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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Value Type Gene description Interaction Map Rank Network Comparison Type red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1962 to 2011 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
red
green
network_comparison
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] 914 210.863 218.878 1.03801
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 925 215.665 207.942 1.03714
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 2460 235.812 235.088 1.00308
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 928 225.976 218.017 1.03651
peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [swissprot;acc:q9hbh1] 2884 0.00001 0.00001 1
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] 1753 220.091 217.362 1.01256
peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] 1939 198.258 196.319 1.00988
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] 2400 182.4 183.083 1.00374
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 1078 174.387 179.697 1.03045
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] 2076 221.703 223.483 1.00803
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] 695 226.135 214.405 1.05471
peregrin (bromodomain and phd finger-containing protein 1) (br140 protein). [swissprot;acc:p55201] 2820 0.00001 0.00001 1
pericentrin 1; frount; nucleoporin nup75. [refseq;acc:nm_024844] 3015
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 673 226.497 214.355 1.05664
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] 2573 213.347 213.005 1.00161
peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] 1124 207.553 213.256 1.02748
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 2688 194.557 194.392 1.00085
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] 1851 218.448 216.08 1.01096
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 1849 218.445 216.074 1.01097
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 1010 217.523 210.648 1.03264
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 841 198.781 190.66 1.04259
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 2177 210.961 209.563 1.00667
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] 1147 208.651 203.109 1.02729
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 1362 228.644 223.736 1.02194
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 664 229.072 216.576 1.0577
peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] 2447 206.084 206.752 1.00324
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 351 242.14 265.696 1.09728
pescadillo homolog 1. [swissprot;acc:o00541] 515 251.297 234.941 1.06962
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] 1082 220.118 213.685 1.03011
phd finger protein 9. [refseq;acc:nm_018062] 1345 216.772 221.594 1.02224
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 235 227.357 254.15 1.11785
phenylalanine-trna synthetase. [refseq;acc:nm_006567] 895 217.491 209.323 1.03902
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] 894
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] 2330 214.213 213.235 1.00459
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 2220 221.509 220.108 1.00637
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 403 207.908 226.218 1.08807
phosducin-like protein (phlp). [swissprot;acc:q13371] 400
phosphate carrier protein, mitochondrial precursor (ptp). [swissprot;acc:q00325] 3176 0.00001 0.00001 1
phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] 2459 204.653 205.286 1.00309
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] 2449 204.717 205.371 1.00319
phosphatidylethanolamine-binding protein (pebp) (prostatic binding protein) (hcnppp) (neuropolypeptide h3) (raf kinase inhibitor protein) (rkip) [contains: hippocampal cholinergic neurostimulating peptide (hcnp)]. [swissprot;acc:p30086] 3162 0.00001 0.00001 1
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] 1651 219.062 215.942 1.01445
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] 1656
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] 1653
phosphatidylinositol glycan class t precursor. [refseq;acc:nm_015937] 3024 0.00001 0.00001 1
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 2080 215.967 214.28 1.00787
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] 2079
phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] 1391 218.47 213.875 1.02148
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 627 214.256 202.139 1.05994
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] 1774 223.032 225.739 1.01214

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/