Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3820 rpmA

Ribosomal protein L27 (NCBI)

CircVis
Functional Annotations (6)
Function System
Ribosomal protein L27 cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
L27 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3820
(Mouseover regulator name to see its description)

RSP_3820 is regulated by 19 influences and regulates 0 modules.
Regulators for RSP_3820 rpmA (19)
Regulator Module Operator
RSP_0386 169 tf
RSP_0698 169 tf
RSP_1163 169 tf
RSP_1669 169 tf
RSP_1704 169 tf
RSP_1739 169 tf
RSP_2236 169 tf
RSP_2591 169 tf
RSP_3606 169 tf
RSP_0395 309 tf
RSP_0443 309 tf
RSP_0489 309 tf
RSP_1163 309 tf
RSP_1231 309 tf
RSP_1274 309 tf
RSP_1704 309 tf
RSP_1890 309 tf
RSP_2410 309 tf
RSP_3324 309 tf

Warning: RSP_3820 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
8058 5.00e-01 AAaacgaAagaacg
Loader icon
8059 6.60e+03 TCaCagtCGAA
Loader icon
8332 2.70e-08 AatggGgCGag.TTcCcCcTT
Loader icon
8333 7.00e-03 tCCTgtTTcgCaGgA
Loader icon
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 RSP_3820

RSP_3820 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Ribosomal protein L27 cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
L27 tigr/ tigrfam
Module neighborhood information for RSP_3820

RSP_3820 has total of 48 gene neighbors in modules 169, 309
Gene neighbors (48)
Gene Common Name Description Module membership
RSP_0123 cerI Autoinducer synthesis protein (NCBI) 97, 309
RSP_0124 RSP_0124 hypothetical protein (NCBI) 161, 309
RSP_0140 RSP_0140 30S ribosomal protein S18 (NCBI) 169, 312
RSP_0141 RSP_0141 50S ribosomal protein L9 (NCBI) 104, 169
RSP_0217 int possible phage-related integrase (NCBI) 171, 309
RSP_0890 RSP_0890 possible protein yrbC precursor (NCBI) 182, 309
RSP_0891 vacJ putative lipoprotein (NCBI) 182, 309
RSP_0892 RSP_0892 ABC protein toxin exporter, fused ATPase and inner membrane domain (NCBI) 182, 309
RSP_0893 RSP_0893 RTX secretion protein D, HlyD family (NCBI) 182, 309
RSP_0929 accD Acetyl-CoA carboxylase carboxyl transferase, beta subunit (NCBI) 309, 360
RSP_1043 rpmE ribosomal protein L31 (NCBI) 169, 310
RSP_1044 rplS 50s ribosomal protein L19 (NCBI) 169, 310
RSP_1111 rpsO Ribosomal protein S15 (NCBI) 169, 310
RSP_1162 RSP_1162 hypothetical protein (NCBI) 104, 169
RSP_1163 nusA N-utilization substance protein A (NCBI) 104, 169
RSP_1165 InfB Translation Initiation factor 2 (NCBI) 104, 169
RSP_1699 rpoB DNA-directed RNA polymerase, beta subunit (NCBI) 104, 169
RSP_1701 rplJ Ribosomal protein L10 (NCBI) 169, 310
RSP_1702 rplA Ribosomal protein L1 (NCBI) 104, 169
RSP_1703 rplK Ribosomal protein L11 (NCBI) 104, 169
RSP_1707 tufA Elongation factor Tu (EF-Tu) (NCBI) 169, 310
RSP_1737 rpsM Ribosomal protein S13 (NCBI) 151, 169
RSP_1738 rpsK Ribosomal protein S11 (NCBI) 151, 169
RSP_1764 rplT Ribosomal protein L20 (NCBI) 169, 310
RSP_1765 rpmI Ribosomal protein L35 (NCBI) 169, 310
RSP_1843 ftsY Signal recognition particle-docking protein FtsY (NCBI) 71, 309
RSP_1864 RSP_1864 hypothetical protein (NCBI) 48, 309
RSP_1948 RSP_1948 Protein of unknown function, HesB/YadR/YfhF (NCBI) 161, 309
RSP_1949 RSP_1949 hypothetical protein (NCBI) 161, 309
RSP_1986 gatB Glutamyl-tRNA amidotransferase subunit B (NCBI) 25, 309
RSP_1991 RSP_1991 Putative Ornithine decarboxylase (NCBI) 309, 365
RSP_1994 gltA Citrate synthase (NCBI) 279, 309
RSP_2193 gcvT predicted aminomethyltransferase, tetrahydrofolate dependent (NCBI) 71, 309
RSP_2283 rpsD Ribosomal protein S4 (NCBI) 169, 312
RSP_2329 mreB Cell shape determining protein MreB/Mrl (NCBI) 93, 309
RSP_2646 RSP_2646 None 286, 309
RSP_2718 RSP_2718 possible outer membrane protein (NCBI) 3, 309
RSP_2783 lipA lipoic acid synthetase (NCBI) 161, 309
RSP_2860 rpsB Ribosomal protein S2 (NCBI) 104, 169
RSP_2861 TSF Translation elongation factor Ts (NCBI) 104, 169
RSP_2914 RSP_2914 Nucleoside hydrolase (NCBI) 126, 309
RSP_2921 RSP_2921 phospho-2-dehydro-3-deoxyheptonate (NCBI) 182, 309
RSP_2922 RSP_2922 Transcriptional regulator, AraC family (NCBI) 182, 309
RSP_2975 RSP_2975 hypothetical protein (NCBI) 71, 309
RSP_3074 ilvD Dihydroxy-acid and 6-phosphogluconate dehydratase (NCBI) 15, 309
RSP_3819 rplU Ribosomal protein L21 (NCBI) 169, 312
RSP_3820 rpmA Ribosomal protein L27 (NCBI) 169, 309
RSP_3821 RSP_3821 Putative acetyltransferase (NCBI) 297, 309
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 RSP_3820
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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