Organism : Bacillus cereus ATCC14579 | Module List :
BC4422

Nicotinate-nucleotide pyrophosphorylase [carboxylating] (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Nicotinate-nucleotide pyrophosphorylase cog/ cog
nicotinate-nucleotide diphosphorylase (carboxylating) activity go/ molecular_function
NAD biosynthetic process go/ biological_process
Nicotinate and nicotinamide metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
nadC tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4422
(Mouseover regulator name to see its description)

BC4422 is regulated by 28 influences and regulates 0 modules.
Regulators for BC4422 (28)
Regulator Module Operator
BC0882 9 tf
BC0954 9 tf
BC1622 9 tf
BC2379 9 tf
BC2470 9 tf
BC2526 9 tf
BC2558 9 tf
BC2904 9 tf
BC3434 9 tf
BC3449 9 tf
BC3961 9 tf
BC4650 9 tf
BC0114 55 tf
BC0518 55 tf
BC0607 55 tf
BC1075 55 tf
BC1337 55 tf
BC1987 55 tf
BC2401 55 tf
BC2964 55 tf
BC3982 55 tf
BC4010 55 tf
BC4356 55 tf
BC4650 55 tf
BC4930 55 tf
BC5143 55 tf
BC5173 55 tf
BC5340 55 tf

Warning: BC4422 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
3940 2.40e+05 GCAccTcAC
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3941 7.80e-02 AGGaGG
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4030 2.00e+00 aaAAcaAgAaagGtt
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4031 2.50e+04 CTATCaTATTCcaAtGT
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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 BC4422

BC4422 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Nicotinate-nucleotide pyrophosphorylase cog/ cog
nicotinate-nucleotide diphosphorylase (carboxylating) activity go/ molecular_function
NAD biosynthetic process go/ biological_process
Nicotinate and nicotinamide metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
nadC tigr/ tigrfam
Module neighborhood information for BC4422

BC4422 has total of 57 gene neighbors in modules 9, 55
Gene neighbors (57)
Gene Common Name Description Module membership
BC0022 BC0022 Pyrazinamidase (NCBI ptt file) 9, 256
BC0212 BC0212 hypothetical protein (NCBI ptt file) 9, 128
BC0312 BC0312 UDP-glucose 4-epimerase (NCBI ptt file) 9, 263
BC0314 BC0314 Glycosyltransferase (NCBI ptt file) 9, 506
BC0364 BC0364 tRNA (Uracil-5-) -methyltransferase (NCBI ptt file) 55, 242
BC0460 BC0460 hypothetical protein (NCBI ptt file) 9, 364
BC0484 BC0484 hypothetical protein (NCBI ptt file) 9, 25
BC0563 BC0563 Biotin carboxyl carrier protein (NCBI ptt file) 9, 85
BC0771 BC0771 Protein erfK/srfK precursor (NCBI ptt file) 9, 85
BC0903 BC0903 Methyltransferase (NCBI ptt file) 55, 249
BC0927 BC0927 hypothetical protein (NCBI ptt file) 55, 249
BC0934 BC0934 hypothetical protein (NCBI ptt file) 9, 85
BC1020 BC1020 hypothetical Membrane Associated Protein (NCBI ptt file) 9, 150
BC1040 BC1040 hypothetical protein (NCBI ptt file) 9, 146
BC1046 BC1046 hypothetical protein (NCBI ptt file) 9, 489
BC1119 BC1119 Two-component response regulator yvrH (NCBI ptt file) 55, 230
BC1130 BC1130 hypothetical protein (NCBI ptt file) 9, 440
BC1254 BC1254 hypothetical protein (NCBI ptt file) 9, 428
BC1678 BC1678 JEMB (NCBI ptt file) 9, 123
BC1837 BC1837 Methylmalonyl CoA epimerase (NCBI ptt file) 55, 177
BC1848 BC1848 Prophage helix-turn-helix protein (NCBI ptt file) 9, 85
BC1935 BC1935 hypothetical protein (NCBI ptt file) 9, 85
BC2115 BC2115 Transglutaminase-like enzymes, hypothetical cysteine proteases (NCBI ptt file) 9, 225
BC2172 BC2172 IG hypothetical 18880 (NCBI ptt file) 55, 159
BC2173 BC2173 hypothetical Membrane Spanning Protein (NCBI ptt file) 55, 159
BC2379 BC2379 Transcriptional regulator (NCBI ptt file) 9, 85
BC2445 BC2445 hypothetical protein (NCBI ptt file) 55, 308
BC2496 BC2496 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 9, 139
BC2620 BC2620 Penicillin-binding protein transpeptidase (NCBI ptt file) 9, 141
BC2716 BC2716 Glucose dehydrogenase [pyrroloquinoline-quinone] (NCBI ptt file) 55, 308
BC2742 BC2742 Transcriptional regulator, GntR family (NCBI ptt file) 9, 453
BC2857 BC2857 hypothetical protein (NCBI ptt file) 9, 416
BC2895 BC2895 hypothetical protein (NCBI ptt file) 10, 55
BC2915 BC2915 hypothetical protein (NCBI ptt file) 55, 453
BC3105 BC3105 Transcriptional regulator, AraC family (NCBI ptt file) 9, 141
BC3114 BC3114 Two-component sensor kinase ycbA (NCBI ptt file) 55, 265
BC3120 BC3120 Succinoglycan biosynthesis protein (NCBI ptt file) 9, 341
BC3146 BC3146 Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) 9, 428
BC3227 BC3227 Two component system histidine kinase (NCBI ptt file) 55, 256
BC3228 BC3228 Two-component response regulator (NCBI ptt file) 55, 242
BC3301 BC3301 hypothetical Cytosolic Protein (NCBI ptt file) 9, 230
BC3434 BC3434 Transcriptional regulator, DeoR family (NCBI ptt file) 9, 85
BC3514 BC3514 Glucose-1-phosphate cytidylyltransferase (NCBI ptt file) 9, 487
BC3528 BC3528 Sporulation kinase (NCBI ptt file) 8, 55
BC3584 BC3584 Oligopeptide-binding protein oppA (NCBI ptt file) 55, 63
BC3703 BC3703 Phage protein (NCBI ptt file) 9, 141
BC3985 BC3985 hypothetical Cytosolic Protein (NCBI ptt file) 55, 449
BC4021 BC4021 hypothetical protein (NCBI ptt file) 55, 249
BC4022 BC4022 ABC transporter ATP-binding protein (NCBI ptt file) 55, 249
BC4246 BC4246 hypothetical protein (NCBI ptt file) 55, 449
BC4247 BC4247 hypothetical protein (NCBI ptt file) 6, 55
BC4356 BC4356 Transcriptional regulator, MerR family (NCBI ptt file) 55, 148
BC4421 BC4421 Quinolinate synthetase A (NCBI ptt file) 55, 177
BC4422 BC4422 Nicotinate-nucleotide pyrophosphorylase [carboxylating] (NCBI ptt file) 9, 55
BC4617 BC4617 hypothetical Membrane Spanning Protein (NCBI ptt file) 9, 141
BC4945 BC4945 None 9, 85
BC5411 BC5411 Two-component response regulator yhcZ (NCBI ptt file) 55, 177
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 BC4422
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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