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.

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

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Showing element 968 to 1017 of 3228 in total

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

Rank	description	network_comparison	green	red
968	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	1.03426	204.964	211.987
969	tbc1 domain family member 5. [swissprot;acc:q92609]
970	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]
971	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]
972	numb-like protein (numb-r). [swissprot;acc:q9y6r0]
973	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]
974	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]
975	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
976	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	1.03407	235.322	243.34
977	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	1.03402	221.421	228.953
978	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
979	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	1.03399	195.386	202.027
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]	1.03396	134.713	130.289
981	exocyst complex component sec6. [swissprot;acc:o60645]	1.03387	200.398	207.186
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	1.03383	235.351	243.312
983	pbk1 protein. [sptrembl;acc:o76021]	1.03382	235.353
984	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	1.03379	120.654	116.71
985	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	1.03375	225.782	233.402
986	exocyst complex component sec5. [swissprot;acc:q96kp1]	1.03371	120.707	116.771
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]	1.03369	211.338	218.459
988	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	1.03368	211.343	218.461
989	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	1.03367	211.345	218.462
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]		235.373	243.297
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]	1.03365	196.76	203.381
992	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	1.03364	211.357	218.468
993	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	1.03362	204.205	211.071
994	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	1.03361	120.772	116.845
995	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	1.03345	212.547	219.656
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]	1.03338	218.271	225.557
999	vinculin (metavinculin). [swissprot;acc:p18206]	1.03336	208.95	215.92
1000	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	1.03325	217.922	225.167
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]	1.03318	231.059	238.725
1005	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	1.03307	218.232	225.448
1006	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	1.03305	120.375	116.524
1007	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	1.03296	156.884	162.055
1008	wd-repeat protein bing4. [swissprot;acc:o15213]	1.03292	235.475	243.227
1009	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	1.03288	221.823	229.116
1010	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	1.03264	210.648	217.523
1011	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	1.03253	210.189	217.026
1012	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	1.03252	210.185	217.021
1013	protein bap28. [swissprot;acc:q9h583]	1.03239	236.647	244.312
1014	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	1.03238	235.422	243.045
1015	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	1.03236	228.906	221.73
1016	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	1.03233	210.561	217.369
1017	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]		210.558	217.365

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.