Organism : Methanococcus maripaludis S2 | Module List :
MMP0042

H/ACA RNA-protein complex component Gar1

CircVis
Functional Annotations (4)
Function System
RNA-binding protein involved in rRNA processing cog/ cog
small nucleolar ribonucleoprotein complex go/ cellular_component
rRNA processing go/ biological_process
rRNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0042
(Mouseover regulator name to see its description)

MMP0042 is regulated by 11 influences and regulates 0 modules.
Regulators for MMP0042 (11)
Regulator Module Operator
MMP0018
MMP1100		 19 combiner
MMP0052
Formate		 19 combiner
MMP0097
Formate		 19 combiner
MMP1100 19 tf
H2 108 ef
MMP0052
MMP0097		 108 combiner
MMP0086
MMP0097		 108 combiner
MMP0097
MMP0631		 108 combiner
MMP0097
MMP1376		 108 combiner
MMP0168
MMP1100		 108 combiner
MMP1347 108 tf

Warning: MMP0042 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
699 7.40e+01 TaTaTaaa.tTTtctAtTtga.tt
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700 1.10e+04 GCCGGA
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873 0.00e+00 gGGGgAt
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874 8.30e-02 AtAttgcCc.agg.gGggAAt
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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 MMP0042

MMP0042 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
RNA-binding protein involved in rRNA processing cog/ cog
small nucleolar ribonucleoprotein complex go/ cellular_component
rRNA processing go/ biological_process
rRNA binding go/ molecular_function
Module neighborhood information for MMP0042

MMP0042 has total of 53 gene neighbors in modules 19, 108
Gene neighbors (53)
Gene Common Name Description Module membership
Antisense_27 None 19, 50
MMP0029 hypothetical protein MMP0029 108, 131
MMP0041 tfb transcription initiation factor IIB 19, 160
MMP0042 H/ACA RNA-protein complex component Gar1 19, 108
MMP0194 hypothetical protein MMP0194 31, 108, 131
MMP0278 putative CBS domain-containing signal transduction protein 19, 90
MMP0335 hypothetical protein MMP0335 108, 156
MMP0344 hypothetical protein MMP0344 19, 90
MMP0405 gch3 GTP cyclohydrolase III 19, 92
MMP0407 hypothetical protein MMP0407 8, 19, 89
MMP0542 hypothetical protein MMP0542 108, 156
MMP0628 TOBE domain-containing protein 108, 123, 156
MMP0632 ATP/GTP-binding motif-containing protein 19, 115
MMP0634 hypothetical protein MMP0634 43, 108
MMP0635 ABC transporter ATPase 75, 108
MMP0711 corA magnesium/cobalt transporter CorA 43, 108
MMP0736 PRC-barrel domain-containing protein 8, 19, 38
MMP0762 hypothetical protein MMP0762 19, 43
MMP0964 hypothetical protein MMP0964 43, 108
MMP0988 RNA methyltransferase-like protein 108, 131
MMP1015 transcription factor CBF/NF-Y 72, 108
MMP1067 succinate dehydrogenase/fumarate reductase iron-sulfur subunit 19, 123
MMP1156 carboxymuconolactone decarboxylase 74, 84, 108, 123
MMP1162 beta-lactamase domain-containing protein 75, 108
MMP1223 hypothetical protein MMP1223 19, 123
MMP1244 fwdH tungsten containing formylmethanofuran dehydrogenase subunit H 19, 89
MMP1245 fwdF tungsten containing formylmethanofuran dehydrogenase subunit F 19, 89
MMP1246 fwdG tungsten containing formylmethanofuran dehydrogenase subunit G 19, 89
MMP1247 fwdD tungsten containing formylmethanofuran dehydrogenase subunit D 19, 89
MMP1248 fwdA tungsten containing formylmethanofuran dehydrogenase subunit A 19, 89
MMP1249 fwdC tungsten containing formylmethanofuran dehydrogenase subunit C 19, 89
MMP1257 NERD domain-containing protein 19, 43
MMP1258 hemB delta-aminolevulinic acid dehydratase 19, 124
MMP1385 fruB coenzyme F420-reducing hydrogenase subunit beta 108, 113
MMP1475 hypothetical protein MMP1475 19, 50
MMP1486 mechanosensitive ion channel MscS 108, 131
MMP1511 amino acid carrier protein 19, 92
MMP1555 mcrB methyl-coenzyme M reductase I subunit beta 19, 89
MMP1556 mcrD methyl-coenzyme M reductase I, protein D 19, 89
MMP1557 mcrC methyl coenzyme M reductase I, protein C 19, 89
MMP1558 mcrG methyl-coenzyme M reductase I subunit gamma 19, 89
MMP1559 mcrA methyl-coenzyme M reductase I subunit alpha 19, 89
MMP1586 hypothetical protein MMP1586 19, 100
MMP1609 ftr formylmethanofuran--tetrahydromethanopterin formyltransferase 19, 89
MMP1610 hypothetical protein MMP1610 19, 139
MMP1637 hypothetical protein MMP1637 13, 19
MMP1660 hypothetical protein MMP1660 42, 108, 123, 131
MMP1703 hypothetical protein MMP1703 43, 108
MMP1712 LysR family transcriptional regulator 19, 106
Unanno_18 None 9, 108
Unanno_20 None 108, 114
Unanno_25 None 108, 114
Unanno_50 None 9, 108
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 MMP0042
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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