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 4858 to 4907 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
2429 SLC20A1 solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415] Subtracted 235.812 235.088 0.724
2430 EPN1 epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] Divided 217.873 218.644 1.00354
LMBR1L lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Subtracted 235.812 235.088 0.724
2431 GLI1 zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]
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] Divided 213.048 212.3 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] 215.807 216.556 1.00347
SUFU suppressor of fused. [refseq;acc:nm_016169] Subtracted 235.812 235.088 0.724
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] Divided 217.366 218.117 1.00346
GLI3 zinc finger protein gli3. [swissprot;acc:p10071] Subtracted 235.812 235.088 0.724
2434 LMBR1 limb region 1 protein; limb region 1. [refseq;acc:nm_022458]
MTHFR methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Divided 213.021 212.286 1.00346
2435 PGC gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142] Subtracted 235.812 235.088 0.724
ZNF259 zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] Divided 217.366 218.117 1.00346
2436 EEF1A2 elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]
GLI2 zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] Subtracted 235.812 235.088 0.724
2437 ACOX2 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] 193.389 194.105 0.716
GUK1 guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] Divided 219.361 220.116 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] 214.049 213.323 1.0034
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] Subtracted 217.073 216.364 0.709
2439 no value dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 194.407 193.706 0.701
YWHAB 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Divided 220.681 221.425 1.00337
2440 GLO1 lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] Subtracted 194.407 193.706 0.701
PSMD3 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] Divided 217.645 218.376 1.00336
2441 ETFA electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 180.137 180.732 1.0033
LYPLA1 lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330] Subtracted 194.407 193.706 0.701
2442 PBLD mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039]
TAF6 transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Divided 204.419 203.748 1.00329
2443 LYPLA2P1 lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260] Subtracted 194.407 193.706 0.701
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] Divided 217.073 216.364 1.00328
2444 STAM signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Subtracted 182.266 182.962 0.696
ZBTB20 zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] Divided 206.086 206.753 1.00324
2445 no value alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Subtracted 192.871 193.555 0.684
ZBTB7B kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872] Divided 206.088 206.756 1.00324
2446 EPHX1 epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] 182.272 181.683
ESD esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Subtracted 192.871 193.555 0.684
2447 PEX7 peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] Divided 206.084 206.752 1.00324
PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Subtracted 182.395 183.079 0.684
2448 no value glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Divided 212.446 211.766 1.00321
PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Subtracted 182.4 183.083 0.683
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] Divided 204.717 205.371 1.00319
PPIB peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Subtracted 182.4 183.083 0.683
2450 OGT udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294]
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] Divided 213.85 213.177 1.00316
2451 COX4I1 cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Subtracted 182.4 183.083 0.683
SCAMP2 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Divided 204.688 205.333 1.00315
2452 COX4I2 cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Subtracted 182.4 183.083 0.683
SCAMP3 secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Divided 204.688 205.333 1.00315
2453 no value glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Subtracted 212.446 211.766 0.68
SCAMP1 secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Divided 204.688 205.332 1.00315
2454 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] Subtracted 213.85 213.177 0.673

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/