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 8764 to 8813 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2191 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Measured 5285.38 5034.86 1.04976
2192 hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282] Ranked 209.54 208.162 1.00662
lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358] Rooted 62.2377 63.6038 1.02195
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Squared 27346 29649.9 1.08425
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Measured 5285.38 5034.86 1.04976
2193 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Squared 27346 29649.9 1.08425
hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Rooted 65.292 66.7239 1.02193
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Measured 5285.38 5034.86 1.04976
prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Ranked 209.54 208.162 1.00662
2194 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] Rooted 65.292 66.7239 1.02193
beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] Squared 27346 29649.9 1.08425
dna repair protein rad52 homolog. [swissprot;acc:p43351] Measured 5285.38 5034.86 1.04976
homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786] Ranked 209.54 208.162 1.00662
2195 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Squared 27346 29649.9 1.08425
guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] Rooted 65.292 66.7239 1.02193
rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853] Ranked 209.54 208.162 1.00662
ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] Measured 6197.11 6504.93 1.04967
2196 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 6688.64 7020.02 1.04954
prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Ranked 209.54 208.162 1.00662
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] Squared 27346 29649.9 1.08425
testis-specific protein tex28. [swissprot;acc:o15482] Rooted 62.412 61.0748 1.02189
2197 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Measured 5285.79 5036.39 1.04952
indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Squared 27346 29649.9 1.08425
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Rooted 62.412 61.0748 1.02189
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] Ranked 193.787 195.064 1.00659
2198 a kindred of iglon. [refseq;acc:nm_173808] Rooted 62.412 61.0748 1.02189
complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021] Measured 6344.31 6657.98 1.04944
creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] Squared 58521.9 53975.7 1.08423
kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679] Ranked 193.787 195.064 1.00659
2199 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Rooted 62.412 61.0748 1.02189
fuse binding protein 3 (fragment). [sptrembl;acc:q92946] Squared 26428.2 28654 1.08422
sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238] Measured 6344.31 6657.98 1.04944
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] Ranked 193.787 195.064 1.00659
2200 inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Rooted 62.412 61.0748 1.02189
insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] Ranked 196.748 195.466 1.00656
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Measured 5076.73 5326.29 1.04916
visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235] Squared 23472.1 25448.8 1.08421
2201 cytochrome c. [swissprot;acc:p00001] Measured 5076.73 5326.29 1.04916
far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Squared 26427.3 28652.4 1.0842
p47 protein isoform a. [refseq;acc:nm_016143] Ranked 213.642 212.254 1.00654
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Rooted 62.412 61.0748 1.02189
2202 beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Measured 5076.73 5326.29 1.04916
neurocalcin delta. [swissprot;acc:p29554] Squared 23465.1 25440.8 1.0842
tumor susceptibility gene 101 protein. [swissprot;acc:q99816] Ranked 195.97 194.7 1.00652
2203 heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Measured 5076.73 5326.29 1.04916
neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076] Squared 23466.1 25441.8 1.08419
symplekin. [swissprot;acc:q92797] Ranked 162.741 163.8 1.00651
syntaxin 16 (syn16). [swissprot;acc:o14662] Rooted 62.412 61.0748 1.02189
2204 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]

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/