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 3151 to 3200 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
788	ubiquitin-activating enzyme e1 (a1s9 protein). [source:swissprot;acc:p22314]	Squared	27407.7	31927.7	1.16492	
788	vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [source:swissprot;acc:q13488]	Measured	5890.41	6547.81	1.11161	
789	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	Ranked	224.244	234.511	1.04578	
789	atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [source:refseq;acc:nm_020632]	Measured	5890.59	6547.99	1.1116	
789	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [source:swissprot;acc:o75746]	Squared	27407.7	31927.7	1.16492	
789	midasin (midas-containing protein). [source:swissprot;acc:q9nu22]	Rooted	54.2779	57.8311	1.06546	
790	40s ribosomal protein s21. [source:swissprot;acc:p35265]	Ranked	224.244	234.511	1.04578	
790	melanoma antigen recognized by t cells 2. [source:refseq;acc:nm_018194]	Squared	27407.7	31927.7	1.16492	
790	parafibromin. [source:refseq;acc:nm_024529]	Rooted	53.2852	56.7723	1.06544	
790	vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [source:swissprot;acc:q93050]	Measured	5890.88	6548.28	1.1116	
791	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [source:swissprot;acc:p13196]	Squared	27407.7	31927.7	1.16492	
791	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [source:swissprot;acc:q15642]	Rooted	62.5007	58.6648	1.06539	
791	cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [source:swissprot;acc:p50453]	Ranked	224.244	234.511	1.04578	
791	transducin beta-like 3; wd-repeat protein sazd. [source:refseq;acc:nm_006453]	Measured	4025.3	4474.3	1.11154	
792	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [source:swissprot;acc:o14645]	Measured	6772.75	7526.2	1.11125	
792	calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [source:swissprot;acc:q9ujs0]	Squared	27407.7	31927.7	1.16492	
792	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	Ranked	224.244	234.511	1.04578	
792	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [source:swissprot;acc:p28066]	Rooted	63.8039	67.9633	1.06519	
793	acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [source:swissprot;acc:o14561]	Squared	27407.7	31927.7	1.16492	
793	beta-catenin (pro2286). [source:swissprot;acc:p35222]	Rooted	60.2378	64.1631	1.06516	
793	bomapin (protease inhibitor 10) (serpin b10). [source:swissprot;acc:p48595]	Ranked	224.244	234.511	1.04578	
793	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [source:swissprot;acc:q9y5n5]	Measured	5036.92	5596.36	1.11107	
794	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Rooted	57.9449	61.719	1.06513	
794	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [source:swissprot;acc:q16531]	Squared	29554.6	34419.4	1.1646	
794	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [source:swissprot;acc:p11388]	Measured	6441.17	7154.55	1.11075	
794	plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [source:swissprot;acc:p05120]	Ranked	224.244	234.511	1.04578	
795	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	Measured	6441.14	7154.13	1.11069	
795	polymerase (rna) iii (dna directed) (62kd). [source:refseq;acc:nm_006468]	Rooted	52.1577	48.9787	1.06491	
795	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [source:swissprot;acc:p05166]	Squared	29554.6	34419.4	1.1646	
795	serpin b11. [source:swissprot;acc:q96p15]	Ranked	224.244	234.511	1.04578	
796	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Measured	6834.54	7590.49	1.11061	
796	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [source:swissprot;acc:p35237]	Ranked	224.244	234.511	1.04578	
796	set domain and mariner transposase fusion gene. [source:refseq;acc:nm_006515]	Rooted	54.765	51.4319	1.06481	
796	xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [source:refseq;acc:nm_020385]	Squared	25842.1	30093.4	1.16451	
797	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	Ranked	224.244	234.511	1.04578	
797	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [source:swissprot;acc:q14974]	Measured	6834.54	7590.49	1.11061	
797	limbic system-associated membrane protein precursor (lsamp). [source:swissprot;acc:q13449]	Squared	22535.2	26238.4	1.16433	
797	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [source:swissprot;acc:q08945]	Rooted	54.1622	57.6725	1.06481	
798	cd209 antigen-like; putative type ii membrane protein. [source:refseq;acc:nm_014257]	Rooted	54.765	51.4319	1.06481	
798	leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [source:swissprot;acc:p30740]	Ranked	224.244	234.511	1.04578	
798	opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [source:swissprot;acc:q14982]	Squared	22587.2	26296.1	1.1642	
798	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [source:swissprot;acc:o60907]	Measured	6834.54	7590.49	1.11061	
799	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [source:swissprot;acc:p06734]	Rooted	54.765	51.4319	1.06481	
799	neurotrimin precursor (hnt). [source:swissprot;acc:q9p121]	Squared	22623.7	26336.8	1.16412	
799	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [source:refseq;acc:nm_003900]	Ranked	221.965	212.404	1.04501	
799	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Measured	6834.54	7590.49	1.11061	
800	chromatin-specific transcription elongation factor large subunit. [source:refseq;acc:nm_007192]	Rooted	54.1622	57.6725	1.06481	
800	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [source:swissprot;acc:p22307]	Ranked	221.965	212.404	1.04501	
800	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	Measured	6075.55	6746.92	1.1105	
800	phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [source:swissprot;acc:o15305]	Squared	22210.6	25839.9	1.1634	

Legend:
- Rank is the rank after comparing the two networks
- 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/