Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 2913 to 2962 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	Hugo	description	
2913	AUH	au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [source:refseq;acc:nm_001698]	
2914	LACTB2	lactamase, beta 2. [source:refseq;acc:nm_016027]	
2915	SLC25A37	mitochondrial solute carrier protein. [source:refseq;acc:nm_016612]	
2916	PRPS1L1	ribose-phosphate pyrophosphokinase i (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase i) (ppribp) (prs-i). [source:swissprot;acc:p09329]	
2917	CCT6A	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [source:swissprot;acc:p40227]	
2918	GBAS	nipsnap2 protein (glioblastoma amplified sequence). [source:swissprot;acc:o75323]	
2919	GLRA1	glycine receptor alpha-1 chain precursor (glycine receptor 48 kda subunit) (strychnine binding subunit). [source:swissprot;acc:p23415]	
2920	GLRA3	glycine receptor alpha-3 chain precursor. [source:swissprot;acc:o75311]	
2921	EAF2	ell-associated factor 2; uncharacterized bone marrow protein bm040; testosterone regulated apoptosis inducer and tumor suppressor. [source:refseq;acc:nm_018456]	
2922	ALDH1L1	10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [source:swissprot;acc:o75891]	
2923	TMEM4	transmembrane protein 4. [source:refseq;acc:nm_014255]	
2924	RQCD1	rcd1 required for cell differentiation1 homolog; protein involved in sexual development; rcd1 (required for cell differentiation, s.pombe) homolog 1. [source:refseq;acc:nm_005444]	
2925	RALB	ras-related protein ral-b. [source:swissprot;acc:p11234]	
2926	DUSP11	dual specificity protein phosphatase 11 (ec 3.1.3.48) (rna/rnp complex-intereracting phosphatase) (phosphatase that interacts with rna/rnp complex 1). [source:swissprot;acc:o75319]	
2927	CIAO1	wd-repeat containing protein ciao 1. [source:swissprot;acc:o76071]	
2928		calmodulin. [source:swissprot;acc:p02593]	
2929	LYST	lysosomal trafficking regulator (beige homolog). [source:swissprot;acc:q99698]	
2930	ILF2	interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [source:refseq;acc:nm_004515]	
2931	TPM3	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [source:swissprot;acc:p06753]	
2932	POGZ	pogo transposable element with znf domain isoform 1. [source:refseq;acc:nm_015100]	
2933	SEMA6C	semaphorin 6c precursor (semaphorin y) (sema y). [source:swissprot;acc:q9h3t2]	
2934	PPOX	protoporphyrinogen oxidase (ec 1.3.3.4) (ppo). [source:swissprot;acc:p50336]	
2935	TMCO1	putative membrane protein. [source:refseq;acc:nm_019026]	
2936	RXRG	retinoic acid receptor rxr-gamma. [source:swissprot;acc:p48443]	
2937	MOBKL2C	similar to mob-lak. [source:refseq;acc:nm_145279]	
2938	CYR61	cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [source:swissprot;acc:o00622]	
2939	FBN3	fibrillin 3. [source:refseq;acc:nm_032447]	
2940		transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [source:swissprot;acc:p15884]	
2941	TAF4B	transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [source:swissprot;acc:q92750]	
2942	SS18	ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [source:swissprot;acc:q15532]	
2943	PRPSAP2	phosphoribosyl pyrophosphate synthetase-associated protein 2 (prpp synthetase-associated protein 2) (41 kda phosphoribosypyrophosphate synthetase-associated protein) (pap41). [source:swissprot;acc:o60256]	
2944	TIGD7	tigger transposable element derived 7; jerky (mouse) homolog-like. [source:refseq;acc:nm_033208]	
2945	TPM1	tropomyosin 1 alpha chain (alpha-tropomyosin). [source:swissprot;acc:p09493]	
2946	GTF2A2	transcription initiation factor iia gamma chain (tfiia p12 subunit) (tfiia-12) (tfiias) (tfiia-gamma). [source:swissprot;acc:p52657]	
2947	SERF2	small edrk-rich factor 2. [source:refseq;acc:nm_005770]	
2948	TCF12	transcription factor 12 (transcription factor htf-4) (e-box-binding protein) (dna-binding protein htf4). [source:swissprot;acc:q99081]	
2949	MFAP1	microfibrillar-associated protein 1. [source:swissprot;acc:p55081]	
2950	TEGT	bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [source:swissprot;acc:p55061]	
2951	ITGB7	integrin beta-7 precursor. [source:swissprot;acc:p26010]	
2952	ACVRL1	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). [source:swissprot;acc:p37023]	
2953	GLIPR1	glioma pathogenesis-related protein (glipr) (rtvp-1 protein). [source:swissprot;acc:p48060]	
2954	NDUFA9	nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [source:swissprot;acc:q16795]	
2955	FBN2	fibrillin 2 precursor. [source:swissprot;acc:p35556]	
2956	SEC24B	protein transport protein sec24b (sec24-related protein b). [source:swissprot;acc:o95487]	
2957	ENPEP	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [source:swissprot;acc:q07075]	
2958	CNOT6L	ccr4-not transcription complex, subunit 6-like. [source:refseq;acc:nm_144571]	
2959		60s ribosomal protein l37a. [source:swissprot;acc:p12751]	
2960	AOX1	aldehyde oxidase (ec 1.2.3.1). [source:swissprot;acc:q06278]	
2961	RAB1A	ras-related protein rab-1a (ypt1-related protein). [source:swissprot;acc:p11476]	
2962	DYNC2LI1	dynein 2 light intermediate chain. [source:refseq;acc:nm_016008]	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/