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

Results: HTML CSV LaTeX

Showing element 6408 to 6457 of 29840 in total

Interaction Map

: High confidence

Rank	Value Type	description	Network Comparison Type	green	Filtered	red	network_comparison
401	Ranked	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Divided	11904.9	0	12305.9	1.03368
	Squared	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]		40524.8	1	33044.3	1.22638
		camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]		4136.72	0	3862.64	1.07096
		phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205]	Subtracted	33982.7	1	28188.7	5794
		sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]		5.42219	0	12.5892	7.16701
	Rooted	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]		17.1002		17.8274	0.7272
		dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]	Divided	22.6039		21.8861	1.0328
		serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	Divided	106.044	1	116.707	1.10055
		u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Subtracted	62.0565		55.9231	6.1334
402	Measured	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	Subtracted	7168.2		6230.94	937.26
		leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Divided	4479.76		5201.41	1.16109
		lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Subtracted	39.8063	0	12.6208	27.1855
		myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Divided	527.5		548.5	1.03981
	Ranked	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	Divided	10918		10562.4	1.03367
			Subtracted	10918		10562.4	355.6
		highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	Subtracted	249.983	1	231.802	18.181
		replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]	Divided	226.218	1	207.908	1.08807
	Squared	brain protein 16. [refseq;acc:nm_016458]	Divided	2371.77	0	2538.95	1.07049
		cab2. [refseq;acc:nm_033419]	Subtracted	7.16592	0	0	7.16592
		endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]	Divided	48393.1	1	39472	1.22601
		gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104]	Subtracted	33984.1	1	28190.4	5793.7
	Rooted	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	Divided	22.4088	0	21.6987	1.03273
		eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537]	Divided	55.2294	1	50.1918	1.10037
		ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	Subtracted	65.604	1	59.5128	6.0912
		uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Subtracted	17.1002	0	17.8274	0.7272
403	Measured	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Divided	4479.76	1	5201.41	1.16109
		maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Subtracted	2264.37	0	2290.09	25.72
		myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Divided	527.5	0	548.5	1.03981
		ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Subtracted	7190.91	1	6259.3	931.61
	Ranked	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Subtracted	246.338		228.468	17.87
		phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]	Divided	226.218		207.908	1.08807
		scribble. [refseq;acc:nm_015356]	Subtracted	12719	0	12370.5	348.5
		udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	Divided	10111.2	0	9783.63	1.03348
	Squared	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]	Subtracted	33984.1	1	28190.4	5793.7
		glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	Divided	48362.1	1	39463.9	1.22548
		ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	Divided	1754.91	0	1872.12	1.06679
		protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	Subtracted	87.5656	0	94.678	7.1124
	Rooted	calcyphosine. [swissprot;acc:q13938]		65.604	1	59.5128	6.0912
		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]		14.7645	0	15.4896	0.7251
		nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	Divided	65.6741	1	59.6834	1.10037
		poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Divided	20.0671	0	19.4322	1.03267
404	Measured	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]	Subtracted	8731.82	1	7802.31	929.51
		leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Divided	4479.76	1	5201.41	1.16109
		spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	Subtracted	56.278	0	31.1429	25.1351
		thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	Divided	1278.36	0	1229.57	1.03968
	Ranked	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]	Subtracted	246.33	1	228.463	17.867
		dna repair protein rad52 homolog. [swissprot;acc:p43351]	Divided	226.218	1	207.908	1.08807
		similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	Subtracted	10945.3	0	10598.5	346.8
		udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	Divided	10111.2	0	9783.63	1.03348
	Squared	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	Divided	32855.4	1	26819.1	1.22507

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/