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	Rank	description	Network Comparison Type	green	Interaction Map	network_comparison	red	Filtered

Results: HTML CSV LaTeX

Showing element 501 to 550 of 2061 in total

Network Comparison Type  : Subtracted
green  : 0
network_comparison  : 0
red  : 0
Filtered  : 1

Value Type	Rank	description	Interaction Map
Measured	5047	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	Low confidence
	5048	double-stranded rna-binding zinc finger protein jaz. [refseq;acc:nm_012279]
	5049	mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [swissprot;acc:q9uha4]
	5050	lipin 2. [swissprot;acc:q92539]
	5051	sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3]
	5052	tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922]
	5053	gamma-glutamyltransferase. [sptrembl;acc:q14390]
	5054	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
	5055	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
	5056	putative nadh oxidoreductase complex i subunit homolog. [sptrembl;acc:q96q80]
	5057	leucine rich repeat (in flii) interacting protein 2. [refseq;acc:nm_006309]
	5058	carcinoma related gene. [refseq;acc:nm_016041]
	5059	core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [swissprot;acc:q13951]
	5060	homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011]
	5061	runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761]
Ranked	2756	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	High confidence
	2757	nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]
	2758	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]
	2759	retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]
	2760	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]
	2761	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]
	2762	developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295]
	2763	ring finger protein 3. [refseq;acc:nm_006315]
	2764	ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]
	2765	histone h2a.e (h2a/e). [swissprot;acc:q99878]
	2766	ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]
	2767	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
	2768	histone h2a.x (h2a/x). [swissprot;acc:p16104]
	2769	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]
	2770	nipsnap1 protein. [swissprot;acc:q9bpw8]
	2771	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]
	2772	uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]
	2773	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]
	2774	dc12 protein. [refseq;acc:nm_020187]
	2775	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]
	2776	bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745]
	2777	guanine nucleotide exchange factor mss4 (rab interacting factor). [swissprot;acc:p47224]
	2778	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [sptrembl;acc:q8nhw3]
	2779	caveolin-3 (m-caveolin). [swissprot;acc:p56539]
	2780	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]
	2781	exocyst complex component exo70. [swissprot;acc:q9upt5]
	2782	vacuolar atp synthase membrane sector associated protein m8-9 (v-atpase m8.9 subunit). [swissprot;acc:o75787]
	2783	mab-21-like protein 2; mab-21-like 2. [refseq;acc:nm_006439]
	2784	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
	2785	nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [swissprot;acc:p06748]
	2786	mab-21-like protein 1; mab-21-like 1. [refseq;acc:nm_005584]
	2787	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]
	2788	a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588]
	2789	protein-tyrosine phosphatase, non-receptor type 11 (ec 3.1.3.48) (protein-tyrosine phosphatase 2c) (ptp-2c) (ptp-1d) (sh-ptp3) (sh- ptp2) (shp-2). [swissprot;acc:q06124]
	2790	transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3]

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.