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 4558 to 4607 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2279 ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Divided 5783.73 6048.91 1.04585
2280 rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156]
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Subtracted 5076.73 5326.29 249.56
2281 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] Divided 5783.73 6048.91 1.04585
2282 adaptor-associated kinase 1. [refseq;acc:nm_014911]
rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Subtracted 5076.73 5326.29 249.56
2283 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Divided 5783.7 6048.88 1.04585
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Subtracted 5285.79 5036.39 249.4
2284 alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 5607.81 5855.72 247.91
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Divided 5783.73 6048.91 1.04585
2285 heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792] Subtracted 5606.66 5854.45 247.79
rho-gtpase activating protein 10. [refseq;acc:nm_020824] Divided 5783.73 6048.91 1.04585
2286 deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] Subtracted 4644.58 4892.06 247.48
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Divided 5783.76 6048.94 1.04585
2287 phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Subtracted 4374.32 4126.96 247.36
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Divided 5783.7 6048.88 1.04585
2288 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] 5783.76 6048.94
pp3111 protein. [refseq;acc:nm_022156] Subtracted 4374.32 4126.96 247.36
2289 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] Divided 5783.76 6048.94 1.04585
syntaxin 18. [swissprot;acc:q9p2w9] Subtracted 4374.32 4126.96 247.36
2290 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Divided 5783.75 6048.93 1.04585
rd protein. [swissprot;acc:p18615] Subtracted 4374.32 4126.96 247.36
2291 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Divided 5783.71 6048.89 1.04585
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Subtracted 4374.32 4126.96 247.36
2292 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Divided 5783.76 6048.94 1.04585
2293 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Subtracted 4374.32 4126.96 247.36
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] Divided 5783.76 6048.94 1.04585
2294 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] 5783.73 6048.91
j domain containing protein 1. [swissprot;acc:q9ukb3] Subtracted 4374.32 4126.96 247.36
2295 glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211] Divided 6066.61 6344.65 1.04583
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Subtracted 4374.32 4126.96 247.36
2296 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
eyes absent homolog 4. [swissprot;acc:o95677] Divided 5784.9 6049.99 1.04582
2297 rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] 6570.31 6871.29 1.04581
rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701] Subtracted 7139.06 7384.85 245.79
2298 rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407] Divided 6570.74 6871.6 1.04579
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Subtracted 5309.65 5066.82 242.83
2299 eyes absent homolog 2. [swissprot;acc:o00167] Divided 5786.15 6050.71 1.04572
signal transducer and activator of transcription 5b. [swissprot;acc:p51692] Subtracted 5516.82 5758.48 241.66
2300 rh type c glycoprotein. [refseq;acc:nm_016321] Divided 6573.3 6873.48 1.04567
signal transducer and activator of transcription 5a. [swissprot;acc:p42229] Subtracted 5516.67 5758.22 241.55
2301 hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] Divided 6946.6 7263.68 1.04565
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Subtracted 3600.99 3360.33 240.66
2302 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] Divided 6946.6 7263.68 1.04565
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Subtracted 3600.99 3360.33 240.66
2303 hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] Divided 6946.6 7263.68 1.04565
signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] Subtracted 5515.12 5755.63 240.51
2304 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Divided 6946.38 7263.48 1.04565

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/