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 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1790 dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] Subtracted 217.011 214.481 2.53
1791 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] 217.009 214.482 2.527
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Divided 217.866 215.295 1.01194
1792 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] Subtracted 217.008 214.482 2.526
elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] Divided 217.766 215.199 1.01193
1793 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 193.1 190.823
serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Subtracted 207.757 210.274 2.517
1794 cyclin c. [swissprot;acc:p24863] 217.071 214.564 2.507
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] Divided 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
polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Subtracted 216.854 214.35 2.504
1796 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Divided 203.759 201.357 1.01193
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] Subtracted 216.854 214.35 2.504
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] Divided 193.111 190.834 1.01193
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Subtracted 218.36 215.874 2.486
1798 elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Divided 217.807 215.242 1.01192
eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] Subtracted 221.525 224.001 2.476
1799 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] Divided 217.016 214.481 1.01182
helicase (fragment). [sptrembl;acc:q92771] Subtracted 187.204 189.679 2.475
1800 dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 187.205 2.474
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] Divided 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
ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Subtracted 218.984 221.446 2.462
1802 elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] Divided 217.011 214.481 1.0118
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Subtracted 218.984 221.446 2.462
1803 dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] Divided 217.011 214.481 1.0118
pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] Subtracted 206.332 203.874 2.458
1804 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] Divided 217.984 215.442 1.0118
germ cell-less. [refseq;acc:nm_022471] Subtracted 206.335 203.877 2.458
1805 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] Divided 217.008 214.482 1.01178
pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] Subtracted 206.332 203.874 2.458
1806 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] Divided 217.009 214.482 1.01178
hyporthetical protein mgc27169. [refseq;acc:nm_176782] Subtracted 206.332 203.874 2.458
1807 homeobox protein meis1. [swissprot;acc:o00470]
ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636] Divided 211.102 208.651 1.01175
1808 homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] Subtracted 206.332 203.874 2.458
ral-a exchange factor ralgps2. [refseq;acc:nm_152663] Divided 211.102 208.651 1.01175
1809 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] Subtracted 206.332 203.874 2.458
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] Divided 211.102 208.651 1.01175
1810 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 223.214 225.827 1.01171
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Subtracted 206.332 203.874 2.458
1811 polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Divided 216.854 214.35 1.01168
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] Subtracted 206.332 203.874 2.458
1812 cyclin c. [swissprot;acc:p24863] Divided 217.071 214.564 1.01168
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Subtracted 206.332 203.874 2.458
1813 ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636] 211.102 208.651 2.451
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] Divided 216.854 214.35 1.01168
1814 ral-a exchange factor ralgps2. [refseq;acc:nm_152663] Subtracted 211.102 208.651 2.451
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Divided 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/