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

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Showing element 1627 to 1676 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
814	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	Divided	212.386	221.785	1.04425
	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	Subtracted	244.155	234.96	9.195
815	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821]		246.354	237.223	9.131
	syntaxin 1b. [swissprot;acc:q15531]	Divided	212.386	221.785	1.04425
816	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152]	Subtracted	246.354	237.223	9.131
	melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	Divided	212.386	221.785	1.04425
817	dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	Subtracted	110.689	101.613	9.076
818	60s ribosomal protein l39. [swissprot;acc:p02404]		234.025	224.958	9.067
	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	Divided	168.592	161.452	1.04422
819	60s ribosomal protein l18a. [swissprot;acc:q02543]	Subtracted	234.025	224.958	9.067
	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954]	Divided	228.563	238.668	1.04421
820	40s ribosomal protein s19. [swissprot;acc:p39019]	Subtracted	234.025	224.958	9.067
	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399]	Divided	221.716	231.501	1.04413
821	60s ribosomal protein l31. [swissprot;acc:p12947]	Subtracted	234.025	224.958	9.067
	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	Divided	221.676	231.453	1.0441
822	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]		243.067	232.805	1.04408
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Subtracted	55	46	9
823	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]
	transcription factor iib. [refseq;acc:nm_013242]	Divided	206.068	197.471	1.04354
824	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Subtracted	55	46	9
	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]	Divided	206.068	197.471	1.04354
825	40s ribosomal protein s3a. [swissprot;acc:p49241]	Subtracted	225.689	234.674	8.985
	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	Divided	206.214	197.614	1.04352
826	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993]		223.186	213.912	1.04335
	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]	Subtracted	230.811	239.785	8.974
827	jm1 protein. [refseq;acc:nm_014008]		219.762	210.806	8.956
	loh1cr12. [refseq;acc:nm_058169]	Divided	230.087	220.579	1.0431
828	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Subtracted	135.087	144.041	8.954
	unr protein. [swissprot;acc:o75534]	Divided	230.087	220.579	1.0431
829	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715]	Subtracted	252.873	261.821	8.948
	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	Divided	135.844	130.259	1.04288
830	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]		231.734	222.222	1.0428
	wd-repeat protein 3. [swissprot;acc:q9unx4]	Subtracted	243.896	234.96	8.936
831	60s acidic ribosomal protein p1. [swissprot;acc:p05386]		229.171	238.048	8.877
	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]	Divided	231.734	222.222	1.0428
832	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]	Subtracted	229.171	238.048	8.877
833	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	Divided	231.734	222.222	1.0428
	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]	Subtracted	229.171	238.048	8.877
834	60s ribosomal protein l8. [swissprot;acc:p25120]	Divided	231.734	222.222	1.0428
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Subtracted	230.768	239.632	8.864
835	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	Divided	231.734	222.222	1.0428
	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	Subtracted	224.413	233.272	8.859
836	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	Divided	231.734	222.222	1.0428
	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]	Subtracted	224.413	233.272	8.859
837	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	Divided	231.734	222.222	1.0428
	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945]	Subtracted	237.62	228.762	8.858
838	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
	rw1 protein (fragment). [swissprot;acc:q92545]	Divided	231.734	222.222	1.0428

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.