Organism : Bacillus cereus ATCC14579 | Module List :
BC4405

Protein translocase subunit SecD / Protein translocase subunit SecF (NCBI ptt file)

CircVis
Functional Annotations (12)
Function System
Preprotein translocase subunit SecD cog/ cog
proteolysis go/ biological_process
intracellular protein transport go/ biological_process
serine-type peptidase activity go/ molecular_function
Gram-negative-bacterium-type cell wall go/ cellular_component
P-P-bond-hydrolysis-driven protein transmembrane transporter activity go/ molecular_function
type II protein secretion system complex go/ cellular_component
protein secretion by the type II secretion system go/ biological_process
membrane go/ cellular_component
Protein export kegg/ kegg pathway
Bacterial secretion system kegg/ kegg pathway
2A0604s01 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4405
(Mouseover regulator name to see its description)

BC4405 is regulated by 25 influences and regulates 0 modules.
Regulators for BC4405 (25)
Regulator Module Operator
BC0123 201 tf
BC1080 201 tf
BC1818 201 tf
BC1998 201 tf
BC2410 201 tf
BC2903 201 tf
BC4603 201 tf
BC5282 201 tf
BC5339 201 tf
BC5483 201 tf
BC0158 180 tf
BC1059 180 tf
BC1356 180 tf
BC2340 180 tf
BC2434 180 tf
BC2672 180 tf
BC3244 180 tf
BC3813 180 tf
BC3814 180 tf
BC4124 180 tf
BC4508 180 tf
BC4652 180 tf
BC4703 180 tf
BC4902 180 tf
BC5173 180 tf

Warning: BC4405 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
4276 4.00e-01 AAGGtgG
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4277 2.60e+00 GCTtcctTaCTACtcatt.tTATa
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4318 2.00e-04 AGGgGG
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4319 1.00e+04 GCGTGGcAcG
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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 BC4405

BC4405 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
Preprotein translocase subunit SecD cog/ cog
proteolysis go/ biological_process
intracellular protein transport go/ biological_process
serine-type peptidase activity go/ molecular_function
Gram-negative-bacterium-type cell wall go/ cellular_component
P-P-bond-hydrolysis-driven protein transmembrane transporter activity go/ molecular_function
type II protein secretion system complex go/ cellular_component
protein secretion by the type II secretion system go/ biological_process
membrane go/ cellular_component
Protein export kegg/ kegg pathway
Bacterial secretion system kegg/ kegg pathway
2A0604s01 tigr/ tigrfam
Module neighborhood information for BC4405

BC4405 has total of 38 gene neighbors in modules 180, 201
Gene neighbors (38)
Gene Common Name Description Module membership
BC0002 BC0002 DNA polymerase III, beta chain (NCBI ptt file) 88, 201
BC0106 BC0106 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (NCBI ptt file) 22, 201
BC0850 BC0850 Oxidoreductase (NCBI ptt file) 201, 474
BC1086 BC1086 Lipoate-protein ligase A (NCBI ptt file) 180, 227
BC1295 BC1295 hypothetical protein (NCBI ptt file) 201, 474
BC1369 BC1369 Protein dltD precursor (NCBI ptt file) 201, 283
BC1370 BC1370 D-alanyl carrier protein (NCBI ptt file) 201, 283
BC1371 BC1371 Protein dltB (NCBI ptt file) 201, 474
BC1381 BC1381 hypothetical protein (NCBI ptt file) 180, 224
BC1382 BC1382 hypothetical protein (NCBI ptt file) 126, 180
BC1465 BC1465 Lysyltransferase (NCBI ptt file) 201, 300
BC1934 BC1934 hypothetical protein (NCBI ptt file) 41, 180
BC1998 BC1998 Transcriptional regulator, ArsR family (NCBI ptt file) 201, 262
BC2018 BC2018 IolS protein (NCBI ptt file) 180, 491
BC2019 BC2019 Low-affinity zinc transport protein (NCBI ptt file) 74, 180
BC2022 BC2022 Oxidoreductase (NCBI ptt file) 118, 180
BC2340 BC2340 Transcriptional regulator, TetR family (NCBI ptt file) 180, 480
BC2439 BC2439 Aminoacyl-histidine dipeptidase (NCBI ptt file) 180, 227
BC2657 BC2657 None 6, 180
BC3149 BC3149 1,4-dihydroxy-2-naphthoate octaprenyltransferase (NCBI ptt file) 201, 208
BC3368 BC3368 6-phosphogluconolactonase (NCBI ptt file) 110, 180
BC3453 BC3453 N-acyl homoserine lactone hydrolase (NCBI ptt file) 173, 180
BC3463 BC3463 Arsenical pump membrane protein (NCBI ptt file) 110, 180
BC3950 BC3950 hypothetical protein (NCBI ptt file) 152, 180
BC4000 BC4000 Multidrug resistance protein B (NCBI ptt file) 201, 312
BC4009 BC4009 Aromatic amino acid aminotransferase (NCBI ptt file) 180, 480
BC4096 BC4096 D-threo-aldose 1-dehydrogenase (NCBI ptt file) 110, 180
BC4103 BC4103 transport protein (NCBI ptt file) 79, 201
BC4405 BC4405 Protein translocase subunit SecD / Protein translocase subunit SecF (NCBI ptt file) 180, 201
BC4506 BC4506 None 15, 180
BC4601 BC4601 Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha (NCBI ptt file) 22, 201
BC4602 BC4602 Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (NCBI ptt file) 22, 201
BC4604 BC4604 NAD-dependent malic enzyme (NCBI ptt file) 201, 403
BC4907 BC4907 Superoxide dismutase [Cu-Zn] (NCBI ptt file) 155, 180
BC5188 BC5188 Bacterial Peptide Chain Release Factor 2 (RF-2) (NCBI ptt file) 201, 474
BC5380 BC5380 Ferrichrome-binding protein (NCBI ptt file) 90, 201
BC5431 BC5431 Multidrug resistance protein B (NCBI ptt file) 79, 201
BC5432 BC5432 Bactoprenol glucosyl transferase (NCBI ptt file) 201, 300
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 BC4405
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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