Yun Jiang1, Cunshuan Xu. 1. Key Laboratory of Bioengineering, Henan Normal University, Henan, China. ryanyunjiang@hotmail.com
Abstract
BACKGROUND: It is difficult to measure precisely the phenotypic complexity of living organisms. Here we propose a method to calculate the minimal amount of genomic information needed to construct organism (effective information) as a measure of organismal complexity, by using permutation and combination formulas and Shannon's information concept. RESULTS: The results demonstrate that the calculated information correlates quite well with the intuitive organismal phenotypic complexity defined by traditional taxonomy and evolutionary theory. From viruses to human beings, the effective information gradually increases, from thousands of bits to hundreds of millions of bits. The simpler the organism is, the less the information; the more complex the organism, the more the information. About 13% of human genome is estimated as effective information or functional sequence. CONCLUSIONS: The effective information can be used as a quantitative measure of phenotypic complexity of living organisms and also as an estimate of functional fraction of genome.
BACKGROUND: It is difficult to measure precisely the phenotypic complexity of living organisms. Here we propose a method to calculate the minimal amount of genomic information needed to construct organism (effective information) as a measure of organismal complexity, by using permutation and combination formulas and Shannon's information concept. RESULTS: The results demonstrate that the calculated information correlates quite well with the intuitive organismal phenotypic complexity defined by traditional taxonomy and evolutionary theory. From viruses to human beings, the effective information gradually increases, from thousands of bits to hundreds of millions of bits. The simpler the organism is, the less the information; the more complex the organism, the more the information. About 13% of human genome is estimated as effective information or functional sequence. CONCLUSIONS: The effective information can be used as a quantitative measure of phenotypic complexity of living organisms and also as an estimate of functional fraction of genome.
Authors: Jean-Marc Aury; Olivier Jaillon; Laurent Duret; Benjamin Noel; Claire Jubin; Betina M Porcel; Béatrice Ségurens; Vincent Daubin; Véronique Anthouard; Nathalie Aiach; Olivier Arnaiz; Alain Billaut; Janine Beisson; Isabelle Blanc; Khaled Bouhouche; Francisco Câmara; Sandra Duharcourt; Roderic Guigo; Delphine Gogendeau; Michael Katinka; Anne-Marie Keller; Roland Kissmehl; Catherine Klotz; France Koll; Anne Le Mouël; Gersende Lepère; Sophie Malinsky; Mariusz Nowacki; Jacek K Nowak; Helmut Plattner; Julie Poulain; Françoise Ruiz; Vincent Serrano; Marek Zagulski; Philippe Dessen; Mireille Bétermier; Jean Weissenbach; Claude Scarpelli; Vincent Schächter; Linda Sperling; Eric Meyer; Jean Cohen; Patrick Wincker Journal: Nature Date: 2006-11-01 Impact factor: 49.962
Authors: V Wood; R Gwilliam; M-A Rajandream; M Lyne; R Lyne; A Stewart; J Sgouros; N Peat; J Hayles; S Baker; D Basham; S Bowman; K Brooks; D Brown; S Brown; T Chillingworth; C Churcher; M Collins; R Connor; A Cronin; P Davis; T Feltwell; A Fraser; S Gentles; A Goble; N Hamlin; D Harris; J Hidalgo; G Hodgson; S Holroyd; T Hornsby; S Howarth; E J Huckle; S Hunt; K Jagels; K James; L Jones; M Jones; S Leather; S McDonald; J McLean; P Mooney; S Moule; K Mungall; L Murphy; D Niblett; C Odell; K Oliver; S O'Neil; D Pearson; M A Quail; E Rabbinowitsch; K Rutherford; S Rutter; D Saunders; K Seeger; S Sharp; J Skelton; M Simmonds; R Squares; S Squares; K Stevens; K Taylor; R G Taylor; A Tivey; S Walsh; T Warren; S Whitehead; J Woodward; G Volckaert; R Aert; J Robben; B Grymonprez; I Weltjens; E Vanstreels; M Rieger; M Schäfer; S Müller-Auer; C Gabel; M Fuchs; A Düsterhöft; C Fritzc; E Holzer; D Moestl; H Hilbert; K Borzym; I Langer; A Beck; H Lehrach; R Reinhardt; T M Pohl; P Eger; W Zimmermann; H Wedler; R Wambutt; B Purnelle; A Goffeau; E Cadieu; S Dréano; S Gloux; V Lelaure; S Mottier; F Galibert; S J Aves; Z Xiang; C Hunt; K Moore; S M Hurst; M Lucas; M Rochet; C Gaillardin; V A Tallada; A Garzon; G Thode; R R Daga; L Cruzado; J Jimenez; M Sánchez; F del Rey; J Benito; A Domínguez; J L Revuelta; S Moreno; J Armstrong; S L Forsburg; L Cerutti; T Lowe; W R McCombie; I Paulsen; J Potashkin; G V Shpakovski; D Ussery; B G Barrell; P Nurse; L Cerrutti Journal: Nature Date: 2002-02-21 Impact factor: 49.962
Authors: Nicholas H Putnam; Thomas Butts; David E K Ferrier; Rebecca F Furlong; Uffe Hellsten; Takeshi Kawashima; Marc Robinson-Rechavi; Eiichi Shoguchi; Astrid Terry; Jr-Kai Yu; E Lia Benito-Gutiérrez; Inna Dubchak; Jordi Garcia-Fernàndez; Jeremy J Gibson-Brown; Igor V Grigoriev; Amy C Horton; Pieter J de Jong; Jerzy Jurka; Vladimir V Kapitonov; Yuji Kohara; Yoko Kuroki; Erika Lindquist; Susan Lucas; Kazutoyo Osoegawa; Len A Pennacchio; Asaf A Salamov; Yutaka Satou; Tatjana Sauka-Spengler; Jeremy Schmutz; Tadasu Shin-I; Atsushi Toyoda; Marianne Bronner-Fraser; Asao Fujiyama; Linda Z Holland; Peter W H Holland; Nori Satoh; Daniel S Rokhsar Journal: Nature Date: 2008-06-19 Impact factor: 49.962
Authors: Vishvanath Nene; Jennifer R Wortman; Daniel Lawson; Brian Haas; Chinnappa Kodira; Zhijian Jake Tu; Brendan Loftus; Zhiyong Xi; Karyn Megy; Manfred Grabherr; Quinghu Ren; Evgeny M Zdobnov; Neil F Lobo; Kathryn S Campbell; Susan E Brown; Maria F Bonaldo; Jingsong Zhu; Steven P Sinkins; David G Hogenkamp; Paolo Amedeo; Peter Arensburger; Peter W Atkinson; Shelby Bidwell; Jim Biedler; Ewan Birney; Robert V Bruggner; Javier Costas; Monique R Coy; Jonathan Crabtree; Matt Crawford; Becky Debruyn; David Decaprio; Karin Eiglmeier; Eric Eisenstadt; Hamza El-Dorry; William M Gelbart; Suely L Gomes; Martin Hammond; Linda I Hannick; James R Hogan; Michael H Holmes; David Jaffe; J Spencer Johnston; Ryan C Kennedy; Hean Koo; Saul Kravitz; Evgenia V Kriventseva; David Kulp; Kurt Labutti; Eduardo Lee; Song Li; Diane D Lovin; Chunhong Mao; Evan Mauceli; Carlos F M Menck; Jason R Miller; Philip Montgomery; Akio Mori; Ana L Nascimento; Horacio F Naveira; Chad Nusbaum; Sinéad O'leary; Joshua Orvis; Mihaela Pertea; Hadi Quesneville; Kyanne R Reidenbach; Yu-Hui Rogers; Charles W Roth; Jennifer R Schneider; Michael Schatz; Martin Shumway; Mario Stanke; Eric O Stinson; Jose M C Tubio; Janice P Vanzee; Sergio Verjovski-Almeida; Doreen Werner; Owen White; Stefan Wyder; Qiandong Zeng; Qi Zhao; Yongmei Zhao; Catherine A Hill; Alexander S Raikhel; Marcelo B Soares; Dennis L Knudson; Norman H Lee; James Galagan; Steven L Salzberg; Ian T Paulsen; George Dimopoulos; Frank H Collins; Bruce Birren; Claire M Fraser-Liggett; David W Severson Journal: Science Date: 2007-05-17 Impact factor: 47.728
Authors: Erica Sodergren; George M Weinstock; Eric H Davidson; R Andrew Cameron; Richard A Gibbs; Robert C Angerer; Lynne M Angerer; Maria Ina Arnone; David R Burgess; Robert D Burke; James A Coffman; Michael Dean; Maurice R Elphick; Charles A Ettensohn; Kathy R Foltz; Amro Hamdoun; Richard O Hynes; William H Klein; William Marzluff; David R McClay; Robert L Morris; Arcady Mushegian; Jonathan P Rast; L Courtney Smith; Michael C Thorndyke; Victor D Vacquier; Gary M Wessel; Greg Wray; Lan Zhang; Christine G Elsik; Olga Ermolaeva; Wratko Hlavina; Gretchen Hofmann; Paul Kitts; Melissa J Landrum; Aaron J Mackey; Donna Maglott; Georgia Panopoulou; Albert J Poustka; Kim Pruitt; Victor Sapojnikov; Xingzhi Song; Alexandre Souvorov; Victor Solovyev; Zheng Wei; Charles A Whittaker; Kim Worley; K James Durbin; Yufeng Shen; Olivier Fedrigo; David Garfield; Ralph Haygood; Alexander Primus; Rahul Satija; Tonya Severson; Manuel L Gonzalez-Garay; Andrew R Jackson; Aleksandar Milosavljevic; Mark Tong; Christopher E Killian; Brian T Livingston; Fred H Wilt; Nikki Adams; Robert Bellé; Seth Carbonneau; Rocky Cheung; Patrick Cormier; Bertrand Cosson; Jenifer Croce; Antonio Fernandez-Guerra; Anne-Marie Genevière; Manisha Goel; Hemant Kelkar; Julia Morales; Odile Mulner-Lorillon; Anthony J Robertson; Jared V Goldstone; Bryan Cole; David Epel; Bert Gold; Mark E Hahn; Meredith Howard-Ashby; Mark Scally; John J Stegeman; Erin L Allgood; Jonah Cool; Kyle M Judkins; Shawn S McCafferty; Ashlan M Musante; Robert A Obar; Amanda P Rawson; Blair J Rossetti; Ian R Gibbons; Matthew P Hoffman; Andrew Leone; Sorin Istrail; Stefan C Materna; Manoj P Samanta; Viktor Stolc; Waraporn Tongprasit; Qiang Tu; Karl-Frederik Bergeron; Bruce P Brandhorst; James Whittle; Kevin Berney; David J Bottjer; Cristina Calestani; Kevin Peterson; Elly Chow; Qiu Autumn Yuan; Eran Elhaik; Dan Graur; Justin T Reese; Ian Bosdet; Shin Heesun; Marco A Marra; Jacqueline Schein; Michele K Anderson; Virginia Brockton; Katherine M Buckley; Avis H Cohen; Sebastian D Fugmann; Taku Hibino; Mariano Loza-Coll; Audrey J Majeske; Cynthia Messier; Sham V Nair; Zeev Pancer; David P Terwilliger; Cavit Agca; Enrique Arboleda; Nansheng Chen; Allison M Churcher; F Hallböök; Glen W Humphrey; Mohammed M Idris; Takae Kiyama; Shuguang Liang; Dan Mellott; Xiuqian Mu; Greg Murray; Robert P Olinski; Florian Raible; Matthew Rowe; John S Taylor; Kristin Tessmar-Raible; D Wang; Karen H Wilson; Shunsuke Yaguchi; Terry Gaasterland; Blanca E Galindo; Herath J Gunaratne; Celina Juliano; Masashi Kinukawa; Gary W Moy; Anna T Neill; Mamoru Nomura; Michael Raisch; Anna Reade; Michelle M Roux; Jia L Song; Yi-Hsien Su; Ian K Townley; Ekaterina Voronina; Julian L Wong; Gabriele Amore; Margherita Branno; Euan R Brown; Vincenzo Cavalieri; Véronique Duboc; Louise Duloquin; Constantin Flytzanis; Christian Gache; François Lapraz; Thierry Lepage; Annamaria Locascio; Pedro Martinez; Giorgio Matassi; Valeria Matranga; Ryan Range; Francesca Rizzo; Eric Röttinger; Wendy Beane; Cynthia Bradham; Christine Byrum; Tom Glenn; Sofia Hussain; Gerard Manning; Esther Miranda; Rebecca Thomason; Katherine Walton; Athula Wikramanayke; Shu-Yu Wu; Ronghui Xu; C Titus Brown; Lili Chen; Rachel F Gray; Pei Yun Lee; Jongmin Nam; Paola Oliveri; Joel Smith; Donna Muzny; Stephanie Bell; Joseph Chacko; Andrew Cree; Stacey Curry; Clay Davis; Huyen Dinh; Shannon Dugan-Rocha; Jerry Fowler; Rachel Gill; Cerrissa Hamilton; Judith Hernandez; Sandra Hines; Jennifer Hume; Laronda Jackson; Angela Jolivet; Christie Kovar; Sandra Lee; Lora Lewis; George Miner; Margaret Morgan; Lynne V Nazareth; Geoffrey Okwuonu; David Parker; Ling-Ling Pu; Rachel Thorn; Rita Wright Journal: Science Date: 2006-11-10 Impact factor: 47.728
Authors: S G Gregory; K F Barlow; K E McLay; R Kaul; D Swarbreck; A Dunham; C E Scott; K L Howe; K Woodfine; C C A Spencer; M C Jones; C Gillson; S Searle; Y Zhou; F Kokocinski; L McDonald; R Evans; K Phillips; A Atkinson; R Cooper; C Jones; R E Hall; T D Andrews; C Lloyd; R Ainscough; J P Almeida; K D Ambrose; F Anderson; R W Andrew; R I S Ashwell; K Aubin; A K Babbage; C L Bagguley; J Bailey; H Beasley; G Bethel; C P Bird; S Bray-Allen; J Y Brown; A J Brown; D Buckley; J Burton; J Bye; C Carder; J C Chapman; S Y Clark; G Clarke; C Clee; V Cobley; R E Collier; N Corby; G J Coville; J Davies; R Deadman; M Dunn; M Earthrowl; A G Ellington; H Errington; A Frankish; J Frankland; L French; P Garner; J Garnett; L Gay; M R J Ghori; R Gibson; L M Gilby; W Gillett; R J Glithero; D V Grafham; C Griffiths; S Griffiths-Jones; R Grocock; S Hammond; E S I Harrison; E Hart; E Haugen; P D Heath; S Holmes; K Holt; P J Howden; A R Hunt; S E Hunt; G Hunter; J Isherwood; R James; C Johnson; D Johnson; A Joy; M Kay; J K Kershaw; M Kibukawa; A M Kimberley; A King; A J Knights; H Lad; G Laird; S Lawlor; D A Leongamornlert; D M Lloyd; J Loveland; J Lovell; M J Lush; R Lyne; S Martin; M Mashreghi-Mohammadi; L Matthews; N S W Matthews; S McLaren; S Milne; S Mistry; M J F Moore; T Nickerson; C N O'Dell; K Oliver; A Palmeiri; S A Palmer; A Parker; D Patel; A V Pearce; A I Peck; S Pelan; K Phelps; B J Phillimore; R Plumb; J Rajan; C Raymond; G Rouse; C Saenphimmachak; H K Sehra; E Sheridan; R Shownkeen; S Sims; C D Skuce; M Smith; C Steward; S Subramanian; N Sycamore; A Tracey; A Tromans; Z Van Helmond; M Wall; J M Wallis; S White; S L Whitehead; J E Wilkinson; D L Willey; H Williams; L Wilming; P W Wray; Z Wu; A Coulson; M Vaudin; J E Sulston; R Durbin; T Hubbard; R Wooster; I Dunham; N P Carter; G McVean; M T Ross; J Harrow; M V Olson; S Beck; J Rogers; D R Bentley; R Banerjee; S P Bryant; D C Burford; W D H Burrill; S M Clegg; P Dhami; O Dovey; L M Faulkner; S M Gribble; C F Langford; R D Pandian; K M Porter; E Prigmore Journal: Nature Date: 2006-05-18 Impact factor: 49.962
Authors: M D Adams; S E Celniker; R A Holt; C A Evans; J D Gocayne; P G Amanatides; S E Scherer; P W Li; R A Hoskins; R F Galle; R A George; S E Lewis; S Richards; M Ashburner; S N Henderson; G G Sutton; J R Wortman; M D Yandell; Q Zhang; L X Chen; R C Brandon; Y H Rogers; R G Blazej; M Champe; B D Pfeiffer; K H Wan; C Doyle; E G Baxter; G Helt; C R Nelson; G L Gabor; J F Abril; A Agbayani; H J An; C Andrews-Pfannkoch; D Baldwin; R M Ballew; A Basu; J Baxendale; L Bayraktaroglu; E M Beasley; K Y Beeson; P V Benos; B P Berman; D Bhandari; S Bolshakov; D Borkova; M R Botchan; J Bouck; P Brokstein; P Brottier; K C Burtis; D A Busam; H Butler; E Cadieu; A Center; I Chandra; J M Cherry; S Cawley; C Dahlke; L B Davenport; P Davies; B de Pablos; A Delcher; Z Deng; A D Mays; I Dew; S M Dietz; K Dodson; L E Doup; M Downes; S Dugan-Rocha; B C Dunkov; P Dunn; K J Durbin; C C Evangelista; C Ferraz; S Ferriera; W Fleischmann; C Fosler; A E Gabrielian; N S Garg; W M Gelbart; K Glasser; A Glodek; F Gong; J H Gorrell; Z Gu; P Guan; M Harris; N L Harris; D Harvey; T J Heiman; J R Hernandez; J Houck; D Hostin; K A Houston; T J Howland; M H Wei; C Ibegwam; M Jalali; F Kalush; G H Karpen; Z Ke; J A Kennison; K A Ketchum; B E Kimmel; C D Kodira; C Kraft; S Kravitz; D Kulp; Z Lai; P Lasko; Y Lei; A A Levitsky; J Li; Z Li; Y Liang; X Lin; X Liu; B Mattei; T C McIntosh; M P McLeod; D McPherson; G Merkulov; N V Milshina; C Mobarry; J Morris; A Moshrefi; S M Mount; M Moy; B Murphy; L Murphy; D M Muzny; D L Nelson; D R Nelson; K A Nelson; K Nixon; D R Nusskern; J M Pacleb; M Palazzolo; G S Pittman; S Pan; J Pollard; V Puri; M G Reese; K Reinert; K Remington; R D Saunders; F Scheeler; H Shen; B C Shue; I Sidén-Kiamos; M Simpson; M P Skupski; T Smith; E Spier; A C Spradling; M Stapleton; R Strong; E Sun; R Svirskas; C Tector; R Turner; E Venter; A H Wang; X Wang; Z Y Wang; D A Wassarman; G M Weinstock; J Weissenbach; S M Williams; K C Worley; D Wu; S Yang; Q A Yao; J Ye; R F Yeh; J S Zaveri; M Zhan; G Zhang; Q Zhao; L Zheng; X H Zheng; F N Zhong; W Zhong; X Zhou; S Zhu; X Zhu; H O Smith; R A Gibbs; E W Myers; G M Rubin; J C Venter Journal: Science Date: 2000-03-24 Impact factor: 47.728
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