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 red green network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
398	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Squared	Subtracted	26157.6	20236.2	5921.4	
398	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Ranked	Divided	218.818	238.358	1.0893	
398	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	Ranked	Subtracted	207.908	226.218	18.31	
398	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [source:swissprot;acc:q16537]	Rooted	Divided	116.707	106.044	1.10055	
398	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	Measured	Divided	5084.26	5904.1	1.16125	
399	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	Ranked	Divided	207.889	226.226	1.08821	
399	cyclin g2. [source:swissprot;acc:q16589]	Rooted	Divided	116.707	106.044	1.10055	
399	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	Ranked	Subtracted	207.908	226.218	18.31	
399	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	Squared	Divided	18929.1	23222.8	1.22683	
399	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Measured	Divided	5201.41	4479.76	1.16109	
399	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Squared	Subtracted	26157.6	20236.2	5921.4	
399	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	Rooted	Subtracted	63.2134	69.352	6.1386	
399	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	Measured	Subtracted	4633.92	5572.85	938.93	
400	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Measured	Divided	5201.41	4479.76	1.16109	
400	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	Ranked	Subtracted	207.931	226.209	18.278	
400	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	Rooted	Divided	116.707	106.044	1.10055	
400	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	Squared	Divided	39478.8	48419	1.22646	
400	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Measured	Subtracted	1834.73	895.893	938.837	
400	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	Rooted	Subtracted	79.931	86.0693	6.1383	
400	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [source:swissprot;acc:q9y6m9]	Squared	Subtracted	33024.9	38867.8	5842.9	
400	phosducin-like protein (phlp). [source:swissprot;acc:q13371]	Ranked	Divided	207.908	226.218	1.08807	
401	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Measured	Divided	5201.41	4479.76	1.16109	
401	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [source:swissprot;acc:o14645]	Squared	Divided	33044.3	40524.8	1.22638	
401	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	Measured	Subtracted	1835.3	896.972	938.328	
401	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [source:refseq;acc:nm_032390]	Ranked	Subtracted	254.434	236.224	18.21	
401	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [source:swissprot;acc:p07205]	Squared	Subtracted	28188.7	33982.7	5794	
401	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [source:swissprot;acc:p27694]	Ranked	Divided	207.908	226.218	1.08807	
401	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [source:swissprot;acc:q15172]	Rooted	Divided	116.707	106.044	1.10055	
401	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Rooted	Subtracted	55.9231	62.0565	6.1334	
402	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	Measured	Subtracted	6230.94	7168.2	937.26	
402	endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	Squared	Divided	39472	48393.1	1.22601	
402	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	Rooted	Divided	50.1918	55.2294	1.10037	
402	gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [source:swissprot;acc:p09104]	Squared	Subtracted	28190.4	33984.1	5793.7	
402	highly expressed in cancer, rich in leucine heptad repeats. [source:refseq;acc:nm_006101]	Ranked	Subtracted	231.802	249.983	18.181	
402	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	Measured	Divided	5201.41	4479.76	1.16109	
402	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	Rooted	Subtracted	59.5128	65.604	6.0912	
402	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [source:swissprot;acc:p15927]	Ranked	Divided	207.908	226.218	1.08807	
403	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [source:swissprot;acc:p13929]	Squared	Subtracted	28190.4	33984.1	5793.7	
403	calcyphosine. [source:swissprot;acc:q13938]	Rooted	Subtracted	59.5128	65.604	6.0912	
403	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	Measured	Divided	5201.41	4479.76	1.16109	
403	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	Squared	Divided	39463.9	48362.1	1.22548	
403	microtubule-actin crosslinking factor 1, isoform 4. [source:swissprot;acc:q96pk2]	Ranked	Subtracted	228.468	246.338	17.87	
403	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Rooted	Divided	59.6834	65.6741	1.10037	
403	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	Ranked	Divided	207.908	226.218	1.08807	
403	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	Measured	Subtracted	6259.3	7190.91	931.61	
404	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [source:swissprot;acc:p30520]	Squared	Divided	26819.1	32855.4	1.22507	
404	alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [source:swissprot;acc:p06733]	Squared	Subtracted	28190.4	33984.1	5793.7	
404	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [source:swissprot;acc:q03001]	Ranked	Subtracted	228.463	246.33	17.867	
404	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	Rooted	Subtracted	59.5128	65.604	6.0912	
404	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	Ranked	Divided	207.908	226.218	1.08807	

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/