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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5158 to 5207 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
1290 PPP1R12B protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Divided Low confidence 195.789 191.498 1.02241
SESN1 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] High confidence 218.368 213.22 1.02414
SPCS2 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Subtracted Low confidence 205.491 201.077 4.414
1291 ACSL4 long-chain-fatty-acid--coa ligase 4 (ec 6.2.1.3) (long-chain acyl-coa synthetase 4) (lacs 4). [swissprot;acc:o60488] Divided 201.117 196.709 1.02241
HAS2 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] High confidence 221.093 226.399 1.024
SMOX polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Subtracted 228.644 223.736 4.908
UMPS uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Low confidence 205.491 201.077 4.414
1292 no value protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] 200.75 196.336
CASP7 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Divided High confidence 233.942 228.46 1.024
HCCS cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Subtracted 228.644 223.736 4.908
NONO 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Divided Low confidence 200.544 196.152 1.02239
1293 CASP3 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] High confidence 233.942 228.46 1.024
COX10 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Subtracted Low confidence 199.952 195.538 4.414
PSPC1 paraspeckle protein 1. [refseq;acc:nm_018282] Divided 200.543 196.152 1.02239
TPD52L2 tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] Subtracted High confidence 206.852 211.757 4.905
1294 ACSL3 long-chain-fatty-acid--coa ligase 3 (ec 6.2.1.3) (long-chain acyl-coa synthetase 3) (lacs 3). [swissprot;acc:o95573] Low confidence 201.127 196.714 4.413
GSTT1 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] High confidence 228.646 223.744 4.902
HAS1 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Divided 221.093 226.399 1.024
SEC31A yeast sec31p homolog. [refseq;acc:nm_014933] Low confidence 204.144 199.676 1.02238
1295 HAS3 hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] High confidence 221.093 226.399 1.024
IRX4 iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Subtracted Low confidence 195.344 190.932 4.412
OXA1L cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] High confidence 220.681 215.78 4.901
SLC3A1 neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Divided Low confidence 199.695 195.323 1.02238
1296 MRPL34 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] Subtracted High confidence 220.681 215.78 4.901
SDCCAG1 serologically defined colon cancer antigen 1. [refseq;acc:nm_004713] Low confidence 202.396 197.985 4.411
SEC31B secretory pathway component sec31b-1. [refseq;acc:nm_015490] Divided 204.174 199.705 1.02238
SLC37A1 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] High confidence 209.062 204.174 1.02394
1297 ACSL4 long-chain-fatty-acid--coa ligase 4 (ec 6.2.1.3) (long-chain acyl-coa synthetase 4) (lacs 4). [swissprot;acc:o60488] Subtracted Low confidence 201.117 196.709 4.408
MAPK11 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Divided 200.193 195.812 1.02237
PRODH proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] High confidence 209.062 204.174 1.02394
SF3B4 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Subtracted 232.752 237.65 4.898
1298 DLAT dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] Divided 206.482 211.404 1.02384
GLI1 zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Low confidence 203.074 198.63 1.02237
PI4K2B phosphatidylinositol 4-kinase type-ii beta; likely ortholog of mouse phosphatidylinositol 4-kinase type 2 beta. [refseq;acc:nm_018323] Subtracted 198.635 194.227 4.408
SLC37A1 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] High confidence 209.062 204.174 4.888
1299 ACO2 aconitate hydratase, mitochondrial precursor (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:q99798] Divided Low confidence 200.342 195.959 1.02237
ALDH1B1 aldehyde dehydrogenase x, mitochondrial precursor (ec 1.2.1.3) (aldh class 2). [swissprot;acc:p30837] Subtracted 205.089 209.494 4.405
GSR glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] High confidence 207.387 212.275 4.888
PMPCB mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Divided 217.635 212.575 1.0238
1300 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Low confidence 199.276 194.918 1.02236
PI4K2A phosphatidylinositol 4-kinase type ii. [refseq;acc:nm_018425] Subtracted 198.639 194.235 4.404
PMPCA mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Divided High confidence 217.634 212.576 1.02379
PRODH proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] Subtracted 209.062 204.174 4.888
1301 CETN3 centrin 3. [swissprot;acc:o15182] Low confidence 197.302 192.899 4.403
COPE coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] High confidence 187.964 192.849 4.885
HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Divided Low confidence 199.276 194.918 1.02236
TPD52L2 tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] High confidence 206.852 211.757 1.02371
1302 CSMD1 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Subtracted 218.509 213.648 4.861
FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Divided Low confidence 199.276 194.918 1.02236
RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted 208.899 213.298 4.399

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
- Hugo is the HGNC identifier if it exists
- 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/