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

Results: HTML CSV LaTeX

Showing element 2175 to 2224 of 3228 in total

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

Rank	description	red	network_comparison	green	
2175	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	1.00671	208.808	
2176	serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [source:swissprot;acc:p53350]	218.089	1.00669	216.64	
2177	peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [source:swissprot;acc:q9nr77]	210.961	1.00667	209.563	
2178	heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [source:swissprot;acc:p54652]	210.961	1.00667	209.563	
2179	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	210.961	1.00667	209.563	
2180	heat shock cognate 71 kda protein. [source:swissprot;acc:p11142]	210.961	1.00667	209.563	
2181	calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [source:swissprot;acc:p27797]	227.117	1.00664	225.62	
2182	twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [source:refseq;acc:nm_021830]	218.062	1.00664	216.624	
2183	rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [source:refseq;acc:nm_004703]	218.062	1.00664	216.624	
2184	suppressor of var1, 3-like 1. [source:refseq;acc:nm_003171]	211.713	1.00663	210.318	
2185	bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [source:swissprot;acc:q99933]	211.713	1.00663	210.318	
2186	glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [source:swissprot;acc:p49840]	211.713	1.00663	210.318	
2187	glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [source:swissprot;acc:p49841]	211.713	1.00663	210.318	
2188	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	1.00662	208.162	
2189	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	1.00662	208.162	
2190	zinc finger protein-like 1; zinc-finger protein in men1 region. [source:refseq;acc:nm_006782]	209.54	1.00662	208.162	
2191	hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [source:refseq;acc:nm_004507]	209.54	1.00662	208.162	
2192	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	1.00662	208.162	
2193	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	1.00662	208.162	
2194	homeobox prospero-like protein prox1 (prox 1). [source:swissprot;acc:q92786]	209.54	1.00662	208.162	
2195	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	1.00662	208.162	
2196	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	1.00662	208.162	
2197	ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [source:swissprot;acc:q9y2z9]	193.787	1.00659	195.064	
2198	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [source:refseq;acc:nm_003679]	193.787	1.00659	195.064	
2199	squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [source:swissprot;acc:q14534]	193.787	1.00659	195.064	
2200	insulin gene enhancer protein isl-2 (islet-2). [source:swissprot;acc:q96a47]	196.748	1.00656	195.466	
2201	p47 protein isoform a. [source:refseq;acc:nm_016143]	213.642	1.00654	212.254	
2202	tumor susceptibility gene 101 protein. [source:swissprot;acc:q99816]	195.97	1.00652	194.7	
2203	symplekin. [source:swissprot;acc:q92797]	162.741	1.00651	163.8	
2204	ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [source:swissprot;acc:q9y230]	219.377	1.00649	220.8	
2205	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [source:swissprot;acc:p35268]	199.129	1.00645	200.413	
2206	transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [source:swissprot;acc:p55072]	215.571	1.00645	214.19	
2207	sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [source:refseq;acc:nm_003864]	199.129	1.00645	200.413	
2208	clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [source:swissprot;acc:p20172]	199.129	1.00645	200.413	
2209	atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [source:refseq;acc:nm_033450]	199.129	1.00645	200.413	
2210	lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [source:swissprot;acc:o00754]	199.129	1.00645	200.413	
2211	rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	199.129	1.00645	200.413	
2212	28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [source:swissprot;acc:q9y3d3]	224.411	1.00643	225.854	
2213	dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [source:refseq;acc:nm_014475]	210.127	1.00642	211.475	
2214	fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [source:swissprot;acc:p15090]	221.509	1.00637	220.108	
2215	fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [source:swissprot;acc:q01469]	221.509	1.00637	220.108	
2216	fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [source:swissprot;acc:o15540]	221.509	1.00637	220.108	
2217	wd-repeat protein 4. [source:swissprot;acc:p57081]	221.509	1.00637	220.108	
2218	myelin p2 protein. [source:swissprot;acc:p02689]	221.509	1.00637	220.108	
2219	kelch-like protein 8. [source:swissprot;acc:q9p2g9]	221.509	1.00637	220.108	
2220	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [source:swissprot;acc:p11086]	221.509	1.00637	220.108	
2221	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [source:refseq;acc:nm_031938]	221.509	1.00637	220.108	
2222	beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [source:refseq;acc:nm_017429]	221.509	1.00637	220.108	
2223	fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [source:swissprot;acc:p05413]	221.509	1.00637	220.108	
2224	retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [source:refseq;acc:nm_000329]	221.509	1.00637	220.108	

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/