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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2551 to 2600 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
319	scratch; scratch 1. [source:refseq;acc:nm_031309]	Squared	0	5976.46	5135.5	1.16375	
319	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [source:swissprot;acc:q9y5x1]	Ranked	0	8918.54	9465.32	1.06131	
320	40s ribosomal protein s29. [source:swissprot;acc:p30054]	Rooted	1	50.2784	45.294	1.11005	
320	adp-ribosylation factor 3. [source:swissprot;acc:p16587]	Ranked	0	11627.8	10958.2	1.0611	
320	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [source:sptrembl;acc:q9h5b6]	Squared	0	5127.13	5964.46	1.16331	
320	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	Ranked	1	241.892	265.96	1.0995	
320	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [source:swissprot;acc:p07099]	Squared	1	87971.9	69563.1	1.26463	
320	mevalonate kinase (ec 2.7.1.36) (mk). [source:swissprot;acc:q03426]	Rooted	0	28.7027	26.9929	1.06334	
320	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Measured	1	20911	24908.5	1.19117	
320	syntaxin 1a (neuron-specific antigen hpc-1). [source:swissprot;acc:q16623]	Measured	0	142.802	156.3	1.09452	
321	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [source:swissprot;acc:p07741]	Ranked	0	11634.4	10989.9	1.05864	
321	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [source:swissprot;acc:o15143]	Squared	0	5671.94	6590.82	1.162	
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	Ranked	1	241.892	265.959	1.09949	
321	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	Measured	0	628.072	686.693	1.09333	
321	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Squared	1	33526	42390.2	1.2644	
321	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Measured	1	20911	24908.5	1.19117	
321	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [source:refseq;acc:nm_016538]	Rooted	0	42.9302	40.4104	1.06236	
321	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Rooted	1	55.9231	62.0565	1.10968	
322	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Measured	0	1621.1	1771.04	1.09249	
322	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Measured	1	20911	24908.5	1.19117	
322	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	Squared	0	7795.92	9052.52	1.16119	
322	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Ranked	1	86.7483	78.8995	1.09948	
322	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [source:swissprot;acc:p14061]	Ranked	0	11634.4	10989.9	1.05864	
322	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [source:swissprot;acc:p15531]	Squared	1	33522.8	42384.8	1.26436	
322	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	Rooted	0	46.9819	44.2892	1.0608	
322	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Rooted	1	60.594	67.2244	1.10942	
323	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	Ranked	1	241.884	265.945	1.09947	
323	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	Rooted	1	50.3803	45.4193	1.10923	
323	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [source:sptrembl;acc:q9nq03]	Squared	0	5936.62	5112.71	1.16115	
323	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	Rooted	0	27.5028	29.1579	1.06018	
323	histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	Measured	0	2056.14	2244.06	1.09139	
323	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	Squared	1	33514.4	42370.8	1.26426	
323	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [source:swissprot;acc:p15154]	Ranked	0	17387.1	16427.3	1.05843	
323	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Measured	1	4620.76	5501.94	1.1907	
324	40s ribosomal protein s23. [source:swissprot;acc:p39028]	Ranked	1	243.944	268.195	1.09941	
324	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [source:swissprot;acc:o95376]	Squared	0	1742.44	1500.84	1.16098	
324	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Measured	1	28136.5	33457.6	1.18912	
324	fad synthetase. [source:refseq;acc:nm_025207]	Rooted	1	50.3803	45.4193	1.10923	
324	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [source:swissprot;acc:p49590]	Squared	1	34527.9	43507.9	1.26008	
324	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [source:swissprot;acc:p12829]	Rooted	0	27.5028	29.1579	1.06018	
324	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [source:swissprot;acc:o14658]	Ranked	0	17387.1	16427.3	1.05843	
324	testis-specific chromodomain y protein 1. [source:swissprot;acc:q9y6f8]	Measured	0	3036.29	2784.08	1.09059	
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	Ranked	1	243.944	268.195	1.09941	
325	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Rooted	1	50.3803	45.4193	1.10923	
325	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [source:swissprot;acc:p12081]	Squared	1	34506.3	43476	1.25994	
325	mstp028 protein. [source:refseq;acc:nm_031954]	Ranked	0	7965.66	7528.21	1.05811	
325	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	Measured	1	16177.9	19235.4	1.18899	
325	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [source:refseq;acc:nm_003075]	Rooted	0	16.5182	17.4854	1.05855	
325	testis-specific chromodomain protein y protein 2. [source:swissprot;acc:q9y6f7]	Measured	0	3036.85	2784.59	1.09059	
325	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [source:swissprot;acc:p51966]	Squared	0	1742.44	1500.84	1.16098	

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/