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 3551 to 3600 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1776 elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Subtracted 217.807 215.242 2.565
nucleoporin like 1. [refseq;acc:nm_014089] Divided 216.878 214.286 1.0121
1777 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Subtracted 240.317 242.881 2.564
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Divided 216.878 214.286 1.0121
1778 cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185]
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] Subtracted 217.984 215.441 2.543
1779 pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] Divided 206.332 203.874 1.01206
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Subtracted 210.997 213.539 2.542
1780 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] 217.984 215.442
germ cell-less. [refseq;acc:nm_022471] Divided 206.335 203.877 1.01206
1781 dpy-30-like protein. [swissprot;acc:q9c005] Subtracted 220.462 217.926 2.536
pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] Divided 206.332 203.874 1.01206
1782 hyporthetical protein mgc27169. [refseq;acc:nm_176782]
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Subtracted 220.462 217.926 2.536
1783 gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470]
homeobox protein meis1. [swissprot;acc:o00470] Divided 206.332 203.874 1.01206
1784 homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770]
neighbor of cox4. [swissprot;acc:o43402] Subtracted 220.462 217.926 2.536
1785 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] Divided 206.332 203.874 1.01206
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Subtracted 220.462 217.926 2.536
1786 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Divided 206.332 203.874 1.01206
1787 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] Subtracted 217.016 214.481 2.535
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] Divided 206.332 203.874 1.01206
1788 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] Subtracted 217.011 214.481 2.53
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Divided 206.332 203.874 1.01206
1789 elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] Subtracted 217.011 214.481 2.53
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Divided 210.997 213.539 1.01205
1790 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 203.759 201.349 1.01197
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

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/