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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Network Comparison Type Gene Value Type description Rank network_comparison Filtered green Interaction Map red
Results: HTML CSV LaTeX Showing element 1951 to 2000 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
green
red
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 25 1.31818 44 58
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 26
pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [swissprot;acc:q9nve7] 2883 1 0.00001 0.00001
parafibromin. [refseq;acc:nm_024529] 917 1.03772 230.991 239.704
paraspeckle protein 1. [refseq;acc:nm_018282] 2533 1.00214 190.824 190.417
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 830 1.0428 222.222 231.734
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 965 1.03426 204.964 211.987
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] 1555 1.01656 192.996 196.192
paxillin. [swissprot;acc:p49023] 436 1.07909 205.286 221.522
pbk1 protein. [sptrembl;acc:o76021] 983 1.03382 235.353 243.312
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 833 1.0428 222.222 231.734
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 1.03801 218.878 210.863
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 925 1.03714 207.942 215.665
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 2460 1.00308 235.088 235.812
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 928 1.03651 218.017 225.976
peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [swissprot;acc:q9hbh1] 2884 1 0.00001 0.00001
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] 1753 1.01256 217.362 220.091
peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] 1939 1.00988 196.319 198.258
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 1.00374 183.083 182.4
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 1078 1.03045 179.697 174.387
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] 2076 1.00803 223.483 221.703
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 1.05471 214.405 226.135
peregrin (bromodomain and phd finger-containing protein 1) (br140 protein). [swissprot;acc:p55201] 2820 1 0.00001 0.00001
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 1.05664 214.355 226.497
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 1.00161 213.005 213.347
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 1.02748 213.256 207.553
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 1.00085 194.392 194.557
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] 1851 1.01096 216.08 218.448
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 1849 1.01097 216.074 218.445
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 1010 1.03264 210.648 217.523
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 841 1.04259 190.66 198.781
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 2177 1.00667 209.563 210.961
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] 1147 1.02729 203.109 208.651
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 1362 1.02194 223.736 228.644
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 1.0577 216.576 229.072
peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] 2447 1.00324 206.752 206.084
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 351 1.09728 265.696 242.14
pescadillo homolog 1. [swissprot;acc:o00541] 515 1.06962 234.941 251.297
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] 1082 1.03011 213.685 220.118
phd finger protein 9. [refseq;acc:nm_018062] 1345 1.02224 221.594 216.772
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 235 1.11785 254.15 227.357
phenylalanine-trna synthetase. [refseq;acc:nm_006567] 895 1.03902 209.323 217.491
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 1.00459 213.235 214.213
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] 2220 1.00637 220.108 221.509
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 403 1.08807 226.218 207.908
phosducin-like protein (phlp). [swissprot;acc:q13371] 400
phosphate carrier protein, mitochondrial precursor (ptp). [swissprot;acc:q00325] 3176 1 0.00001 0.00001
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 1.00309 205.286 204.653

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/