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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green 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	red	green	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	6.25494	141.944	22.6931
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Rooted		Low confidence	1	53.5555	66.8994	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	25.6987	43.561	1.69507
	serpin b12. [swissprot;acc:q96p63]	Squared		High confidence	0	23.5744	0.0289898	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	124602	133193	8591
	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	Rooted	Subtracted		1	32.2966	47.9763	15.6797
	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Ranked	Divided			304.548	246.824	1.23387
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Squared				332411	473408	1.42416
20	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Measured			0	570	139	4.10072
		Rooted	Subtracted	High confidence		23.8747	11.7898	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		37661.1	29380.4	8280.7
	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Rooted	Divided	High confidence		11.3774	1.80368	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	203.673	182.638	21.035
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared	Divided	Low confidence		299771	424645	1.41656
		Rooted	Subtracted	Low confidence		173.58	189.17	15.59
	ero1-like. [refseq;acc:nm_014584]	Measured	Divided	High confidence	0	82	0.00001	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	5.54059	103.726	18.7211
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Measured	Subtracted	High confidence	1	23421.5	17580.4	5841.1
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Ranked	Divided	High confidence	1	185.678	245.247	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	22422	14964	1.4984
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152]		Subtracted	High confidence	1	266.868	336.159	69.291
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Rooted	Divided	High confidence	1	40.3337	24.2744	1.66157
	hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]	Ranked	Subtracted	Low confidence	0	11485.6	15984.3	4498.7
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Ranked	Divided	High confidence	0	22286	13216	1.68629
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Squared	Subtracted	Low confidence	1	122475	159767	37292
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Squared	Divided	High confidence	0	23.4957	0.0297673	789.312
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Rooted	Divided	Low confidence	0	16.1288	34.2643	2.12442
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Squared	Subtracted	High confidence	1	219048	129762	89286
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Rooted	Subtracted	Low confidence	0	61.6393	70.9983	9.359
	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [swissprot;acc:q07326]	Rooted	Divided	Low confidence	1	57.2538	71.1231	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	8763	7608	1155
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Measured	Divided		1	677.5	1865.5	2.75351
		Squared	Divided			108.641	823.69	7.58176
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Measured	Subtracted	Low confidence		15464.1	17572.7	2108.6
	retinoblastoma-associated factor 600. [refseq;acc:nm_020765]	Measured	Divided	Low confidence		7256.71	9368.87	1.29106
	serpin b12. [swissprot;acc:q96p63]	Ranked	Subtracted	High confidence	0	14604.2	21138.6	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	38799.5	25982	12817.5
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Ranked		Low confidence	1	297.273	258.59	38.683
	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	Ranked	Divided		1	304.359	246.737	1.23354
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Measured	Subtracted		0	2376	3169.35	793.35
21	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	Ranked	Divided	High confidence		6313.38	10621.4	1.68236
		Rooted	Subtracted			44.2946	32.7593	11.5353
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Rooted	Divided			36.9188	6.85565	5.38516
	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	Squared	Divided	Low confidence		76.8994	4.57302	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	13689.1	11788.6	1900.5
		Rooted	Subtracted	High confidence		153.602	133.195	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		3035.43	3917.88	1.29072
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Ranked			0	3859	2582	1.49458
	dna helicase homolog (fragment). [sptrembl;acc:q9y645]	Rooted			0	6.65832	3.18113	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	677.5	1865.5	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/