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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 951 to 1000 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
951	triple functional domain protein (ptprf interacting protein). [source:swissprot;acc:o75962]	217.253	209.827	1.03539	
952	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [source:refseq;acc:nm_144678]	217.252	209.83	1.03537	
953	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [source:swissprot;acc:q01780]	198.494	205.466	1.03512	
954	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [source:swissprot;acc:o43708]	267.447	276.773	1.03487	
955	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [source:swissprot;acc:q9p0m9]	231.163	239.205	1.03479	
956	vinexin (sh3-containing adaptor molecule-1) (scam-1). [source:swissprot;acc:o60504]	211.812	204.732	1.03458	
957	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	129.913	134.399	1.03453	
958	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	129.921	134.406	1.03452	
959	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [source:swissprot;acc:p25388]	237.558	229.677	1.03431	
960	zuotin related factor-1 (m-phase phosphoprotein 11). [source:swissprot;acc:q99543]	237.558	229.677	1.03431	
961	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]	130.066	134.527	1.0343	
962	cyclin g2. [source:swissprot;acc:q16589]	130.066	134.527	1.0343	
963	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	130.066	134.527	1.0343	
964	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]	130.066	134.527	1.0343	
965	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	211.987	204.964	1.03426	
966	tubby protein homolog. [source:swissprot;acc:p50607]	211.987	204.964	1.03426	
967	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [source:swissprot;acc:p41743]	211.987	204.964	1.03426	
968	numb protein homolog (h-numb) (protein s171). [source:swissprot;acc:p49757]	211.987	204.964	1.03426	
969	tbc1 domain family member 5. [source:swissprot;acc:q92609]	211.987	204.964	1.03426	
970	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	211.987	204.964	1.03426	
971	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	211.987	204.964	1.03426	
972	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	211.987	204.964	1.03426	
973	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	211.987	204.964	1.03426	
974	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	211.987	204.964	1.03426	
975	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	211.987	204.964	1.03426	
976	t-cell activation wd repeat protein. [source:refseq;acc:nm_139281]	243.34	235.322	1.03407	
977	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [source:swissprot;acc:q99471]	228.953	221.421	1.03402	
978	prefoldin subunit 6 (protein ke2). [source:swissprot;acc:o15212]	228.953	221.421	1.03402	
979	gcn5-like protein 1 (rt14 protein). [source:swissprot;acc:p78537]	202.027	195.386	1.03399	
980	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]	130.289	134.713	1.03396	
981	exocyst complex component sec6. [source:swissprot;acc:o60645]	207.186	200.398	1.03387	
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [source:refseq;acc:nm_032830]	243.312	235.351	1.03383	
983	pbk1 protein. [source:sptrembl;acc:o76021]	243.312	235.353	1.03382	
984	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	116.71	120.654	1.03379	
985	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [source:swissprot;acc:o14737]	233.402	225.782	1.03375	
986	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	116.771	120.707	1.03371	
987	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	218.459	211.338	1.03369	
988	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	218.461	211.343	1.03368	
989	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	218.462	211.345	1.03367	
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [source:refseq;acc:nm_007010]	243.297	235.373	1.03367	
991	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]	203.381	196.76	1.03365	
992	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	218.468	211.357	1.03364	
993	pinin, desmosome associated protein; pinin. [source:refseq;acc:nm_002687]	211.071	204.205	1.03362	
994	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	116.845	120.772	1.03361	
995	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [source:swissprot;acc:q9ui95]	219.656	212.547	1.03345	
996	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	219.656	212.547	1.03345	
997	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [source:swissprot;acc:q99567]	219.656	212.547	1.03345	
998	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	225.557	218.271	1.03338	
999	vinculin (metavinculin). [source:swissprot;acc:p18206]	215.92	208.95	1.03336	
1000	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	225.167	217.922	1.03325	

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/