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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 11264 to 11313 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2314 very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] Measured 6960.99 7273.72 1.04493
2315 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] Ranked 194.825 195.787 1.00494
calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746] Rooted 70.5239 71.8706 1.0191
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Squared 26202.1 28200.6 1.07627
solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] Measured 6961.11 7273.85 1.04493
2316 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Ranked 217.241 218.311 1.00493
melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194] Rooted 70.5239 71.8706 1.0191
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Squared 26202.1 28200.1 1.07625
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Measured 6960.74 7273.48 1.04493
2317 5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Rooted 70.5239 71.8706 1.0191
ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] Squared 26202.2 28199.1 1.07621
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Ranked 194.834 195.794 1.00493
solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] Measured 6961.44 7274.17 1.04492
2318 calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0] Rooted 70.5239 71.8706 1.0191
n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] Squared 20767.9 22344.9 1.07593
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Ranked 194.834 195.794 1.00493
ubiquitin. [swissprot;acc:p02248] Measured 7484.98 7821.11 1.04491
2319 acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] Ranked 194.842 195.8 1.00492
acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561] Rooted 70.5239 71.8706 1.0191
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Squared 20767.9 22344.9 1.07593
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Measured 6362.48 6647.42 1.04478
2320 electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Rooted 77.0412 78.4884 1.01878
mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] Squared 20767.9 22344.9 1.07593
rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Ranked 219.292 218.218 1.00492
t54 protein. [swissprot;acc:q92917] Measured 6362.48 6647.42 1.04478
2321 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 3496.21 3652.28 1.04464
fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Squared 20767.9 22344.9 1.07593
glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] Rooted 66.2571 65.036 1.01878
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Ranked 203.909 202.925 1.00485
2322 glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506] Rooted 66.2571 65.036 1.01878
mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] Measured 6773.67 7075.51 1.04456
probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] Squared 20767.8 22344.6 1.07593
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Ranked 236.023 234.905 1.00476
2323 asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] 192.773 193.691
cbf1 interacting corepressor. [refseq;acc:nm_004882] Squared 32891.4 30575.7 1.07574
mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797] Measured 6773.67 7075.51 1.04456
ubiquilin 1 isoform 1. [refseq;acc:nm_013438] Rooted 76.0828 77.5093 1.01875
2324 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] 76.0984 77.5217 1.0187
cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833] Measured 6773.67 7075.51 1.04456
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Squared 32891.4 30575.7 1.07574
proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618] Ranked 212.129 211.129 1.00474
2325 creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] Rooted 75.0965 76.4933 1.0186
methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Ranked 221.728 220.685 1.00473
mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] Measured 6773.67 7075.51 1.04456
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Squared 43306.1 40270.4 1.07538
2326 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 20706.1 22261.9 1.07514
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Rooted 75.1012 76.4968 1.01858
dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Ranked 220.076 219.05 1.00468
histone deacetylase 11 (hd11). [swissprot;acc:q96db2] Measured 6773.67 7075.51 1.04456
2327 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] Ranked 217.413 218.426 1.00466

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
- 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/