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

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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	Hugo	description	red	green	network_comparison
968	NUMB	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	211.987	204.964	1.03426
969	TBC1D5	tbc1 domain family member 5. [swissprot;acc:q92609]
970	TULP1	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]
971	VPS29	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]
972	NUMBL	numb-like protein (numb-r). [swissprot;acc:q9y6r0]
973	TULP3	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]
974	VPS35	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]
975	PRKCZ	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
976	WDR36	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	243.34	235.322	1.03407
977	PFDN5	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	228.953	221.421	1.03402
978	no value	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
979	BLOC1S1	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	202.027	195.386	1.03399
980	BRAF	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	EXOC3	exocyst complex component sec6. [swissprot;acc:o60645]	207.186	200.398	1.03387
982	CIRH1A	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	243.312	235.351	1.03383
983	RSL1D1	pbk1 protein. [sptrembl;acc:o76021]		235.353	1.03382
984	PAPOLA	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	116.71	120.654	1.03379
985	PDCD5	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	EXOC2	exocyst complex component sec5. [swissprot;acc:q96kp1]	116.771	120.707	1.03371
987	HTRA2	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	HTRA4	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	218.461	211.343	1.03368
989	HTRA3	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	218.462	211.345	1.03367
990	DDX52	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	243.297	235.373
991	DPM1	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	HTRA1	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	218.468	211.357	1.03364
993	PNN	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	211.071	204.205	1.03362
994	PAPOLG	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	MAD2L2	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	219.656	212.547	1.03345
996	no value	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
997	NUP88	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]
998	DYNC1I2	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	225.557	218.271	1.03338
999	VCL	vinculin (metavinculin). [swissprot;acc:p18206]	215.92	208.95	1.03336
1000	no value	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	225.167	217.922	1.03325
1001	SPRY3	sprouty homolog 3 (spry-3). [swissprot;acc:o43610]
1002	SPRY1	sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]
1003	SPRY2	sprouty homolog 2 (spry-2). [swissprot;acc:o43597]
1004	no value	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	238.725	231.059	1.03318
1005	DYNC1I1	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	225.448	218.232	1.03307
1006	CPSF3	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	116.524	120.375	1.03305
1007	RALGDS	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	162.055	156.884	1.03296
1008	WDR46	wd-repeat protein bing4. [swissprot;acc:o15213]	243.227	235.475	1.03292
1009	no value	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	CROT	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	217.523	210.648	1.03264
1011	RBL2	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	217.026	210.189	1.03253
1012	RBL1	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	217.021	210.185	1.03252
1013	HEATR1	protein bap28. [swissprot;acc:q9h583]	244.312	236.647	1.03239
1014	AATF	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]	243.045	235.422	1.03238
1015	MAGI1	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	KPNA4	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629]	217.369	210.561	1.03233
1017	TOE1	target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077]	217.365	210.558

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
- 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.