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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Value Type Interaction Map description Network Comparison Type Rank Gene Filtered red green network_comparison

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Showing element 825 to 874 of 3228 in total

Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	2194	5285.38	5034.86	1.04976	
dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [source:swissprot;acc:p25205]	1492	4619.81	4965.45	1.07482	
dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [source:swissprot;acc:p33992]	2001	5047.2	5344.68	1.05894	
dna replication licensing factor mcm8 (minichromosome maintenance 8). [source:swissprot;acc:q9uja3]	3011	0.00001	0.00001	1	
dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [source:refseq;acc:nm_012135]	1265	5894.47	6383.73	1.083	
dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [source:swissprot;acc:p11388]	794	6441.17	7154.55	1.11075	
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	795	6441.14	7154.13	1.11069	
dna topoisomerase iii alpha (ec 5.99.1.2). [source:swissprot;acc:q13472]	1433	5692.34	6131.71	1.07719	
dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [source:swissprot;acc:p27695]	1065	6393.81	6984.94	1.09245	
dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [source:swissprot;acc:p16989]	2095	6682.05	7051.02	1.05522	
dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [source:swissprot;acc:o14593]	2728	5603.24	5583.64	1.00351	
dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [source:swissprot;acc:q9h9y6]	2533	3847.84	3759.28	1.02356	
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [source:swissprot;acc:q9y2s0]	2069	4632.65	4892.66	1.05613	
dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	2523	3803.04	3710.01	1.02508	
dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	2381	3667.94	3521.41	1.04161	
dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [source:swissprot;acc:p52435]	2371	4668.29	4868.52	1.04289	
dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [source:swissprot;acc:p41584]	2629	4582.38	4649.17	1.01458	
dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [source:swissprot;acc:p36954]	2546	4763.99	4868.66	1.02197	
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	2306	3619.07	3461.21	1.04561	
dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]	2446	4031.94	4166.99	1.0335	
dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]	2581	4570.81	4654.97	1.01841	
dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [source:swissprot;acc:p19388]	2582	3899.28	3829.53	1.01821	
dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [source:swissprot;acc:p19387]	2555	3852.99	3775.86	1.02043	
dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [source:swissprot;acc:p52436]	2667	4071.9	4099.01	1.00666	
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	2163	3569.06	3392.22	1.05213	
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	2374	3669.57	3520.86	1.04224	
dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [source:swissprot;acc:p52434]	2740	4200.59	4210.94	1.00246	
dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [source:swissprot;acc:q9y2y1]	1795	5501.3	5866.02	1.0663	
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [source:swissprot;acc:q9h1d9]	2633	4000.73	3947.54	1.01347	
dna-repair protein complementing xp-a cells (xeroderma pigmentosum group a complementing protein). [source:swissprot;acc:p23025]	2971	0.00001	0.00001	1	
dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [source:swissprot;acc:q92889]	2801	0.00001	0.00001	1	
dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [source:swissprot;acc:p28715]	2641	3377.01	3411.47	1.0102	
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [source:swissprot;acc:o43542]	1550	6025.86	6464.16	1.07274	
dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [source:swissprot;acc:p25685]	2620	5599.85	5683	1.01485	
dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [source:swissprot;acc:q9ubs4]	845	6276.97	6934.8	1.1048	
dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [source:swissprot;acc:q9udy4]	2617	5599.85	5683	1.01485	
dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [source:swissprot;acc:o75953]	2619	5599.85	5683	1.01485	
doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	48	779.167	1390.33	1.78438	
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	410	6102.59	7081.46	1.1604	
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	409	6102.59	7081.46	1.1604	
dok-like protein. [source:refseq;acc:nm_024872]	408	6102.59	7081.46	1.1604	
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [source:swissprot;acc:o60762]	549	5865.79	6671.23	1.13731	
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	190	4571.89	5864.86	1.28281	
dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [source:swissprot;acc:p40126]	1228	5998.58	6509.65	1.0852	
double-strand break repair protein mre11a (mre11 homolog 1). [source:swissprot;acc:p49959]	1371	10231.8	9487.34	1.07847	
double-stranded rna-binding zinc finger protein jaz. [source:refseq;acc:nm_012279]	3054	0.00001	0.00001	1	
doublecortin (lissencephalin-x) (lis-x) (doublin). [source:swissprot;acc:o43602]	1748	6301.03	6724.63	1.06723	
doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [source:refseq;acc:nm_021240]	3187	0.00001	0.00001	1	
down-regulated in metastasis. [source:refseq;acc:nm_014503]	747	4086.6	4557.68	1.11527	
dpy-30-like protein. [source:swissprot;acc:q9c005]	1448	5602.01	6031.05	1.07659	

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/