Organism : Bacillus cereus ATCC14579 | Module List :
BC1415

Glyoxylate reductase (NADP+) (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Lactate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
metabolic process go/ biological_process
NAD binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1415
(Mouseover regulator name to see its description)

BC1415 is regulated by 30 influences and regulates 0 modules.
Regulators for BC1415 (30)
Regulator Module Operator
BC0433 511 tf
BC0586 511 tf
BC0613 511 tf
BC0856 511 tf
BC1047 511 tf
BC1296 511 tf
BC1356 511 tf
BC1490 511 tf
BC1715 511 tf
BC2340 511 tf
BC2386 511 tf
BC2480 511 tf
BC2794 511 tf
BC3194 511 tf
BC3404 511 tf
BC3668 511 tf
BC4001 511 tf
BC4073 511 tf
BC5097 511 tf
BC5175 511 tf
BC0648 480 tf
BC0880 480 tf
BC1302 480 tf
BC1356 480 tf
BC1710 480 tf
BC1715 480 tf
BC2340 480 tf
BC2480 480 tf
BC4256 480 tf
BC4670 480 tf

Warning: BC1415 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
4870 2.30e-02 AAAGGAG
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4871 3.70e+04 GGGaaTACGG
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4932 2.90e-02 AAGgAGg
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4933 4.40e+03 ctcacCccTC
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for BC1415

BC1415 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Lactate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
metabolic process go/ biological_process
NAD binding go/ molecular_function
Module neighborhood information for BC1415

BC1415 has total of 45 gene neighbors in modules 480, 511
Gene neighbors (45)
Gene Common Name Description Module membership
BC0191 BC0191 hypothetical Membrane Spanning Protein (NCBI ptt file) 211, 511
BC0424 BC0424 IG hypothetical 16092 (NCBI ptt file) 467, 511
BC0665 BC0665 Transaldolase (NCBI ptt file) 224, 480
BC1023 BC1023 Transporter, LysE family (NCBI ptt file) 41, 480
BC1095 BC1095 hypothetical protein (NCBI ptt file) 449, 511
BC1193 BC1193 Oligoendopeptidase F (NCBI ptt file) 302, 511
BC1307 BC1307 hypothetical protein (NCBI ptt file) 511, 527
BC1415 BC1415 Glyoxylate reductase (NADP+) (NCBI ptt file) 480, 511
BC1460 BC1460 hypothetical protein (NCBI ptt file) 227, 480
BC1510 BC1510 DNA-binding protein HU (NCBI ptt file) 166, 480
BC2101 BC2101 Formate--tetrahydrofolate ligase (NCBI ptt file) 322, 511
BC2156 BC2156 Thioredoxin (NCBI ptt file) 40, 511
BC2158 BC2158 Protein-L-isoD(D-D) O-methyltransferase (NCBI ptt file) 71, 511
BC2241 BC2241 Succinate-semialdehyde dehydrogenase [NADP+] (NCBI ptt file) 6, 511
BC2293 BC2293 hypothetical protein (NCBI ptt file) 450, 511
BC2340 BC2340 Transcriptional regulator, TetR family (NCBI ptt file) 180, 480
BC2371 BC2371 Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) 56, 511
BC2479 BC2479 ABC transporter permease protein (NCBI ptt file) 302, 511
BC2480 BC2480 Transcriptional regulator, TetR family (NCBI ptt file) 385, 480
BC2556 BC2556 DNA integration/recombination/invertion protein (NCBI ptt file) 286, 511
BC2576 BC2576 hypothetical protein (NCBI ptt file) 15, 480
BC2578 BC2578 Phage protein (NCBI ptt file) 449, 480
BC2616 BC2616 Cytochrome P450(MEG) (NCBI ptt file) 491, 511
BC2954 BC2954 Lactoylglutathione lyase (NCBI ptt file) 116, 511
BC2955 BC2955 hypothetical protein (NCBI ptt file) 449, 511
BC3026 BC3026 Tetracycline resistance protein tetP (NCBI ptt file) 286, 511
BC3070 BC3070 Signal peptidase I (NCBI ptt file) 47, 480
BC3073 BC3073 hypothetical protein (NCBI ptt file) 47, 480
BC3140 BC3140 Carbonic anhydrase (NCBI ptt file) 302, 480
BC3141 BC3141 hypothetical protein (NCBI ptt file) 302, 480
BC3142 BC3142 NADH-quinone oxidoreductase chain L (NCBI ptt file) 302, 480
BC3143 BC3143 hypothetical Cytosolic Protein (NCBI ptt file) 47, 511
BC3144 BC3144 hypothetical Cytosolic Protein (NCBI ptt file) 47, 511
BC3194 BC3194 Transcriptional regulator, MarR family (NCBI ptt file) 414, 511
BC4009 BC4009 Aromatic amino acid aminotransferase (NCBI ptt file) 180, 480
BC4017 BC4017 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 304, 480
BC4019 BC4019 hypothetical protein (NCBI ptt file) 414, 511
BC4084 BC4084 Magnesium and cobalt transport protein corA (NCBI ptt file) 491, 511
BC4092 BC4092 Stage II sporulation protein M (NCBI ptt file) 233, 511
BC4098 BC4098 Glutamate-rich protein grpB (NCBI ptt file) 268, 511
BC4791 BC4791 Carbonic anhydrase (NCBI ptt file) 227, 480
BC4804 BC4804 hypothetical protein (NCBI ptt file) 491, 511
BC4807 BC4807 Ferrous iron transport protein A (NCBI ptt file) 491, 511
BC5061 BC5061 NADH dehydrogenase (NCBI ptt file) 385, 480
BC5279 BC5279 Tyrosine-protein kinase (capsular polysaccharide biosynthesis) (NCBI ptt file) 43, 511
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for BC1415
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend