Organism : Bacillus cereus ATCC14579 | Module List :
BC0374

Amidohydrolase amhX (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Metal-dependent amidase/aminoacylase/carboxypeptidase cog/ cog
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
protein dimerization activity go/ molecular_function
amidohydrolases tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0374
(Mouseover regulator name to see its description)

BC0374 is regulated by 18 influences and regulates 0 modules.
Regulators for BC0374 (18)
Regulator Module Operator
BC0099 139 tf
BC1302 139 tf
BC2386 139 tf
BC3084 139 tf
BC3792 139 tf
BC4010 139 tf
BC4652 139 tf
BC4703 139 tf
BC5481 139 tf
BC0954 218 tf
BC1032 218 tf
BC1427 218 tf
BC1490 218 tf
BC2632 218 tf
BC2979 218 tf
BC3493 218 tf
BC4010 218 tf
BC5097 218 tf

Warning: BC0374 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
4194 1.60e-04 gAgGgGga
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4195 1.30e+04 GGGTGGTAaCaCGG
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4352 9.70e-05 agagaGG.Gata.aa
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4353 2.00e+04 CCATCGcccCTTGC
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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 BC0374

BC0374 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Metal-dependent amidase/aminoacylase/carboxypeptidase cog/ cog
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
protein dimerization activity go/ molecular_function
amidohydrolases tigr/ tigrfam
Module neighborhood information for BC0374

BC0374 has total of 67 gene neighbors in modules 139, 218
Gene neighbors (67)
Gene Common Name Description Module membership
BC0041 BC0041 Corrin/porphyrin methyltransferase (NCBI ptt file) 139, 388
BC0374 BC0374 Amidohydrolase amhX (NCBI ptt file) 139, 218
BC0398 BC0398 Benzoate transport protein (NCBI ptt file) 76, 218
BC0494 BC0494 hypothetical Cytosolic Protein (NCBI ptt file) 85, 139
BC0582 BC0582 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 96, 218
BC0590 BC0590 hypothetical protein (NCBI ptt file) 48, 218
BC0820 BC0820 Branched-chain amino acid transport system carrier protein (NCBI ptt file) 139, 197
BC0827 BC0827 hypothetical protein (NCBI ptt file) 141, 218
BC0829 BC0829 hypothetical protein (NCBI ptt file) 86, 218
BC0859 BC0859 Oligopeptide-binding protein oppA (NCBI ptt file) 137, 139
BC1127 BC1127 Malate synthase (NCBI ptt file) 163, 218
BC1128 BC1128 Isocitrate lyase (NCBI ptt file) 218, 400
BC1202 BC1202 Serine/threonine protein phosphatase (NCBI ptt file) 72, 218
BC1230 BC1230 Bacterial Ig-like domain protein (NCBI ptt file) 86, 139
BC1231 BC1231 Sodium/proline symporter (NCBI ptt file) 139, 399
BC1340 BC1340 Sporulation kinase (NCBI ptt file) 218, 434
BC1441 BC1441 Branched-chain amino acid transport system carrier protein (NCBI ptt file) 139, 412
BC1675 BC1675 Branched-chain amino acid transport protein azlD (NCBI ptt file) 218, 416
BC1817 BC1817 CAAX amino terminal protease family (NCBI ptt file) 86, 139
BC1985 BC1985 None 139, 311
BC2013 BC2013 Alpha/beta hydrolase (NCBI ptt file) 52, 218
BC2042 BC2042 putative NAD-dependent dehydrogenase (NCBI ptt file) 218, 243
BC2094 BC2094 Acetyltransferase (NCBI ptt file) 137, 139
BC2160 BC2160 hypothetical protein (NCBI ptt file) 139, 517
BC2217 BC2217 Two-component response regulator yhcZ (NCBI ptt file) 218, 279
BC2281 BC2281 Multimodular transpeptidase-transglycosylase PBP 1A (NCBI ptt file) 218, 375
BC2395 BC2395 hypothetical protein (NCBI ptt file) 218, 321
BC2464 BC2464 S-layer protein / Peptidoglycan endo-beta-N-acetylglucosaminidase (NCBI ptt file) 139, 517
BC2496 BC2496 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 9, 139
BC2663 BC2663 None 218, 225
BC2699 BC2699 None 139, 428
BC2715 BC2715 hypothetical Membrane Spanning Protein (NCBI ptt file) 139, 175
BC2757 BC2757 Tryptophan 2,3-dioxygenase (NCBI ptt file) 137, 218
BC2759 BC2759 L-kynurenine hydrolase (NCBI ptt file) 137, 218
BC2838 BC2838 hypothetical protein (NCBI ptt file) 76, 218
BC2899 BC2899 2'-5' RNA ligase (NCBI ptt file) 52, 218
BC3022 BC3022 hypothetical protein (NCBI ptt file) 127, 218
BC3075 BC3075 EpiH/GdmH-related protein (NCBI ptt file) 75, 139
BC3117 BC3117 Arsenical pump membrane protein (NCBI ptt file) 139, 341
BC3124 BC3124 Isochorismatase family (NCBI ptt file) 218, 313
BC3162 BC3162 Bicyclomycin resistance protein (NCBI ptt file) 150, 218
BC3248 BC3248 D-3-phosphoglycerate dehydrogenase (NCBI ptt file) 218, 359
BC3524 BC3524 S-layer protein / N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 67, 139
BC3594 BC3594 PhnB protein (NCBI ptt file) 141, 218
BC3656 BC3656 Methyltransferase (NCBI ptt file) 218, 303
BC3657 BC3657 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme (NCBI ptt file) 218, 359
BC3788 BC3788 Nucleoside transport system permease protein (NCBI ptt file) 139, 234
BC3789 BC3789 None 139, 234
BC3893 lspA lipoprotein signal peptidase (RefSeq) 139, 192
BC3939 BC3939 Amidase (NCBI ptt file) 218, 461
BC3993 BC3993 Polyphosphate kinase (NCBI ptt file) 57, 218
BC4003 BC4003 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (NCBI ptt file) 194, 218
BC4010 BC4010 Transcriptional regulator, LacI family (NCBI ptt file) 139, 432
BC4042 BC4042 3-hydroxyisobutyrate dehydrogenase (NCBI ptt file) 193, 218
BC4082 BC4082 hypothetical protein (NCBI ptt file) 218, 361
BC4121 BC4121 Tyrosine transporter (NCBI ptt file) 139, 412
BC4122 BC4122 None 139, 277
BC4449 BC4449 hypothetical Membrane Spanning Protein (NCBI ptt file) 139, 464
BC4598 BC4598 FxsA protein (NCBI ptt file) 31, 218
BC4668 BC4668 Virulence factor mviM (NCBI ptt file) 125, 218
BC4767 BC4767 hypothetical protein (NCBI ptt file) 218, 405
BC4852 BC4852 hypothetical protein (NCBI ptt file) 139, 415
BC5051 BC5051 Sodium/proton-dependent alanine carrier protein (NCBI ptt file) 139, 213
BC5062 BC5062 Tyrosyl-tRNA synthetase (NCBI ptt file) 139, 297
BC5302 BC5302 Sensory box/GGDEF family protein (NCBI ptt file) 139, 321
BC5350 BC5350 Transcriptional activator plcR (NCBI ptt file) 139, 506
BC5366 BC5366 Muramoyltetrapeptide carboxypeptidase (NCBI ptt file) 139, 218
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 BC0374
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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