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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2150 to 2199 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison	
2150	PSMD14	26s proteasome-associated pad1 homolog. [source:refseq;acc:nm_005805]	217.871	219.366	1.00686	
2151	APOB	apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [source:swissprot;acc:p04114]	217.871	219.366	1.00686	
2152	VAMP2	vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [source:swissprot;acc:p19065]	200.063	198.71	1.00681	
2153	VAMP1	vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [source:swissprot;acc:p23763]	200.063	198.71	1.00681	
2154	VAMP4	vesicule-associated membrane protein 4 (vamp-4). [source:swissprot;acc:o75379]	200.063	198.71	1.00681	
2155	CDIPT	cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [source:swissprot;acc:o14735]	200.063	198.71	1.00681	
2156	ARFGAP1	adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [source:swissprot;acc:q8n6t3]	200.063	198.71	1.00681	
2157	VAMP3	vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [source:swissprot;acc:q15836]	200.063	198.71	1.00681	
2158	LGALS4	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [source:swissprot;acc:p56470]	206.401	207.796	1.00676	
2159	MAPK3	mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [source:swissprot;acc:p27361]	215.921	214.474	1.00675	
2160	RPS6KA3	ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [source:swissprot;acc:p51812]	215.925	214.481	1.00673	
2161	CAMK2G	calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [source:swissprot;acc:q13555]	215.925	214.481	1.00673	
2162	CAMK2D	calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [source:swissprot;acc:q13557]	215.925	214.481	1.00673	
2163	MAP3K6	mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [source:swissprot;acc:o95382]	215.925	214.481	1.00673	
2164		signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	215.925	214.481	1.00673	
2165	RPS6KA1	ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [source:swissprot;acc:q15418]	215.925	214.481	1.00673	
2166	ABCD3	atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [source:swissprot;acc:p28288]	215.925	214.481	1.00673	
2167	GCDH	glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [source:swissprot;acc:q92947]	215.925	214.481	1.00673	
2168	MAPK1	mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [source:swissprot;acc:p28482]	215.929	214.486	1.00673	
2169	HAL	histidine ammonia-lyase (ec 4.3.1.3) (histidase). [source:swissprot;acc:p42357]	215.925	214.481	1.00673	
2170	RPS6KA6	ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [source:swissprot;acc:q9uk32]	215.925	214.481	1.00673	
2171	RPS6KA2	ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [source:swissprot;acc:q15349]	215.925	214.481	1.00673	
2172	CAMK2A	calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [source:swissprot;acc:q9uqm7]	215.925	214.481	1.00673	
2173	CAMK2B	calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [source:swissprot;acc:q13554]	215.925	214.481	1.00673	
2174		mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [source:swissprot;acc:q99683]	215.925	214.481	1.00673	
2175	PSMD2	26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [source:swissprot;acc:q13200]	210.209	208.808	1.00671	
2176	PLK1	serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [source:swissprot;acc:p53350]	218.089	216.64	1.00669	
2177	PXMP2	peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [source:swissprot;acc:q9nr77]	210.961	209.563	1.00667	
2178	HSPA2	heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [source:swissprot;acc:p54652]	210.961	209.563	1.00667	
2179		heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	210.961	209.563	1.00667	
2180	HSPA8	heat shock cognate 71 kda protein. [source:swissprot;acc:p11142]	210.961	209.563	1.00667	
2181	CALR	calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [source:swissprot;acc:p27797]	227.117	225.62	1.00664	
2182	PEO1	twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [source:refseq;acc:nm_021830]	218.062	216.624	1.00664	
2183	RABEP1	rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [source:refseq;acc:nm_004703]	218.062	216.624	1.00664	
2184	SUPV3L1	suppressor of var1, 3-like 1. [source:refseq;acc:nm_003171]	211.713	210.318	1.00663	
2185	BAG1	bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [source:swissprot;acc:q99933]	211.713	210.318	1.00663	
2186	GSK3A	glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [source:swissprot;acc:p49840]	211.713	210.318	1.00663	
2187	GSK3B	glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [source:swissprot;acc:p49841]	211.713	210.318	1.00663	
2188	P4HB	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [source:swissprot;acc:p07237]	209.54	208.162	1.00662	
2189	HAAO	3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	209.54	208.162	1.00662	
2190	ZFPL1	zinc finger protein-like 1; zinc-finger protein in men1 region. [source:refseq;acc:nm_006782]	209.54	208.162	1.00662	
2191	HUS1	hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [source:refseq;acc:nm_004507]	209.54	208.162	1.00662	
2192	HABP4	hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [source:refseq;acc:nm_014282]	209.54	208.162	1.00662	
2193	P4HA1	prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [source:swissprot;acc:p13674]	209.54	208.162	1.00662	
2194	PROX1	homeobox prospero-like protein prox1 (prox 1). [source:swissprot;acc:q92786]	209.54	208.162	1.00662	
2195	RAD1	rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [source:refseq;acc:nm_002853]	209.54	208.162	1.00662	
2196	P4HA2	prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [source:swissprot;acc:o15460]	209.54	208.162	1.00662	
2197	COQ6	ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [source:swissprot;acc:q9y2z9]	193.787	195.064	1.00659	
2198	KMO	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [source:refseq;acc:nm_003679]	193.787	195.064	1.00659	
2199	SQLE	squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [source:swissprot;acc:q14534]	193.787	195.064	1.00659	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/