Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2518 rplM

50S ribosomal protein L13

CircVis
Functional Annotations (6)
Function System
Ribosomal protein L13 cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
rplM_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2518
(Mouseover regulator name to see its description)

DVU2518 is regulated by 22 influences and regulates 0 modules.
Regulators for DVU2518 rplM (22)
Regulator Module Operator
DVU0653
DVU2275
151 combiner
DVU1547
DVU2690
151 combiner
DVU2086 151 tf
DVU2195 151 tf
DVU2275 151 tf
DVU2532
DVU2275
151 combiner
DVU2547 151 tf
DVU2547
DVU2588
151 combiner
DVU3167 151 tf
DVU3167
DVU1584
151 combiner
DVU3167
DVU2582
151 combiner
DVU0744
DVU0230
45 combiner
DVU0744
DVU3142
45 combiner
DVU1402 45 tf
DVU1547
DVUA0024
45 combiner
DVU1584 45 tf
DVU2195 45 tf
DVU2275 45 tf
DVU2423
DVU0619
45 combiner
DVU2547 45 tf
DVU3167
DVU1949
45 combiner
DVU3167
DVU2582
45 combiner

Warning: DVU2518 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (4)
Motif Id e-value Consensus Motif Logo RegPredict
89 9.30e+01 AagGAttctAaCCCcCaaa
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RegPredict
90 2.30e+03 CtTccTTggtc.aGC
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RegPredict
287 1.80e+02 ATGAaGGtga.AatTacatg
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RegPredict
288 3.20e+03 TcCtTCC.cCCC.GCCATttC
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RegPredict
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 DVU2518

DVU2518 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Ribosomal protein L13 cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
rplM_bact tigr/ tigrfam
Module neighborhood information for DVU2518

DVU2518 has total of 27 gene neighbors in modules 45, 151
Gene neighbors (27)
Gene Common Name Description Module membership
DVU0873 tsf elongation factor Ts 151, 186
DVU0874 rpsB 30S ribosomal protein S2 151, 186
DVU0956 rpsF 30S ribosomal protein S6 151, 306
DVU1287 reductase, iron-sulfur binding subunit 151, 306
DVU1288 cytochrome c family protein 151, 306
DVU1289 reductase, iron-sulfur binding subunit 151, 306
DVU1293 None 151, 323
DVU1303 rplC 50S ribosomal protein L3 45, 177
DVU1325 rpmJ 50S ribosomal protein L36 45, 177
DVU1326 rpsM 30S ribosomal protein S13 45, 177
DVU1327 rpsK 30S ribosomal protein S11 45, 177
DVU1328 rpsD 30S ribosomal protein S4 45, 177
DVU1329 rpoA DNA-directed RNA polymerase subunit alpha 45, 177
DVU1330 rplQ 50S ribosomal protein L17 45, 177
DVU1574 rplY 50S ribosomal protein L25 45, 151
DVU1575 prsA ribose-phosphate pyrophosphokinase 10, 45
DVU2231 typA GTP-binding protein TypA 10, 151
DVU2518 rplM 50S ribosomal protein L13 45, 151
DVU2519 rpsI 30S ribosomal protein S9 151, 186
DVU2922 secE preprotein translocase subunit SecE 151, 237
DVU2923 nusG transcription antitermination protein NusG 10, 151
DVU2924 rplK 50S ribosomal protein L11 45, 151
DVU2925 rplA 50S ribosomal protein L1 151, 297
DVU2926 rplJ 50S ribosomal protein L10 45, 151
DVU2927 rplL 50S ribosomal protein L7/L12 151, 306
DVU2928 rpoB DNA-directed RNA polymerase subunit beta 151, 306
DVU2929 rpoC DNA-directed RNA polymerase subunit beta' 151, 248
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 DVU2518
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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