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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2551 to 2600 of 6456 in total
Value Type	Ranked
Interaction Map High confidence
Filtered 1
Rank Hugo description Network Comparison Type red green network_comparison 1276 CHRNA3 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [source:swissprot;acc:p32297] Divided 171.231 167.177 1.02425 1276 PPP3CB serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [source:swissprot;acc:p16299] Subtracted 218.44 213.44 5 1277 POLE3 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [source:swissprot;acc:q9nrf9] Subtracted 250.854 255.842 4.988 1277 SPHK2 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [source:swissprot;acc:q9nra0] Divided 171.231 167.177 1.02425 1278 NDST2 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [source:swissprot;acc:p52849] Subtracted 228.409 223.475 4.934 1278 SESN3 sestrin 3. [source:swissprot;acc:p58005] Divided 218.368 213.219 1.02415 1279 NDST3 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [source:refseq;acc:nm_004784] Subtracted 228.409 223.475 4.934 1279 SESN2 sestrin 2 (hi95). [source:swissprot;acc:p58004] Divided 218.368 213.219 1.02415 1280 CYP4A11 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [source:swissprot;acc:q02928] Divided 218.368 213.22 1.02414 1280 NDST4 n-deacetylase/n-sulfotransferase 4. [source:refseq;acc:nm_022569] Subtracted 228.409 223.475 4.934 1281 CYP4F3 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:q08477] Divided 218.368 213.22 1.02414 1281 NDST1 heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [source:swissprot;acc:p52848] Subtracted 228.409 223.475 4.934 1282 CDC27 protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260] Subtracted 228.409 223.475 4.934 1282 CYP4F8 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187] Divided 218.368 213.22 1.02414 1283 CYP4X1 likely ortholog of rat cytochrome p450 4x1. [source:refseq;acc:nm_178033] Divided 218.368 213.22 1.02414 1283 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). [source:swissprot;acc:p10515] Subtracted 206.482 211.404 4.922 1284 CYP4F12 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [source:swissprot;acc:q9hcs2] Divided 218.368 213.22 1.02414 1284 GSTT2B glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712] Subtracted 228.642 223.726 4.916 1285 CYP4F2 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329] Divided 218.368 213.22 1.02414 1285 TGFBR1 tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [source:swissprot;acc:p36897] Subtracted 223.89 228.805 4.915 1286 ACVR1B serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [source:swissprot;acc:p36896] Subtracted 223.885 228.797 4.912 1286 CYP4F11 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6] Divided 218.368 213.22 1.02414 1287 CYP4A22 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [source:sptrembl;acc:q9ntl5] Divided 218.368 213.22 1.02414 1287 FREQ neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [source:swissprot;acc:p36610] Subtracted 223.887 228.799 4.912 1288 ACVR1C activin a receptor, type ic; activin receptor-like kinase 7. [source:refseq;acc:nm_145259] Subtracted 223.884 228.795 4.911 1288 CYP4B1 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [source:swissprot;acc:p13584] Divided 218.368 213.22 1.02414 1289 FLOT1 flotillin-1. [source:swissprot;acc:o75955] Divided 218.368 213.22 1.02414 1289 PAOX peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911] Subtracted 228.644 223.736 4.908 1290 ATPIF1 atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2] Subtracted 228.644 223.736 4.908 1290 SESN1 sestrin 1 (p53-regulated protein pa26). [source:swissprot;acc:q9y6p5] Divided 218.368 213.22 1.02414 1291 HAS2 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [source:swissprot;acc:q92819] Divided 221.093 226.399 1.024 1291 SMOX polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [source:refseq;acc:nm_019025] Subtracted 228.644 223.736 4.908 1292 CASP7 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [source:swissprot;acc:p55210] Divided 233.942 228.46 1.024 1292 HCCS cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [source:swissprot;acc:p53701] Subtracted 228.644 223.736 4.908 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). [source:swissprot;acc:p42574] Divided 233.942 228.46 1.024 1293 TPD52L2 tumor protein d54 (hd54) (d52-like 2). [source:swissprot;acc:o43399] Subtracted 206.852 211.757 4.905 1294 GSTT1 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [source:swissprot;acc:p30711] Subtracted 228.646 223.744 4.902 1294 HAS1 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [source:swissprot;acc:q92839] Divided 221.093 226.399 1.024 1295 HAS3 hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [source:swissprot;acc:o00219] Divided 221.093 226.399 1.024 1295 OXA1L cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [source:swissprot;acc:q15070] Subtracted 220.681 215.78 4.901 1296 MRPL34 60s ribosomal protein l34, mitochondrial precursor (l34mt). [source:swissprot;acc:q9bq48] Subtracted 220.681 215.78 4.901 1296 SLC37A1 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [source:swissprot;acc:p57057] Divided 209.062 204.174 1.02394 1297 PRODH proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [source:swissprot;acc:o43272] Divided 209.062 204.174 1.02394 1297 SF3B4 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [source: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). [source:swissprot;acc:p10515] Divided 206.482 211.404 1.02384 1298 SLC37A1 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [source:swissprot;acc:p57057] Subtracted 209.062 204.174 4.888 1299 GSR glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [source:swissprot;acc:p00390] Subtracted 207.387 212.275 4.888 1299 PMPCB mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [source:swissprot;acc:o75439] Divided 217.635 212.575 1.0238 1300 PMPCA mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [source:swissprot;acc:q10713] Divided 217.634 212.576 1.02379 1300 PRODH proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [source:swissprot;acc:o43272] Subtracted 209.062 204.174 4.888 Legend: - Rank is the rank after comparing the two networks - 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/