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 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
148	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Rooted	0	8.52047	10.0173	1.17567
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Rooted	1	42.0577	50.424	1.19892
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Squared		103496	146848	1.41888
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Ranked		296.677	247.559	1.19841
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Ranked	0	6755.71	7863.63	1.164
149	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Squared	1	103496	146848	1.41888
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Ranked	1	142	170	1.19718
	block 23. [sptrembl;acc:q8nhw5]	Ranked	0	11469.3	13334.8	1.16265
	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]	Measured	0	293.178	379.474	1.29435
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Rooted	1	42.0684	50.4323	1.19882
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Rooted	0	8.52047	10.0173	1.17567
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Measured	1	11068	8508.5	1.30082
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Squared	0	8.27669	4.90793	1.68639
150	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Squared		274.947	163.071	1.68606
	metaxin 1. [swissprot;acc:q13505]	Measured		933.395	723.368	1.29035
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Ranked	1	55	46	1.19565
	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	Squared		121200	85473.4	1.41799
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Measured		11068	8508.5	1.30082
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	Rooted	0	26.8649	22.8761	1.17437
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Rooted	1	63.5827	53.0856	1.19774
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Ranked	0	8730	7516	1.16152
151	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Rooted	1	38.8223	46.4975	1.1977
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Squared	0	25050	42114.6	1.68122
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared	1	250303	354894	1.41786
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Ranked		55	46	1.19565
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Measured		4578.09	5939.91	1.29746
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	Rooted	0	16.3248	19.168	1.17416
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Ranked		7502.08	6461.83	1.16098
	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	Measured		2230.13	1729.7	1.28932
152	40s ribosomal protein s26. [swissprot;acc:p02383]	Squared		8.80383	5.24885	1.67729
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Rooted		13.8773	11.824	1.17366
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Rooted	1	55.2859	65.9288	1.19251
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Measured		23693.7	18263	1.29736
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Ranked		55	46	1.19565
	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	Squared		90226	126939	1.4069
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	Ranked	0	11438	13277.1	1.16079
	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	Measured	0	2230.13	1729.7	1.28932
153	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Ranked	1	249.663	298.263	1.19466
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Measured		23693.7	18263	1.29736
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Rooted		55.297	65.9236	1.19217
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Squared	0	81.4343	135.97	1.66969
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Squared	1	70011	49783	1.40632
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	Rooted	0	10.3441	8.83176	1.17124
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	Ranked		7879.3	6789.92	1.16044
	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]	Measured		2230.13	1729.7	1.28932
154	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	Rooted	1	43.5479	51.5473	1.18369
	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]	Measured	0	2230.13	1729.7	1.28932
	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	Rooted	0	14.1274	16.5305	1.1701
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Measured	1	23693.7	18263	1.29736
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Ranked	0	10883	12622.8	1.15986

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/