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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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 2925 to 2974 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
red  : 0.00001
green  : 0.00001
network_comparison  : 1

Rank	description
2925	ras-related protein ral-b. [swissprot;acc:p11234]
2926	dual specificity protein phosphatase 11 (ec 3.1.3.48) (rna/rnp complex-intereracting phosphatase) (phosphatase that interacts with rna/rnp complex 1). [swissprot;acc:o75319]
2927	wd-repeat containing protein ciao 1. [swissprot;acc:o76071]
2928	calmodulin. [swissprot;acc:p02593]
2929	lysosomal trafficking regulator (beige homolog). [swissprot;acc:q99698]
2930	interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [refseq;acc:nm_004515]
2931	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753]
2932	pogo transposable element with znf domain isoform 1. [refseq;acc:nm_015100]
2933	semaphorin 6c precursor (semaphorin y) (sema y). [swissprot;acc:q9h3t2]
2934	protoporphyrinogen oxidase (ec 1.3.3.4) (ppo). [swissprot;acc:p50336]
2935	putative membrane protein. [refseq;acc:nm_019026]
2936	retinoic acid receptor rxr-gamma. [swissprot;acc:p48443]
2937	similar to mob-lak. [refseq;acc:nm_145279]
2938	cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [swissprot;acc:o00622]
2939	fibrillin 3. [refseq;acc:nm_032447]
2940	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]
2941	transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750]
2942	ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [swissprot;acc:q15532]
2943	phosphoribosyl pyrophosphate synthetase-associated protein 2 (prpp synthetase-associated protein 2) (41 kda phosphoribosypyrophosphate synthetase-associated protein) (pap41). [swissprot;acc:o60256]
2944	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]
2945	tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493]
2946	transcription initiation factor iia gamma chain (tfiia p12 subunit) (tfiia-12) (tfiias) (tfiia-gamma). [swissprot;acc:p52657]
2947	small edrk-rich factor 2. [refseq;acc:nm_005770]
2948	transcription factor 12 (transcription factor htf-4) (e-box-binding protein) (dna-binding protein htf4). [swissprot;acc:q99081]
2949	microfibrillar-associated protein 1. [swissprot;acc:p55081]
2950	bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061]
2951	integrin beta-7 precursor. [swissprot;acc:p26010]
2952	serine/threonine-protein kinase receptor r3 precursor (ec 2.7.1.37) (skr3) (activin receptor-like kinase 1) (alk-1) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:p37023]
2953	glioma pathogenesis-related protein (glipr) (rtvp-1 protein). [swissprot;acc:p48060]
2954	nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795]
2955	fibrillin 2 precursor. [swissprot;acc:p35556]
2956	protein transport protein sec24b (sec24-related protein b). [swissprot;acc:o95487]
2957	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]
2958	ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571]
2959	60s ribosomal protein l37a. [swissprot;acc:p12751]
2960	aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278]
2961	ras-related protein rab-1a (ypt1-related protein). [swissprot;acc:p11476]
2962	dynein 2 light intermediate chain. [refseq;acc:nm_016008]
2963	geranylgeranyl transferase type ii beta subunit (ec 2.5.1.-) (rab geranylgeranyltransferase beta subunit) (rab geranyl- geranyltransferase beta subunit) (rab gg transferase beta) (rab ggtase beta). [swissprot;acc:p53611]
2964	semaphorin 6d isoform 3 precursor. [refseq;acc:nm_153617]
2965	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]
2966	protease inhibitor 15 preproprotein; 25 kda trypsin inhibitor. [refseq;acc:nm_015886]
2967	taube nuss. [refseq;acc:nm_138572]
2968	ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39]
2969	transcription factor ap-2 alpha (ap2-alpha) (activating enhancer- binding protein 2 alpha) (ap-2 transcription factor) (activator protein-2) (ap-2). [swissprot;acc:p05549]
2970	nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [swissprot;acc:p48745]
2971	dna-repair protein complementing xp-a cells (xeroderma pigmentosum group a complementing protein). [swissprot;acc:p23025]
2972	steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285]
2973	fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062]
2974	cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750]

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.