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 1651 to 1700 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
826	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993]	Divided	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
839	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Subtracted	230.764	239.62	8.856
	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	Divided	177.776	170.499	1.04268
840	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398]	Subtracted	236.741	245.547	8.806
	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388]	Divided	198.781	190.66	1.04259
841	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]
	rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480]	Subtracted	236.741	245.547	8.806
842	jm1 protein. [refseq;acc:nm_014008]	Divided	219.762	210.806	1.04248
	map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650]	Subtracted	236.741	245.547	8.806
843	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954]
	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102]	Divided	218.521	227.796	1.04244
844	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]		178.033	170.82	1.04223
	meiotic recombination protein spo11. [swissprot;acc:q9y5k1]	Subtracted	236.741	245.547	8.806
845	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3]		232.512	241.288	8.776
	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	Divided	228.599	219.399	1.04193
846	methyltransferase like 2. [refseq;acc:nm_018396]		147.211	153.371	1.04184
	parafibromin. [refseq;acc:nm_024529]	Subtracted	239.704	230.991	8.713
847	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]	Divided	147.211	153.371	1.04184
	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	Subtracted	227.604	219.001	8.603
848	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	Divided	147.211	153.371	1.04184
	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	Subtracted	206.214	197.614	8.6
849	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Divided	147.211	153.371	1.04184
	transcription factor iib. [refseq;acc:nm_013242]	Subtracted	206.068	197.471	8.597
850	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Divided	107.842	112.329	1.04161
	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]	Subtracted	206.068	197.471	8.597

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.