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.


Navigation/Query Panel:
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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7164 to 7213 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1791 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
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Rooted 61.0608 62.9579 1.03107
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Ranked 193.111 190.834 1.01193
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Measured 5096.02 5432.63 1.06605
1798 60s ribosomal protein l32. [swissprot;acc:p02433] 3618.02 3394.29 1.06591
elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Ranked 217.807 215.242 1.01192
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Squared 30559.5 33585.8 1.09903
importin 8; ran-binding protein 8. [refseq;acc:nm_006390] Rooted 61.0608 62.9579 1.03107
1799 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] Ranked 217.016 214.481 1.01182
brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Rooted 61.0608 62.9579 1.03107
interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Squared 24759.8 27209.3 1.09893
translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770] Measured 5456.57 5816.14 1.0659
1800 dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] Ranked 217.011 214.481 1.0118
hsgcn1 (fragment). [sptrembl;acc:q99736] Rooted 61.0608 62.9579 1.03107
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Squared 27451.6 30163.1 1.09877
translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] Measured 5424.3 5781.58 1.06587
1801 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] Squared 27297.6 29991.6 1.09869
brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] Rooted 61.0608 62.9579 1.03107
cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879] Ranked 217.984 215.441 1.0118
epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] Measured 5881.33 6268.57 1.06584
1802 dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] Squared 27297 29990.5 1.09867
elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] Ranked 217.011 214.481 1.0118
gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Rooted 63.065 65.0219 1.03103
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Measured 4980.54 5307.81 1.06571
1803 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] Ranked 217.011 214.481 1.0118
elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] Squared 27297 29990.5 1.09867
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Rooted 63.065 65.0219 1.03103
1804 60s ribosomal protein l28. [swissprot;acc:p46779] Squared 27555.4 30274.3 1.09867

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/