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 Filtered Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 2430 to 2479 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence
Rank
Hugo
description
green
red
network_comparison
2430 EPN1 epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] 218.644 217.873 1.00354
2431 PSMA2 proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] 212.3 213.048 1.00352
2432 PSMD6 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] 216.556 215.807 1.00347
2433 EEF1AL3 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] 218.117 217.366 1.00346
2434 MTHFR methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] 212.286 213.021
2435 ZNF259 zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] 218.117 217.366
2436 EEF1A2 elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]
2437 GUK1 guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] 220.116 219.361 1.00344
2438 PSMA4 proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] 213.323 214.049 1.0034
2439 YWHAB 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] 221.425 220.681 1.00337
2440 PSMD3 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] 218.376 217.645 1.00336
2441 ETFA electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 180.732 180.137 1.0033
2442 TAF6 transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] 203.748 204.419 1.00329
2443 UBE2I 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] 216.364 217.073 1.00328
2444 ZBTB20 zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] 206.753 206.086 1.00324
2445 ZBTB7B kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872] 206.756 206.088
2446 EPHX1 epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] 181.683 182.272
2447 PEX7 peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] 206.752 206.084
2448 no value glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] 211.766 212.446 1.00321
2449 CDS2 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] 205.371 204.717 1.00319
2450 PSMB6 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] 213.177 213.85 1.00316
2451 SCAMP2 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 205.333 204.688 1.00315
2452 SCAMP3 secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]
2453 SCAMP1 secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 205.332
2454 SLC13A4 solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] 205.326 204.683 1.00314
2455 SLC13A3 solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9]
2456 SLC13A1 solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2]
2457 NSF vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] 212.92 213.588
2458 SLC13A2 solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] 205.326 204.683
2459 CDS1 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] 205.286 204.653 1.00309
2460 no value pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 235.088 235.812 1.00308
2461 SLC20A2 solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749]
2462 FDPS farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324]
2463 PCDH15 protocadherin 15 precursor. [swissprot;acc:q96qu1]
2464 SLC20A1 solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415]
2465 LMBR1L lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]
2466 GLI1 zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]
2467 SUFU suppressor of fused. [refseq;acc:nm_016169]
2468 GLI3 zinc finger protein gli3. [swissprot;acc:p10071]
2469 LMBR1 limb region 1 protein; limb region 1. [refseq;acc:nm_022458]
2470 PGC gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142]
2471 GLI2 zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]
2472 TNS3 tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] 217.564 218.218 1.00301
2473 MAPK8IP3 c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] 217.991 218.644 1.003
2474 PSMC3 26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] 217.285 216.64 1.00298
2475 TENC1 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] 217.571 218.219
2476 XYLB xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] 210.577 211.205
2477 MRPL30 mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212] 216.801 216.177 1.00289
2478 PSMC6 26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]
2479 PRR5 rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0] 218.72 218.093 1.00287

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/