Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_1425

Plasmid replication initiation protein (NCBI)

CircVis
Functional Annotations (3)
Function System
DNA-directed DNA polymerase activity go/ molecular_function
extrachromosomal circular DNA go/ cellular_component
DNA-dependent DNA replication initiation go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_1425
(Mouseover regulator name to see its description)

RSP_1425 is regulated by 22 influences and regulates 0 modules.
Regulators for RSP_1425 (22)
Regulator Module Operator
RSP_0068 68 tf
RSP_0402 68 tf
RSP_0607 68 tf
RSP_0641 68 tf
RSP_0760 68 tf
RSP_1092 68 tf
RSP_1785 68 tf
RSP_2130 68 tf
RSP_2182 68 tf
RSP_2610 68 tf
RSP_3024 68 tf
RSP_3094 68 tf
RSP_3341 68 tf
RSP_3667 68 tf
RSP_3731 68 tf
RSP_0728 42 tf
RSP_1077 42 tf
RSP_2533 42 tf
RSP_3022 42 tf
RSP_3064 42 tf
RSP_3109 42 tf
RSP_3317 42 tf

Warning: RSP_1425 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
7804 3.60e+02 CtGaAaAA
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7805 2.50e+02 CgcATccCcTT
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7856 7.40e+03 ATTCACGAAGCGCGAAT
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7857 1.80e+04 TTTtCcGCAA
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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_1425

RSP_1425 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
DNA-directed DNA polymerase activity go/ molecular_function
extrachromosomal circular DNA go/ cellular_component
DNA-dependent DNA replication initiation go/ biological_process
Module neighborhood information for RSP_1425

RSP_1425 has total of 34 gene neighbors in modules 42, 68
Gene neighbors (34)
Gene Common Name Description Module membership
RSP_0013 RSP_0013 hypothetical protein (NCBI) 68, 91
RSP_0144 RSP_0144 None 42, 101
RSP_0220 RSP_0220 hypothetical protein (NCBI) 68, 327
RSP_0301 RSP_0301 ABC branched chain amino acid transporter, substrate binding protein (NCBI) 68, 300
RSP_0326 RSP_0326 hypothetical protein (NCBI) 68, 188
RSP_0571 RSP_0571 tRNA pseudouridine synthase (NCBI) 68, 108
RSP_0748 RSP_0748 N-6 Adenine-specific DNA methylase (NCBI) 68, 288
RSP_1013 RSP_1013 possible Hemolysin (NCBI) 68, 267
RSP_1137 RSP_1137 Histone deacetylase family protein (NCBI) 68, 108
RSP_1215 ilvE putative IlvE, Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase (NCBI) 68, 381
RSP_1224 hemN putative Coproporphyrinogen III oxidase and related Fe-S oxidoreductases (NCBI) 68, 187
RSP_1423 RSP_1423 ParA family ATPase (NCBI) 68, 293
RSP_1425 RSP_1425 Plasmid replication initiation protein (NCBI) 42, 68
RSP_1443 RSP_1443 ABC sugar transporter, inner membrane subunit (NCBI) 68, 89
RSP_1445 RSP_1445 ABC sugar transporter, ATPase subunit (NCBI) 68, 89
RSP_1525 RSP_1525 putative Helicase/Exonuclease (NCBI) 42, 265
RSP_1577 putR Proline dehydrogenase transcriptional activator (NCBI) 68, 112
RSP_1752 RSP_1752 Putative creatinase (NCBI) 68, 346
RSP_1778 RSP_1778 TPR domain protein (NCBI) 68, 285
RSP_1779 ispE Putative 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (NCBI) 68, 285
RSP_2204 RSP_2204 multidrug efflux pump, MATE family (NCBI) 13, 42
RSP_2239 RSP_2239 tRNA/rRNA metyltransferase (NCBI) 42, 187
RSP_2316 dadA D-amino acid dehydrogenase (NCBI) 68, 375
RSP_2339 RSP_2339 hypothetical protein (NCBI) 28, 68
RSP_2348 RSP_2348 hypothetical protein (NCBI) 68, 293
RSP_2732 RSP_2732 Major facilitator superfamily (MFS) transporter (NCBI) 68, 292
RSP_3024 RSP_3024 transcriptional regulator, IclR family/MhpR (NCBI) 68, 73
RSP_3120 RSP_3120 hypothetical protein (NCBI) 2, 42
RSP_3190 RSP_3190 2Fe-2S ferredoxin (NCBI) 68, 244
RSP_3373 RSP_3373 ABC efflux transporter, inner membrane subunit (NCBI) 42, 267
RSP_3374 RSP_3374 ABC efflux transporter, ATPase subunit (NCBI) 22, 42
RSP_3625 RSP_3625 None 42, 315
RSP_3650 RSP_3650 Periplasmic serine proteases (ClpP class) (NCBI) 68, 196
RSP_3790 RSP_3790 hypothetical protein (NCBI) 42, 68
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_1425
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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