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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 936 to 985 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	green	red	network_comparison	
468	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	1	267.226	248.152	1.07686	
469	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	1	267.226	248.152	1.07686	
469	histone h2a; h2a histone family, member r. [source:refseq;acc:nm_170745]	0	20914	21205	1.01391	
470	h2a histone family, member j isoform 1. [source:refseq;acc:nm_018267]	0	20914	21205	1.01391	
470	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	1	267.226	248.152	1.07686	
471	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [source:swissprot;acc:p56470]	0	11463	11319.2	1.0127	
471	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	1	267.226	248.152	1.07686	
472	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [source:swissprot;acc:p49753]	0	7165.6	7080.27	1.01205	
472	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	1	267.226	248.152	1.07686	
473	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [source:swissprot;acc:q13098]	0	825	816	1.01103	
473	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [source:refseq;acc:nm_015629]	1	209.651	225.661	1.07637	
474	lipocalin-interacting membrane receptor. [source:refseq;acc:nm_018113]	0	11167.6	11290.1	1.01097	
474	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [source:swissprot;acc:p16389]	1	210.818	226.789	1.07576	
475	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [source:swissprot;acc:p56559]	0	18500	18667	1.00903	
475	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [source:swissprot;acc:q09470]	1	210.816	226.727	1.07547	
476	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	0	8329	8403	1.00888	
476	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [source:swissprot;acc:p22459]	1	210.814	226.681	1.07527	
477	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	1	234.547	251.926	1.0741	
477	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [source:swissprot;acc:p47986]	0	15780.2	15920	1.00886	
478	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	0	10243.1	10156.4	1.00854	
478	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [source:swissprot;acc:q92994]	1	212.321	228.051	1.07409	
479	aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]	0	15031.7	15155.8	1.00826	
479	nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	1	212.321	228.051	1.07409	
480	neuropilin- and tolloid-like protein 2 precursor. [source:refseq;acc:nm_018092]	1	254.667	237.109	1.07405	
480	uncharacterized bone marrow protein bm033. [source:refseq;acc:nm_018452]	0	15031.7	15155.8	1.00826	
481	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [source:refseq;acc:nm_138966]	1	254.667	237.109	1.07405	
481	uridine kinase-like 1. [source:swissprot;acc:q9nwz5]	0	11462.4	11554.3	1.00802	
482	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [source:swissprot;acc:q00839]	1	254.667	237.109	1.07405	
482	kinesin-like protein kif13b (kinesin-like protein gakin). [source:swissprot;acc:q9nqt8]	0	6205.67	6156.33	1.00801	
483	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [source:swissprot;acc:q13950]	1	254.667	237.109	1.07405	
483	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	0	12127.5	12223.8	1.00794	
484	e1b-55kda-associated protein 5 isoform a. [source:refseq;acc:nm_007040]	1	254.667	237.109	1.07405	
484	protein c20orf45 (cgi-107). [source:swissprot;acc:q9y3b1]	0	11414.3	11489.7	1.00661	
485	60s ribosomal protein l18. [source:swissprot;acc:q07020]	1	254.667	237.109	1.07405	
485	pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790]	0	12542.3	12461.5	1.00648	
486	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	0	13288.3	13372.4	1.00633	
486	mct-1 protein. [source:refseq;acc:nm_014060]	1	243.03	226.313	1.07387	
487	mitochondrial ribosomal protein l22. [source:refseq;acc:nm_014180]	1	243.03	226.313	1.07387	
487	survival motor neuron protein (component of gems 1) (gemin1). [source:swissprot;acc:q16637]	0	13159.3	13236.8	1.00589	
488	heat shock factor binding protein 1. [source:swissprot;acc:o75506]	0	15127.8	15204.2	1.00505	
488	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	1	209.798	225.026	1.07258	
489	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	0	8811.09	8854.04	1.00487	
489	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	1	215.627	231.276	1.07257	
490	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [source:swissprot;acc:q9y2s0]	0	10338.7	10388.7	1.00484	
490	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [source:swissprot;acc:q14155]	1	236.015	220.183	1.0719	
491	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	1	234.951	251.83	1.07184	
491	rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm_015952]	0	21880	21970	1.00411	
492	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [source:swissprot;acc:q13177]	1	235.979	220.171	1.0718	
492	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [source:swissprot;acc:q96gm5]	0	6829.74	6802.96	1.00394	
493	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [source:swissprot;acc:q9up83]	1	235.98	220.172	1.0718	

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/