A transcription factor as displayed in a network graph.
What is a node?
100
A method to group genes together with similar expression patterns.
What is clustering?
100
The number of times a given nucleotide is sequenced.
What is coverage?
100
Illumina sequencing utilizes this number of fluorophores to sequence.
What is four?
100
For Illumina or 454 sequencing this term refers to the number of base pairs of a sequence.
What is read length?
200
An interaction between a transcription factor and its target promoter in a network graph.
What is an edge?
200
A gene that is expressed more highly in one sample vs. another.
What is differentially expressed?
200
Coverage is not an appropriate metric for transcriptome sequencing because of this.
What is expression in multiple tissues or time points?
200
This molecule is released after formation of a phosphodiester bond and used as a substrate in 454 sequencing.
What is pyrophosphate?
200
In Illumina sequencing this term describes the number of sequences obtained for a particular library in one well relative to another.
What is sequencing depth?
300
A pattern that occurs more frequently in a network than expected by chance.
What is a network motif?
300
This distribution more closely approximates that of RNAseq data.
What is a negative binomial distribution?
300
Transcriptome assembly identifies this portion of a gene that is not exonic and that has polarity.
What is a UTR?
300
Occasionally a blotch of light can be produced which needs to be accounted for in this gene expression profiling data quality step.
What is within array normalization?
300
In the normalization method, FPKM, the number of reads that are aligned to a given gene are divided over this term.
What is transcript length or kilobase per million?
400
A pattern that occurs more frequently in a network than expected by chance.
What is a network motif?
400
A distance metric that groups genes together based on similarity in expression pattern (or shape) across multiple conditions.
What is Pearson correlation?
400
This feature of a gene is not easily annotated in sequence-based gene annotation algorithms and can change depending on developmental stage, tissue type or stimulus.
What are intron/exon junctions or alternatively spliced variants?
400
Illumina and 454 sequencing both use this step after addition of adapters.
What is clonal amplification?
400
In order to achieve as comprehensive of a transcriptome for assembly purposes it is ideal to sequence this.
What are multiple tissues or time points?
500
A network that was created by switching edges between nodes.
What is a randomized network?
500
A normalization method that looks at the distribution of quartiles.
What is scaling?
500
The study of other genomes to assist in annotation of de novo assembled transcriptomes.
What is comparative genomics?
500
This enzyme coverts pyrophosphate and uses this substrate to produce light indicative of formation of a phosphodiester bond.
What is ATP sulfyrase and luciferin?
500
This position of cDNA sequence is rarely sequenced because of reverse transcriptase fidelity.