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 3580 to 3629 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1790 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] High confidence 203.759 201.349 1.01197
1791 elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] 217.866 215.295 1.01194
translin. [swissprot;acc:q15631] Low confidence 202.745 198.743 1.02014
1792 aquaporin 5. [swissprot;acc:p55064] 195.447 191.588
elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] High confidence 217.766 215.199 1.01193
1793 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Low confidence 204.337 200.302 1.02014
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] High confidence 193.1 190.823 1.01193
1794 cda11 protein. [refseq;acc:nm_032026] Low confidence 199.338 195.403 1.02014
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] High confidence 193.138 190.861 1.01193
1795 elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] 217.724 215.158
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Low confidence 195.447 191.589 1.02014
1796 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] High confidence 203.759 201.357 1.01193
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Low confidence 202.745 198.743 1.02014
1797 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] High confidence 193.111 190.834 1.01193
polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Low confidence 202.745 198.743 1.02014
1798 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556] 200.037 196.088
elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] High confidence 217.807 215.242 1.01192
1799 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] 217.016 214.481 1.01182
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] Low confidence 199.606 195.666 1.02014
1800 af-6 protein. [swissprot;acc:p55196] 203.545 199.529 1.02013
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] High confidence 217.011 214.481 1.0118
1801 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] 217.984 215.441
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Low confidence 196.761 192.879 1.02013
1802 elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] High confidence 217.011 214.481 1.0118
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Low confidence 199.594 195.657 1.02012
1803 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 199.592 195.655
dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] High confidence 217.011 214.481 1.0118
1804 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Low confidence 195.454 191.599 1.02012
cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561] High confidence 217.984 215.442 1.0118
1805 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] 217.008 214.482 1.01178
glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Low confidence 199.294 195.368 1.0201
1806 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] High confidence 217.009 214.482 1.01178
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Low confidence 198.893 194.978 1.02008
1807 ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]
ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636] High confidence 211.102 208.651 1.01175
1808 ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Low confidence 198.888 194.973 1.02008
ral-a exchange factor ralgps2. [refseq;acc:nm_152663] High confidence 211.102 208.651 1.01175
1809 glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Low confidence 199.322 195.398 1.02008
stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] High confidence 211.102 208.651 1.01175
1810 double-strand-break repair protein rad21 homolog (hhr21) (nuclear matrix protein 1) (nxp-1) (scc1 homolog). [swissprot;acc:o60216] Low confidence 202.127 198.153 1.02006
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] High confidence 223.214 225.827 1.01171
1811 polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] 216.854 214.35 1.01168
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Low confidence 192.58 188.792 1.02006
1812 cyclin c. [swissprot;acc:p24863] High confidence 217.071 214.564 1.01168
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Low confidence 192.58 188.792 1.02006
1813 dj545l17.2 (novel protein similar to rad21 (s. pombe) homolog (kiaa0078)) (fragment). [sptrembl;acc:q9h4i0] 202.127 198.153
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] High confidence 216.854 214.35 1.01168
1814 dj467n11.1 protein. [refseq;acc:nm_022091] Low confidence 199.184 195.266 1.02006
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] High confidence 122.3 123.727 1.01167
1815 dpy-30-like protein. [swissprot;acc:q9c005] 220.462 217.926 1.01164

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/