Organism : Methanococcus maripaludis S2 | Module List :
MMP0648 rtcA

RNA 3'-terminal-phosphate cyclase

CircVis
Functional Annotations (4)
Function System
RNA 3'-terminal phosphate cyclase cog/ cog
RNA-3'-phosphate cyclase activity go/ molecular_function
RNA processing go/ biological_process
RNA_3prim_cycl tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0648
(Mouseover regulator name to see its description)

MMP0648 is regulated by 5 influences and regulates 0 modules.
Regulators for MMP0648 rtcA (5)
Regulator Module Operator
MMP0031
MMP0402		 67 combiner
MMP0031
MMP1704		 67 combiner
MMP0607
MMP1442		 67 combiner
MMP1137 67 tf
MMP1210
MMP1704		 67 combiner

Warning: MMP0648 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
795 3.10e+03 GGGCGA
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796 1.70e+04 CTGcGGAG
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943 1.30e+00 CtCCCCct
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944 1.90e+04 GGtAcgagCTTT.Ac.aG
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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 MMP0648

MMP0648 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
RNA 3'-terminal phosphate cyclase cog/ cog
RNA-3'-phosphate cyclase activity go/ molecular_function
RNA processing go/ biological_process
RNA_3prim_cycl tigr/ tigrfam
Module neighborhood information for MMP0648

MMP0648 has total of 55 gene neighbors in modules 67, 146
Gene neighbors (55)
Gene Common Name Description Module membership
Antisense_6 None 52, 67
MMP0017 hypothetical protein MMP0017 67, 142
MMP0035 hypothetical protein MMP0035 23, 67
MMP0108 ABC-type Iron(III)-binding periplasmic protein precursor 41, 67, 95
MMP0122 hypothetical protein MMP0122 57, 102, 146
MMP0124 membrane-bound metal-dependent hydrolase 14, 67
MMP0128 cyclase family protein 73, 146, 153
MMP0202 permease 52, 67
MMP0203 hypothetical protein MMP0203 52, 67
MMP0204 hypothetical protein MMP0204 67, 99
MMP0227 nrdD anaerobic ribonucleoside-triphosphate reductase 15, 67
MMP0262 hypothetical protein MMP0262 52, 67
MMP0274 hypE hydrogenase expression/formation protein HypE 67, 70
MMP0280 hisI phosphoribosyl-AMP cyclohydrolase 67, 90
MMP0322 rfcB replication factor C large subunit 23, 67
MMP0341 pycA pyruvate carboxylase subunit A 67, 86, 120
MMP0446 nitrogen fixation-like protein 52, 67
MMP0447 nitrogenase-like protein 4, 146
MMP0455 amino-acid ABC transporter 54, 146
MMP0488 low molecular weight phosphotyrosine protein phosphatase 52, 67
MMP0489 hypothetical protein MMP0489 52, 67
MMP0499 hypothetical protein MMP0499 22, 28, 144, 146, 153
MMP0514 modA molybdenum ABC transporter periplasmic molybdate-binding protein 99, 146
MMP0520 HAD superfamily ATPase 73, 146
MMP0522 hypothetical protein MMP0522 42, 85, 146, 153
MMP0523 ABC transporter ATP-binding protein 42, 85, 146, 153
MMP0524 hypothetical protein MMP0524 4, 58, 146, 153, 163
MMP0525 hypothetical protein MMP0525 4, 146, 163
MMP0617 radB DNA repair and recombination protein RadB 52, 67
MMP0648 rtcA RNA 3'-terminal-phosphate cyclase 67, 146
MMP0682 hypothetical protein MMP0682 67, 92
MMP0757 hypothetical protein MMP0757 58, 146
MMP0760 hypothetical protein MMP0760 22, 67, 92
MMP0775 hypothetical protein MMP0775 42, 146, 153, 163
MMP0785 dop chymotrypsin serine protease 2, 146, 159
MMP0811 hypothetical protein MMP0811 52, 67
MMP0813 hypothetical protein MMP0813 146, 166
MMP0835 hypothetical protein MMP0835 85, 146
MMP0863 CBS domain-containing protein 2, 54, 146
MMP0864 napA-2 Na+/H+ exchanger 50, 146, 166
MMP0993 XRE family transcriptional regulator 67, 144
MMP0994 hypothetical protein MMP0994 67, 144, 153
MMP1079 glycosyl transferase family protein 64, 67
MMP1110 hypothetical protein MMP1110 31, 146
MMP1120 ATPase-like ATP-binding protein 52, 67
MMP1123 radical SAM domain-containing protein 64, 67
MMP1124 thiamine-monophosphate kinase 102, 146
MMP1243 UBA/THIF-type NAD/FAD binding protein 89, 146
MMP1346 basic helix-loop-helix dimerization domain-containing protein 49, 67, 142
MMP1605 pyruvate kinase 1, 54, 146, 166
MMP1664 hypothetical protein MMP1664 42, 146
MMP1686 cbf5 H/ACA RNA-protein complex component Cbf5p 22, 67
Mma-sR04 None 100, 146
Unanno_10 None 64, 146
Unanno_14 None 52, 67
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 MMP0648
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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