Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2068

putative ClpP-like protease (NCBI)

CircVis
Functional Annotations (3)
Function System
Protease subunit of ATP-dependent Clp proteases cog/ cog
proteolysis go/ biological_process
endopeptidase Clp activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2068
(Mouseover regulator name to see its description)

RSP_2068 is regulated by 23 influences and regulates 0 modules.
Regulators for RSP_2068 (23)
Regulator Module Operator
RSP_1077 235 tf
RSP_1231 235 tf
RSP_1607 235 tf
RSP_1660 235 tf
RSP_3064 235 tf
RSP_3179 235 tf
RSP_3238 235 tf
RSP_3418 235 tf
RSP_3464 235 tf
RSP_3676 235 tf
RSP_3684 235 tf
RSP_0511 304 tf
RSP_1607 304 tf
RSP_1660 304 tf
RSP_2922 304 tf
RSP_2932 304 tf
RSP_3001 304 tf
RSP_3055 304 tf
RSP_3418 304 tf
RSP_3464 304 tf
RSP_3616 304 tf
RSP_3676 304 tf
RSP_3684 304 tf

Warning: RSP_2068 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
8188 8.60e-02 agtatcTgCtTgaGctt
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8189 4.00e+02 GttcGcgCAcaAtctCGcGAcGA
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8322 4.80e+04 AAACCTTA
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8323 6.20e+04 ACATGAAGA
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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_2068

RSP_2068 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Protease subunit of ATP-dependent Clp proteases cog/ cog
proteolysis go/ biological_process
endopeptidase Clp activity go/ molecular_function
Module neighborhood information for RSP_2068

RSP_2068 has total of 65 gene neighbors in modules 235, 304
Gene neighbors (65)
Gene Common Name Description Module membership
RSP_0206 RSP_0206 hypothetical protein (NCBI) 235, 303
RSP_0234 tlpL TlpL, putative cytoplasmic chemoreceptor (NCBI) 138, 235
RSP_0297 RSP_0297 ABC branched chain amino acid transporter, ATPase subunit (NCBI) 103, 304
RSP_0512 RSP_0512 multisensor hybrid histidine kinase (NCBI) 94, 304
RSP_0609 RSP_0609 hypothetical protein (NCBI) 146, 304
RSP_0856 btaA S-adenosylmethionine-diacylglycerol 3-amino-3-carboxypropyl transferase (NCBI) 6, 304
RSP_0938 RSP_0938 hypothetical protein (NCBI) 304, 313
RSP_1323 RSP_1323 hypothetical protein (NCBI) 116, 304
RSP_1332 RSP_1332 H+-transporting two-sector ATPase, alpha/beta subunit (NCBI) 235, 359
RSP_1500 RSP_1500 possible anti-sigma regulatory kinase (NCBI) 29, 304
RSP_1618 RSP_1618 hypothetical protein (NCBI) 62, 304
RSP_1619 RSP_1619 hypothetical protein (NCBI) 189, 235
RSP_1620 RSP_1620 hypothetical protein (NCBI) 235, 342
RSP_1651 RSP_1651 hypothetical protein (NCBI) 304, 313
RSP_1694 RSP_1694 Probable short-chain dehydrogenase/reductase (NCBI) 233, 304
RSP_1753 RSP_1753 hypothetical protein (NCBI) 304, 355
RSP_1782 RSP_1782 hypothetical membrane protein (NCBI) 233, 235
RSP_1783 RSP_1783 Predicted membrane protein (NCBI) 233, 235
RSP_1954 RSP_1954 hypothetical protein (NCBI) 155, 304
RSP_1957 RSP_1957 hypothetical protein (NCBI) 138, 235
RSP_1961 RSP_1961 hypothetical protein (NCBI) 235, 355
RSP_2023 RSP_2023 hypothetical protein (NCBI) 229, 304
RSP_2034 RSP_2034 possible CAAX amino terminal protease family (NCBI) 235, 380
RSP_2040 RSP_2040 possible Transposase fragment (NCBI) 138, 235
RSP_2043 RSP_2043 hypothetical protein (NCBI) 235, 380
RSP_2068 RSP_2068 putative ClpP-like protease (NCBI) 235, 304
RSP_2070 RSP_2070 Putative Phage-related terminase (NCBI) 77, 304
RSP_2071 RSP_2071 hypothetical protein (NCBI) 77, 304
RSP_2259 RSP_2259 Transmembrane protein (NCBI) 288, 304
RSP_2441 tlpS Putative transducer like protein (NCBI) 304, 320
RSP_2466 RSP_2466 hypothetical protein (NCBI) 193, 235
RSP_2471 RSP_2471 Predicted phage phi-C31 gp36 major capsid-like protein (NCBI) 193, 235
RSP_2472 RSP_2472 hypothetical protein (NCBI) 193, 235
RSP_2478 RSP_2478 hypothetical protein (NCBI) 193, 235
RSP_2479 RSP_2479 putative phage host specificity protein (NCBI) 235, 320
RSP_2480 RSP_2480 hypothetical protein (NCBI) 193, 235
RSP_2769 RSP_2769 probable 5,10-methylenetetrahydrofolate reductase (NCBI) 238, 304
RSP_2813 mttB putative trimethylamine methyltransferase protein (NCBI) 73, 304
RSP_2871 aglG ABC alpha-glucoside transporter, inner membrane subunit AglG (NCBI) 229, 235
RSP_2930 RSP_2930 hypothetical protein (NCBI) 235, 238
RSP_2990 RSP_2990 hypothetical protein (NCBI) 235, 380
RSP_2996 RSP_2996 putative prohead protease (NCBI) 14, 235
RSP_2997 RSP_2997 putative head portal protein (NCBI) 14, 235
RSP_3014 RSP_3014 putative aldolase protein (NCBI) 137, 304
RSP_3018 RSP_3018 putative acyl-CoA dehydrogenase (NCBI) 304, 370
RSP_3064 RSP_3064 transcriptional regulator, DeoR family (NCBI) 235, 292
RSP_3096 RSP_3096 hypothetical protein (NCBI) 168, 304
RSP_3098 qoxB QoxB, Quinol oxidase subunit II (NCBI) 168, 304
RSP_3103 RSP_3103 hypothetical protein (NCBI) 19, 304
RSP_3104 fdh Putative Glutathione-dependent formaldehyde dehydrogenase (NCBI) 288, 304
RSP_3201 RSP_3201 putative oxidoreductase (NCBI) 138, 235
RSP_3204 RSP_3204 putative Oxidoreductase (NCBI) 124, 304
RSP_3283 RSP_3283 myo-inositol 2-dehydrogenase (NCBI) 116, 304
RSP_3357 gpU putative phage tail protein U (NCBI) 40, 304
RSP_3358 gpX Phage tail component protein X (NCBI) 282, 304
RSP_3390 RSP_3390 ABC Fe3+-siderophores transporter, ATPase subunit (NCBI) 146, 235
RSP_3417 RSP_3417 TonB dependent outer membrane ferrichrome-iron receptor (NCBI) 235, 380
RSP_3577 gvpG putative gas vesicle synthesis protein (NCBI) 253, 304
RSP_3624 RSP_3624 hypothetical protein (NCBI) 235, 307
RSP_3659 RSP_3659 Predicted amidohydrolase (NCBI) 288, 304
RSP_3682 RSP_3682 hypothetical protein (NCBI) 74, 304
RSP_3684 solR transcriptional regulator, LuxR family (NCBI) 116, 235
RSP_3774 RSP_3774 hypothetical protein (NCBI) 304, 380
RSP_3775 RSP_3775 hypothetical protein (NCBI) 304, 380
RSP_3814 RSP_3814 hypothetical protein (NCBI) 189, 304
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_2068
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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