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.

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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 6358 to 6407 of 77072 in total

Rank	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison
199	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Measured	Divided	High confidence	1	4916.8	3888.18	1.26455
	single-stranded dna-binding protein 4. [swissprot;acc:q9bwg4]	Squared	Subtracted	Low confidence		52164.3	47095.3	5069
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Rooted	Divided	High confidence		61.2893	70.3856	1.14842
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Squared	Subtracted		0	799.337	432.882	366.455
	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	Squared	Divided		1	71062.2	95488.6	1.34373
	tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226]	Rooted	Divided	Low confidence	1	70.8512	75.1709	1.06097
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	Rooted	Subtracted	High confidence	0	10.9527	8.13999	2.81271
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Ranked	Subtracted	Low confidence		12294.5	13531.6	1237.1
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	Squared	Divided			7130.54	9625.93	1.34996
	zinc finger protein 431. [swissprot;acc:q8tf32]	Measured	Divided			2350.86	1967.99	1.19455
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Measured	Subtracted	High confidence		385	543	158
200	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Ranked	Subtracted	High confidence	1	241.808	267.335	25.527
	60s ribosomal protein l27. [swissprot;acc:p08526]	Rooted	Divided	Low confidence		69.691	73.939	1.06095
	alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511]	Ranked	Divided			219.543	208.868	1.05111
	anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]	Ranked	Subtracted			213.495	203.244	10.251
	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	Measured	Subtracted	High confidence		10635.3	12111.4	1476.1
	bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	Squared	Divided	Low confidence		54179.7	48910.9	1.10772
	cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363]	Measured	Subtracted	Low confidence		9810.95	10381.3	570.35
	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	Measured	Divided	High confidence		4808.79	6074.21	1.26315
	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]	Squared	Subtracted	Low confidence	0	14084.8	15189.4	1104.6
		Rooted	Divided	Low confidence		20.6112	23.3431	1.13254
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Measured		High confidence		578.056	482.7	1.19755
	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Ranked			1	242.718	276.018	1.1372
	gk001 protein. [refseq;acc:nm_020198]	Squared			1	71062.2	95488.6	1.34373
	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]	Measured	Subtracted		0	1705.19	1547.2	157.99
	guanine nucleotide-binding protein g(s), alpha subunit (adenylate cyclase-stimulating g alpha protein). [swissprot;acc:p04895]	Squared	Divided	Low confidence		2610.94	3520.09	1.34821
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Rooted	Subtracted	Low confidence		9.84765	5.80678	4.04087
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Rooted	Divided	High confidence		23.8722	20.9333	1.14039
	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]	Squared	Subtracted		1	42411.6	55802.1	13390.5
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Squared			0	129.158	488.851	359.693
	nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8]	Rooted		Low confidence	1	69.9166	74.219	4.3024
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Measured		Low confidence	0	286	0	286
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Rooted	Divided	High confidence	1	61.2893	70.3856	1.14842
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Ranked		High confidence	0	8786.74	7870.3	1.11644
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured		Low confidence	1	6926.74	7434.04	1.07324
	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	Subtracted	High confidence	1	63.5827	53.0856	10.4971
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Rooted		High confidence	0	11.5003	8.68906	2.81124
	tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105]	Squared		Low confidence	1	52164	47095.1	5068.9
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Ranked		High confidence	0	13483.3	14685.4	1202.1
	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	Squared	Divided	High confidence		5317.39	3738.08	1.42249
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Ranked	Subtracted	Low confidence		13558.4	14792.7	1234.3
	zinc finger protein 221. [swissprot;acc:q9uk13]	Ranked	Divided			4251.37	4847.95	1.14033
	zinc finger protein 267 (zinc finger protein hzf2). [swissprot;acc:q14586]	Measured	Divided			2350.86	1967.99	1.19455
201	60s ribosomal protein l11. [swissprot;acc:p39026]	Ranked	Subtracted	High confidence	1	241.828	267.346	25.518
	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Measured	Divided	Low confidence		10392.7	9683.56	1.07323
	aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]	Measured	Subtracted			9249.74	9818.95	569.21
	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Squared			0	16325.1	17416.9	1091.8
	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Ranked		High confidence		6814	8009	1195
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	Squared	Divided			351.996	499.177	1.41813
	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	Squared	Divided		1	71033.4	95440.2	1.3436

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/