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 7136 to 7185 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1784 homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] Ranked 206.332 203.874 1.01206
1785 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816]
nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] Measured 5386.37 5744.89 1.06656
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Rooted 67.1523 69.2654 1.03147
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Squared 19340.3 21267.5 1.09965
1786 actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747] Measured 5386.37 5744.89 1.06656
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Squared 19340.3 21267.5 1.09965
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Ranked 206.332 203.874 1.01206
proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] Rooted 63.6258 65.628 1.03147
1787 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] 67.1494 69.2625
interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894] Measured 5386.48 5744.78 1.06652
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Squared 19340.3 21267.5 1.09965
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] Ranked 206.332 203.874 1.01206
1788 arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] Measured 5386.49 5744.76 1.06651
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Rooted 63.9873 65.9937 1.03136
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Squared 19340.3 21267.5 1.09965
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Ranked 206.332 203.874 1.01206
1789 enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Squared 24761.4 27226.6 1.09956
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Ranked 210.997 213.539 1.01205
serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4] Measured 5839.72 6227.33 1.06637
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Rooted 85.2289 82.6464 1.03125
1790 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Ranked 203.759 201.349 1.01197
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Rooted 85.2289 82.6464 1.03125
f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Squared 30558.1 33599.6 1.09953
kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] Measured 5839.72 6227.33 1.06637
1791 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] Rooted 60.4164 62.3011 1.0312
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Ranked 217.866 215.295 1.01194
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] Squared 21739.2 23895.5 1.09919
serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9] Measured 5839.72 6227.33 1.06637
1792 elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] Ranked 217.766 215.199 1.01193
presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] Squared 19888.3 21859.5 1.09911
serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965] Measured 5839.72 6227.33 1.06637
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Rooted 63.1543 65.1233 1.03118
1793 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Measured 5839.72 6227.33 1.06637
gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Squared 19888.3 21859.5 1.09911
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Ranked 193.1 190.823 1.01193
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Rooted 63.1543 65.1233 1.03118
1794 brachyury protein (t protein). [swissprot;acc:o15178] 64.9125 66.9337 1.03114
epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] Measured 5948.26 6342.84 1.06634
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Ranked 193.138 190.861 1.01193
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Squared 19888.3 21859.5 1.09911
1795 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 26807.7 29463.6 1.09907
dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1] Measured 5501.3 5866.02 1.0663
elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] Ranked 217.724 215.158 1.01193
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Rooted 64.9125 66.9337 1.03114
1796 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Ranked 203.759 201.357 1.01193
thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] Squared 26479.8 29102.5 1.09905
tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Measured 5387.64 5743.5 1.06605
tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Rooted 54.9766 53.3184 1.0311
1797 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Squared 27596.4 30329.5 1.09904

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/