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 1180 to 1229 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
148	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [source:refseq;acc:nm_004980]	Rooted	Subtracted	41.6879	28.9554	12.7325	
148	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Squared	Divided	103496	146848	1.41888	
148	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	Squared	Subtracted	70011	49783	20228	
148	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	Ranked	Divided	296.677	247.559	1.19841	
148	symplekin. [source:swissprot;acc:q92797]	Measured	Subtracted	15213.4	13418.1	1795.3	
149	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Squared	Divided	103496	146848	1.41888	
149	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Ranked	Divided	142	170	1.19718	
149	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Rooted	Divided	42.0684	50.4323	1.19882	
149	metaxin 1. [source:swissprot;acc:q13505]	Squared	Subtracted	60401.6	79875.7	19474.1	
149	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	Measured	Divided	11068	8508.5	1.30082	
149	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [source:refseq;acc:nm_004979]	Rooted	Subtracted	41.6969	28.9696	12.7273	
149	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Ranked	Subtracted	226.582	198.444	28.138	
149	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	Measured	Subtracted	11736.6	13531.9	1795.3	
150	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	Rooted	Subtracted	42.2825	54.9687	12.6862	
150	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [source:swissprot;acc:p30084]	Squared	Subtracted	57913.5	76336.3	18422.8	
150	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	Ranked	Divided	55	46	1.19565	
150	pre-mrna cleavage complex ii protein clp1. [source:swissprot;acc:q92989]	Squared	Divided	121200	85473.4	1.41799	
150	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Ranked	Subtracted	226.582	198.444	28.138	
150	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Measured	Divided	11068	8508.5	1.30082	
150	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	Rooted	Divided	63.5827	53.0856	1.19774	
150	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Measured	Subtracted	4172.91	5954.48	1781.57	
151	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Rooted	Divided	38.8223	46.4975	1.1977	
151	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Squared	Divided	250303	354894	1.41786	
151	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [source:swissprot;acc:p07099]	Squared	Subtracted	87971.9	69563.1	18408.8	
151	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Rooted	Subtracted	50.3065	62.9788	12.6723	
151	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	Ranked	Divided	55	46	1.19565	
151	pre-mrna cleavage complex ii protein clp1. [source:swissprot;acc:q92989]	Measured	Subtracted	14830.5	13050.3	1780.2	
151	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Ranked	Subtracted	226.582	198.444	28.138	
151	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	Measured	Divided	4578.09	5939.91	1.29746	
152	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Measured	Subtracted	5136.78	6895.98	1759.2	
152	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Rooted	Divided	55.2859	65.9288	1.19251	
152	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	Measured	Divided	23693.7	18263	1.29736	
152	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Ranked	Divided	55	46	1.19565	
152	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Squared	Subtracted	73995.1	56003.7	17991.4	
152	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	Squared	Divided	90226	126939	1.4069	
152	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Ranked	Subtracted	226.582	198.444	28.138	
152	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Rooted	Subtracted	50.3247	62.9892	12.6645	
153	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	Ranked	Divided	249.663	298.263	1.19466	
153	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Ranked	Subtracted	226.582	198.444	28.138	
153	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Measured	Divided	23693.7	18263	1.29736	
153	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Rooted	Subtracted	50.3333	62.9942	12.6609	
153	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Rooted	Divided	55.297	65.9236	1.19217	
153	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	Measured	Subtracted	9035	7279.6	1755.4	
153	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	Squared	Subtracted	73510.2	55607.3	17902.9	
153	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	Squared	Divided	70011	49783	1.40632	
154	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Rooted	Divided	43.5479	51.5473	1.18369	
154	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Rooted	Subtracted	50.339	62.9975	12.6585	
154	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Measured	Divided	23693.7	18263	1.29736	
154	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Ranked	Subtracted	227.491	199.458	28.033	
154	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	Measured	Subtracted	9035	7279.6	1755.4	

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/