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 133 to 182 of 3228 in total
Value Type: Measured
Network Comparison Type: Divided
Interaction Map: High confidence
Filtered: 1
\def\wcA{0.16666666666667\textwidth} \def\wcB{0.16666666666667\textwidth} \def\wcC{0.16666666666667\textwidth} \def\wcD{0.16666666666667\textwidth} \def\wcE{0.16666666666667\textwidth} \begin{longtable}{|c|c|c|c|c|} \hline \parbox{\wcA}{\vspace{3pt}\noindent Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent description\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent red\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent green\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent network\_comparison\vspace{3pt}}\\ \hline \hline \parbox{\wcA}{\vspace{3pt}\noindent 133\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm\_007278]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 23421.5\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 17580.4\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.33225\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 134\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcC}{\vspace{3pt}\noindent 21785.2\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent 16426.1\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent 1.32626\vspace{3pt}}}\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 135\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent apg3p; pc3-96 protein. [source:refseq;acc:nm\_022488]\vspace{3pt}}&&&\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 136\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcC}{\vspace{3pt}\noindent 3620.77\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent 4763.34\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent 1.31556\vspace{3pt}}}\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 137\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]\vspace{3pt}}&&&\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 138\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm\_014592]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 2755.15\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 2094.3\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.31555\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 139\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm\_147183]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 2759.61\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 2099.49\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.31442\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 140\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm\_173193]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 2760.28\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 2100.27\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.31425\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 141\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 4405.4\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 5782.08\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.3125\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 142\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm\_014889]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 9276.47\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 7090.37\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.30832\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 143\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent beta-1,4 mannosyltransferase. [source:refseq;acc:nm\_019109]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 9275.1\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 7089.65\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.30826\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 144\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 3349.9\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 4362.61\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.30231\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 145\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm\_006395]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 16771.5\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 12889.1\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.30122\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 146\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm\_020799]\vspace{3pt}}&\multirow{5}{*}{\parbox{\wcC}{\vspace{3pt}\noindent 11068\vspace{3pt}}}&\multirow{5}{*}{\parbox{\wcD}{\vspace{3pt}\noindent 8508.5\vspace{3pt}}}&\multirow{5}{*}{\parbox{\wcE}{\vspace{3pt}\noindent 1.30082\vspace{3pt}}}\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 147\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm\_014453]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 148\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent associated molecule with the sh3 domain of stam. [source:refseq;acc:nm\_006463]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 149\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm\_016079]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 150\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]\vspace{3pt}}&&&\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 151\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm\_005489]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 4578.09\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 5939.91\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.29746\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 152\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm\_030801]\vspace{3pt}}&\multirow{21}{*}{\parbox{\wcC}{\vspace{3pt}\noindent 23693.7\vspace{3pt}}}&\multirow{21}{*}{\parbox{\wcD}{\vspace{3pt}\noindent 18263\vspace{3pt}}}&\multirow{21}{*}{\parbox{\wcE}{\vspace{3pt}\noindent 1.29736\vspace{3pt}}}\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 153\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm\_138703]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 154\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 155\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 156\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 157\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm\_020932]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 158\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 159\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent necdin. [source:swissprot;acc:q99608]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 160\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 161\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 162\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma antigen, family b, 6. [source:refseq;acc:nm\_173523]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 163\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 164\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 165\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 166\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 167\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 168\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 169\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 170\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 171\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 172\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent trophinin. [source:swissprot;acc:q12816]\vspace{3pt}}&&&\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 173\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent breast cancer antiestrogen resistance 3. [source:refseq;acc:nm\_003567]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 4579.34\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 5940.64\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.29727\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 174\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent mad protein (max dimerizer). [source:swissprot;acc:q05195]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 4455.95\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 5774.03\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.2958\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 175\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 4456.67\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 5773.77\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.29553\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 176\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 4456.93\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 5773.67\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.29544\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 177\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm\_031300]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 4457.06\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 5773.63\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.29539\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 178\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]\vspace{3pt}}&\multirow{3}{*}{\parbox{\wcC}{\vspace{3pt}\noindent 21591.5\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcD}{\vspace{3pt}\noindent 27904.5\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcE}{\vspace{3pt}\noindent 1.29238\vspace{3pt}}}\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 179\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]\vspace{3pt}}&&&\\\cline{1-2} \parbox{\wcA}{\vspace{3pt}\noindent 180\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]\vspace{3pt}}&&&\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 181\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm\_003760]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 4068.56\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 5252.6\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.29102\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 182\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent rna-binding protein. [source:refseq;acc:nm\_019027]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent 4069.83\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent 5252.17\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent 1.29051\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/