Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2016 rpmB

50S ribosomal protein L28 (NCBI)

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 RSP_2016
(Mouseover regulator name to see its description)

RSP_2016 is regulated by 28 influences and regulates 0 modules.
Regulators for RSP_2016 rpmB (28)
Regulator Module Operator
RSP_0591 327 tf
RSP_1032 327 tf
RSP_1055 327 tf
RSP_1669 327 tf
RSP_1776 327 tf
RSP_1871 327 tf
RSP_1945 327 tf
RSP_2494 327 tf
RSP_3022 327 tf
RSP_3109 327 tf
RSP_3324 327 tf
RSP_3621 327 tf
RSP_3694 327 tf
RSP_0395 248 tf
RSP_0607 248 tf
RSP_0755 248 tf
RSP_1607 248 tf
RSP_1663 248 tf
RSP_1866 248 tf
RSP_2165 248 tf
RSP_2533 248 tf
RSP_2610 248 tf
RSP_2840 248 tf
RSP_2922 248 tf
RSP_3022 248 tf
RSP_3042 248 tf
RSP_3203 248 tf
RSP_3505 248 tf

Warning: RSP_2016 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
8214 4.50e-62 GATATTTGggCCAGaaTGAAaGgG
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8215 4.80e-10 cGGGGGTcCGGGGGc.g.aaacCC
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8362 9.20e-02 AAAAAC
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8363 4.40e-01 AttGacGaCaCGGtGaaAAcTCaA
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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 RSP_2016

RSP_2016 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 RSP_2016

RSP_2016 has total of 49 gene neighbors in modules 248, 327
Gene neighbors (49)
Gene Common Name Description Module membership
RSP_0007 RSP_0007 putative outer membrane protein (NCBI) 190, 248
RSP_0205 RSP_0205 hypothetical protein (NCBI) 213, 327
RSP_0220 RSP_0220 hypothetical protein (NCBI) 68, 327
RSP_0236 RSP_0236 AgaE protein (NCBI) 156, 248
RSP_0237 argE acetylornithine deacetylase (NCBI) 248, 262
RSP_0370 RSP_0370 hypothetical protein (NCBI) 210, 327
RSP_0389 folA Dihydrofolate reductase (NCBI) 159, 248
RSP_0390 RSP_0390 Thymidylate synthase (NCBI) 159, 248
RSP_0395 rpoD RNA polymerase sigma factor RpoD (NCBI) 159, 248
RSP_0396 RSP_0396 hypothetical protein (NCBI) 159, 248
RSP_0397 dnaG DNA primase (DnaG) (NCBI) 159, 248
RSP_0447 RSP_0447 hypothetical protein (NCBI) 159, 248
RSP_0591 RSP_0591 Cold-shock protein (NCBI) 56, 327
RSP_0597 RSP_0597 Probable molybdopterin biosynthesis protein (NCBI) 159, 248
RSP_0598 RSP_0598 Probable deoxyuridine-triphosphatase (NCBI) 159, 248
RSP_0626 infA Probable translation initiation factor 1 (IF-1) (NCBI) 75, 327
RSP_0814 RSP_0814 Acetyltransferase (NCBI) 215, 248
RSP_0815 aspS Aspartyl-tRNA synthetase (NCBI) 166, 248
RSP_0867 rnhA ribonuclease H (NCBI) 213, 327
RSP_1059 rpmH 50S ribosomal protein L34 (NCBI) 75, 327
RSP_1104 RSP_1104 hypothetical protein (NCBI) 35, 327
RSP_1201 RSP_1201 hypothetical protein (NCBI) 43, 327
RSP_1277 RSP_1277 hypothetical protein (NCBI) 172, 248
RSP_1278 cbbZ phosphoglycolate phosphatase (NCBI) 248, 264
RSP_1279 cbbY CbbY family protein (NCBI) 248, 264
RSP_1341 rpsT Ribosomal protein S20 (NCBI) 75, 327
RSP_1388 RSP_1388 DNA-binding protein HU, form N (NCBI) 327, 345
RSP_1398 rpmJ ribosomal protein L36 (NCBI) 75, 327
RSP_1496 RSP_1496 hypothetical protein (NCBI) 181, 327
RSP_1498 RSP_1498 hypothetical protein (NCBI) 181, 327
RSP_1517 spbA Histone-like protein of HNS family (NCBI) 48, 327
RSP_1529 trxA Thioredoxin (NCBI) 327, 345
RSP_1669 rpoZ RNA polymerase omega subunit (NCBI) 75, 327
RSP_1859 ppdK Pyruvate phosphate dikinase (NCBI) 248, 341
RSP_1887 RSP_1887 Ribosomal protein L33 (NCBI) 75, 327
RSP_2016 rpmB 50S ribosomal protein L28 (NCBI) 248, 327
RSP_2266 rluB Pseudouridine synthase, (predicted) (NCBI) 156, 248
RSP_2340 RSP_2340 MiaB-like Radical SAM protein (NCBI) 159, 248
RSP_2424 RSP_2424 ferredoxin II (NCBI) 75, 327
RSP_2463 acpP Acyl carrier protein (ACP) (NCBI) 327, 345
RSP_2978 mrcA Penicillin-binding protein 1A (PBP-1a) (NCBI) 159, 248
RSP_2979 amiC Probable N-acetylmuramoyl-L-alanine amidase (NCBI) 113, 248
RSP_4300 RSP_4300 tRNA-Ser (NCBI) 327, 336
RSP_4301 RSP_4301 tRNA-Leu (NCBI) 48, 327
RSP_4309 RSP_4309 tRNA-Val (NCBI) 75, 327
RSP_4311 RSP_4311 tRNA-Pro (NCBI) 75, 327
RSP_4323 RSP_4323 tRNA-OTHER (NCBI) 75, 327
RSP_4332 RSP_4332 tRNA-Leu (NCBI) 75, 327
RSP_6181 RSP_6181 None 190, 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 RSP_2016
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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