Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph

scientific article

Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph is …
instance of (P31):
scholarly articleQ13442814

External links are
P8978DBLP publication IDjournals/bioinformatics/RichardsMSCRL10
P356DOI10.1093/BIOINFORMATICS/BTQ203
P932PMC publication ID2881388
P698PubMed publication ID20529941
P5875ResearchGate publication ID44655694

P2093author name stringXinghua Lu
L Ashley Cowart
Adam J Richards
Brian Muller
Matthew Shotwell
Bäerbel Rohrer
P2860cites workSemantic similarity in biomedical ontologiesQ21145359
Gene ontology: tool for the unification of biologyQ23781406
From genomics to chemical genomics: new developments in KEGGQ24538628
Cluster analysis and display of genome-wide expression patternsQ24644463
Network biology: understanding the cell's functional organizationQ27861027
Knowledge-based analysis of microarray gene expression data by using support vector machinesQ27939386
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene listsQ28131785
Systematic determination of genetic network architectureQ28138580
Semantic similarity measures as tools for exploring the gene ontologyQ28211764
Thy-1 is critical for normal retinal developmentQ28594633
On Estimating RegressionQ29303512
Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptronsQ30745866
Ontological analysis of gene expression data: current tools, limitations, and open problemsQ30993399
Improved scoring of functional groups from gene expression data by decorrelating GO graph structureQ31036410
A multivariate approach for integrating genome-wide expression data and biological knowledgeQ31050518
GOGrapher: A Python library for GO graph representation and analysisQ33479340
Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene OntologyQ33490282
Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine.Q34363246
The genomics of yeast responses to environmental stress and starvationQ34794209
Novel metrics for evaluating the functional coherence of protein groups via protein semantic networkQ36570652
Neural reprogramming in retinal degeneration.Q36692268
A literature-based method for assessing the functional coherence of a gene groupQ37160519
GS2: an efficiently computable measure of GO-based similarity of gene setsQ37168032
Multidestructive pathways triggered in photoreceptor cell death of the rd mouse as determined through gene expression profilingQ38339652
A new method to measure the semantic similarity of GO termsQ38398724
Multiple testing on the directed acyclic graph of gene ontology.Q38514569
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applicationsQ38516098
A graph-theoretic modeling on GO space for biological interpretation of gene clustersQ38522164
Gene expression profiles of mouse retinas during the second and third postnatal weeksQ40315875
From mice to men: the cyclic GMP phosphodiesterase gene in vision and disease. The Proctor Lecture.Q40584439
Transcriptional regulation and function during the human cell cycleQ43515454
Dopamine has a critical role in photoreceptor degeneration in the rd mouseQ44038221
POWER_SAGE: comparing statistical tests for SAGE experimentsQ52068990
The Structure and Function of Complex NetworksQ55879008
An analysis of variance test for normality (complete samples)Q57253423
Silhouettes: A graphical aid to the interpretation and validation of cluster analysisQ57380611
P433issue12
P407language of work or nameEnglishQ1860
P921main subjectontologyQ324254
Gene OntologyQ135085
P304page(s)i79-87
P577publication date2010-06-01
P1433published inBioinformaticsQ4914910
P1476titleAssessing the functional coherence of gene sets with metrics based on the Gene Ontology graph
P478volume26

Reverse relations

cites work (P2860)
Q33911818Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis
Q35101877Conceptualization of molecular findings by mining gene annotations
Q30620822From Data towards Knowledge: Revealing the Architecture of Signaling Systems by Unifying Knowledge Mining and Data Mining of Systematic Perturbation Data
Q27321393Functional coherence metrics in protein families
Q34008003GO-based functional dissimilarity of gene sets
Q51511475GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets
Q40855428Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits.
Q30874969Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model
Q34149135Identifying informative subsets of the Gene Ontology with information bottleneck methods
Q30531263Literature aided determination of data quality and statistical significance threshold for gene expression studies
Q33817492RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis
Q34530741Revealing functionally coherent subsets using a spectral clustering and an information integration approach
Q38385125Semantic Similarity in the Gene Ontology
Q28685216The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation

Search more.