Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3565

Glycoside hydrolase, family 25 (NCBI)

CircVis
Functional Annotations (5)
Function System
Lyzozyme M1 (1,4-beta-N-acetylmuramidase) cog/ cog
lysozyme activity go/ molecular_function
peptidoglycan catabolic process go/ biological_process
cell wall macromolecule catabolic process go/ biological_process
cation binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3565
(Mouseover regulator name to see its description)

RSP_3565 is regulated by 12 influences and regulates 0 modules.
Regulators for RSP_3565 (12)
Regulator Module Operator
RSP_0386 84 tf
RSP_0755 84 tf
RSP_1660 84 tf
RSP_3238 84 tf
RSP_3341 84 tf
RSP_0507 221 tf
RSP_1225 221 tf
RSP_1890 221 tf
RSP_2346 221 tf
RSP_2838 221 tf
RSP_2840 221 tf
RSP_3665 221 tf

Warning: RSP_3565 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
7888 1.20e-01 aGAtCGgTCAgCTtccGccCCcG
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7889 9.10e+00 CcgAAGGcTcG.aacaaccCGCGg
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8162 4.10e-01 CtcATCCcgTtgCAAcgtTgCG
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8163 1.40e+01 CGCATCcgcGAtGGCaActtcG
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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_3565

RSP_3565 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Lyzozyme M1 (1,4-beta-N-acetylmuramidase) cog/ cog
lysozyme activity go/ molecular_function
peptidoglycan catabolic process go/ biological_process
cell wall macromolecule catabolic process go/ biological_process
cation binding go/ molecular_function
Module neighborhood information for RSP_3565

RSP_3565 has total of 48 gene neighbors in modules 84, 221
Gene neighbors (48)
Gene Common Name Description Module membership
RSP_0015 RSP_0015 ABC spermidine/putrescine transporter, ATPase subunit (NCBI) 221, 358
RSP_0202 RSP_0202 putative membrane protein (NCBI) 221, 340
RSP_0677 RSP_0677 Putative malonate transporter, mdcF, AEC family (NCBI) 130, 221
RSP_0923 map1 Methionine aminopeptidase, subfamily 1 (NCBI) 84, 286
RSP_0925 yobR Putative acetyl transferase (NCBI) 84, 286
RSP_0926 RSP_0926 OmpA/MotB family protein (NCBI) 84, 286
RSP_0963 RSP_0963 Inner membrane protein (NCBI) 208, 221
RSP_0987 RSP_0987 Putative transporter, RarD family, DMT superfamily (NCBI) 84, 126
RSP_1263 RSP_1263 hypothetical protein (NCBI) 84, 307
RSP_1264 RSP_1264 hypothetical protein (NCBI) 84, 307
RSP_1265 kdpA Potassium-transporting P-type ATPase, A chain, KdpA (NCBI) 84, 307
RSP_1266 kdpB Potassium-transporting P-type ATPase, B chain, KdpB (NCBI) 84, 307
RSP_1267 kdpC Potassium-transporting P-type ATPase C chain, kdpC (NCBI) 84, 307
RSP_1268 kdpD Osmosensitive K+ channel histidine kinase (NCBI) 84, 307
RSP_1269 kdpE two component transcriptional regulator, winged helix family (NCBI) 84, 307
RSP_1339 RSP_1339 Formamidopyrimidine-DNA glycolase (NCBI) 84, 331
RSP_1462 lpxK Putative Tetraacyldisaccharide-1-P 4'-kinase (NCBI) 84, 234
RSP_1470 rnhB ribonuclease HII (NCBI) 84, 164
RSP_1677 RSP_1677 hypothetical protein (NCBI) 221, 383
RSP_1810 mviN putative virulence factor, MviN (NCBI) 221, 374
RSP_1811 glnD uridylyltransferase (NCBI) 221, 374
RSP_1812 RSP_1812 hypothetical protein (NCBI) 81, 221
RSP_1813 RSP_1813 hypothetical protein (NCBI) 121, 221
RSP_1814 RSP_1814 hypothetical protein (NCBI) 197, 221
RSP_1815 gshB glutathione synthetase (NCBI) 184, 221
RSP_1909 RSP_1909 Outer membrane general secretion pathway protein, Secretin (NCBI) 221, 381
RSP_1970 RSP_1970 Phosphoribosylglycinamide formyltransferase (NCBI) 84, 209
RSP_2107 murG UDP-N-acetylglucosamine:N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI) 221, 349
RSP_2108 murC UDP-N-acetylmuramate-alanine ligase (NCBI) 5, 221
RSP_2109 RSP_2109 hypothetical protein (NCBI) 5, 221
RSP_2110 murB UDP-N-acetylenolpyruvoylglucosamine reductase/dehydrogenase (NCBI) 5, 221
RSP_2111 ddlA D-alanine--D-alanine ligase (NCBI) 221, 349
RSP_2256 dtd D-tyrosyl-tRNA(Tyr) deacylase (NCBI) 221, 374
RSP_2257 RSP_2257 putative Fructokinase (NCBI) 221, 374
RSP_2358 RSP_2358 possible phage phi-C31 gp36-like protein / Major capsid protein, HK97 family (NCBI) 221, 331
RSP_2534 RSP_2534 Predicted hydrolase of the metallo-beta-lactamase superfamily (NCBI) 84, 361
RSP_2583 RSP_2583 hypothetical protein (NCBI) 26, 221
RSP_2584 RSP_2584 hypothetical protein (NCBI) 221, 363
RSP_2599 phoB Phosphate regulon transcriptional regulator, PhoR (NCBI) 84, 155
RSP_2790 RSP_2790 hypothetical protein (NCBI) 84, 356
RSP_2815 xerD Probable integrase/recombinase XerD (NCBI) 84, 326
RSP_2818 aroB Putative 3-dehydroquinate synthase (NCBI) 84, 234
RSP_2941 RSP_2941 Putative Glycoside hydrolase (NCBI) 221, 259
RSP_3091 RSP_3091 Coserved hypothetical protein (NCBI) 54, 84
RSP_3448 RSP_3448 transcriptional regulator, GntR-family (NCBI) 84, 220
RSP_3449 RSP_3449 Putative allophanate hydrolase subunit 2 (NCBI) 61, 84
RSP_3450 RSP_3450 hypothetical protein (NCBI) 61, 84
RSP_3565 RSP_3565 Glycoside hydrolase, family 25 (NCBI) 84, 221
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_3565
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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