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 1132 to 1181 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
283	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	Measured	5221.28	6314.35	1.20935	
284	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	Squared	59464	76120.8	1.28012	
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Ranked	224.657	203.235	1.10541	
284	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	Rooted	51.8647	46.3161	1.1198	
284	paxillin. [source:swissprot;acc:p49023]	Measured	5221.28	6314.35	1.20935	
285	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	Rooted	48.4278	54.2262	1.11973	
285	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Squared	6680.89	8549.44	1.27969	
285	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Measured	23326.5	19296.4	1.20885	
285	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Ranked	224.647	203.242	1.10532	
286	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Ranked	224.633	203.251	1.1052	
286	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Measured	23316	19288.8	1.20878	
286	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	Rooted	51.8717	46.3287	1.11965	
286	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	Squared	6693.64	8564.94	1.27956	
287	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Ranked	240.758	266.079	1.10517	
287	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Squared	6693.64	8564.94	1.27956	
287	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	Rooted	51.8714	46.3281	1.11965	
287	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Measured	23303.1	19279.5	1.2087	
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Ranked	240.758	266.078	1.10517	
288	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	Measured	23422.4	19380.3	1.20857	
288	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Squared	6693.64	8564.94	1.27956	
288	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	Rooted	51.8789	46.3416	1.11949	
289	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	Ranked	272.781	246.892	1.10486	
289	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Squared	6693.64	8564.94	1.27956	
289	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [source:refseq;acc:nm_015629]	Rooted	57.4274	64.2609	1.11899	
289	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	Measured	4682.88	5646.19	1.20571	
290	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Squared	15734.4	20126.8	1.27916	
290	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Rooted	75.6323	67.6572	1.11788	
290	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [source:swissprot;acc:p31350]	Ranked	231.969	210.064	1.10428	
290	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Measured	4991.48	6014.08	1.20487	
291	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	Ranked	251.679	228.037	1.10368	
291	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Measured	44490.5	36927.5	1.20481	
291	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	Squared	59016.1	75486.9	1.27909	
291	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Rooted	113.983	101.979	1.11771	
292	40s ribosomal protein s15a. [source:swissprot;acc:p39027]	Ranked	241.411	266.414	1.10357	
292	neuralized-like. [source:refseq;acc:nm_004210]	Squared	6828.26	8728.66	1.27831	
292	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Measured	4641.09	5588.75	1.20419	
292	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	Rooted	56.48	63.119	1.11755	
293	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	Ranked	240.782	265.717	1.10356	
293	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	Squared	35991.8	46002.9	1.27815	
293	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Measured	4641.09	5588.75	1.20419	
293	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	Rooted	63.0715	56.4506	1.11729	
294	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [source:swissprot;acc:o15120]	Squared	30826.5	39383.9	1.2776	
294	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [source:refseq;acc:nm_016567]	Ranked	240.782	265.717	1.10356	
294	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Measured	22515.5	18702.6	1.20387	
294	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Rooted	59.0296	65.951	1.11725	
295	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [source:swissprot;acc:q99943]	Squared	30807.7	39351.7	1.27733	
295	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	Ranked	223.273	202.423	1.103	
295	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [source:swissprot;acc:q9nzl6]	Measured	13261.9	11017.8	1.20368	
295	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	Rooted	59.029	65.9421	1.11711	
296	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	Rooted	63.0663	56.4667	1.11688	

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/