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

Results: HTML CSV LaTeX

Showing element 582 to 631 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	Hugo	Network Comparison Type	description	Value Type	red	network_comparison	green
73	PPP1CC	Subtracted	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	Measured	22268.8	3708.4	18560.4
	PPP1R8	Subtracted	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	Squared	148058	48429.6	99628.4
	PPP2R2B	Divided	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	Measured	4556.83	1.54711	2945.38
74	no value	Subtracted	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	20446.1	3690.3	24136.4
	ARAF	Subtracted	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Squared	117858	47287.9	70570.1
	JPH2	Divided	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Ranked	288	1.25694	362
	NEUROD4	Divided	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Rooted	27.9136	1.33581	37.2872
	PBK	Subtracted	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Rooted	27.7254	16.3045	44.0299
	PPP2R1A	Subtracted	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]	Ranked	189.07	53.383	242.453
	PPP2R2C	Divided	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	Measured	4556.99	1.54694	2945.8
	TRO	Divided	trophinin. [swissprot;acc:q12816]	Squared	219048	1.68808	129762
75	CACNG8	Subtracted	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Ranked	254.693	52.025	202.668
	CHD5	Divided	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Rooted	27.9136	1.33581	37.2872
	HOXB4	Subtracted	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Measured	20446.1	3690.3	24136.4
	KHDRBS3	Subtracted	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Rooted	27.7254	16.3045	44.0299
	MYO5B	Divided	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Squared	110342	1.67024	184298
	NDUFS4	Divided	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	Measured	1920.75	1.5137	2907.43
	RAF1	Subtracted	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Squared	117850	47283.2	70566.8
	SMPD2	Divided	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Ranked	288	1.25694	362
76	CACNG3	Subtracted	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Ranked	254.693	52.025	202.668
	CCNG1	Subtracted	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Squared	117718	47212.2	70505.8
	CDK2AP1	Divided	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	Rooted	27.9136	1.33581	37.2872
	HOXC5	Subtracted	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Measured	20446.1	3690.3	24136.4
	KHDRBS1	Subtracted	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Rooted	27.7254	16.3045	44.0299
	MYO5C	Divided	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Squared	110342	1.67024	184298
	PPP2R1B		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]	Measured	4599.26	1.50373	3058.57
	TMEM33		db83 protein. [swissprot;acc:p57088]	Ranked	288	1.25694	362
77	no value		myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Squared	110342	1.67024	184298
	no value	Subtracted	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured	20446.1	3690.3	24136.4
	CACNG2	Divided	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Ranked	254.692	1.2567	202.668
	CACNG2	Subtracted		Ranked	254.692	52.024	202.668
	KHDRBS2	Subtracted	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Rooted	27.7254	16.3045	44.0299
	PPP2R1A	Divided	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]	Measured	4612.39	1.49095	3093.6
	PPP2R5E	Subtracted	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	Squared	117718	47212.1	70505.9
	UNC84A	Divided	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Rooted	39.9725	1.32584	52.9973
78	no value	Subtracted	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Rooted	177.987	16.303	194.29
	ARAF	Divided	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Squared	117858	1.67008	70570.1
	ATF3	Divided	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Measured	4800.81	1.48573	7132.71
	CACNG4	Subtracted	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Ranked	254.691	52.023	202.668
	CACNG8	Divided	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Ranked	254.693	1.2567	202.668
	CCNG2	Subtracted	cyclin g2. [swissprot;acc:q16589]	Squared	117718	47212.1	70505.9
	HOXD4	Subtracted	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Measured	20446.1	3690.3	24136.4
	PPP2R2D	Divided	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Rooted	63.7477	1.3237	48.1589
79	no value		serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	Rooted	63.7477	1.3237	48.1588
	CACNG3		voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Ranked	254.693	1.2567	202.668
	CACNG5	Subtracted	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Ranked	254.614	51.968	202.646
	HOXB5		homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Measured	20446.1	3690.3	24136.4
	NEURL		neuralized-like. [refseq;acc:nm_004210]	Rooted	27.9107	16.2549	44.1656
	PPP2R5A		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	47212.1	70505.9
	RAF1	Divided	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Squared	117850	1.67005	70566.8

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
- Hugo is the HGNC identifier if it exists
- 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/