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1. Human Protein Reference Database - 2009 update.

Author

T. S. Keshava Prasad, Renu Goel, Kumaran Kandasamy, Shivakumar Keerthikumar, Sameer Kumar 0002, Suresh Mathivanan, Deepthi Telikicherla, Rajesh Raju, Beema Shafreen, Abhilash Venugopal, Lavanya Balakrishnan, Arivusudar Marimuthu, Sutopa Banerjee, Devi S. Somanathan, Aimy Sebastian, Sandhya Rani, Somak Ray, C. J. Harrys Kishore, Sashi Kanth, Mukhtar Ahmed, Manoj K. Kashyap, Riaz Mohmood, Y. L. Ramachandra, V. Krishna, B. Abdul Rahiman, S. Sujatha Mohan, Prathibha Ranganathan, Subhashri Ramabadran, Raghothama Chaerkady, and Akhilesh Pandey

Published
2009
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2. NetSlim: high-confidence curated signaling maps.

Author

Rajesh Raju, Vishalakshi Nanjappa, Lavanya Balakrishnan, Aneesha Radhakrishnan, Joji Kurian Thomas, Jyoti Sharma, Maozhen Tian, Shyam Mohan Palapetta, Tejaswini Subbannayya, Nirujogi Raja Sekhar, Babylakshmi Muthusamy, Renu Goel, Yashwanth Subbannayya, Deepthi Telikicherla, Mitali Bhattacharjee, Sneha M. Pinto, Nazia Syed, Srinivas Manda Srikanth, Gajanan J. Sathe, Sartaj Ahmad, Sandip N. Chavan, Ghantasala S. Sameer Kumar, Arivusudar Marimuthu, T. S. Keshava Prasad, H. C. Harsha, B. Abdul Rahiman, Osamu Ohara, Gary D. Bader, S. Sujatha Mohan, William P. Schiemann, and Akhilesh Pandey

Published
2011
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5. A pathway map of prolactin signaling

Author

Aneesha Radhakrishnan, Kulkarni Kale Urmila, Joji Kurian Thomas, B. Abdul Rahiman, Premendu P. Mathur, Shyam Mohan Palapetta, Deepthi Telikicherla, T. S. Keshava Prasad, Nirvana Tuladhar, Akhilesh Pandey, H. C. Harsha, Carrie S. Shemanko, Aditi Chatterjee, Tejaswini Subbannayya, Rajesh Raju, Desai Dattatraya Venkatesh, and Renu Goel

Subjects
endocrine system, medicine.medical_specialty, Prolactin receptor, Cell Biology, Biology, Biochemistry, Prolactin, Prolactin signaling pathway, Technical Report, Endocrinology, medicine.anatomical_structure, Anterior pituitary, Internal medicine, medicine, Placental lactogen, Kinase activity, Signal transduction, Receptor, Molecular Biology, hormones, hormone substitutes, and hormone antagonists
Abstract

Prolactin (PRL) is a pleiotropic polypeptide hormone secreted primarily by the lactotrophic cells of anterior pituitary gland in vertebrates (Freeman et al. 2000). This hormone family includes placental lactogen (PL) and growth hormone (GH) (Corbacho et al. 2002). Prolactin plays a major role in lactation and reproduction and has been shown to have a multitude of effects relating to growth, development, metabolism, immunoregulation and protection (Ben-Jonathan et al. 2006). The prolactin signaling pathway is initiated by the binding of prolactin with the prolactin receptor (PRLR), a member of class I cytokine receptor superfamily (Binart et al. 2000), which is expressed in a variety of tissues. The PRLR comprises of an extracellular ligand binding domain, a transmembrane domain and an intracellular domain. The PRLR lacks intrinsic kinase activity and transduces signal through kinases that interact with its cytoplasmic tail. Three constitutively active variants of the receptor have been reported in humans (Goffin et al. 2010). Though the signaling reactions downstream of the longest isoform of prolactin receptor have been well established, little is known about prolactin signaling initiated by six other isoforms (Bouilly et al. 2011). Studies also indicate that binding affinity of the human prolactin receptor to nonhuman prolactin is lower than human prolactin (Utama et al. 2009). The prolactin receptor also binds to hPL and hGH leading to the activation of downstream pathways. However, we have not considered these reactions in the current study. This study reports only those reactions, which occur upon stimulation of prolactin receptor with prolactin, based on the criteria described previously (Nanjappa et al. 2011). Availability of signaling pathway information is useful to the biomedical research community, especially for systems biology approaches. Considering this, we have developed ‘NetPath’ as a resource of ligand-receptor specific signal transduction pathways (Kandasamy et al. 2010). As a part of this, we have carried out manual annotation of available information from the published literature for ligand-receptor signaling pathways (Raju et al. 2011a; Nanjappa et al. 2011; Telikicherla et al. 2011; Goel et al. 2012). Similarly, in this study, we enriched publicly available information pertaining to prolactin-prolactin receptor dependent signaling pathways and also generated a graphic map depicting the prolactin signaling pathway.

Published
2012
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6. Human Proteinpedia enables sharing of human protein data

Author

Ron Bose, Jean-Charles Sanchez, Young Jin Lee, Marcus Bantscheff, Pia Hønnerup Jensen, Yunping Zhu, Jonathan C. Trinidad, Juan Martínez-Heredia, Michael Moran, Samir K. Brahmachari, Pierre Gagné, Kripa Shankari, Jeffrey C. Smith, Jose-Manuel Vidal-Taboada, James P. DeLany, Shi Jun Sheng, Ragna Rönnholm, Xosé R. Bustelo, Helene L. Cardasis, Erik Björling, Ole N. Jensen, Pavel Gromov, Michael J. Dunn, Xiaoyue Wang, Guy G. Poirier, Greg T. Cantin, Richard J. Simpson, Kenny Helsens, Ming Zhou, Sumio Sugano, Samir M. Hanash, Prashantha Hebbar, Y. L. Ramachandra, Jennifer E. Van Eyk, Rafael Oliva, Philip C. Andrews, Lennart Martens, Julio E. Celis, B. Abdul Rahiman, Alexander Mehrle, Feixia Chu, Richard D. Smith, Philip A. Cole, Leroi V. DeSouza, Stefan Wiemann, Joseph A. Loo, Bernhard Kuster, Mauno Vihinen, Peter Jung, David C. Muddiman, Jayson A. Falkner, Osamu Ohara, Fredrik Levander, Gerald W. Hart, Mukhtar Ahmed, T. S. Keshava Prasad, Eric W. Deutsch, Riaz Mohmood, Indu Kheterpal, Jeffrey M. Gimble, John R. Yates, Catherine Fenselau, Timothy D. Veenstra, Julian Vasilescu, Brian M. Balgley, Heiko Hermeking, Johanna Salonen, Rainer Pepperkok, Michael Lefevre, William S. Hancock, Visith Thongboonkerd, Tao Xu, Beerelli Seshi, Christine A. Miller, Florian Gnad, Ravi Sirdeshmukh, Arnaud Droit, Renu Goel, Maarit Takatalo, Emanuel F. Petricoin, Mathias Uhlén, Vitor M. Faça, Billy Wu, Robert J. Cotter, Angelo M. De Marzo, Mark E. McComb, Alma S Burlingame, Oliver Hofmann, Martine Morzel, Rajasree Menon, Denis F. Hochstrasser, Peter James, Matthew J. Sullivan, Robin Wait, K. W. Michael Siu, H. C. Harsha, Hainard Alexandre, Megan S. Lim, Winston Hide, Kris Gevaert, Harald Mischak, Thierry Sayd, Matthias Mann, Blagoy Blagoev, Gerard Cagney, Xiangming Fang, Ralph H. Hruban, James D. Morgan, Joel S. Bader, Samuel O. Purvine, Fuchu He, Robert Moritz, Rob M. Ewing, Daniel Figeys, Min-Seok Kwon, Kumaran Kandasamy, Reiko F. Kikuno, Masaaki Oyama, Cecilia Gelfi, Gilbert S. Omenn, James P. McRedmond, Pierre Lescuyer, Kojo S.J. Elenitoba-Johnson, Akhilesh Pandey, Joël Vandekerckhove, Karin Hjernø, Subburaman Mohan, Jens Rick, Kyla Pennington, Raghothama Chaerkady, Henrik Molina, David M Horn, Faith A. Hays, Young Ki Paik, Balamurugan Periaswamy, Giulio Superti-Furga, Roman Körner, Gerard Drewes, Jun Zhong, E. Dransfield, Suresh Mathivanan, Robert H. Rice, David K. Crockett, Thomas A. Neubert, Minna Lehvaslaiho, K. Shivakumar, Catherine E. Costello, Hyoung Joo Lee, Christian Löbke, Keiryn L. Bennett, Nieves Ibarrola, Ramars Amanchy, Petra Zürbig, Vivekananda Shetty, Natalie G. Ahn, Ulrike Korf, J. Daniel Navarro, Anuradha Nalli, Prasanna Ramachandran, David J. States, Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Biological Systems Engineering, University of Wisconsin-Madison, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria, Royal Institute of Technology [Stockholm] (KTH ), University of California [San Francisco] (UC San Francisco), University of California (UC), Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Radiothérapie moléculaire (UMR 1030), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Université Laval [Québec] (ULaval), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Chemistry and Biochemistry Department (University of Maryland), University of Maryland [College Park], University of Maryland System-University of Maryland System, Ottawa Institute of Systems Biology, University of Ottawa [Ottawa], Cabinet de Médecine Générale (Cabinet PG), Ville, Flanders Institute for Biotechnology, Beijing Institute of Radiation medicine, South African National Bioinformatics Institute (SANBI), University of the Western Cape (UWC), Département de science des protéines humaines [Genève], Université de Genève = University of Geneva (UNIGE)-Faculté de médecine [Genève], Donders Institute for Brain, Cognition and Behaviour, Radboud University [Nijmegen], Fraunhofer German-Sino Lab for Mobile Communications (MCI), Fraunhofer Institute for Manufacturing Engineering and Automation (Fraunhofer IPA), Fraunhofer (Fraunhofer-Gesellschaft)-Fraunhofer (Fraunhofer-Gesellschaft), Max Planck Institute for Human Cognitive and Brain Sciences [Leipzig] (IMPNSC), Max-Planck-Gesellschaft, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Hôpitaux Universitaires de Genève (HUG), Department of Pathology, University of Utah, University of California [Los Angeles] (UCLA), Universiteit Gent = Ghent University (UGENT), Protein Analysis for Clinical Diagnosis and Pharmaceutical Research, Mosaiques Diagnostics and Therapeutics AG, Proteomics Resource Center, Rockfeller University, Auteur indépendant, Section des Sciences de la Terre, Université de Genève = University of Geneva (UNIGE), RIKEN Research Center for Allergy and Immunology, Yokohama (RCAI), Research Unit for Immune Homeostasis, Yonsei Proteome Research Center and Department of Biochemistry, Yonsei University, European Molecular Biology Laboratory [Heidelberg] (EMBL), Department of Molecular Pathology and Microbiology, Center for Applied Proteomics and Molecular Medicine-George Mason University [Fairfax], Axe cancer, Université Laval [Québec] (ULaval)-CHUQ Research Center, The University of Arizona Medical Center, University of Arizona, The University of Tokyo (UTokyo), Research Center for Molecular Medicine of the Austrian Academy of Sciences [Vienna, Austria] (CeMM ), Austrian Academy of Sciences (OeAW), Faculty of Biological and Environmental Sciences [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Medical Molecular Biology Unit, Mahidol University [Bangkok], National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH), Department of Experimental Medical Science, Lund University [Lund], Tsinghua University [Beijing] (THU), Deutsches Krebsforschungszentrum, Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Institut Européen des membranes (IEM), Université Montpellier 2 - Sciences et Techniques (UM2)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Mosaiques Diagnostics & Therapeutics AG, University of California [San Francisco] (UCSF), University of California, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Gustave Roussy (IGR)-Université Paris-Sud - Paris 11 (UP11), University of the Western Cape, Université de Genève (UNIGE)-Faculté de médecine [Genève], Radboud university [Nijmegen], Universiteit Gent = Ghent University [Belgium] (UGENT), University of Geneva [Switzerland], University of Helsinki, Université Montpellier 2 - Sciences et Techniques (UM2)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Hochstrasser, Denis, Lescuyer, Pierre, Moritz, Robert, Pepperkok, Rainer, and Sanchez, Jean-Charles

Subjects
Proteomics, Proteomics methods, Internationality, Magnetic Resonance Spectroscopy, Proteome, Information storage, [SDV]Life Sciences [q-bio], Biomedical Engineering, Information Storage and Retrieval, Proteome/*chemistry/classification/*metabolism, Bioengineering, Computational biology, Biology, Bioinformatics, Databases, Protein, Applied Microbiology and Biotechnology, Data type, Peptide Mapping, 03 medical and health sciences, User-Computer Interface, ddc:576, ComputingMilieux_MISCELLANEOUS, Database Management Systems, Magnetic Resonance Spectroscopy/methods, 030304 developmental biology, 0303 health sciences, Internet, business.industry, Peptide mapping, Gene Expression Profiling, 030302 biochemistry & molecular biology, Information Storage and Retrieval/*methods, Peptide Mapping/methods, Gene Expression Profiling/*methods, Molecular Medicine, The Internet, Proteomics/methods, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Software, Biotechnology
Abstract

Proteomic technologies, such as yeast two-hybrid, mass spectrometry (MS), protein/peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories.

Published
2008
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7. Wound healing activity of embelin isolated from the ethanol extract of leaves of Embelia ribes Burm

Author

K. L. Mankani, H. Raja Naika, H.M. Kumara Swamy, Kittappa M. Mahadevan, K. Shankarmurthy, B. Abdul Rahiman, Venkatarangaiah Krishna, and B.G. Harish

Subjects
Male, medicine.medical_specialty, Embelia ribes, Embelia, Ribes, Pharmacognosy, chemistry.chemical_compound, Granulation, Mice, Drug Discovery, medicine, Benzoquinones, Animals, Rats, Wistar, Pharmacology, Wound Healing, Ethanol, integumentary system, biology, Traditional medicine, Plant Extracts, Granulation tissue, biology.organism_classification, Surgery, Rats, Plant Leaves, medicine.anatomical_structure, chemistry, Female, Collagen, Wound healing
Abstract

Ethanol extract of the leaves of Embelia ribes Burm. (Myrsinaceae) and its isolated quinone compound embelin were screened for wound healing activity by excision, incision and dead space wound models on Swiss Albino Rats. Significant wound healing activity was observed in both ethanol crude extract (30 mg/ml) and the constituent treated groups. In embelin treated groups (4 mg/ml of 0.2% sodium alginate gel), epithelialization of the incision wound was faster with a high rate of wound contraction. The tensile strength of the incision wound was significantly increased than the ethanol extract. In dead space wound model also the weight of the granulation was increased indicating increase in collagenation. The histological examination of the granulation tissue of embelin treated group showed increased cross-linking of collagen fibers and absence of monocytes. The wound healing effect was comparatively evaluated with the standard skin ointment Framycetin.

Published
2006

8. NetPath: a public resource of curated signal transduction pathways

Author

Masato Kubo, Lavanya Balakrishnan, Rajesh Raju, Jon C. D. Houtman, Toshio Hirano, Deepthi Telikicherla, Christian Pecquet, Harrys K.C. Jacob, Daniel J. Navarro, Kumaran Kandasamy, Ghantasala S. Sameer Kumar, Roopashree Subbaiah, Sashi Kanth Gollapudi, Shyam Mohan, Raja Sekhar, B. Abdul Rahiman, Jian Xin Lin, T. S. Keshava Prasad, Subburaman Mohan, Sorin Draghici, S. Singh, Purvesh Khatri, Warren J. Leonard, Sudhir Gopal Tattikota, Vishalakshi Nanjappa, Abhilash K. Venugopal, Stephen Desiderio, Akhilesh Pandey, Suresh Mathivanan, Y. L. Ramachandra, Renu Goel, Osamu Ohara, Hariprasad Padhukasahasram, Shivakumar Keerthikumar, Jun Zhong, Yashwanth Subbannayya, Chris Sander, Gary D. Bader, Stefan N. Constantinescu, Jean-Christophe Renauld, and UCL - SSS/DDUV - Institut de Duve

Subjects
Immune signaling, Transcription, Genetic, Databases, Factual, Energy and redox metabolism [NCMLS 4], WikiPathways : Pathways for the people, Systems biology, Method, Apoptosis, Computational biology, Biology, Models, Biological, Biochemistry, Netpath, Access to Information, 03 medical and health sciences, 0302 clinical medicine, Cell Movement, Protein Interaction Mapping, Humans, Animals, 030304 developmental biology, Public resource, 0303 health sciences, Models, Genetic, Computational Biology, biochemical phenomena, metabolism, and nutrition, Mitochondrial medicine [IGMD 8], 030220 oncology & carcinogenesis, Immune System, Interleukin-2, Signal transduction, Software, Signal Transduction
Abstract

NetPath, a novel community resource of curated human signaling pathways is presented and its utility demonstrated using immune signaling data., We have developed NetPath as a resource of curated human signaling pathways. As an initial step, NetPath provides detailed maps of a number of immune signaling pathways, which include approximately 1,600 reactions annotated from the literature and more than 2,800 instances of transcriptionally regulated genes - all linked to over 5,500 published articles. We anticipate NetPath to become a consolidated resource for human signaling pathways that should enable systems biology approaches.

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9. Wound healing activity of embelin isolated from the ethanol extract of leaves of Embelia ribes Burm.

Author

Kumara Swamy HM, Krishna V, Shankarmurthy K, Abdul Rahiman B, Mankani KL, Mahadevan KM, Harish BG, and Raja Naika H

Subjects
Animals, Benzoquinones isolation & purification, Benzoquinones toxicity, Collagen metabolism, Ethanol chemistry, Female, Male, Mice, Plant Extracts chemistry, Plant Extracts pharmacology, Plant Extracts toxicity, Plant Leaves chemistry, Rats, Rats, Wistar, Benzoquinones pharmacology, Embelia chemistry, Wound Healing drug effects
Abstract

Ethanol extract of the leaves of Embelia ribes Burm. (Myrsinaceae) and its isolated quinone compound embelin were screened for wound healing activity by excision, incision and dead space wound models on Swiss Albino Rats. Significant wound healing activity was observed in both ethanol crude extract (30 mg/ml) and the constituent treated groups. In embelin treated groups (4 mg/ml of 0.2% sodium alginate gel), epithelialization of the incision wound was faster with a high rate of wound contraction. The tensile strength of the incision wound was significantly increased than the ethanol extract. In dead space wound model also the weight of the granulation was increased indicating increase in collagenation. The histological examination of the granulation tissue of embelin treated group showed increased cross-linking of collagen fibers and absence of monocytes. The wound healing effect was comparatively evaluated with the standard skin ointment Framycetin.

Published
2007
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