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

Results: HTML CSV LaTeX

Showing element 2651 to 2700 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
663	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [source:swissprot;acc:q9ubu9]	Rooted	68.8197	74.1413	1.07733	
663	tubby protein homolog. [source:swissprot;acc:p50607]	Measured	6374.65	7145.59	1.12094	
664	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [source:refseq;acc:nm_005863]	Rooted	51.6042	55.574	1.07693	
664	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [source:swissprot;acc:p50542]	Ranked	229.072	216.576	1.0577	
664	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [source:swissprot;acc:p41743]	Measured	6374.65	7145.59	1.12094	
664	ubiquitin-like protein smt3a. [source:swissprot;acc:p55854]	Squared	23948	28164.1	1.17605	
665	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm_012259]	Ranked	229.072	216.576	1.0577	
665	numb protein homolog (h-numb) (protein s171). [source:swissprot;acc:p49757]	Measured	6374.65	7145.59	1.12094	
665	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [source:refseq;acc:nm_019555]	Rooted	51.6042	55.574	1.07693	
665	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	Squared	18960.3	22298	1.17604	
666	down-regulated in metastasis. [source:refseq;acc:nm_014503]	Rooted	51.6042	55.574	1.07693	
666	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [source:swissprot;acc:p57057]	Squared	29224	34362.1	1.17582	
666	tbc1 domain family member 5. [source:swissprot;acc:q92609]	Measured	6374.65	7145.59	1.12094	
666	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	Ranked	229.072	216.576	1.0577	
667	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	Ranked	229.072	216.576	1.0577	
667	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [source:swissprot;acc:o43272]	Squared	29224	34362.1	1.17582	
667	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	Measured	6374.65	7145.59	1.12094	
667	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [source:swissprot;acc:p47985]	Rooted	51.2483	47.5889	1.0769	
668	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	Ranked	229.072	216.576	1.0577	
668	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Rooted	95.4476	102.785	1.07687	
668	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [source:swissprot;acc:p41252]	Squared	23969.3	28175.3	1.17547	
668	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	Measured	6374.65	7145.59	1.12094	
669	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	Rooted	79.931	86.0693	1.07679	
669	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	Measured	6374.65	7145.59	1.12094	
669	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	Ranked	229.072	216.576	1.0577	
669	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Squared	18548.7	21798.2	1.17519	
670	autoantigen ngp-1. [source:swissprot;acc:q13823]	Ranked	250.302	236.817	1.05694	
670	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	Rooted	51.2122	47.5637	1.07671	
670	dok-like protein. [source:refseq;acc:nm_024872]	Squared	28911	33971.3	1.17503	
670	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	Measured	6374.65	7145.59	1.12094	
671	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	Squared	28911	33971.3	1.17503	
671	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Ranked	210.739	199.398	1.05688	
671	proline synthetase co-transcribed bacterial homolog protein. [source:swissprot;acc:o94903]	Rooted	68.6822	73.8955	1.0759	
671	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	Measured	6374.65	7145.59	1.12094	
672	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [source:swissprot;acc:q9h9y6]	Rooted	51.4203	47.7936	1.07588	
672	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	Squared	28911	33971.3	1.17503	
672	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Ranked	210.739	199.398	1.05688	
672	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	Measured	6374.65	7145.59	1.12094	
673	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	Ranked	226.497	214.355	1.05664	
673	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Rooted	132.156	122.835	1.07588	
673	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	Measured	6933.17	7766.54	1.1202	
673	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	Squared	28911	33971.3	1.17503	
674	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	Squared	42467.5	36156.7	1.17454	
674	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Rooted	132.114	122.802	1.07583	
674	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	Ranked	226.497	214.355	1.05664	
674	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	Measured	5549.2	6215.42	1.12006	
675	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Rooted	132.063	122.761	1.07577	
675	single-minded homolog 1. [source:swissprot;acc:p81133]	Ranked	226.497	214.355	1.05664	
675	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	Measured	5549.2	6215.42	1.12006	
675	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [source:swissprot;acc:o14874]	Squared	22347.6	26247.3	1.1745	

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