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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3151 to 3200 of 29840 in total 
Interaction Map	High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison	
197	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	Squared	Divided	1	71062.4	95488.9	1.34373	
197	zinc finger protein-like 1; zinc-finger protein in men1 region. [source:refseq;acc:nm_006782]	Ranked	Subtracted	0	8730	7516	1214	
198	40s ribosomal protein s29. [source:swissprot;acc:p30054]	Ranked	Subtracted	1	241.849	267.642	25.793	
198	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Ranked	Subtracted	0	11844.9	10636.3	1208.6	
198	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	Measured	Subtracted	1	10639.9	12117.4	1477.5	
198	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	Measured	Divided	1	17710.9	13977.7	1.26708	
198	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	Rooted	Subtracted	1	116.576	105.948	10.628	
198	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Ranked	Divided	1	263.191	231.394	1.13741	
198	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Rooted	Divided	1	59.6399	51.9242	1.1486	
198	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [source:swissprot;acc:p15104]	Squared	Divided	0	1679.15	1177.18	1.42642	
198	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	Rooted	Divided	0	23.8722	20.9331	1.1404	
198	lipocalin-interacting membrane receptor. [source:refseq;acc:nm_018113]	Measured	Subtracted	0	734.025	574.372	159.653	
198	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	Rooted	Subtracted	0	25.4117	22.5968	2.8149	
198	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	Squared	Divided	1	71062.2	95488.6	1.34373	
198	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Ranked	Divided	0	11781.5	10545.3	1.11723	
198	secreted modular calcium-binding protein 1. [source:refseq;acc:nm_022137]	Measured	Divided	0	247.333	206	1.20065	
198	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [source:swissprot;acc:q92502]	Squared	Subtracted	1	42411.6	55802.1	13390.5	
198	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	Squared	Subtracted	0	451.156	817.981	366.825	
199	40s ribosomal protein s11. [source:swissprot;acc:p04643]	Ranked	Subtracted	1	241.399	267.088	25.689	
199	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Ranked	Divided	0	11781.8	10545.7	1.11721	
199	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	Ranked	Subtracted	0	11846.3	10638.4	1207.9	
199	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [source:swissprot;acc:p15104]	Measured	Divided	0	1230.54	1026.18	1.19915	
199	keratin associated protein 1-3; keratin associated protein 1.3. [source:refseq;acc:nm_030966]	Rooted	Divided	0	23.8722	20.9331	1.1404	
199	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [source:swissprot;acc:p30301]	Measured	Subtracted	1	10639.8	12117.3	1477.5	
199	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Rooted	Subtracted	1	55.297	65.9236	10.6266	
199	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [source:refseq;acc:nm_015650]	Squared	Divided	0	21.8736	31.1879	1.42582	
199	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [source:swissprot;acc:q15822]	Squared	Subtracted	1	42411.6	55802.1	13390.5	
199	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source:swissprot;acc:q9umr5]	Ranked	Divided	1	242.735	276.059	1.13729	
199	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	Measured	Divided	1	4916.8	3888.18	1.26455	
199	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Rooted	Divided	1	61.2893	70.3856	1.14842	
199	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Squared	Subtracted	0	799.337	432.882	366.455	
199	thymus-specific serine protease precursor (ec 3.4.-.-). [source:swissprot;acc:q9nqe7]	Squared	Divided	1	71062.2	95488.6	1.34373	
199	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	Rooted	Subtracted	0	10.9527	8.13999	2.81271	
199	zinc finger protein-like 1; zinc-finger protein in men1 region. [source:refseq;acc:nm_006782]	Measured	Subtracted	0	385	543	158	
200	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Ranked	Subtracted	1	241.808	267.335	25.527	
200	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [source:swissprot;acc:p29972]	Measured	Subtracted	1	10635.3	12111.4	1476.1	
200	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Measured	Divided	1	4808.79	6074.21	1.26315	
200	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Measured	Divided	0	578.056	482.7	1.19755	
200	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	Ranked	Divided	1	242.718	276.018	1.1372	
200	gk001 protein. [source:refseq;acc:nm_020198]	Squared	Divided	1	71062.2	95488.6	1.34373	
200	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [source:swissprot;acc:q06210]	Measured	Subtracted	0	1705.19	1547.2	157.99	
200	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	Rooted	Divided	0	23.8722	20.9333	1.14039	
200	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [source:refseq;acc:nm_004635]	Squared	Subtracted	1	42411.6	55802.1	13390.5	
200	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Squared	Subtracted	0	129.158	488.851	359.693	
200	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Rooted	Divided	1	61.2893	70.3856	1.14842	
200	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	Ranked	Divided	0	8786.74	7870.3	1.11644	
200	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	Rooted	Subtracted	1	63.5827	53.0856	10.4971	
200	syntaxin 1a (neuron-specific antigen hpc-1). [source:swissprot;acc:q16623]	Rooted	Subtracted	0	11.5003	8.68906	2.81124	
200	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	Ranked	Subtracted	0	13483.3	14685.4	1202.1	
200	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [source:swissprot;acc:q9y690]	Squared	Divided	0	5317.39	3738.08	1.42249	

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/