Organism : Geobacter sulfurreducens | Module List :
GSU0645 rimM

16S rRNA processing protein RimM (NCBI)

CircVis
Functional Annotations (5)
Function System
RimM protein, required for 16S rRNA processing cog/ cog
ribosome go/ cellular_component
rRNA processing go/ biological_process
ribosome binding go/ molecular_function
16S_RimM tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0645
(Mouseover regulator name to see its description)

GSU0645 is regulated by 16 influences and regulates 0 modules.
Regulators for GSU0645 rimM (16)
Regulator Module Operator
GSU0551 87 tf
GSU0770 87 tf
GSU1495 87 tf
GSU1989 87 tf
GSU2033 87 tf
GSU2262 87 tf
GSU2506 87 tf
GSU0551 200 tf
GSU1320 200 tf
GSU1569 200 tf
GSU1940 200 tf
GSU1989 200 tf
GSU1992 200 tf
GSU2262 200 tf
GSU3087 200 tf
GSU3089 200 tf

Warning: GSU0645 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
2334 2.60e+00 a.ttaaGTgAAtAta
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2335 3.50e+02 aTtaTtagTTt.Tt
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2560 3.40e+02 AAaaaatA
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2561 8.90e+02 Aa.TC.cTgaAta.cttAGgTtAT
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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 GSU0645

GSU0645 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
RimM protein, required for 16S rRNA processing cog/ cog
ribosome go/ cellular_component
rRNA processing go/ biological_process
ribosome binding go/ molecular_function
16S_RimM tigr/ tigrfam
Module neighborhood information for GSU0645

GSU0645 has total of 44 gene neighbors in modules 87, 200
Gene neighbors (44)
Gene Common Name Description Module membership
GSU0005 GSU0005 hypothetical protein (VIMSS) 68, 87
GSU0055 GSU0055 conserved hypothetical protein (VIMSS) 87, 318
GSU0065 GSU0065 cytidine/deoxycytidylate deaminase family protein (VIMSS) 81, 200
GSU0103 GSU0103 sensory box histidine kinase (VIMSS) 200, 216
GSU0104 GSU0104 response regulator, putative (VIMSS) 200, 279
GSU0115 pdxA pyridoxal phosphate biosynthetic protein PdxA (NCBI) 200, 335
GSU0116 GSU0116 transglycosylase (VIMSS) 95, 200
GSU0255 GSU0255 sensory box histidine kinase (VIMSS) 87, 145
GSU0358 GSU0358 iron-sulfur cluster-binding protein (VIMSS) 61, 200
GSU0642 ffh signal recognition particle protein (NCBI) 107, 200
GSU0645 rimM 16S rRNA processing protein RimM (NCBI) 87, 200
GSU0646 trmD tRNA (guanine-N1)-methyltransferase (NCBI) 107, 200
GSU0650 GSU0650 conserved hypothetical protein TIGR00252 (VIMSS) 87, 145
GSU0781 GSU0781 twin-arginine translocation protein, TatA/E family (NCBI) 33, 87
GSU0807 GSU0807 apo-citrate lyase phosphoribosyl-dephospho-CoA transferase, putative (NCBI) 81, 200
GSU0953 GSU0953 hypothetical protein (VIMSS) 87, 198
GSU1090 GSU1090 signal transduction protein-related protein (VIMSS) 200, 294
GSU1113 GSU1113 carbohydrate kinase, PfkB family (VIMSS) 87, 102
GSU1231 GSU1231 response regulator (VIMSS) 87, 158
GSU1362 GSU1362 hypothetical protein (VIMSS) 33, 87
GSU1449 GSU1449 hypothetical protein (VIMSS) 87, 260
GSU1495 GSU1495 sigma-54 dependent DNA-binding response regulator (VIMSS) 87, 198
GSU1673 GSU1673 hypothetical protein (VIMSS) 53, 200
GSU1744 GSU1744 hypothetical protein (VIMSS) 87, 318
GSU1790 loN-2 ATP-dependent protease La (NCBI) 87, 324
GSU1796 GSU1796 DHH family protein (VIMSS) 200, 229
GSU1849 GSU1849 hypothetical protein (VIMSS) 87, 232
GSU1990 GSU1990 sensor histidine kinase (VIMSS) 53, 200
GSU2248 GSU2248 conserved hypothetical protein (VIMSS) 87, 102
GSU2315 GSU2315 hypothetical protein (VIMSS) 200, 319
GSU2442 GSU2442 RelA/SpoT domain protein (NCBI) 114, 200
GSU2543 GSU2543 polysaccharide deacetylase domain protein (NCBI) 87, 318
GSU2550 drpA DNA processing protein DprA (NCBI) 87, 145
GSU2678 hsp heat shock protein, Hsp20 family (NCBI) 53, 200
GSU2897 GSU2897 hypothetical protein (VIMSS) 162, 200
GSU3020 GSU3020 hexapeptide transferase family protein (VIMSS) 200, 229
GSU3065 ftsQ cell division protein FtsQ (NCBI) 200, 264
GSU3074 murE UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate ligase (NCBI) 200, 267
GSU3075 GSU3075 penicillin-binding protein (VIMSS) 200, 267
GSU3076 GSU3076 cell division protein FtsL, putative (NCBI) 188, 200
GSU3077 mraW S-adenosyl-methyltransferase MraW (NCBI) 200, 267
GSU3078 GSU3078 mraZ protein, putative (NCBI) 200, 267
GSU3087 GSU3087 transcriptional regulator, Sir2 family (VIMSS) 200, 324
GSU3090 dnaG DNA primase (NCBI) 200, 267
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 GSU0645
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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