MK5 Microarray Data

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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 975 to 1024 of 3228 in total

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

Rank	description	red	green	network_comparison
975	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]	211.987	204.964	1.03426
976	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	243.34	235.322	1.03407
977	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	228.953	221.421	1.03402
978	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
979	gcn5-like protein 1 (rt14 protein). [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). [swissprot;acc:p15056]	130.289	134.713	1.03396
981	exocyst complex component sec6. [swissprot;acc:o60645]	207.186	200.398	1.03387
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	243.312	235.351	1.03383
983	pbk1 protein. [sptrembl;acc:o76021]		235.353	1.03382
984	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [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). [swissprot;acc:o14737]	233.402	225.782	1.03375
986	exocyst complex component sec5. [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). [swissprot;acc:o43464]	218.459	211.338	1.03369
988	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	218.461	211.343	1.03368
989	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	218.462	211.345	1.03367
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	243.297	235.373
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). [swissprot;acc:o60762]	203.381	196.76	1.03365
992	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	218.468	211.357	1.03364
993	pinin, desmosome associated protein; pinin. [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). [swissprot;acc:q9bwt3]	116.845	120.772	1.03361
995	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	219.656	212.547	1.03345
996	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
997	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]
998	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	225.557	218.271	1.03338
999	vinculin (metavinculin). [swissprot;acc:p18206]	215.92	208.95	1.03336
1000	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	225.167	217.922	1.03325
1001	sprouty homolog 3 (spry-3). [swissprot;acc:o43610]
1002	sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]
1003	sprouty homolog 2 (spry-2). [swissprot;acc:o43597]
1004	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	238.725	231.059	1.03318
1005	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	225.448	218.232	1.03307
1006	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	116.524	120.375	1.03305
1007	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	162.055	156.884	1.03296
1008	wd-repeat protein bing4. [swissprot;acc:o15213]	243.227	235.475	1.03292
1009	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	229.116	221.823	1.03288
1010	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	217.523	210.648	1.03264
1011	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	217.026	210.189	1.03253
1012	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	217.021	210.185	1.03252
1013	protein bap28. [swissprot;acc:q9h583]	244.312	236.647	1.03239
1014	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	243.045	235.422	1.03238
1015	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	221.73	228.906	1.03236
1016	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	217.369	210.561	1.03233
1017	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	217.365	210.558
1018	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505]	217.361	210.554
1019	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	221.302	214.409	1.03215
1020	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126]	221.28		1.03205
1021	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	221.278		1.03204
1022	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	205.632	199.266	1.03195
1023	transforming protein rhoc (h9). [swissprot;acc:p08134]
1024	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.