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 3408 to 3457 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
426	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	Squared	1	20267.8	24644.8	1.21596
427	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Ranked	0	11276.1	11582.7	1.02719
	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	Ranked	1	239.977	259.525	1.08146
	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]	Squared	0	14907.5	15522.7	1.04127
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Rooted	0	22.1458	22.7768	1.02849
	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	Rooted	1	54.4927	49.6125	1.09837
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Squared	1	25380.3	30835.9	1.21495
	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	Measured	0	1195.87	1161.29	1.02978
	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	Measured	1	11736.6	13531.9	1.15297
428	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	Rooted		54.4927	49.6125	1.09837
	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	Ranked		253.852	234.808	1.0811
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Ranked	0	11982.7	12301.2	1.02658
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Measured		14267.5	14688.8	1.02953
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Rooted		22.1458	22.7768	1.02849
	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]	Measured	1	3721.19	4288.17	1.15237
	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	Squared	1	29101.9	35347	1.21459
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Squared	0	110.893	106.547	1.04079
429	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Ranked	0	12318.7	12631.5	1.02539
	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	Rooted	1	54.4927	49.6125	1.09837
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Rooted	0	22.1458	22.7768	1.02849
	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	Ranked	1	239.709	259.038	1.08064
	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	Squared	1	29101.9	35347	1.21459
	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	Measured	0	472.351	485.852	1.02858
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Squared	0	4841.65	4659.88	1.03901
	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	Measured	1	6272.91	7226.06	1.15195
430	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Squared		29098.8	35342.6	1.21457
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Rooted		54.4927	49.6125	1.09837
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Rooted	0	22.1458	22.7768	1.02849
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Ranked		11621.7	11913.4	1.0251
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Measured		10247.8	10535	1.02803
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Measured	1	3804.09	4379.37	1.15123
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	Squared	0	366.279	352.536	1.03898
	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Ranked	1	227.748	210.888	1.07995
431	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	Measured		3849.94	4431.36	1.15102
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Rooted		54.4927	49.6125	1.09837
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Ranked	0	10043.7	9799.17	1.02495
	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Squared		14421.3	14982.3	1.0389
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Measured		146.622	150.709	1.02787
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Squared	1	29096	35338.7	1.21456
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	Rooted	0	25.6478	26.3666	1.02803
	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	Ranked	1	236.245	255.113	1.07987
432	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	Squared		29095.3	35337.6	1.21455
	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	Ranked		212.547	229.411	1.07934
	fibrillin 3. [refseq;acc:nm_032447]	Ranked	0	930	953	1.02473
	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	Squared		25936.7	26909.5	1.03751
	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	Measured		100.5	103.25	1.02736
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Rooted	1	54.4927	49.6125	1.09837
	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439]	Measured	1	5244.71	6036.27	1.15093
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	Rooted	0	12.5074	12.1701	1.02772
433	grancalcin. [swissprot;acc:p28676]	Squared	1	29095.7	35338.3	1.21455

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/