Organism : Bacillus cereus ATCC14579 | Module List :
BC3550

Argininosuccinate lyase (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Argininosuccinate lyase cog/ cog
argininosuccinate lyase activity go/ molecular_function
arginine biosynthetic process via ornithine go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
argH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3550
(Mouseover regulator name to see its description)

BC3550 is regulated by 18 influences and regulates 0 modules.
Regulators for BC3550 (18)
Regulator Module Operator
BC0607 265 tf
BC0801 265 tf
BC1033 265 tf
BC1889 265 tf
BC2340 265 tf
BC2401 265 tf
BC3095 265 tf
BC3976 265 tf
BC4204 265 tf
BC4356 265 tf
BC5200 265 tf
BC0116 461 tf
BC1337 461 tf
BC3207 461 tf
BC3706 461 tf
BC3813 461 tf
BC3826 461 tf
BC4499 461 tf

Warning: BC3550 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
4446 1.00e-01 gttTatAAtGgAtga
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4447 5.90e+02 CCTCtcTgcAc
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4832 2.60e+00 TattAgGGggAG
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4833 6.40e+03 AAgA.g.TcaAGAgagctcC
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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 BC3550

BC3550 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Argininosuccinate lyase cog/ cog
argininosuccinate lyase activity go/ molecular_function
arginine biosynthetic process via ornithine go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
argH tigr/ tigrfam
Module neighborhood information for BC3550

BC3550 has total of 42 gene neighbors in modules 265, 461
Gene neighbors (42)
Gene Common Name Description Module membership
BC0014 BC0014 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 257, 461
BC0201 BC0201 L-gulonolactone oxidase (NCBI ptt file) 461, 462
BC0202 BC0202 Multidrug resistance protein B (NCBI ptt file) 461, 462
BC0394 BC0394 hypothetical protein (NCBI ptt file) 261, 265
BC0416 BC0416 Phage infection protein (NCBI ptt file) 10, 461
BC0565 BC0565 Ankyrin (NCBI ptt file) 63, 265
BC0669 BC0669 Potassium channel protein (NCBI ptt file) 265, 288
BC0752 BC0752 hypothetical protein (NCBI ptt file) 265, 449
BC0834 BC0834 hypothetical protein (NCBI ptt file) 64, 265
BC0835 BC0835 hypothetical protein (NCBI ptt file) 97, 265
BC1479 BC1479 hypothetical Cytosolic Protein (NCBI ptt file) 96, 461
BC1550 BC1550 Multimodular transpeptidase-transglycosylase PBP 1A (NCBI ptt file) 351, 461
BC1682 BC1682 hypothetical protein (NCBI ptt file) 64, 461
BC1720 BC1720 Cell surface protein (NCBI ptt file) 261, 265
BC1974 BC1974 Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) 221, 461
BC1975 BC1975 hypothetical Exported Protein (NCBI ptt file) 294, 461
BC2181 BC2181 Transcriptional regulator, Cro/CI family (NCBI ptt file) 10, 461
BC2493 BC2493 hypothetical protein (NCBI ptt file) 265, 308
BC2538 BC2538 Two-component response regulator yxdJ (NCBI ptt file) 265, 449
BC2756 BC2756 6-aminohexanoate-dimer hydrolase (NCBI ptt file) 265, 402
BC2862 BC2862 Protein export protein prsA precursor (NCBI ptt file) 10, 265
BC2863 BC2863 Two component system histidine kinase (NCBI ptt file) 265, 465
BC2921 BC2921 hypothetical protein (NCBI ptt file) 100, 461
BC3114 BC3114 Two-component sensor kinase ycbA (NCBI ptt file) 55, 265
BC3170 BC3170 Transposase (NCBI ptt file) 453, 461
BC3435 BC3435 Daunorubicin resistance transmembrane protein (NCBI ptt file) 313, 461
BC3550 BC3550 Argininosuccinate lyase (NCBI ptt file) 265, 461
BC3939 BC3939 Amidase (NCBI ptt file) 218, 461
BC4173 BC4173 None 161, 265
BC4275 BC4275 hypothetical protein (NCBI ptt file) 257, 461
BC4351 BC4351 Minor extracellular protease VPR precursor (NCBI ptt file) 221, 461
BC4509 BC4509 Sodium export permease protein (NCBI ptt file) 346, 461
BC4510 BC4510 Sodium export ATP-binding protein (NCBI ptt file) 346, 461
BC4541 BC4541 Methyltransferase (NCBI ptt file) 10, 265
BC4582 BC4582 S-adenosylmethionine decarboxylase proenzyme (NCBI ptt file) 225, 265
BC4626 BC4626 hypothetical protein (NCBI ptt file) 147, 265
BC4698 BC4698 putative choline kinase involved in lipopolysaccharide biosynthesis (NCBI ptt file) 265, 308
BC4741 BC4741 DNA integration/recombination/invertion protein (NCBI ptt file) 97, 265
BC4811 BC4811 Fimbria-associated protein (NCBI ptt file) 242, 461
BC4966 BC4966 hypothetical Cytosolic Protein (NCBI ptt file) 265, 308
BC5018 BC5018 hypothetical Membrane Spanning Protein (NCBI ptt file) 265, 477
BC5131 BC5131 Protein translocase subunit SecG (NCBI ptt file) 265, 274
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 BC3550
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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