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

Results: HTML CSV LaTeX

Showing element 580 to 629 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	Hugo	description	Network Comparison Type	Value Type	red	green	network_comparison
73	MAGED2	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Divided	Squared	219048	129762	1.68808
	NEUROD1	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Divided	Rooted	27.9136	37.2872	1.33581
	PPP1CC	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	Subtracted	Measured	22268.8	18560.4	3708.4
	PPP1R8	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]	Subtracted	Squared	148058	99628.4	48429.6
	PPP2R2B	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]	Divided	Measured	4556.83	2945.38	1.54711
74	no value	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Subtracted	Measured	20446.1	24136.4	3690.3
	ARAF	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Subtracted	Squared	117858	70570.1	47287.9
	JPH2	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Divided	Ranked	288	362	1.25694
	NEUROD4	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Divided	Rooted	27.9136	37.2872	1.33581
	PBK	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]	Subtracted	Rooted	27.7254	44.0299	16.3045
	PPP2R1A	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]	Subtracted	Ranked	189.07	242.453	53.383
	PPP2R2C	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]	Divided	Measured	4556.99	2945.8	1.54694
	TRO	trophinin. [swissprot;acc:q12816]	Divided	Squared	219048	129762	1.68808
75	CACNG8	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Subtracted	Ranked	254.693	202.668	52.025
	CHD5	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Divided	Rooted	27.9136	37.2872	1.33581
	HOXB4	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Subtracted	Measured	20446.1	24136.4	3690.3
	KHDRBS3	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Subtracted	Rooted	27.7254	44.0299	16.3045
	MYO5B	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Divided	Squared	110342	184298	1.67024
	NDUFS4	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]	Divided	Measured	1920.75	2907.43	1.5137
	RAF1	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Subtracted	Squared	117850	70566.8	47283.2
	SMPD2	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]	Divided	Ranked	288	362	1.25694
76	CACNG3	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Subtracted	Ranked	254.693	202.668	52.025
	CCNG1	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Subtracted	Squared	117718	70505.8	47212.2
	CDK2AP1	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]	Divided	Rooted	27.9136	37.2872	1.33581
	HOXC5	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Subtracted	Measured	20446.1	24136.4	3690.3
	KHDRBS1	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Subtracted	Rooted	27.7254	44.0299	16.3045
	MYO5C	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Divided	Squared	110342	184298	1.67024
	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	3058.57	1.50373
	TMEM33	db83 protein. [swissprot;acc:p57088]		Ranked	288	362	1.25694
77	no value	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	Measured	20446.1	24136.4	3690.3
	no value	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Divided	Squared	110342	184298	1.67024
	CACNG2	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Divided	Ranked	254.692	202.668	1.2567
	CACNG2		Subtracted	Ranked	254.692	202.668	52.024
	KHDRBS2	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Subtracted	Rooted	27.7254	44.0299	16.3045
	PPP2R1A	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]	Divided	Measured	4612.39	3093.6	1.49095
	PPP2R5E	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]	Subtracted	Squared	117718	70505.9	47212.1
	UNC84A	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Divided	Rooted	39.9725	52.9973	1.32584
78	no value	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	Rooted	177.987	194.29	16.303
	ARAF	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Divided	Squared	117858	70570.1	1.67008
	ATF3	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Divided	Measured	4800.81	7132.71	1.48573
	CACNG4	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Subtracted	Ranked	254.691	202.668	52.023
	CACNG8	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Divided	Ranked	254.693	202.668	1.2567
	CCNG2	cyclin g2. [swissprot;acc:q16589]	Subtracted	Squared	117718	70505.9	47212.1
	HOXD4	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Subtracted	Measured	20446.1	24136.4	3690.3
	PPP2R2D	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Divided	Rooted	63.7477	48.1589	1.3237
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	48.1588	1.3237
	CACNG3	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]		Ranked	254.693	202.668	1.2567
	CACNG5	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Subtracted	Ranked	254.614	202.646	51.968
	HOXB5	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]		Measured	20446.1	24136.4	3690.3
	NEURL	neuralized-like. [refseq;acc:nm_004210]		Rooted	27.9107	44.1656	16.2549

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/