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 9764 to 9813 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2441 jun dimerization protein. [refseq;acc:nm_130469] Squared 21083.2 22381.2 1.06157
2442 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Rooted 60.4127 61.2677 1.01415
breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] Measured 5454.62 5637.88 1.0336
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Squared 25684.8 27256.5 1.06119
transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Ranked 204.419 203.748 1.00329
2443 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] Rooted 60.3943 61.2421 1.01404
gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] Squared 25684.8 27256.5 1.06119
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] Measured 3634.59 3756.67 1.03359
ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] Ranked 217.073 216.364 1.00328
2444 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] Measured 6478.14 6695.67 1.03358
argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] Rooted 61.8651 62.7331 1.01403
inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] Squared 25684.8 27256.5 1.06119
zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] Ranked 206.086 206.753 1.00324
2445 kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872] 206.088 206.756
myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Rooted 74.1169 75.157 1.01403
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] Measured 3633.14 3754.96 1.03353
succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] Squared 27458.4 29134.4 1.06104
2446 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Rooted 74.1169 75.157 1.01403
dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Measured 4031.94 4166.99 1.0335
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Ranked 182.272 181.683 1.00324
integral membrane protein cii-3b. [sptrembl;acc:o75609] Squared 27458.5 29133.6 1.061
2447 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Measured 3730.53 3611.05 1.03309
chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973] Squared 33403.7 31483.8 1.06098
peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] Ranked 206.084 206.752 1.00324
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Rooted 74.1169 75.157 1.01403
2448 40s ribosomal protein s16. [swissprot;acc:p17008] Measured 3730.53 3611.05 1.03309
chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] Squared 33406.5 31491 1.06083
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Ranked 212.446 211.766 1.00321
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Rooted 74.1169 75.157 1.01403
2449 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] Squared 33026.7 35032 1.06072
60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Measured 3730.74 3611.45 1.03303
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] Ranked 204.717 205.371 1.00319
transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206] Rooted 71.2841 72.2606 1.0137
2450 enhancer of rudimentary homolog. [swissprot;acc:q14259] Squared 33026.7 35032 1.06072
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] Ranked 213.85 213.177 1.00316
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Measured 6737.15 6957.34 1.03268
transcription factor relb (i-rel). [swissprot;acc:q01201] Rooted 71.2841 72.2606 1.0137
2451 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694] Measured 6737.15 6957.34 1.03268
nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963] Rooted 71.2841 72.2606 1.0137
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Ranked 204.688 205.333 1.00315
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Squared 33749 35794.2 1.0606
2452 coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551] Rooted 71.2841 72.2606 1.0137
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Ranked 204.688 205.333 1.00315
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Measured 6042.36 6237.19 1.03224
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Squared 37852.3 40124.6 1.06003
2453 60s ribosomal protein l21. [swissprot;acc:p46778] 25226.2 26738.9 1.05997
conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] Measured 6931.15 7152.73 1.03197
ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] Rooted 65.2762 66.1663 1.01364
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Ranked 204.688 205.332 1.00315
2454 homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Measured 8751.01 8480.03 1.03196

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/