Organism : Methanococcus maripaludis S2 | Module List :
MMP0628

TOBE domain-containing protein

CircVis
Functional Annotations (7)
Function System
Molybdopterin-binding protein cog/ cog
ATP binding go/ molecular_function
transport go/ biological_process
molybdate transmembrane-transporting ATPase activity go/ molecular_function
molybdenum ion binding go/ molecular_function
ATP-binding cassette (ABC) transporter complex go/ cellular_component
Mop tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0628
(Mouseover regulator name to see its description)

MMP0628 is regulated by 18 influences and regulates 0 modules.
Regulators for MMP0628 (18)
Regulator Module Operator
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
H2 123 ef
MMP0052
MMP0480		 123 combiner
MMP0086
MMP0097		 123 combiner
MMP0097
MMP0527		 123 combiner
MMP0052
MMP0480		 156 combiner
MMP0086 156 tf
MMP0168
MMP1100		 156 combiner
MMP0217
MMP1023		 156 combiner
MMP0217
MMP1646		 156 combiner
MMP1023 156 tf
MMP1376 156 tf

Warning: MMP0628 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
873 0.00e+00 gGGGgAt
Loader icon
874 8.30e-02 AtAttgcCc.agg.gGggAAt
Loader icon
899 1.50e+03 TGaGacACatCgGc.G
Loader icon
900 4.60e+03 TtGAatTTaAAAc
Loader icon
961 5.00e-06 ggGGGGA
Loader icon
962 1.30e+03 cGGCGcTG
Loader icon
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 MMP0628

MMP0628 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Molybdopterin-binding protein cog/ cog
ATP binding go/ molecular_function
transport go/ biological_process
molybdate transmembrane-transporting ATPase activity go/ molecular_function
molybdenum ion binding go/ molecular_function
ATP-binding cassette (ABC) transporter complex go/ cellular_component
Mop tigr/ tigrfam
Module neighborhood information for MMP0628

MMP0628 has total of 67 gene neighbors in modules 108, 123, 156
Gene neighbors (67)
Gene Common Name Description Module membership
MMP0020 nickel responsive regulator 49, 123
MMP0029 hypothetical protein MMP0029 108, 131
MMP0042 H/ACA RNA-protein complex component Gar1 19, 108
MMP0123 purT phosphoribosylglycinamide formyltransferase 2 50, 123
MMP0194 hypothetical protein MMP0194 31, 108, 131
MMP0215 hypothetical protein MMP0215 54, 156
MMP0283 ndk nucleoside diphosphate kinase 83, 156
MMP0292 hypothetical protein MMP0292 125, 156
MMP0293 aldolase 125, 156
MMP0335 hypothetical protein MMP0335 108, 156
MMP0542 hypothetical protein MMP0542 108, 156
MMP0559 hypothetical protein MMP0559 73, 156
MMP0624 hypothetical protein MMP0624 50, 123
MMP0628 TOBE domain-containing protein 108, 123, 156
MMP0634 hypothetical protein MMP0634 43, 108
MMP0635 ABC transporter ATPase 75, 108
MMP0683 ftsY signal recognition particle-docking protein FtsY 50, 123
MMP0709 hypothetical protein MMP0709 13, 156
MMP0711 corA magnesium/cobalt transporter CorA 43, 108
MMP0763 hypothetical protein MMP0763 43, 123
MMP0772 hypothetical protein MMP0772 42, 123
MMP0820 frcA coenzyme F420-reducing hydrogenase subunit alpha 123, 131
MMP0825 hdrA heterodisulfide reductase subunit A 45, 123
MMP0852 hypothetical protein MMP0852 125, 156
MMP0908 CBS domain-containing protein 45, 123
MMP0961 hypothetical protein MMP0961 74, 156
MMP0962 zinc finger protein 74, 156
MMP0963 MIP family channel protein 74, 156
MMP0964 hypothetical protein MMP0964 43, 108
MMP0988 RNA methyltransferase-like protein 108, 131
MMP1015 transcription factor CBF/NF-Y 72, 108
MMP1016 putative CBS domain-containing signal transduction protein 13, 123
MMP1067 succinate dehydrogenase/fumarate reductase iron-sulfur subunit 19, 123
MMP1134 type A flavoprotein 58, 123
MMP1135 flavodoxin:beta-lactamase-like 58, 123
MMP1136 rubrerythrin 58, 123
MMP1154 hdrC1 heterosulfide reductase subunit C1 74, 84, 123
MMP1156 carboxymuconolactone decarboxylase 74, 84, 108, 123
MMP1158 hypothetical protein MMP1158 74, 84, 123
MMP1160 hypothetical protein MMP1160 74, 84, 156
MMP1162 beta-lactamase domain-containing protein 75, 108
MMP1163 CutA1 divalent ion tolerance protein 74, 156
MMP1174 peroxiredoxin 125, 156
MMP1223 hypothetical protein MMP1223 19, 123
MMP1229 FUN14 family protein 58, 123
MMP1251 putative CBS domain-containing signal transduction protein 123, 145
MMP1252 CBS domain-containing protein 123, 145
MMP1347 HMmB histone B 31, 123
MMP1385 fruB coenzyme F420-reducing hydrogenase subunit beta 108, 113
MMP1439 cofactor-independent phosphoglycerate mutase 58, 123
MMP1486 mechanosensitive ion channel MscS 108, 131
MMP1533 hypothetical protein MMP1533 13, 123
MMP1534 hypothetical protein MMP1534 13, 123
MMP1642 ATP/GTP-binding motif-containing protein 9, 123
MMP1660 hypothetical protein MMP1660 42, 108, 123, 131
MMP1661 hypothetical protein MMP1661 123, 131
MMP1685 hypothetical protein MMP1685 123, 131
MMP1697 hdrA heterodisulfide reductase subunit A 113, 114, 123
MMP1703 hypothetical protein MMP1703 43, 108
MMP1720 hypothetical protein MMP1720 83, 156
MMP1721 hypothetical protein MMP1721 83, 156
Unanno_18 None 9, 108
Unanno_20 None 108, 114
Unanno_25 None 108, 114
Unanno_32 None 65, 123
Unanno_38 None 45, 123
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 MMP0628
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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