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 2418 to 2467 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
2418 SERPINC1 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008] 218.2 218.984 1.00359
2419 EIF2B1 translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232]
2420 SERPINB4 squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508]
2421 AIFM2 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] 210.205 209.454
2422 NR1H3 oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] 218.2 218.984
2423 HDAC5 histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] 220.682 221.471 1.00358
2424 HDAC4 histone deacetylase 4 (hd4). [swissprot;acc:p56524] 221.472
2425 HDAC9 histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0]
2426 no value mesoderm induction early response 1. [refseq;acc:nm_020948] 212.374 211.618 1.00357
2427 PSMA3 proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788]
2428 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] 192.871 193.555 1.00355
2429 ESD esterase d (ec 3.1.1.1). [swissprot;acc:p10768]
2430 EPN1 epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] 217.873 218.644 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] 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
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] 217.366 218.117 1.00346
2434 MTHFR methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] 213.021 212.286
2435 ZNF259 zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] 217.366 218.117
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] 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
2439 YWHAB 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] 220.681 221.425 1.00337
2440 PSMD3 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] 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
2442 TAF6 transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] 204.419 203.748 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] 217.073 216.364 1.00328
2444 ZBTB20 zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] 206.086 206.753 1.00324
2445 ZBTB7B kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872] 206.088 206.756
2446 EPHX1 epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] 182.272 181.683
2447 PEX7 peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] 206.084 206.752
2448 no value glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] 212.446 211.766 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] 204.717 205.371 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] 213.85 213.177 1.00316
2451 SCAMP2 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 204.688 205.333 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] 204.683 205.326 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] 213.588 212.92
2458 SLC13A2 solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] 204.683 205.326
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] 204.653 205.286 1.00309
2460 no value pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 235.812 235.088 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]

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/