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 3630 to 3679 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1815 stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] Subtracted 211.102 208.651 2.451
1816 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 187.582 190.028 2.446
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Divided 220.462 217.926 1.01164
1817 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Subtracted 214.722 212.281 2.441
gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] Divided 220.462 217.926 1.01164
1818 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] Subtracted 212.884 215.323 2.439
neighbor of cox4. [swissprot;acc:o43402] Divided 220.462 217.926 1.01164
1819 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Subtracted 233.828 231.395 2.433
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Divided 220.462 217.926 1.01164
1820 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Subtracted 233.828 231.395 2.433
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 220.462 217.926 1.01164
1821 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Subtracted 201.288 198.86 2.428
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Divided 218.36 215.874 1.01152
1822 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 240.32 243.085 1.01151
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Subtracted 222.215 224.637 2.422
1823 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Divided 202.386 200.086 1.0115
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Subtracted 222.215 224.637 2.422
1824 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Divided 214.722 212.281 1.0115
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Subtracted 214.746 212.328 2.418
1825 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 203.759 201.349 2.41
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Divided 202.386 200.086 1.0115
1826 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 202.393 200.094 1.01149
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Subtracted 223.862 226.271 2.409
1827 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 222.819 225.228
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Divided 191.39 189.219 1.01147
1828 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 202.41 200.115
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Subtracted 223.862 226.271 2.409
1829 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] Divided 212.884 215.323 1.01146
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Subtracted 223.862 226.271 2.409
1830 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] Divided 240.32 243.069 1.01144
dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Subtracted 222.819 225.228 2.409
1831 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Divided 214.746 212.328 1.01139
translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] Subtracted 221.725 224.133 2.408
1832 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] 221.639 224.046 2.407
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Divided 180.409 182.459 1.01136
1833 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Subtracted 203.759 201.357 2.402
1834 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Divided 180.409 182.459 1.01136
tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] Subtracted 188.452 190.845 2.393
1835 brain protein 16. [refseq;acc:nm_016458] 216.811 219.195 2.384
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Divided 194.573 192.396 1.01132
1836 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Subtracted 218.441 216.064 2.377
ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] Divided 208.821 211.17 1.01125
1837 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] Subtracted 217.077 214.702 2.375
ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Divided 218.984 221.446 1.01124
1838 cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Subtracted 220.852 223.225 2.373
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Divided 218.984 221.446 1.01124
1839 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] 221.525 224.001 1.01118
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Subtracted 218.445 216.074 2.371
1840 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Divided 211.882 209.544 1.01116

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/