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LETTER: Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster
- Huaiyu Mi,
- Jody Vandergriff,
- Michael Campbell,
- Apurva Narechania,
- William Majoros,
- Suzanna Lewis,
- Paul D. Thomas,
- and Michael Ashburner
Genome Res. September 2003 13: 2118-2128; doi:10.1101/gr.771603
...makes a different type of homology error: a “low score error.” Four of the eight homology errors made by PANTHER were of this type. Sequences are annotated by scoring proteins against a library of ∼40,000 Hidden Markov Models (HMMs) that represent different families and subfamilies of proteins...
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Resource: The Drosophila brain on cocaine at single-cell resolution
- Brandon M. Baker,
- Sneha S. Mokashi,
- Vijay Shankar,
- Jeffrey S. Hatfield,
- Rachel C. Hannah,
- Trudy F.C. Mackay,
- and Robert R.H. Anholt
Genome Res. October 2021 31: 1927-1937; Published in Advance May 25, 2021, doi:10.1101/gr.268037.120
...Markers function (test.use equals; “MAST”, assay equals; “SCT”, slot equals; “scale.data”) for each cluster to calculate DE. Clusters with a sufficient number of DEGs were subjected to pathway enrichment analysis using the statistical overrepresentation test using PANTHER (Thomas et al. 2003) and Reactome...
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Resource: Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling
- Jian Ming Khor,
- Jennifer Guerrero-Santoro,
- William Douglas,
- and Charles A. Ettensohn
Genome Res. September 2021 31: 1680-1692; Published in Advance July 30, 2021, doi:10.1101/gr.275684.121
...://github.com/anderssonrobin/enhancers/blob/master/scripts/bidir_enhancers).Additional bioinformatic analysisManipulation of peak and gene BED files was performed using BEDTools (v2.19.1) (Quinlan and Hall 2010). Distances between eRNA peaks and genes were determined using the “closest” and “intersect” utilities in BEDTools. GO term enrichment analyses were performed using the PANTHER webtool (Mi...
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Method: Time course regulatory analysis based on paired expression and chromatin accessibility data
- Zhana Duren,
- Xi Chen,
- Jingxue Xin,
- Yong Wang,
- and Wing Hung Wong
Genome Res. April 2020 30: 622-634; Published in Advance March 18, 2020, doi:10.1101/gr.257063.119
...expression level of the ith gene in RA time course data, FPKMi,t represents the expression level of the ith gene on the tth time point. We select the top specific 200 genes and GO enrichment analysis based on PANTHER Version 14.1 (Thomas et al. 2003).Reprogramming...
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Research: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes
- Joe R. Harman,
- Ross Thorne,
- Max Jamilly,
- Marta Tapia,
- Nicholas T. Crump,
- Siobhan Rice,
- Ryan Beveridge,
- Edward Morrissey,
- Marella F.T.R. de Bruijn,
- Irene Roberts,
- Anindita Roy,
- Tudor A. Fulga,
- and Thomas A. Milne
Genome Res. July 2021 31: 1159-1173; Published in Advance June 4, 2021, doi:10.1101/gr.268490.120
...PANTHER (v. 15) (Thomas et al. 2003). Published expression data was sourced from NCBI Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) accessions GSE85988, GSE83671, and GSE139437 (Supplemental Table S3).Chromatin Immunoprecipitation (ChIP)The cells (1 × 107–8) were fixed and sonicated...
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Research: Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells
- Tate Tunstall,
- Richard Kock,
- Jiri Vahala,
- Mark Diekhans,
- Ian Fiddes,
- Joel Armstrong,
- Benedict Paten,
- Oliver A. Ryder,
- and Cynthia C. Steiner
Genome Res. June 2018 28: 780-788; Published in Advance May 24, 2018, doi:10.1101/gr.227603.117
...the HGNC code and Gene Ontology for all genes that contained SNPs that fall within transcribed regions. Specific Tunstall et al. 786 Genome Research www..org enrichment for a particular class of genes was identified using PANTHER (Mi et al. 2013). Data access The data generated from this study have been...
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Resource: Multiparameter functional diversity of human C2H2 zinc finger proteins
- Frank W. Schmitges,
- Ernest Radovani,
- Hamed S. Najafabadi,
- Marjan Barazandeh,
- Laura F. Campitelli,
- Yimeng Yin,
- Arttu Jolma,
- Guoqing Zhong,
- Hongbo Guo,
- Tharsan Kanagalingam,
- Wei F. Dai,
- Jussi Taipale,
- Andrew Emili,
- Jack F. Greenblatt,
- and Timothy R. Hughes
Genome Res. December 2016 26: 1742-1752; Published in Advance November 16, 2016, doi:10.1101/gr.209643.116
...excluded proteins with low variation among all samples (see Supplemental Methods and Supplemental Tables S5–S8). PANTHER (Thomas et al. 2003) overrepresentation analysis of the 344 remaining preys indicates predominantly nuclear roles of the C2H2-ZF proteins in this study, consistent with the fact that all...
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Research: Gene regulation underlies environmental adaptation in house mice
- Katya L. Mack,
- Mallory A. Ballinger,
- Megan Phifer-Rixey,
- and Michael W. Nachman
Genome Res. November 2018 28: 1636-1645; Published in Advance September 7, 2018, doi:10.1101/gr.238998.118
...expression by annotating genes to pathways using the PANTHER database (Thomas et al. 2003). We saw a 1.57-fold enrichment of genes in this pathway compared to a background set of genes expressed in the liver (hypergeometric test, P = 0.018). We also find that the gene that encodes the only known...
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Research: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast
- Gregory T. Booth,
- Isabel X. Wang,
- Vivian G. Cheung,
- and John T. Lis
Genome Res. June 2016 26: 799-811; Published in Advance May 12, 2016, doi:10.1101/gr.204578.116
...(Supplemental Fig. S1B; Pelechano et al. 2013).To assess the amount of signal attributable to background in our PRO-cap experiments, we simultaneously prepared PRO-cap libraries from the same starting material in which nascent RNAs were not treated with Tobacco Acid Pyrophosphatase (TAP) prior to 5′ adaptor...
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Method: Massively parallel cis-regulatory analysis in the mammalian central nervous system
- Susan Q. Shen,
- Connie A. Myers,
- Andrew E.O. Hughes,
- Leah C. Byrne,
- John G. Flannery,
- and Joseph C. Corbo
Genome Res. February 2016 26: 238-255; Published in Advance November 17, 2015, doi:10.1101/gr.193789.115
...in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted...

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