FTFD: An informatics pipeline supporting phylogenomic analysis of fungal transcription factors

Jongsun Park; Jaejin Park; Suwang Jang; Seryun Kim; Sunghyung Kong; Jaeyoung Choi; Kyohun Ahn; Juhyeon Kim; Seungmin Lee; Sunggon Kim; Bongsoo Park; Kyongyong Jung; Soonok Kim; Seogchan Kang; Yong Hwan Lee

doi:10.1093/bioinformatics/btn058

FTFD: An informatics pipeline supporting phylogenomic analysis of fungal transcription factors

Jongsun Park, Jaejin Park, Suwang Jang, Seryun Kim, Sunghyung Kong, Jaeyoung Choi, Kyohun Ahn, Juhyeon Kim, Seungmin Lee, Sunggon Kim, Bongsoo Park, Kyongyong Jung, Soonok Kim, Seogchan Kang, Yong Hwan Lee

Research output: Contribution to journal › Article › peer-review

129 Scopus citations

Abstract

Summary: Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31 832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species.

Original language	English (US)
Pages (from-to)	1024-1025
Number of pages	2
Journal	Bioinformatics
Volume	24
Issue number	7
DOIs	https://doi.org/10.1093/bioinformatics/btn058
State	Published - Apr 2008

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btn058

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title = "FTFD: An informatics pipeline supporting phylogenomic analysis of fungal transcription factors",

abstract = "Summary: Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31 832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species.",

author = "Jongsun Park and Jaejin Park and Suwang Jang and Seryun Kim and Sunghyung Kong and Jaeyoung Choi and Kyohun Ahn and Juhyeon Kim and Seungmin Lee and Sunggon Kim and Bongsoo Park and Kyongyong Jung and Soonok Kim and Seogchan Kang and Lee, {Yong Hwan}",

note = "Funding Information: This research was partially supported by grants from Crop Functional Genomics Center (CG1141) and Microbial Genomics and Applications Center (0462-20060021) of the 21st Century Frontier Research Program funded by the Ministry of Science and Technology and a grant from Biogreen21 Project (20050401034629) funded by Rural Development Administration to Y.H.L. J.P. thanks a graduate fellowship provided by the Ministry of Education through the Brain Korea 21 Project.",

year = "2008",

month = apr,

doi = "10.1093/bioinformatics/btn058",

language = "English (US)",

volume = "24",

pages = "1024--1025",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "7",

}

TY - JOUR

T1 - FTFD

T2 - An informatics pipeline supporting phylogenomic analysis of fungal transcription factors

AU - Park, Jongsun

AU - Park, Jaejin

AU - Jang, Suwang

AU - Kim, Seryun

AU - Kong, Sunghyung

AU - Choi, Jaeyoung

AU - Ahn, Kyohun

AU - Kim, Juhyeon

AU - Lee, Seungmin

AU - Kim, Sunggon

AU - Park, Bongsoo

AU - Jung, Kyongyong

AU - Kim, Soonok

AU - Kang, Seogchan

AU - Lee, Yong Hwan

N1 - Funding Information: This research was partially supported by grants from Crop Functional Genomics Center (CG1141) and Microbial Genomics and Applications Center (0462-20060021) of the 21st Century Frontier Research Program funded by the Ministry of Science and Technology and a grant from Biogreen21 Project (20050401034629) funded by Rural Development Administration to Y.H.L. J.P. thanks a graduate fellowship provided by the Ministry of Education through the Brain Korea 21 Project.

PY - 2008/4

Y1 - 2008/4

N2 - Summary: Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31 832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species.

AB - Summary: Genomes of more than 60 fungal species have been sequenced to date, yet there has been no systematic approach to analyze fungal transcription factors (TFs) kingdom widely. We developed a standardized pipeline for annotating TFs in fungal genomes. Resulting data have been archived in a new database termed the Fungal Transcription Factor Database (FTFD). In FTFD, 31 832 putative fungal TFs, identified from 62 fungal and 3 Oomycete species, were classified into 61 families and phylogenetically analyzed. The FTFD will serve as a community resource supporting comparative analyses of the distribution and domain structure of TFs within and across species.

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DO - 10.1093/bioinformatics/btn058

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SP - 1024

EP - 1025

JO - Bioinformatics

JF - Bioinformatics

IS - 7

ER -

FTFD: An informatics pipeline supporting phylogenomic analysis of fungal transcription factors

Abstract

All Science Journal Classification (ASJC) codes

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