the fragment or peak. If there is an intersecting gene, no downstream gene will be listed.

F, P

end

The end position of the fragment along the template sequence.

F, P

Ensembl_gene

Ensembl gene ID, from the HUGO Gene Nomenclature Committee (HGNC).

G⁴

Entrez_gene_id

Entrez gene ID, from the HUGO Gene Nomenclature Committee (HGNC).

G⁴

ESP6500_MAF

Alternative allele frequency for a given population, from the NHLBI Exome Sequencing Project’s ESP6500 data set. The main category at the top of the tree displays alternative allele frequencies for all populations combined. Below this are the two super populations:

•      AA – African American population only.

•      EA – European American population only.

S¹

essential_gene

Essential I or Non-essential (N) phenotype-changing based on Mouse Genome Informatics (MGI) database (Georgi et al., 2013|topic=Research References).

G⁴

evidence code

See the GO Annotation File Format 2.0 Guide for a description.

G²

experiment ID

The name of the experiment for the peak, as shown in the Experiment List.

P

expression (egenetics)

Tissues/organs in which the gene is expressed, from egenetics data from BioMart.

G⁴

Expression(GNF/Atlas)

Tissues/organs in which the gene is expressed, from GNF/Atlas data from BioMart.

G⁴

FDR

The False Discovery Rate (FDR) represents the likelihood that the peak is not valid. The FDR signal value is only available if control data are present and MACS Peak Detection is used for peak discovery.

F

feature type

The type of feature as annotated in the template sequence for the gene (e.g. CDS, attenuator, C_region, etc.). The genes for the template are defined during Set Up Preprocessing.

The annotations available in the drop-down list will vary based on the annotations you have imported. If the data in your project was imported through the Data Import Wizard, any columns you designated as Description during import will appear in this list.

E¹², G¹², I¹²

fold enrichment

This column is available only in the Peak Table for ChIP-Seq experiments and is available through the Add/Manage Columns under IP Peak Values. Fold Enrichment is calculated from the enriched tags in that peak region and the local lambda of Poisson distribution from the nearby regions. Note that it is not the same analysis used for the MFOLD value. Many reported peaks may have Fold Enrichment values less than the MFOLD cutoff.

P

fragment ID

The ID for the fragment of the genome along which the peak occurs. See the Fragment Table or more information.

G¹¹, P

frameshift¹⁴

This change is caused by indels that are not evenly divisible by three.

G¹³

full alleles⁶

The set of raw alleles as recorded in the VCF file, including the flanking 5’ anchor base that is considered extraneous by ArrayStar.

S⁵

full ref seq⁶

The reference sequence of the raw coalesced/combined SNP sequence as recorded by SeqMan NGen.

S⁵

function_description

Function description of the gene from Uniprot.

G⁴

gene_full_name

Gene full name from the HUGO Gene Nomenclature Committee (HGNC).

G⁴, S⁴

gene_name, gene name

Gene symbol (e.g. recA, thrL, etc.), from the HUGO Gene Nomenclature Committee (HGNC).

G⁴, S⁴

gene_old_names

Old gene symbol, from the HUGO Gene Nomenclature Committee (HGNC).

G⁴

gene_other_names

Other gene names, from the HUGO Gene Nomenclature Committee (HGNC).

G⁴

genotype

Whether this SNP call indicates the reference or not, and (for diploids) whether this calls a homozygous or heterozygous genotype.

S

GERP Score

Genomic Evolutionary Rate Profiling (GERP) score.

S⁵

GERP++_NR

Genomic Evolutionary Rate Profiling (GERP++¹⁰) neutral rate (NR) – the number of substitutions expected under conditions of neutrality.

S¹

GERP++_RS

Genomic Evolutionary Rate Profiling (GERP++¹⁰) rejected substitutions (RS) – the number of substitutions expected under neutrality minus the number of substitutions ‘‘observed’’ at the position. Scores range from 1 to 6.18.The larger the score, the more conserved the site.

S¹

GERP++_RS_rankscore

Genomic Evolutionary Rate Profiling (GERP++¹⁰) RS scores were ranked among all GERP++ RS scores in dbNSFP. The “rankscore” is the ratio of the rank of the score over the total number of GERP++ RS scores in dbNSFP.

S¹

GO ID

See the GO Annotation File Format 2.0 Guide for a description.

G²

GO_Slim_biological_process

Terms for biological process from Gene Ontology (GO) Slim.

G⁴

GO_Slim_cellular_component

Terms for cellular component from Gene Ontology (GO) Slim.

G⁴

GO_Slim_molecular_function

Terms for molecular function from Gene Ontology (GO) Slim.

G⁴

highest exon

The largest copy number value of any discovered exon in the gene. For RPKM-CN or zRPKM-normalized workflows, exons are ignored if they are below 1 RPKM. For zRPKM workflows, exons are also ignored if there is a systematic lack of depth across the same exon in all experiments.

G⁹

inframe indel¹⁴

An insertion or deletion within a coding region whose length is divisible by 3.

•      For insertions, the type is followed by the word Conservative when inserted bases occur between two codons, and by the word Disruptive when the inserted bases occur within a codon.

•      For deletions, the type is followed by the word Conservative when deleted bases begin at the first position of a codon and end at the last position of a codon, and by the word Disruptive when the deleted bases start at position 2 or 3 of a codon and end at position 1 or 2, respectively, of another codon.

G¹³

Interactions (BioGRID)

Other genes with which the gene interacts, from BioGRID. The gene name is followed by the PubMed ID in square brackets.

G⁴

Interactions (ConsensusPathDB)

Other genes with which the gene interacts, from ConsensusPathDB. The gene name is followed by the PubMed ID in square brackets.

G⁴

Interactions (IntAct):

Other genes with which the gene interacts, from IntAct. The gene name is followed by the PubMed ID in square brackets.

G⁴

Interpro_domain

The domain or conserved site on which the variant is located. Domain annotations come from Interpro database. The number in the brackets following a specific domain is the count of times Interpro assigns the variant position to that domain, typically coming from different predicting databases.

S¹

intersecting genes

The names of any genes in the template that intersect the fragment or peak. The genes for the template are defined during Set Up Preprocessing.

F, P

known_rec_info

Known recessive status of the gene (MacArthur et al., 2012).

•      lof-tolerant – seen in homozygous state in at least one 1000G individual.

•      recessive – known OMIM recessive disease.

G⁴

lfc SE

The standard error estimate for the log₂ fold change estimate.

G²⁵, I²⁵

length

The length of the fragment, equal to the end position minus the start position.

F, P

linear expression level

Though the log₂ format is displayed by default, the option for displaying linear values is available in some workflows (see Using the Manage Columns Dialog). The linear signal is equal to (total_)raw_count + repeat_distrib_count, with any selected normalization applied.

linear rlog reads

The rlog values for each gene transformed back into the linear scale. The linear rlog value for the control set is also displayed. This value differs from raw DESeq2 in that it also includes any user-applied data transformations.

G²⁵, I²⁵

log₂ expression level

The log₂ signal columns in the Gene Table, Fragment Table, Peak Table, Exon Table and Isoform Table can display positive or negative values:

•      Positive – the underlying value is greater than one. A value of +1 indicates a two-fold increase. If you have loaded data which comprise a ratio, a positive value in this column denotes up-regulated gene expression.

•      Negative – the underlying value is less than one. A value of -1 indicates a two-fold decrease. If you have loaded data which comprise a ratio, a negative value in this column denotes down-regulated gene expression.

Some examples of log₂ equivalents are shown below:

In addition to displaying this column, you can also over the mouse over any signal column to display a tool tip showing both rounded and unrounded log₂ values.

log₂ fold change

The effect size estimate indicating how much the gene expression seems to have changed in the test sample relative to control. This value is reported on a logarithmic scale to base 2.

G²⁵, I²⁵

lowest exon

The smallest copy number value of any discovered exon in the gene. For RPKM-CN or zRPKM-normalized workflows, exons are ignored if they are below 1 RPKM. For zRPKM workflows, exons are also ignored if there is a systematic lack of depth across the same exon in all experiments.

G⁹

LRT_converted_rankscore¹⁵

Likelihood Ratio Test (LRT) scores were first converted as LRTnew = (1 – LRTori * 0.5) if Omega < 1, or LRTnew = (LRT_ori * 0.5) if Omega ≥ 1. Then LRTnew scores were ranked among all LRTnew scores in dbNSFP. The rankscore is the ratio of the rank over the total number of the scores in dbNSFP. The scores range from 0.00166 to 0.85682.

S¹

LRT_pred¹⁵

Likelihood Ratio Test (LRT) predictions are based on several criteria including the LRT score.

•      D(eleterious) – non-synonymous SNP (NS) needs to fulfill three requirements: 1) from a codon defined by LRT as significantly constrained (LRT_ori <0.001 and ω <1); 2) from a site with >10 eutherian mammals’ alignments; 3) the alternative AA is not presented in any of the eutherian mammals

•      N(eutral) – NS needs to fulfill either of the two requirements: (i) the alternative AA is presented in at least one of the eutherian mammals, or (ii) from a codon defined by LRT as not significantly constrained (LRT_ori >0.001 or ω >1) and with >10 eutherian mammals’ alignments

•      U(nknown) – Alternative amino acid from alignment positions with <10 eutherian mammals.

S¹

LRT_score¹⁵

The p-value from the Likelihood Ratio Test (LRT). The smaller the score the more likely the SNP has a damaging effect. Scores range from 0 to 1.

S¹

mean values from DESeq2

This value is used for DNASTAR diagnostic use only.

G²⁵, I²⁵

MIM_disease

MIM disease name(s) with MIM ID(s) in square brackets from Uniprot.

G⁴

MIM_id

MIM gene ID, from the HUGO Gene Nomenclature Committee (HGNC).

G⁴

MIM_phenotype_id

MIM ID(s) of the phenotype the gene causes or with which it is associated, from Uniprot.

G⁴

MM Count 1

Count of articles in the Mastermind Genomic Search Engine with cDNA matches for this specific variant.

S¹

MM Count 2

Count of articles in the Mastermind Genomic Search Engine with variants either explicitly matching at the cDNA level or given only at protein level.

S¹

MM Count 3

Count of Mastermind articles in the Mastermind Genomic Search Engine, including other DNA-level variants resulting in the same amino acid change.

S¹

MM Gene

Genes for this variant from the Mastermind Genomic Search Engine.

S¹

MM HGVS

HGVS genomic notation for this variant from the Mastermind Genomic Search Engine.

S¹

MM ID 3

Variant identifiers in the Mastermind Genomic Search Engine, as gene:key, for MMCNT3.

S¹

MM URI 3

Search URI for articles in the Mastermind Genomic Search Engine, including other DNA-level variants resulting in the same amino acid change.

S¹

mu

Mean fitted count values from individual replicates.

G²⁵, I²⁵

MutationTaster_converted_rankscore¹⁶

MutationTaster MT_ori scores were first converted. If the prediction is “A” or “D,” then Mtnew = MT_ori; if the prediction is “N” or “P”, then Mtnew = (1-Mt_ori). Mtnew scores were then ranked among all Mtnew scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of Mtnew scores in dbNSFP. Scores range from 0.0931 to 0.80722.

S¹

MutationTaster_pred¹⁶

MutationTaster prediction.

S¹

MutationTaster_score¹⁶

The MutationTaster probability that prediction is correct. Scores range from 0 to 1. The larger the score the more likely it is correct.

S¹

nonsense¹⁴

This change results in a premature stop codon and a truncated, incomplete, and usually nonfunctional protein product.

G¹³

non-synonymous¹⁴

This change alters the amino acid sequence coded for in this (translated) coding region. This category includes Nonsense, Frameshift, No-start and No-stop changes. To derive the number of simple substitutions, display all of the options and subtract the four listed changes from the Non-synonymous count.

G¹³

no-start¹⁴

Change resulting in the absence of a start codon.

G¹³

no-stop¹⁴

Change resulting in the absence of a stop codon.

G¹³

notes

User-created notes about the gene.

G

P not ref

The probability that this position does not match the reference. For combined SNPs and indels, P not ref will be the minimum of the P not refs in the used columns.

S⁸

P(HI)

Estimated probability of haploinsufficiency of the gene (Huang N et al., 2010|topic=Research References).

G⁴

P(rec)

Estimated probability that gene is a recessive disease gene (MacArthur et al., 2012|topic=Research References).

G⁴

pathway(ConsensusPathDB)

Pathway(s) to which the gene belongs, from ConsensusPathDB.

G⁴

pathway(Uniprot)

Pathway(s) to which the gene belongs, from Uniprot.

G⁴

peak ID

The IDs of any peaks that are present within the fragment. See the Peak Table for more information.

F, G¹¹

phastCons100way_vertebrate¹⁷

The PhastCons conservation score, based on the multiple alignments of 100 vertebrate genomes (including human) and a phylo-HMM. The larger the score, the more conserved the site. Scores ranges from 0 to 1.

S¹

phastCons100way_vertebrate_rankscore¹⁷

PhastCons100way_vertebrate scores (PhastCons) were ranked among all phastCons100way_vertebrate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons100way_vertebrate scores in dbNSFP.

S¹

phastCons46way_placental¹⁷

The PhastCons conservation score, based on the multiple alignments of 33 placental mammal genomes (including human) and a phylo-HMM. The larger the score, the more conserved the site. Scores ranges from 0 to 1.

S¹

phastCons46way_placental_rankscore¹⁷

PhastCons46way_placental scores (PhastCons)were ranked among all phastCons46way_placental scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons46way_placental scores in dbNSFP.

S¹

phastCons46way_primate¹⁷

The PhastCons conservation score, based on the multiple alignments of 10 primate genomes (including human) and a phylo-HMM. The larger the score, the more conserved the site. Scores ranges from 0 to 1.

S¹

phastCons46way_primate_rankscore¹⁷

PhastCons46way_primate scores (PhastCons) were ranked among all phastCons46way_primate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons46way_primate scores in dbNSFP.

S¹

phyloP100way_vertebrate¹⁸

The phylogenetic p-values (phyloP) conservation score, representing the –log p-value under the null hypothesis of neutral evolution at the site based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site. Scores ranges from -20 to 10.

S¹

phyloP100way_vertebrate_rankscore¹⁸

PhyloP100way_vertebrate scores (phyloP) were ranked among all phyloP100way_vertebrate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP100way_vertebrate scores in dbNSFP.

S¹

phyloP46way_placental¹⁸

The phylogenetic p-values (phyloP) conservation score, which represents the –log p-value under the null hypothesis of neutral evolution at the site based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site. Scores range from –11.958 to 3.

S¹

phyloP46way_placental_rankscore¹⁸

PhyloP46way_placental scores (phyloP) were ranked among all phyloP46way_placental scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP46way_placental scores in dbNSFP.

S¹

phyloP46way_primate¹⁸

The phylogenetic p-values (phyloP) conservation score, which represents the –log p-value under the null hypothesis of neutral evolution at the site based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site. Scores ranges from -8.176 to 0.66.

S¹

phyloP46way_primate_rankscore¹⁸

PhyloP46way_primate scores (phyloP) were ranked among all phyloP46way_primate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP46way_primate scores in dbNSFP.

S¹

Pinnacle

The position on the template sequence where the peak reaches its top height.

P

pValue

For QSeq Peak Finder and MACS Peak Detection results, pValue score for each peak which is equal to the log₁₀ likelihood that the peak is “valid” multiplied by -10.

F

Q call

The Phred-like quality score of the called genotype. It is a measure of the confidence that the SNP is present in the sample on a 0-60 log10 scale. For combined SNPs and indels, Q call will be the minimum of all available columns at that reference position.

S⁸

QSeq ID

QSeq-generated ID used to link data between tables and to link workflows together.

G²⁰, E²⁰, I²⁰

qualifier

See the GO Annotation File Format 2.0 Guide for a description.

G²

raw_count¹⁹

The number of reads that were initially and uniquely assigned to an isoform, fragment or peak (i.e., reads placed only once). The raw_count value is not normalized, and repeated reads are excluded. It remains constant regardless of any normalization applied to the experiment

If there are duplicated genes, none of the reads will map uniquely. This makes it possible for a read to have a raw count of zero, but still have non-zero signal and fold change values. See example at the very bottom of this topic.

Note that the “Uniquely mapped count” is the total number of unique aligned reads with no normalization applied. This value is used in the calculation of (total_)raw_count, but not explicitly displayed in ArrayStar.

E, F, I²¹

raw DESeq2,

raw DESeq2-Gene

The rlog values from individual replicates.

G²⁵, I²⁵

raw P value

The standard non-FDR corrected P value. This column is only available in the Gene and Isoform tables if you choose a Bioconductor statistic (DESeq2, DESeq2-Local, edgeR, or edgeR-Local) in the Set Up Preprocessing page. In cases where the counts for a gene were zero or contained an extreme outlier(s), DESeq2 will return a value of NA (“not available”). ArrayStar displays these values as “-----”.

G²⁵, I²⁵

raw_repeat_count

The total fraction of repeat reads that map to the peak. For example, if one read maps equally well to two peaks, each peak would have a raw_repeat_count of 0.5. If multiple repeat reads map to a single peak, the proportions are summed to get the raw_repeat_count. This column is only available for QSeq Peak Finder results when repeat handling is used.

F, I²¹

read_count

The total number of reads.

I²⁵

ref seq

Reference sequence at the same position as the SNP.

S

ref ID

The base at this position on the reference chromosome.

S

ref pos

The position on the reference chromosome. This data derives from the SNP Position column in the Data Import Wizard.

S

refcodon

The reference codon.

S¹

Refseq_id

Refseq gene ID, from the HUGO Gene Nomenclature Committee (HGNC).

G⁴

Regularized logarithm (rlog) values from Bioconductor

Same as linear rlog reads.

G²⁵, I²⁵

repeat_distrib_count¹⁹

The proportional number of repeated reads assigned to this exon, gene or isoform. This number remains constant regardless of any normalization applied to the experiment. See example at the very bottom of this topic.

E²¹, I²¹

repeat_distrib_percent¹⁹

A rough estimate of the percentage of the total repeated reads which could have been assigned and that were assigned. In other words, he percentage of repeat_distrib_count in raw_repeat_count. This number remains constant regardless of any normalization applied to the experiment. See example at the very bottom of this topic.

E²¹, G²¹, I²¹

rlog

Same as linear rlog reads.

G²⁵, I²⁵

RPKM

The RPKM calculated for each exon (reads per million mapped reads in the experiment per kilobase of the exon). This option is only available if you chose RPKM-CN or zRPKM normalization.

E

RPKM median

The median RPKM of this exon in all applicable experiments (excluding RPKM < 1). This option is only available if you chose zRPKM normalization.

E

RPKM std dev

The standard deviation of RPKM of this exon in all applicable experiments (excluding RPKM < 1). This option is only available if you chose zRPKM normalization.

E

rs_dbSNP141

The reference SNP (rs) number from dbSNP 141.

S¹

SIFT_converted_rankscore²²

To obtain the rankscore, Sorting Intolerant from Tolerant (SIFT) scores were first converted to SIFTnew = (1-SIFT_ori), then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the largest (most damaging) rankscore is presented. Rankscores range from 0.02654 to 0.87932.

S¹

SIFT_pred²²

Sorting Intolerant from Tolerant (SIFT) prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences.

S¹

SIFT_score²²

Sorting Intolerant from Tolerant (SIFT) score is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences. Scores range from 0 to 1. The smaller the score the more likely the SNP has a damaging effect.

S¹

SiPhy_29way_logOdds²³

The SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site. Scores ranges from 0 to 37.9718.

S¹

SiPhy_29way_logOdds_rankscore²³

SiPhy_29way_logOdds scores (SiPhy) were ranked among all SiPhy_29way_logOdds scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of SiPhy_29way_logOdds scores in dbNSFP.

S¹

SiPhy_29way_pi²³

The estimated stationary distribution of A, C, G and T at the site, using a SiPhy algorithm that includes biased substitution patterns based on 29 mammals genomes.

S¹

SNP Base⁶

For diagnostic purposes only.

S⁵

SNP Gene Name

If the data in your project were imported through the Data Import Wizard, any columns you designated as “Gene IDs” will appear in this field.

G¹³

SNP%

The percentage of the sequence at this position in the assembly which varied from the reference.

S

SNPs¹⁴

A single-nucleotide polymorphism. This category is a summation of SNPs from each individual category (e.g. Nonsense, No-stop, etc.). Only substitutions are included in the count; indels are excluded.

G¹³

source file²⁴

The name and location of the template sequence file, or the template sequence on which the fragment occurs. If you downloaded templates from NCBI during Set Up Preprocessing, this will be the accession number for the template. If this column is used in a table, you can hover over the sequence name in the table for more information.

E¹¹, F¹¹, G¹¹, I¹¹, P¹¹

source seq length

The length, in base pairs, of the template sequence.

E¹¹, F¹¹, G¹¹, I¹¹, P¹¹

source sequence

The template sequence on which the gene occurs. If you downloaded templates from NCBI during Set Up Preprocessing, this will be the accession number for the template. If this column is used in a table, you can hover over the sequence name in the table for more information.

E¹¹, F¹¹, G¹¹, I¹¹, P¹¹

splice¹⁴

This change includes all SNPs that modify splicing. This category is a count of flags which can apply to any of the other categories.

G¹³

start

The start position of the fragment along the template sequence.

F, P

synonymous¹⁴

This change does not alter the amino acid sequence coded for in this (translated) coding region.

G¹³

target length

The target length of the fragment, equal to the end position minus the start position.

E¹¹, G¹¹, I¹¹

target range

The coordinate range of each feature or target within a table. May be a single coordinate range or a list of coordinate ranges for spliced features such as Isoforms.

E¹¹, G¹¹, I¹¹

taxon

See the GO Annotation File Format 2.0 Guide for a description.

G²

top height

The depth of the peak, in reads, at its highest point.

P

total RPKM

Total reads assigned per kilobase of target per million mapped reads.

G⁹

total_raw_count

This value can be applied to the Gene Table. It is similar to raw_count, available in the Isoform Table, except that it is totaled across the isoforms for that gene.

G⁹, G²⁵, I²⁵

total_read_count

This value can be applied to the Gene Table. It is similar to read_count, available in the Isoform Table, except that it is totaled across the isoforms for that gene.

G²⁵

total_repeat_distrib_count

This value can be applied to the Gene Table. It is similar to repeat_distrib_count, available in the Isoform Table, except that it is totaled across the isoforms for that gene.

G⁹, G²⁵

trait_association (GWAS)

Trait(s) with which the gene is associated, from the Genome-Wide Association Studies (GWAS) catalog.

G⁴

type

Whether it is a literal SNP or an indel. Available for SeqMan Pro data only.

S

ucsc_id

UCSC gene ID, from the HUGO Gene Nomenclature Committee (HGNC).

G⁴

Uniprot_aapos

Uniprot amino acid position.

S¹

Uniprot_acc

Uniprot accession number.

G⁴, S¹

Uniprot_id

Uniprot ID number.

G⁴, S¹

Upstream Gene

The name of the nearest upstream gene within 100 kilobases of the fragment or peak. If there is an intersecting gene, no upstream gene will be listed.

F, P

user ID

The position ID from a VCF SNP table embedded into an .assembly project that was imported to ArrayStar. This column type is not available if you imported the VCF SNP data into ArrayStar separately.

S⁵

vst

Variance Stabilizing Transformation value in log₂ scale.

G²⁵, I²⁵

Wald stat

Value from the Wald test which divides the log₂ fold change by the standard error to calculate a P value compared to a normal distribution.

G²⁵, I²⁵

with (or) from

See the GO Annotation File Format 2.0 Guide for a description.

G²

Note

Explanation

1

Variants workflow with SeqMan NGen data for users accessing the Variant Annotation Database.

2

All with imported GO annotations. This annotation may be available if you imported annotations post-project setup from the Gene Ontology Consortium (e.g., by using Data > Import Annotations). See the GO Annotation File Format 2.0 Guide for a description.

3

ChIP-Seq workflow only.

4

All with imported dbNSFP annotations (see Import Annotations Post-Project Setup).

5

Availability varies depending on 1) whether or not the ArrayStar project was created from a .assembly project; 2) whether or not that assembly was made using a genome template package; and 3) whether or not VCF data was imported along with the SeqMan NGen assembly and/or imported directly into ArrayStar (see Import Annotations Post-Project Setup).

6

Used for diagnostics of .assembly-based ArrayStar projects. Rather than adding this option to the Gene Table, most users should instead add the Called Seq column.

7

See the Gene Ontology Gene Product Information (GPI) File Format Guide.

8

Variants workflow using SeqMan NGen data only.

9

CNV workflow only, unless other letters appear in this column.

10

Evolutionary conservation Genomic Evolutionary Rate Profiling (GERP++; Cooper et al., 2005) GERP++ identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element had been neutral DNA, but which did not occur because the element was under functional constraint.

11

All workflows except Variants.

12

Availability is dependent on imported annotations.

13

Variants workflow only.

14

To generate the columns in the Variants workflow, ArrayStar gathers SNPs for quantification based on the criteria chosen by the user. (By default, Pnotref ≥ 50%, SNP% ≥ 5%). Then, numbers are generated for genes which have at least one quantifiable SNP. Note that “-----“ in a column denotes that the gene had no quantifiable SNPs. And if the corresponding SNP table entries consist of low-probability “No Change” calls, the Gene Table will display “-----“ in the same column.

15

Chun & Fay, 2009.

16

Schwarz et al., 2014.

17

PhastCons is part of Phylogenetic Analysis with Space/Time models (PHAST; Siepel,A. et al. 2005).

18

Phylogenetic P-values (PhyloP; Pollard KS et al., 2010).

19

ArrayStar divides repeated reads values proportionately amongst their targets, based upon the amount of unique signal value already assigned to those targets. The raw count, repeat distribution count and repeat distribution percentage are used, in part, to generate normalized expression values, typically RPKM. The final signal is raw_count + repeat_distrib_count, with normalization applied.

20

Only QSeq workflows.

21

RNA-Seq workflow only.

22

Sorting Intolerant from Tolerant (SIFT) SIFT prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences.

23

Site-Specific Phylogenetic Analysis (SiPhy; Garber M et al., 2009).

24

The availability of this column type depends on what annotations are included in your template sequences and what features you defined as genes during Set Up Preprocessing.

25

Only for templated RNA-Seq workflow using DESeq2 normalization.

Variable

Value

No normalization

RPKM normalization

RPM normalization

raw_count

137.000

137.000

137.000

repeat_distrib_count

4875.762

4875.762

4875.762

repeat_distrib_percent

51.620

51.620

51.620

Linear expression level

5012.762

81.088

209.207

Log₂ expression level

12.29139

6.34142

7.70879