Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1618

hypothetical protein (NCBI)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1618
(Mouseover regulator name to see its description)

RSP_1618 is regulated by 23 influences and regulates 0 modules.
Regulators for RSP_1618 (23)
Regulator Module Operator
RSP_0607 62 tf
RSP_1014 62 tf
RSP_1435 62 tf
RSP_2780 62 tf
RSP_2867 62 tf
RSP_2882 62 tf
RSP_3322 62 tf
RSP_3339 62 tf
RSP_3400 62 tf
RSP_3464 62 tf
RSP_3528 62 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_1618 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
7844 5.90e-05 tTATaTtgATaccAAaaaa
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7845 1.90e+01 gCagGATGccCCtgcgaAAGGtcG
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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_1618

Warning: No Functional annotations were found!

Module neighborhood information for RSP_1618

RSP_1618 has total of 60 gene neighbors in modules 62, 304
Gene neighbors (60)
Gene Common Name Description Module membership
RSP_0027 RSP_0027 hypothetical protein (NCBI) 62, 251
RSP_0172 RSP_0172 Predicted transcriptional regulators (NCBI) 38, 62
RSP_0226 RSP_0226 Naringenin-chalcone synthase (NCBI) 62, 189
RSP_0297 RSP_0297 ABC branched chain amino acid transporter, ATPase subunit (NCBI) 103, 304
RSP_0456 RSP_0456 hypothetical protein (NCBI) 62, 380
RSP_0512 RSP_0512 multisensor hybrid histidine kinase (NCBI) 94, 304
RSP_0609 RSP_0609 hypothetical protein (NCBI) 146, 304
RSP_0751 RSP_0751 hypothetical protein (NCBI) 62, 97
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_1435 RSP_1435 regulatory protein TetR family (NCBI) 62, 97
RSP_1446 RSP_1446 Putative sugar kinase (NCBI) 62, 89
RSP_1500 RSP_1500 possible anti-sigma regulatory kinase (NCBI) 29, 304
RSP_1618 RSP_1618 hypothetical protein (NCBI) 62, 304
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_1888 RSP_1888 possible acetyltransferase (GNAT) family (NCBI) 38, 62
RSP_1923 bioB Biotin synthase (NCBI) 62, 292
RSP_1954 RSP_1954 hypothetical protein (NCBI) 155, 304
RSP_1996 RSP_1996 Putative Competence protein (NCBI) 62, 380
RSP_2023 RSP_2023 hypothetical protein (NCBI) 229, 304
RSP_2032 RSP_2032 putative hypothetical Gifsy-1 prophage protein (NCBI) 62, 105
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_2649 RSP_2649 Putative Zn-dependent protease (NCBI) 62, 285
RSP_2769 RSP_2769 probable 5,10-methylenetetrahydrofolate reductase (NCBI) 238, 304
RSP_2780 oxyR Transcriptional regulator, OxyR, LysR family (NCBI) 55, 62
RSP_2799 RSP_2799 Putative Zinc-containing alcohol dehydrogenase (NCBI) 62, 379
RSP_2813 mttB putative trimethylamine methyltransferase protein (NCBI) 73, 304
RSP_2882 RSP_2882 two component transcriptional regulator, LuxR family (NCBI) 62, 381
RSP_3014 RSP_3014 putative aldolase protein (NCBI) 137, 304
RSP_3018 RSP_3018 putative acyl-CoA dehydrogenase (NCBI) 304, 370
RSP_3020 RSP_3020 hypothetical protein (NCBI) 38, 62
RSP_3027 rdxA RdxA, iron-sulfur cluster-binding protein (NCBI) 62, 196
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_3109 RSP_3109 transcriptional regulator, MarR family (NCBI) 62, 285
RSP_3110 RSP_3110 Putative Glutathione S-transferase (NCBI) 62, 342
RSP_3111 RSP_3111 Putative Glutathione S-transferase (NCBI) 62, 285
RSP_3112 RSP_3112 hypothetical protein (NCBI) 62, 285
RSP_3204 RSP_3204 putative Oxidoreductase (NCBI) 124, 304
RSP_3278 RSP_3278 Von Willebrand domain containing protein (NCBI) 62, 116
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_3499 RSP_3499 H+-transporting two-sector ATPase, alpha/beta subunit (NCBI) 38, 62
RSP_3577 gvpG putative gas vesicle synthesis protein (NCBI) 253, 304
RSP_3617 RSP_3617 hypothetical protein (NCBI) 38, 62
RSP_3659 RSP_3659 Predicted amidohydrolase (NCBI) 288, 304
RSP_3682 RSP_3682 hypothetical protein (NCBI) 74, 304
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_1618
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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