Organism : Methanococcus maripaludis S2 | Module List :
MMP0475

hypothetical protein MMP0475

CircVis
Functional Annotations (2)
Function System
protein binding go/ molecular_function
regulation of apoptosis go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0475
(Mouseover regulator name to see its description)

MMP0475 is regulated by 2 influences and regulates 0 modules.
Regulators for MMP0475 (2)
Regulator Module Operator
MMP0499
MMP1015		 151 combiner
MMP0499
MMP1065		 151 combiner

Warning: MMP0475 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 12 motifs predicted.

Motif Table (12)
Motif Id e-value Consensus Motif Logo
713 1.80e+02 TCGaGGGG
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714 4.10e+03 GAtaTTTtcGG
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723 7.00e-06 gggGG.Gt
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724 5.10e+02 TGAcTGAgTAGTCAaTCTTA
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751 5.00e+02 agTTcATatATACacCcc
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752 1.70e+03 GGtatgGTaccC.c
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805 1.10e+01 gatAatCCcCtcg
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806 3.70e+04 GcTCcGCC
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825 2.70e-03 gGGGat
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826 4.30e+03 TcGGGC
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951 1.70e-02 CGggGGgA
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952 9.70e+02 ggcgGcTggA
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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 MMP0475

MMP0475 is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
protein binding go/ molecular_function
regulation of apoptosis go/ biological_process
Module neighborhood information for MMP0475

MMP0475 has total of 114 gene neighbors in modules 26, 31, 45, 72, 82, 151
Gene neighbors (114)
Gene Common Name Description Module membership
Antisense_12 None 31, 119
Antisense_16 None 42, 72
Antisense_17 None 37, 82
Antisense_21 None 37, 119, 151
Antisense_28 None 31, 37
MMP0009 putative DNA primase large subunit 75, 151
MMP0063 argB acetylglutamate kinase 49, 151
MMP0071 DNA primase small subunit 72, 152
MMP0090 glycosyl transferase 69, 110, 151
MMP0110 ABC transporter:AAA ATPase 6, 82
MMP0184 riboflavin kinase 45, 50
MMP0194 hypothetical protein MMP0194 31, 108, 131
MMP0195 hypothetical protein MMP0195 6, 31
MMP0196 ABC-type iron(III) transport system periplasmic binding protein 6, 82
MMP0198 ABC-type iron(III) transport system ATP binding protein 26, 31, 82
MMP0201 moeA molybdenum cofactor biosynthesis protein 26, 82, 155
MMP0208 hypothetical protein MMP0208 26, 31, 42, 82
MMP0211 hypothetical protein MMP0211 45, 85
MMP0361 hypothetical protein MMP0361 42, 45, 163
MMP0365 hypothetical protein MMP0365 45, 163
MMP0369 hypothetical protein MMP0369 58, 151
MMP0375 radical SAM domain-containing protein 31, 45
MMP0423 hypothetical protein MMP0423 72, 131
MMP0435 hypothetical protein MMP0435 31, 72
MMP0436 rimK RimK domain-containing protein 6, 31, 42, 72, 82, 110
MMP0437 hypothetical protein MMP0437 6, 31, 42, 53, 82
MMP0463 hypothetical protein MMP0463 45, 131
MMP0473 hypothetical protein MMP0473 31, 42
MMP0474 hypothetical protein MMP0474 31, 131
MMP0475 hypothetical protein MMP0475 26, 31, 45, 72, 82, 151
MMP0484 sodium/hydrogen exchanger 31, 72, 127, 131, 161
MMP0485 hypothetical protein MMP0485 62, 72
MMP0494 helicase family protein 26, 155
MMP0495 hypothetical protein MMP0495 31, 42, 127, 155
MMP0497 hypothetical protein MMP0497 26, 82, 155
MMP0501 hypothetical protein MMP0501 31, 82
MMP0513 MoeA molybdopterin biosynthesis moeA protein 53, 72
MMP0515 modB molybdenum ABC transporter permease 6, 53, 72, 110, 151
MMP0518 hypothetical protein MMP0518 69, 72
MMP0519 hypothetical protein MMP0519 6, 31, 161
MMP0551 binding-protein dependent transport system inner membrane protein 72, 110
MMP0585 UspA domain-containing protein 83, 151, 152
MMP0594 hypothetical protein MMP0594 45, 163
MMP0598 phosphoglycerate mutase-related 106, 151
MMP0614 iron-sulfur flavoprotein 43, 125, 151
MMP0662 hypothetical protein MMP0662 62, 72
MMP0673 hypothetical protein MMP0673 5, 31
MMP0690 polyferredoxin 72, 163
MMP0725 putative integral membrane protein 49, 75, 90, 151
MMP0739 Asp/Glu racemase:aspartate racemase 45, 131
MMP0740 purine NTPase 6, 26, 31, 72, 82
MMP0758 HNH endonuclease:HNH nuclease 45, 166
MMP0759 hypothetical protein MMP0759 45, 166
MMP0766 resP site-specific recombinase 6, 42, 53, 72, 127
MMP0767 hypothetical protein MMP0767 36, 53, 72, 161
MMP0769 hypothetical protein MMP0769 36, 53, 151, 161
MMP0771 hypothetical protein MMP0771 26, 155
MMP0773 hypothetical protein MMP0773 53, 72
MMP0778 hypothetical protein MMP0778 31, 72
MMP0779 hypothetical protein MMP0779 31, 72
MMP0780 hypothetical protein MMP0780 72, 155
MMP0781 hypothetical protein MMP0781 72, 110, 127
MMP0782 hypothetical protein MMP0782 31, 53, 72, 127, 155, 161
MMP0789 codB cytosine permease 72, 85
MMP0790 hypothetical protein MMP0790 36, 53, 72, 161
MMP0800 hypothetical protein MMP0800 53, 72
MMP0801 hypothetical protein MMP0801 31, 72
MMP0802 Iron-containing alcohol dehydrogenase 31, 53
MMP0805 hypothetical protein MMP0805 26, 53, 110, 155
MMP0825 hdrA heterodisulfide reductase subunit A 45, 123
MMP0826 hypothetical protein MMP0826 31, 154
MMP0828 hypothetical protein MMP0828 45, 85, 163
MMP0831 mtbA methylcobalamin:coenzyme M methyltransferase 42, 82
MMP0832 ferredoxin 6, 72
MMP0834 mtbA uroporphyrinogen decarboxylase 26, 36, 42, 72, 155
MMP0838 hypothetical protein MMP0838 53, 82
MMP0845 hypothetical protein MMP0845 45, 163
MMP0886 cobalt ABC transporter inner membrane protein 4, 151
MMP0908 CBS domain-containing protein 45, 123
MMP0939 HAD superfamily (subfamily IA) hydrolase 46, 151
MMP0957 dsbD hypothetical protein MMP0957 69, 72, 110
MMP0998 hypothetical protein MMP0998 31, 131
MMP1015 transcription factor CBF/NF-Y 72, 108
MMP1020 hypothetical protein MMP1020 42, 45
MMP1037 rRNA large subunit methyltransferase 26, 155
MMP1056 hypothetical protein MMP1056 119, 151
MMP1088 group 1 glycosyl transferase 31, 117
MMP1110 hypothetical protein MMP1110 31, 146
MMP1172 DNA protection protein DPS 6, 31, 82
MMP1173 zinc/iron permease 45, 85
MMP1179 methyltransferase 85, 110, 151
MMP1180 hypothetical protein MMP1180 45, 85
MMP1184 N-acetyltransferase-like protein 26, 72
MMP1262 hypothetical protein MMP1262 14, 151
MMP1281 GCN5-like N-acetyltransferase 26, 72
MMP1296 pfkC ADP-specific phosphofructokinase 45, 166
MMP1339 SAM-binding motif-containing protein 53, 72
MMP1343 hypothetical protein MMP1343 49, 151
MMP1347 HMmB histone B 31, 123
MMP1388 redox-active disulfide protein 2 99, 151
MMP1476 hypothetical protein MMP1476 42, 45
MMP1525 modulator of DNA gyrase 100, 151
MMP1526 rncS ribonuclease III family protein 36, 53, 151
MMP1529 type 11 methyltransferase 45, 131
MMP1571 hypothetical protein MMP1571 6, 26, 72, 127, 155
MMP1596 hypothetical protein MMP1596 31, 42, 155
MMP1678 nfo endonuclease IV 42, 72, 82
MMP1679 hypothetical protein MMP1679 117, 151
RNA_23 tRNA-Glu2 Glu tRNA 88, 100, 101, 151, 165
RNA_33 tRNA-Met3 Met tRNA 45, 100
RNA_47 rrnB5S 5S ribosomal RNA 100, 101, 151
Unanno_38 None 45, 123
Unanno_43 None 62, 151
Unanno_53 None 72, 119
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 MMP0475
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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