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 7208 to 7257 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1802 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
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] Ranked 217.984 215.442 1.0118
proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786] Rooted 63.3576 65.3187 1.03095
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Measured 4980.54 5307.81 1.06571
1805 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] Ranked 217.008 214.482 1.01178
dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] Squared 27297 29990.5 1.09867
phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] Rooted 67.051 69.1037 1.03061
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Measured 4980.54 5307.81 1.06571
1806 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] Ranked 217.009 214.482 1.01178
Squared 27296.6 29989.9 1.09867
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Measured 4783.49 5097.66 1.06568
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Rooted 67.0385 69.087 1.03056
1807 alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] Squared 27296.5 29989.7 1.09866
endothelial-derived gene 1. [refseq;acc:nm_025205] Measured 6399.54 6818.17 1.06542
ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636] Ranked 211.102 208.651 1.01175
solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Rooted 67.0387 69.0872 1.03056
1808 lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] Measured 4941.92 5265.09 1.06539
ral-a exchange factor ralgps2. [refseq;acc:nm_152663] Ranked 211.102 208.651 1.01175
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Squared 21399.1 23508.5 1.09857
solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] Rooted 67.0385 69.087 1.03056
1809 dynein light chain 2. [refseq;acc:nm_080677] Squared 21399.1 23508.5 1.09857
epsin 3. [refseq;acc:nm_017957] Measured 5816.12 6196.21 1.06535
solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] Rooted 67.0387 69.0872 1.03056
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] Ranked 211.102 208.651 1.01175
1810 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] Squared 26702.8 29325.9 1.09823
colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] Measured 6520.83 6946.75 1.06532
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Ranked 223.214 225.827 1.01171
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Rooted 67.0364 69.0841 1.03055
1811 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Squared 27506.1 30207.8 1.09822
polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Ranked 216.854 214.35 1.01168
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Rooted 67.0364 69.0841 1.03055
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Measured 7659.42 8156.79 1.06494
1812 cyclin c. [swissprot;acc:p24863] Ranked 217.071 214.564 1.01168
hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] Measured 5514.19 5871.64 1.06482
Squared 24755.6 27183.3 1.09807
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Rooted 67.0367 69.0845 1.03055
1813 dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Squared 16173.9 17758 1.09794
dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Measured 5866.19 6245.4 1.06464
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Rooted 62.0498 63.9432 1.03051
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] Ranked 216.854 214.35 1.01168
1814 heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] Measured 5733.71 6104.26 1.06463
oxidation resistance 1. [refseq;acc:nm_181354] Rooted 62.0498 63.9432 1.03051
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Ranked 122.3 123.727 1.01167
vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] Squared 29263.6 32125.4 1.09779
1815 dpy-30-like protein. [swissprot;acc:q9c005] Ranked 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/