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

Results: HTML CSV LaTeX

Showing element 601 to 650 of 77072 in total

Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison
19	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Squared	Divided	Low confidence	0	141.944	6.25494	22.6931
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Rooted		Low confidence	1	66.8994	53.5555	1.24916
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Rooted		High confidence	1	43.561	25.6987	1.69507
	serpin b12. [swissprot;acc:q96p63]	Squared		High confidence	0	0.0289898	23.5744	813.196
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Squared	Subtracted	Low confidence	0	133193	124602	8591
	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	Rooted	Subtracted		1	47.9763	32.2966	15.6797
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Ranked	Divided			246.824	304.548	1.23387
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Squared				473408	332411	1.42416
20	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Measured			0	139	570	4.10072
		Rooted	Subtracted	High confidence		11.7898	23.8747	12.0849
	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Squared	Subtracted	Low confidence		29380.4	37661.1	8280.7
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Rooted	Divided	High confidence		1.80368	11.3774	6.30788
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Rooted	Subtracted	High confidence	1	182.638	203.673	21.035
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared	Divided	Low confidence		424645	299771	1.41656
		Rooted	Subtracted	Low confidence		189.17	173.58	15.59
	ero1-like. [refseq;acc:nm_014584]	Measured	Divided	High confidence	0	0.00001	82	8200000
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Squared	Divided	Low confidence	0	103.726	5.54059	18.7211
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Measured	Subtracted	High confidence	1	17580.4	23421.5	5841.1
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Ranked	Divided	High confidence	1	245.247	185.678	1.32082
	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]		Divided	Low confidence	0	14964	22422	1.4984
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]		Subtracted	High confidence	1	336.159	266.868	69.291
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Rooted	Divided	High confidence	1	24.2744	40.3337	1.66157
	hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]	Ranked	Subtracted	Low confidence	0	15984.3	11485.6	4498.7
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Ranked	Divided	High confidence	0	13216	22286	1.68629
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Squared	Subtracted	Low confidence	1	159767	122475	37292
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Squared	Divided	High confidence	0	0.0297673	23.4957	789.312
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Rooted	Divided	Low confidence	0	34.2643	16.1288	2.12442
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Squared	Subtracted	High confidence	1	129762	219048	89286
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Rooted	Subtracted	Low confidence	0	70.9983	61.6393	9.359
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Rooted	Divided	Low confidence	1	71.1231	57.2538	1.24224
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Measured	Subtracted	High confidence	0	7608	8763	1155
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Measured	Divided		1	1865.5	677.5	2.75351
		Squared	Divided			823.69	108.641	7.58176
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Measured	Subtracted	Low confidence		17572.7	15464.1	2108.6
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	Measured	Divided	Low confidence		9368.87	7256.71	1.29106
	serpin b12. [swissprot;acc:q96p63]	Ranked	Subtracted	High confidence	0	21138.6	14604.2	6534.4
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Squared		High confidence	0	25982	38799.5	12817.5
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Ranked		Low confidence	1	258.59	297.273	38.683
	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	Ranked	Divided		1	246.737	304.359	1.23354
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Measured	Subtracted		0	3169.35	2376	793.35
21	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	Ranked	Divided	High confidence		10621.4	6313.38	1.68236
		Rooted	Subtracted			32.7593	44.2946	11.5353
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Rooted	Divided			6.85565	36.9188	5.38516
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Squared	Divided	Low confidence		4.57302	76.8994	16.8159
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Measured	Subtracted	Low confidence	1	11788.6	13689.1	1900.5
		Rooted	Subtracted	High confidence		133.195	153.602	20.407
	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318]	Measured	Divided	Low confidence		3917.88	3035.43	1.29072
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Ranked			0	2582	3859	1.49458
	dna helicase homolog (fragment). [sptrembl;acc:q9y645]	Rooted			0	3.18113	6.65832	2.09307
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Measured		High confidence	1	1865.5	677.5	2.75351

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/