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 Filtered Network Comparison Type Interaction Map red green network_comparison

Results: HTML CSV LaTeX

Showing element 651 to 700 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
82	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Squared	1	117718	70505.8	1.66962
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Ranked	0	7706.5	6058	1.27212
	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Ranked	1	267.636	335.359	1.25304
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Measured	0	191.333	115.333	1.65896
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Measured	1	4172.91	5954.48	1.42694
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	Rooted	0	10.9527	8.13999	1.34554
83	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	Rooted		10.9038	8.12243	1.34243
	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Measured		166.114	100.887	1.64654
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Ranked	1	88.2482	110.265	1.24949
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Measured		4932.27	7033.29	1.42597
	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]	Squared		117718	70505.9	1.66962
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Rooted		63.6507	48.7127	1.30666
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Ranked	0	18359.8	14447.8	1.27077
	uridine kinase-like 1. [swissprot;acc:q9nwz5]	Squared	0	269.31	688.46	2.55638
84	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]		1	117515	70412.3	1.66896
	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]		0	33.0303	83.901	2.54012
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Ranked	1	88.2482	110.265	1.24949
	jun dimerization protein. [refseq;acc:nm_130469]	Measured		4932.27	7033.29	1.42597
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	Rooted		46.7419	60.9337	1.30362
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Measured	0	973.698	1601.52	1.64478
	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	Rooted		33.5215	25.0836	1.33639
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Ranked		12460.6	15781	1.26647
85	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	Squared	1	67438.6	40697	1.65709
	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	Squared	0	181.122	444.663	2.45505
	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Rooted	1	46.7419	60.9337	1.30362
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Rooted	0	40.0375	29.9666	1.33607
	fos-related antigen 2. [swissprot;acc:p15408]	Measured	1	4941.95	7037.11	1.42395
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Ranked	1	88.2482	110.265	1.24949
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	Measured	0	679.449	1106.88	1.62908
	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	Ranked		9688.47	12104.2	1.24934
86	60s ribosomal protein l21. [swissprot;acc:p46778]	Squared		146.619	359.589	2.45254
	alpha crystallin a chain. [swissprot;acc:p02489]	Measured		55.3059	89.2447	1.61366
	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	Ranked		5677.96	4546.87	1.24876
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Rooted		9.13761	12.1722	1.3321
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Ranked	1	88.2482	110.265	1.24949
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Measured		4942.49	7037.32	1.42384
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	Rooted		63.6205	48.8838	1.30146
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Squared		105500	64146.3	1.64468
87	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	Rooted		42.2825	54.9687	1.30003
	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	Ranked	0	5677.89	4547.43	1.24859
	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Rooted	0	17.7787	23.6792	1.33189
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Measured	1	4944.3	7038.04	1.42347
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	Squared		105482	64136.9	1.64464
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Ranked		88.2482	110.265	1.24949
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Squared	0	0.668702	1.63441	2.44415
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Measured	0	304.664	483.809	1.58801
88	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Ranked	1	88.2482	110.265	1.24949
	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	Ranked	0	5677.86	4547.66	1.24852
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Rooted	0	3.4819	4.6274	1.32899
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Measured	1	2411.93	1695.45	1.42259

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/