Mycobacterium tuberculosis Pathway/Genome Databases | ![]() |
This website contains 50 Mycobacterium tuberculosis genomes (show list) and associated metabolic pathways. This site is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes. Click the "Change Current Database" button (above) to explore the available databases.
This site includes extensive retrieval, visualization and analysis tools, including a genome browser and a metabolic map diagram. There are tools for analysis of gene expression, metabolomics and ChIP-chip data. You can search and align sequences for Vibrio cholerae and other microbial genomes and perform comparative analysis. You can store groups of genes and pathways into a SmartTable, and then browse, analyze and share with other users.
Learning Library
Tutorial Series
Tutorial #1: Introduction to BioCyc
- BioCyc Overview (14:04) [mp4 video] or [YouTube]
- Searching in BioCyc (17:00) [mp4 video] or [YouTube]
- Genome Browsing, Searching, and Alignment (15:38) [mp4 video] or [YouTube]
- Pathways (13:19) [mp4 video] or [YouTube]
- Reactions (3:37) [mp4 video] or [YouTube]
- Compounds (6:42) [mp4 video] or [YouTube]
Tutorial #2: Introduction to SmartTables
- Part 1: SmartTables Overview (4:30) [mp4 video] or [YouTube]
- Part 2: SmartTables Basics (12:43) [QuickTime Video]
- Part 3: SmartTables Transformations (8:08) [QuickTime Video]
- Part 4: SmartTables Import and Export (9:00) [QuickTime Video]
- Part 5: SmartTables Gene Expression Analysis (7:40) [QuickTime Video]
- Part 6: Metabolomics Analysis with SmartTables (6:45) [QuickTime Video]
Tutorial #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
- Part 1: The Cellular Overview: Navigating metabolic networks (17:15) [mp4 video] or [QuickTime Video] or [YouTube]
- Part 2: Comparative Genomics (21:06) [Windows Media Video] or [QuickTime Video]
- Part 3: Ortholog Viewing (10:02) [Windows Media Video] or [QuickTime Video]
- Part 4: The Regulatory Overview -- exploring transcriptional regulatory networks (15:21) [mp4 video] or [YouTube]
Tutorial #4: Omics Data Analysis
- Transcriptomics Analysis Tools [brief tour (2:40) mp4 video or YouTube] [detailed tutorial (21:36) mp4 video or YouTube]
- Metabolomics Analysis Tools [brief tour (3:26) mp4 video or YouTube] [detailed tutorial (24:09) mp4 video or YouTube]
- Omics Dashboard Part 1 (16:35) [mp4 video], or [YouTube]
- Omics Dashboard Part 2 (24:29) [mp4 video], or [YouTube]
Tutorial #5: Pathway Collages
- Pathway Collages (22:39) [mp4 video], [QuickTime Video] or [YouTube]
Tutorial #6: Creating a Pathway/Genome Database
- Part 1A: Introduction to Database Building and Pathologic (14:04) [MP4 Video] or [YouTube]
- Part 1B: Building a Database: Detailed Pathologic Example (23:53) [MP4 Video] or [YouTube]
- Part 2A: General Editing Strategies (8:00) [Windows Media Video] or [QuickTime Video] or [YouTube]
- Part 2B: Creating and Editing Reactions and Compounds (17:32) [Windows Media Video] or [QuickTime Video] or [YouTube]
- Part 2C: Updating Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10) [Windows Media Video] or [QuickTime Video] or [YouTube]
- Part 2D: Making and Editing Pathways (9:42) [Windows Media Video] or [QuickTime Video] or [YouTube]
Tutorial #7: Using the Structured Advanced Query Page
- Quick Introduction (6:27): "Structured Advanced Query Page Quick Introduction" [Windows Media Video] or [mp4 video] or [YouTube]
- Full Tutorial (42:15): "Structured Advanced Query Page" [Windows Media Video] or [mp4 video] or [YouTube]