Scientific

MK5 Microarray Data


Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3150 to 3199 of 3228 in total
Value Type: Measured
Network Comparison Type: Divided
Interaction Map: High confidence
Filtered: 1
red: 0.00001
green: 0.00001
network\_comparison: 1
\def\wcA{0.33333333333333\textwidth} \def\wcB{0.33333333333333\textwidth} \begin{longtable}{|c|c|} \hline \parbox{\wcA}{\vspace{3pt}\noindent Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent description\vspace{3pt}}\\ \hline \hline \parbox{\wcA}{\vspace{3pt}\noindent 3150\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [source:swissprot;acc:p54108]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3151\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent dna mismatch repair protein msh2. [source:swissprot;acc:p43246]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3152\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent histone deacetylase 6 (hd6). [source:swissprot;acc:q9ubn7]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3153\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent leucine rich repeat (in flii) interacting protein 2. [source:refseq;acc:nm\_006309]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3154\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent nucleoporin 50 kda (nuclear pore-associated protein 60 kda-like) (pro1146). [source:swissprot;acc:q9ukx7]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3155\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent transforming growth factor beta 2 precursor (tgf-beta 2) (glioblastoma-derived t-cell suppressor factor) (g-tsf) (bsc-1 cell growth inhibitor) (polyergin) (cetermin). [source:swissprot;acc:p08112]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3156\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent tektin 2 (tektin-t) (testicular tektin b1-like protein). [source:swissprot;acc:q9uif3]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3157\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent vesicle transport-related protein isoform a; vesicle transport-related protein. [source:refseq;acc:nm\_016106]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3158\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent integrin alpha-6 precursor (vla-6) (cd49f). [source:swissprot;acc:p23229]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3159\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent trinucleotide repeat containing 6; edie; gw182 autoantigen. [source:refseq;acc:nm\_014494]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3160\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent cyclin k. [source:swissprot;acc:o75909]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3161\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent brca1 associated protein. [source:refseq;acc:nm\_006768]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3162\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent phosphatidylethanolamine-binding protein (pebp) (prostatic binding protein) (hcnppp) (neuropolypeptide h3) (raf kinase inhibitor protein) (rkip) [contains: hippocampal cholinergic neurostimulating peptide (hcnp)]. [source:swissprot;acc:p30086]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3163\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [source:refseq;acc:nm\_014516]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3164\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [source:swissprot;acc:q92754]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3165\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [source:swissprot;acc:q96s52]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3166\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent myotubularin-related protein 2 (ec 3.1.3.-). [source:swissprot;acc:q13614]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3167\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent centromere/kinetochore protein zw10 homolog. [source:swissprot;acc:o43264]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3168\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent cop-coated vesicle membrane protein p24 precursor (p24a). [source:swissprot;acc:q15363]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3169\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent transcriptional repressor nf-x1 (ec 6.3.2.-) (nuclear transcription factor, x box-binding, 1). [source:swissprot;acc:q12986]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3170\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ecotropic virus integration 1 site protein. [source:swissprot;acc:q03112]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3171\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent cyclin t2. [source:swissprot;acc:o60583]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3172\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent hormone sensitive lipase (ec 3.1.1.-) (hsl). [source:swissprot;acc:q05469]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3173\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent phosphoinositide-3-kinase, class 3; vps34; phosphatidylinositol 3-kinase, class 3. [source:refseq;acc:nm\_002647]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3174\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [source:swissprot;acc:q9hd45]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3175\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent tubulin alpha-3/alpha-7 chain (alpha-tubulin 3/7). [source:swissprot;acc:p05214]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3176\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent phosphate carrier protein, mitochondrial precursor (ptp). [source:swissprot;acc:q00325]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3177\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ergic-53 protein precursor (er-golgi intermediate compartment 53 kda protein) (lectin, mannose-binding 1) (gp58) (intracellular mannose specific lectin mr60). [source:swissprot;acc:p49257]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3178\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent transcription initiation factor iie, beta subunit (tfiie-beta). [source:swissprot;acc:p29084]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3179\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent carcinoma related gene. [source:refseq;acc:nm\_016041]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3180\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [source:swissprot;acc:q99714]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3181\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [source:swissprot;acc:p51648]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3182\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [source:swissprot;acc:p15923]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3183\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [source:swissprot;acc:q13951]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3184\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [source:swissprot;acc:p23497]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3185\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [source:swissprot;acc:p22830]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3186\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [source:swissprot;acc:q04759]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3187\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [source:refseq;acc:nm\_021240]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3188\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent connective tissue growth factor-like protein precursor (ctgf-l) (wnt1 inducible signaling pathway protein 2) (wisp-2) (connective tissue growth factor-related protein 58). [source:swissprot;acc:o76076]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3189\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ring finger protein 4. [source:swissprot;acc:p78317]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3190\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent myotubularin-related protein 1 (ec 3.1.3.-). [source:swissprot;acc:q13613]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3191\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [source:refseq;acc:nm\_006380]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3192\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ubiquitin carboxyl-terminal hydrolase 13 (ec 3.1.2.15) (ubiquitin thiolesterase 13) (ubiquitin-specific processing protease 13) (deubiquitinating enzyme 13) (isopeptidase t-3) (isot-3). [source:swissprot;acc:q92995]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3193\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [source:swissprot;acc:p50395]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3194\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent muts protein homolog 4. [source:swissprot;acc:o15457]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3195\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [source:swissprot;acc:p05106]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3196\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [source:swissprot;acc:q15011]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3197\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent cisplatin resistance related protein crr9p. [source:refseq;acc:nm\_030782]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3198\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent rp42 homolog; squamous cell carcinoma-related oncogene. [source:refseq;acc:nm\_020640]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3199\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent complement component c6 precursor. [source:swissprot;acc:p13671]\vspace{3pt}}\\\hline nd{longtable}
Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.

- http://analysis.yellowcouch.org/