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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 2408 to 2457 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
network_comparison
green
2408 no value dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 194.407 1.00362 193.706
2409 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]
2410 LYPLA1 lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330]
2411 PBLD mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039]
2412 LYPLA2P1 lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260]
2413 SERPINB12 serpin b12. [swissprot;acc:q96p63] 218.2 1.00359 218.984
2414 SERPINB7 megsin (tp55) (serpin b7). [swissprot;acc:o75635]
2415 no value hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
2416 NR1H2 oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055]
2417 C16orf70 upf0183 protein. [swissprot;acc:q9bsu1]
2418 SERPINC1 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
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 1.00358 221.471
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 1.00357 211.618
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 1.00355 193.555
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 1.00354 218.644
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 1.00352 212.3
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 1.00347 216.556
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 1.00346 218.117
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 1.00344 220.116
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 1.0034 213.323
2439 YWHAB 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] 220.681 1.00337 221.425
2440 PSMD3 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] 217.645 1.00336 218.376
2441 ETFA electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 180.137 1.0033 180.732
2442 TAF6 transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] 204.419 1.00329 203.748
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 1.00328 216.364
2444 ZBTB20 zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] 206.086 1.00324 206.753
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 1.00321 211.766
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 1.00319 205.371
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 1.00316 213.177
2451 SCAMP2 secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 204.688 1.00315 205.333
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 1.00314 205.326
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

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/