Organism : Bacillus cereus ATCC14579 | Module List :
BC1924

L-lactate dehydrogenase (NCBI ptt file)

CircVis
Functional Annotations (13)
Function System
Malate/lactate dehydrogenases cog/ cog
L-lactate dehydrogenase activity go/ molecular_function
cytoplasm go/ cellular_component
glycolysis go/ biological_process
tricarboxylic acid cycle intermediate metabolic process go/ biological_process
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Cysteine and methionine metabolism kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
L-LDH-NAD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1924
(Mouseover regulator name to see its description)

BC1924 is regulated by 28 influences and regulates 0 modules.
Regulators for BC1924 (28)
Regulator Module Operator
BC0742 90 tf
BC0880 90 tf
BC1282 90 tf
BC1363 90 tf
BC1603 90 tf
BC1818 90 tf
BC2218 90 tf
BC2517 90 tf
BC2971 90 tf
BC2988 90 tf
BC4240 90 tf
BC5339 90 tf
BC5481 90 tf
BC0630 100 tf
BC0950 100 tf
BC1850 100 tf
BC1932 100 tf
BC1996 100 tf
BC2122 100 tf
BC2353 100 tf
BC3253 100 tf
BC4010 100 tf
BC4240 100 tf
BC4425 100 tf
BC4826 100 tf
BC4842 100 tf
BC5265 100 tf
BC5402 100 tf

Warning: BC1924 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
4096 1.80e+02 cccCCTtT
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4097 2.30e+04 CcTGCaAATaCGCc
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4116 1.40e-04 AgaaAaAgGgatgtt
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4117 2.00e+03 GGaGaTacgCC
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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 BC1924

BC1924 is enriched for 13 functions in 3 categories.
Enrichment Table (13)
Function System
Malate/lactate dehydrogenases cog/ cog
L-lactate dehydrogenase activity go/ molecular_function
cytoplasm go/ cellular_component
glycolysis go/ biological_process
tricarboxylic acid cycle intermediate metabolic process go/ biological_process
Glycolysis / Gluconeogenesis kegg/ kegg pathway
Cysteine and methionine metabolism kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
L-LDH-NAD tigr/ tigrfam
Module neighborhood information for BC1924

BC1924 has total of 49 gene neighbors in modules 90, 100
Gene neighbors (49)
Gene Common Name Description Module membership
BC0159 BC0159 LSU ribosomal protein L17P (NCBI ptt file) 90, 430
BC0405 BC0405 Arginine repressor, argR (NCBI ptt file) 100, 187
BC0457 BC0457 Tetratricopeptide repeat family protein (NCBI ptt file) 90, 296
BC0546 BC0546 23S rRNA methyltransferase (NCBI ptt file) 90, 380
BC0739 BC0739 hypothetical protein (NCBI ptt file) 90, 478
BC0740 BC0740 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 15, 90
BC1333 BC1333 CBS domain containing protein (NCBI ptt file) 100, 199
BC1386 BC1386 hypothetical protein (NCBI ptt file) 100, 354
BC1598 BC1598 LACX protein (NCBI ptt file) 90, 296
BC1850 BC1850 Transcriptional regulator (NCBI ptt file) 100, 294
BC1924 BC1924 L-lactate dehydrogenase (NCBI ptt file) 90, 100
BC1996 BC1996 Transcription state regulatory protein abrB (NCBI ptt file) 100, 517
BC2210 BC2210 NAD(P)H nitroreductase (NCBI ptt file) 90, 406
BC2261 BC2261 Cobalt-zinc-cadmium resistance protein czcD (NCBI ptt file) 100, 214
BC2263 BC2263 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 100, 354
BC2356 BC2356 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 28, 100
BC2398 BC2398 putative integral membrane protein (NCBI ptt file) 100, 481
BC2527 BC2527 CAAX amino terminal protease family (NCBI ptt file) 100, 354
BC2618 BC2618 hydrolase (HAD superfamily) (NCBI ptt file) 100, 401
BC2671 BC2671 ThiJ/PfpI family (NCBI ptt file) 20, 90
BC2717 BC2717 hypothetical protein (NCBI ptt file) 100, 337
BC2718 BC2718 hypothetical protein (NCBI ptt file) 100, 337
BC2828 BC2828 Acetyltransferase (NCBI ptt file) 90, 426
BC2879 BC2879 hypothetical protein (NCBI ptt file) 90, 227
BC2921 BC2921 hypothetical protein (NCBI ptt file) 100, 461
BC2987 BC2987 hypothetical Membrane Spanning Protein (NCBI ptt file) 90, 304
BC2988 BC2988 Transcriptional regulator, Cro/CI family (NCBI ptt file) 100, 440
BC2989 BC2989 hypothetical protein (NCBI ptt file) 90, 304
BC2995 BC2995 hypothetical protein (NCBI ptt file) 7, 100
BC3318 BC3318 hypothetical protein (NCBI ptt file) 7, 100
BC3665 BC3665 Bacitracin transport permease protein BCRB (NCBI ptt file) 100, 388
BC4062 BC4062 IG hypothetical 17221 (NCBI ptt file) 100, 477
BC4370 BC4370 hypothetical protein (NCBI ptt file) 100, 477
BC4519 BC4519 hypothetical Cytosolic Protein (NCBI ptt file) 90, 304
BC4559 BC4559 Asparaginyl-tRNA synthetase (NCBI ptt file) 100, 412
BC4664 BC4664 hypothetical protein (NCBI ptt file) 100, 228
BC4675 BC4675 Sex pheromone staph-cAM373 precursor (NCBI ptt file) 7, 100
BC4728 BC4728 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 41, 90
BC4815 BC4815 Hypoxanthine-guanine phosphoribosyltransferase (NCBI ptt file) 90, 198
BC4826 BC4826 hypothetical protein (NCBI ptt file) 100, 304
BC4842 BC4842 Transcriptional regulator, GntR family (NCBI ptt file) 100, 304
BC4861 BC4861 hypothetical protein (NCBI ptt file) 90, 380
BC4913 BC4913 hypothetical protein (NCBI ptt file) 15, 90
BC4929 BC4929 Macrolide-efflux protein (NCBI ptt file) 20, 100
BC5220 BC5220 Lactoylglutathione lyase (NCBI ptt file) 90, 198
BC5258 BC5258 Phosphoglycerate transporter protein (NCBI ptt file) 100, 290
BC5349 BC5349 PapR protein (NCBI ptt file) 100, 354
BC5380 BC5380 Ferrichrome-binding protein (NCBI ptt file) 90, 201
BC5397 BC5397 hypothetical Membrane Spanning Protein (NCBI ptt file) 90, 170
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 BC1924
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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