Organism : Bacillus cereus ATCC14579 | Module List :
BC3856

LSU ribosomal protein L28P (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Ribosomal protein L28 cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
L28 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3856
(Mouseover regulator name to see its description)

BC3856 is regulated by 30 influences and regulates 0 modules.
Regulators for BC3856 (30)
Regulator Module Operator
BC0224 251 tf
BC0880 251 tf
BC0993 251 tf
BC2971 251 tf
BC3539 251 tf
BC4053 251 tf
BC4174 251 tf
BC4256 251 tf
BC4289 251 tf
BC4525 251 tf
BC5265 251 tf
BC5332 251 tf
BC0073 207 tf
BC0116 207 tf
BC0122 207 tf
BC0880 207 tf
BC2250 207 tf
BC2971 207 tf
BC3072 207 tf
BC3539 207 tf
BC3706 207 tf
BC3740 207 tf
BC4170 207 tf
BC4174 207 tf
BC4212 207 tf
BC4508 207 tf
BC4525 207 tf
BC4708 207 tf
BC5141 207 tf
BC5339 207 tf

Warning: BC3856 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
4330 1.20e-02 AgGGAGgGaAa
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4331 6.00e+03 cCTTcGCATTtCGAC
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4418 3.70e-02 GGAGgg
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4419 2.70e+03 AACtTCatatATTTtCtATtGaAA
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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 BC3856

BC3856 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Ribosomal protein L28 cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
L28 tigr/ tigrfam
Module neighborhood information for BC3856

BC3856 has total of 20 gene neighbors in modules 207, 251
Gene neighbors (20)
Gene Common Name Description Module membership
BC0019 BC0019 hypothetical Cytosolic Protein (NCBI ptt file) 207, 383
BC0120 BC0120 LSU ribosomal protein L12P (L7/L12) (NCBI ptt file) 251, 360
BC0164 BC0164 LSU ribosomal protein L13P (NCBI ptt file) 207, 360
BC0165 BC0165 SSU ribosomal protein S9P (NCBI ptt file) 207, 251
BC3806 BC3806 SSU ribosomal protein S15P (NCBI ptt file) 207, 251
BC3838 BC3838 LSU ribosomal protein L19P (NCBI ptt file) 207, 251
BC3841 BC3841 RNA binding protein (NCBI ptt file) 207, 251
BC3842 BC3842 SSU ribosomal protein S16P (NCBI ptt file) 207, 251
BC3856 BC3856 LSU ribosomal protein L28P (NCBI ptt file) 207, 251
BC3986 BC3986 hypothetical Cytosolic Protein (NCBI ptt file) 207, 251
BC4306 BC4306 GatB/Yqey domain protein (NCBI ptt file) 166, 207
BC4307 BC4307 SSU ribosomal protein S21P (NCBI ptt file) 207, 383
BC4320 BC4320 SSU ribosomal protein S20P (NCBI ptt file) 207, 251
BC4410 BC4410 Protein translocase subunit YajC (NCBI ptt file) 226, 251
BC4573 BC4573 LSU ribosomal protein L20P (NCBI ptt file) 207, 251
BC4574 BC4574 LSU ribosomal protein L35P (NCBI ptt file) 207, 360
BC4575 BC4575 Bacterial Protein Translation Initiation Factor 3 (IF-3) (NCBI ptt file) 207, 360
BC4655 BC4655 SSU ribosomal protein S4P (NCBI ptt file) 251, 383
BC5331 rpmE2 50S ribosomal protein L31 type B (RefSeq) 251, 383
BC5474 BC5474 SSU ribosomal protein S18P (NCBI ptt file) 207, 251
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 BC3856
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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