Organism : Bacillus cereus ATCC14579 | Module List :
BC4314

Heat-inducible transcription repressor hrcA (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator of heat shock gene cog/ cog
regulation of transcription, DNA-dependent go/ biological_process
hrcA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4314
(Mouseover regulator name to see its description)

BC4314 is regulated by 24 influences and regulates 10 modules.
Regulators for BC4314 (24)
Regulator Module Operator
BC0586 40 tf
BC1302 40 tf
BC1356 40 tf
BC1531 40 tf
BC2133 40 tf
BC2632 40 tf
BC3404 40 tf
BC4211 40 tf
BC4314 40 tf
BC4661 40 tf
BC5141 40 tf
BC5171 40 tf
BC0114 164 tf
BC0123 164 tf
BC1302 164 tf
BC1477 164 tf
BC1531 164 tf
BC2133 164 tf
BC3025 164 tf
BC3449 164 tf
BC4314 164 tf
BC4603 164 tf
BC4832 164 tf
BC5141 164 tf

Warning: BC4314 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
4000 2.50e+02 GAGtGatAAcA
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4001 7.10e+02 gtcaTTTcCG
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4244 1.40e+02 GtcatTTcCg
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4245 1.00e+03 GAGTGCTAACAcAc
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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 BC4314

BC4314 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator of heat shock gene cog/ cog
regulation of transcription, DNA-dependent go/ biological_process
hrcA tigr/ tigrfam
Module neighborhood information for BC4314

BC4314 has total of 21 gene neighbors in modules 40, 164
Gene neighbors (21)
Gene Common Name Description Module membership
BC0294 groES co-chaperonin GroES (RefSeq) 164, 335
BC0295 BC0295 60 kDa chaperonin GROEL (NCBI ptt file) 40, 164
BC1194 BC1194 hypothetical Cytosolic Protein (NCBI ptt file) 40, 507
BC1195 BC1195 Globin Family Protein (NCBI ptt file) 40, 507
BC2155 BC2155 PBS lyase HEAT-like repeat (NCBI ptt file) 40, 71
BC2156 BC2156 Thioredoxin (NCBI ptt file) 40, 511
BC4310 BC4310 Ribosomal protein L11 methyltransferase (NCBI ptt file) 164, 493
BC4311 BC4311 Chaperone protein dnaJ (NCBI ptt file) 40, 164
BC4312 BC4312 Chaperone protein dnaK (NCBI ptt file) 40, 164
BC4313 BC4313 GrpE protein (NCBI ptt file) 40, 164
BC4314 BC4314 Heat-inducible transcription repressor hrcA (NCBI ptt file) 40, 164
BC4584 BC4584 Dephospho-CoA kinase (NCBI ptt file) 164, 302
BC4585 BC4585 Integral membrane protein (NCBI ptt file) 164, 367
BC4586 BC4586 Formamidopyrimidine-DNA glycosylase (NCBI ptt file) 164, 518
BC4587 BC4587 DNA polymerase I (NCBI ptt file) 164, 367
BC4979 BC4979 ABC transporter-associated protein (NCBI ptt file) 152, 164
BC4980 BC4980 IscU protein (NCBI ptt file) 40, 164
BC4981 BC4981 Cysteine desulfhydrase (NCBI ptt file) 40, 164
BC4982 BC4982 ABC transporter-associated protein (NCBI ptt file) 40, 164
BC4983 BC4983 ABC transporter ATP-binding protein (NCBI ptt file) 40, 164
BC5035 BC5035 Phenylacetic acid degradation protein paaD (NCBI ptt file) 40, 507
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 BC4314
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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