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 description Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 3632 to 3681 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
1816 rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Divided 217.926 220.462 1.01164
1817 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Subtracted 212.281 214.722 2.441
gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] Divided 217.926 220.462 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 215.323 212.884 2.439
neighbor of cox4. [swissprot;acc:o43402] Divided 217.926 220.462 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 231.395 233.828 2.433
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Divided 217.926 220.462 1.01164
1820 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Subtracted 231.395 233.828 2.433
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 217.926 220.462 1.01164
1821 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Subtracted 198.86 201.288 2.428
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Divided 215.874 218.36 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] 243.085 240.32 1.01151
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Subtracted 224.637 222.215 2.422
1823 fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Divided 200.086 202.386 1.0115
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Subtracted 224.637 222.215 2.422
1824 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Divided 212.281 214.722 1.0115
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Subtracted 212.328 214.746 2.418
1825 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 201.349 203.759 2.41
fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Divided 200.086 202.386 1.0115
1826 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 200.094 202.393 1.01149
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Subtracted 226.271 223.862 2.409
1827 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 225.228 222.819
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Divided 189.219 191.39 1.01147
1828 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 200.115 202.41
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 226.271 223.862 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 215.323 212.884 1.01146
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Subtracted 226.271 223.862 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 243.069 240.32 1.01144
dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Subtracted 225.228 222.819 2.409
1831 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Divided 212.328 214.746 1.01139
translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] Subtracted 224.133 221.725 2.408
1832 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] 224.046 221.639 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 182.459 180.409 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 201.357 203.759 2.402
1834 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Divided 182.459 180.409 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 190.845 188.452 2.393
1835 brain protein 16. [refseq;acc:nm_016458] 219.195 216.811 2.384
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Divided 192.396 194.573 1.01132
1836 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Subtracted 216.064 218.441 2.377
ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] Divided 211.17 208.821 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 214.702 217.077 2.375
ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Divided 221.446 218.984 1.01124
1838 cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Subtracted 223.225 220.852 2.373
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Divided 221.446 218.984 1.01124
1839 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] 224.001 221.525 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 216.074 218.445 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 209.544 211.882 1.01116
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] Subtracted 216.08 218.448 2.368
1841 presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Divided 210.113 212.455 1.01115

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/