Short tutorials on how to use the web-based tool DAVID - Database for Annotation, Visualization and Integrated Discovery) - http://david.abcc.ncifcrf.gov/
DAVID provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
Information recovery is the recovery of things (objects, Web pages, archives, and so forth) that fulfill explicit conditions set in an ordinary articulation like query. While IR targets fulfilling a bit of client data need generally communicated in common language, information recovery targets figuring out which records contain the specific terms of the user queries.
INTRODUCTION
A PERFECT THERAPEUTIC DRUG
DRUG DISCOVERY- HISTORY
MODERN DRUG DISCOVERY
BIOINFORATICS IN DRUG DISCOVERY
DRUG DISCOVERY BASED ON BIOINFORMATIC TOOLS
BIOINFORMATICS IN COMPUTER-AIDED DRUG DISCOVERY
ECONOMICS OF DRUG DISCOVERY
CONCLUSION
REFERENCES
Information recovery is the recovery of things (objects, Web pages, archives, and so forth) that fulfill explicit conditions set in an ordinary articulation like query. While IR targets fulfilling a bit of client data need generally communicated in common language, information recovery targets figuring out which records contain the specific terms of the user queries.
INTRODUCTION
A PERFECT THERAPEUTIC DRUG
DRUG DISCOVERY- HISTORY
MODERN DRUG DISCOVERY
BIOINFORATICS IN DRUG DISCOVERY
DRUG DISCOVERY BASED ON BIOINFORMATIC TOOLS
BIOINFORMATICS IN COMPUTER-AIDED DRUG DISCOVERY
ECONOMICS OF DRUG DISCOVERY
CONCLUSION
REFERENCES
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
Protein Sequence, Structure, and Functional Databases: UniProtKB, Swiss-Prot, TrEMBL, PIR, MIPS, PROSITE, PRINTS, BLOCKS, Pfam, NDRB, OWL, PDB, SCOP, CATH, NDB, PQS, SYSTERS, and Motif. Presented at UGC Sponsored National Workshop on Bioinformatics and Sequence Analysis conducted by Nesamony Memorial Christian College, Marthandam on 9th and 10th October, 2017 by Prof. T. Ashok Kumar
Drug and Chemical Databases 2018 - Drug DiscoveryGirinath Pillai
Latest collection of Chemical and Drug Databases for Biological Research as well as Drug Design studies. Databases statistics, links and overview data with CADD introduction.
INTRODUCTION
WHAT IS DATA AND DATABASE?
WHAT IS BIOLOGICAL DATABASE?
TYPES OF BIOLOGICAL DATABASE
PRIMARY DATABASE
Nucleic acid sequence database
Protein sequence database
SECONDARY DATABASE
COMPOSITE DATABASE
TERTIARY DATABASE
WHY NEED?
CONCLUSION
REFRENCES
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
Protein Sequence, Structure, and Functional Databases: UniProtKB, Swiss-Prot, TrEMBL, PIR, MIPS, PROSITE, PRINTS, BLOCKS, Pfam, NDRB, OWL, PDB, SCOP, CATH, NDB, PQS, SYSTERS, and Motif. Presented at UGC Sponsored National Workshop on Bioinformatics and Sequence Analysis conducted by Nesamony Memorial Christian College, Marthandam on 9th and 10th October, 2017 by Prof. T. Ashok Kumar
Drug and Chemical Databases 2018 - Drug DiscoveryGirinath Pillai
Latest collection of Chemical and Drug Databases for Biological Research as well as Drug Design studies. Databases statistics, links and overview data with CADD introduction.
INTRODUCTION
WHAT IS DATA AND DATABASE?
WHAT IS BIOLOGICAL DATABASE?
TYPES OF BIOLOGICAL DATABASE
PRIMARY DATABASE
Nucleic acid sequence database
Protein sequence database
SECONDARY DATABASE
COMPOSITE DATABASE
TERTIARY DATABASE
WHY NEED?
CONCLUSION
REFRENCES
Bioinformatics Introduction and Use of BLAST ToolJesminBinti
Hi, I am Jesmin, studying MCSE. I think this file will help you if you want to know the basic information about Bioinformatics and the use of BLAST tool. The BLAST tool is the tool that matches the sequences of DNA,RNA and proteins.
COMPUTATIONAL METHODS FOR FUNCTIONAL ANALYSIS OF GENE EXPRESSIONcsandit
Sequencing projects arising from high throughput technologies including those of sequencing DNA microarrays allowed to simultaneously measure the expression levels of millions of genes of a biological sample as well as annotate and identify the role (function) of those genes. Consequently, to better manage and organize this significant amount of information,
bioinformatics approaches have been developed. These approaches provide a representation and a more 'relevant' integration of data in order to test and validate the hypothesis of researchers throughout the experimental cycle. In this context, this article describes and discusses some of techniques used for the functional analysis of gene expression data.
As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data.
introduction,history scope and applications of
relation to other fields , bioinformatics,biological databases,computers internet,sequence development, and
introduction to sequence development and alignment
Bioinformatics, application by kk sahu sirKAUSHAL SAHU
INTRODUCTION
HISTORY
WHAT IS BIOINFORMATICS
APPLICATIONS
DNA AND RNA LEVELS
CONCLUSION
REFRENCES
"Bioinformatics" to refer to the study of information processes in biotic systems. This definition placed bioinformatics as a field parallel to biophysics or biochemistry (biochemistry is the study of chemical processes in biological systems).
the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. This includes nucleotide and amino acid sequences, protein domains, and protein structures.
Introduction to Gene Mining Part A: BLASTn-off!adcobb
In this lesson, students will learn to use bioinformatics portals and tools to mine plant versions of human genes. Student handout and teacher resource materials are available at www.Araport.org, Teaching Resources (Community tab). Suitable for grades 9-12 or first year undergraduate students.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
1. Extracting biological meaning from large gene list with DAVID Huang et al., CurrProtoc Bioinformatics (2009) http://david.abcc.ncifcrf.gov/home.jsp Francesco Mattia Mancuso (francesco.mancuso@crg.es) Bioinfarmatics Core Facility Short Tutorial
15. Main objectives of GO project Compile and provide GO terms; Use of structured vocabularies in the annotation of gene products; Provide open access to the GO database and Web resource. Independent sets of vocabularies Molecular Function (MF) – elemental activity or task performed, or potentially performed, by individual gene products (e.g. “DNA binding” and “catalytic activity”); Cellular Component (CC) – location of action for a gene product (e.g. “organelle membrane” and “cytoskeleton”); Biological Process (BP) – broad biological objective or goal in which a gene product participates. (e.g. “DNA replication” and “response to stimulus”).
20. Enrichment and p-valuescalculatedwith a hypergeometricdistribution N = all genes (universe) M = all genes belonging to a pathway n = your gene list m = genes of your gene list that belongs to the pathway Other well-known statistical methods: χ2, Fisher’s exact test, Binomial probability
21. A 'good' gene list Contains many important genes (marker genes) as expected; Reasonable number of genes ranging from hundreds to thousands (e.g., 100–2,000 genes), not extremely low or high; Most of the genes significantly pass the statistical threshold; Portion of up- or down-regulated genes are involved in certain interesting biological processes, rather than being randomly spread throughout all possible biological processes; Consistently contain more enriched biology than that of a random list in the same size range; High reproducibility to generate a similar gene list under the same conditions; Data high quality can be confirmed by other independent experiments.
30. Exercise 1 Submit data and convert the IDs Cicala, C. et al. HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication. Proc. Natl. Acad. Sci. USA 99, 9380–9385 (2002). “Freshly isolated peripheral blood mononuclear cells were treated with an HIV envelope protein (gp120) and genome-wide gene expression changes were observed using Affymetrix U95A microarray chips. The aim of the experiment was to investigate cellular responses to viral envelope protein infection, which may help in understanding the mechanisms for HIV replication in resting or sub-optimally activated peripheral blood mononuclear cells.” DOWNLOAD THE DATASET FROM : http://www.nature.com/nprot/journal/v4/n1/suppinfo/nprot.2008.211_S1.html Supplementary Data 2
45. Attention!!!!! DAVID enrichment analysis is more of an exploratory procedure than a pure statistical solution. “The final interpretation and analytic result decisions (in terms of accepting the results that make sense biologically in the context of the study, or rejecting ones that do not) should be made by the biologists/analysts themselves, rather than by any of the tools.” (Huang et al., 2009)
46.
47.
48. EASE Score Threshold (Maximum Probability): the threshold of EASE Score, a modified Fisher Exact P-value, for gene-enrichment analysis. It ranges from 0 to 1. Fisher Exact P-Value = 0 represents perfect enrichment.
49. The Fold Enrichment is defined as the ratio of the two proportions. For example, if 40/400 (i.e. 10%) of your input genes involved in "kinase activity" and the background information is 300/30000 genes (i.e. 1%) associating with "kinase activity", roughly 10% / 1% = 10 fold enrichment.
50. In DAVID annotation system, Fisher Exact is adopted to measure the gene-enrichment in annotation terms. When members of two independent groups can fall into one of two mutually exclusive categories, Fisher Exact test is used to determine whether the proportions of those falling into each category differs by group.
51. Benjamini-Hochberg, Bonferroni, FDR (False Discovery Rate) are different 'standard' statistics for multiple comparison corrections. They correct P-values to be more conservative in order to lower family-wise false discovery rate.
52. LT (list total): number of genes in your gene list mapped to any term in this ontology ("system”)
53. PH (population hits): number of genes with this GO term on the background list (the whole chip)
54. PT (population total): number of genes on the background list (the whole chip) mapped to any term in this ontology ("system”)
Editor's Notes
GoMiner, GOstat, Onto-express, GoToolBox, FatiGO, GFINDer and GSEA
3 - (e.g., selecting genes by comparing gene expression between control and experimental cells with t-test statistics: fold changes greater than or equal to 2 and P-values less than or equal to 0.05)6 - e.g., by independent experiments under the same conditions or by leave-one-out statistical test
Functional classification: ability for investigators to explore and view functionally related genes together, as a unit, to concentrate on the larger biological network rather than at the level of an individual gene.Functional Annotation chart: provides typical gene–term enrichment (overrepresented) analysis to identify the most relevant (overrepresented) biological terms associated with a given gene listFunctional Annotation Clustering: uses a similar fuzzy clustering concept as functional classification by measuring relationships among the annotation terms on the basis of the degree of their coassociation with genes within the user’s list to cluster somewhat heterogeneous, yet highly similar annotation into functional annotation groupsFunctional annotation table: is a query engine for the DAVID knowledgebase, without statistical calculations. For a given gene list, the tool can quickly query corresponding annotation for each gene and present them in a table format.