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 563 to 612 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
71	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Rooted	Subtracted	63.8686	47.2654	16.6032	
71	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04898]	Ranked	Divided	267.144	336.073	1.25802	
71	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Ranked	Subtracted	265.686	319.651	53.965	
71	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Squared	Divided	219048	129762	1.68808	
71	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). [source:swissprot;acc:q00007]	Measured	Divided	4556.78	2945.26	1.54716	
71	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). [source:swissprot;acc:q15172]	Measured	Subtracted	17738.5	13995.7	3742.8	
72	44050 protein. [source:refseq;acc:nm_178832]	Squared	Subtracted	148058	99628.4	48429.6	
72	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	Measured	Subtracted	17710.9	13977.7	3733.2	
72	deltex 2. [source:refseq;acc:nm_020892]	Rooted	Subtracted	27.634	43.9629	16.3289	
72	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [source:swissprot;acc:p08754]	Ranked	Divided	267.144	336.073	1.25802	
72	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Squared	Divided	219048	129762	1.68808	
72	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Rooted	Divided	27.9136	37.2872	1.33581	
72	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Ranked	Subtracted	265.639	319.546	53.907	
72	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Measured	Divided	4556.79	2945.28	1.54715	
73	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Rooted	Subtracted	27.7078	44.017	16.3092	
73	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Ranked	Divided	288	362	1.25694	
73	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm_173193]	Ranked	Subtracted	265.632	319.531	53.899	
73	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	Squared	Divided	219048	129762	1.68808	
73	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Rooted	Divided	27.9136	37.2872	1.33581	
73	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)]. [source:swissprot;acc:q12972]	Squared	Subtracted	148058	99628.4	48429.6	
73	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). [source:swissprot;acc:q00005]	Measured	Divided	4556.83	2945.38	1.54711	
73	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [source:swissprot;acc:p36873]	Measured	Subtracted	22268.8	18560.4	3708.4	
74	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Squared	Subtracted	117858	70570.1	47287.9	
74	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Measured	Subtracted	20446.1	24136.4	3690.3	
74	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Ranked	Divided	288	362	1.25694	
74	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Rooted	Divided	27.9136	37.2872	1.33581	
74	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). [source:swissprot;acc:q9y2t4]	Measured	Divided	4556.99	2945.8	1.54694	
74	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). [source:swissprot;acc:p30153]	Ranked	Subtracted	189.07	242.453	53.383	
74	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	Rooted	Subtracted	27.7254	44.0299	16.3045	
74	trophinin. [source:swissprot;acc:q12816]	Squared	Divided	219048	129762	1.68808	
75	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Rooted	Divided	27.9136	37.2872	1.33581	
75	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Measured	Subtracted	20446.1	24136.4	3690.3	
75	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Rooted	Subtracted	27.7254	44.0299	16.3045	
75	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	Squared	Divided	110342	184298	1.67024	
75	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). [source:swissprot;acc:o43181]	Measured	Divided	1920.75	2907.43	1.5137	
75	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Squared	Subtracted	117850	70566.8	47283.2	
75	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Ranked	Divided	288	362	1.25694	
75	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [source:swissprot;acc:q8wxs5]	Ranked	Subtracted	254.693	202.668	52.025	
76	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	Squared	Subtracted	117718	70505.8	47212.2	
76	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	Rooted	Divided	27.9136	37.2872	1.33581	
76	db83 protein. [source:swissprot;acc:p57088]	Ranked	Divided	288	362	1.25694	
76	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Measured	Subtracted	20446.1	24136.4	3690.3	
76	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Rooted	Subtracted	27.7254	44.0299	16.3045	
76	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	Squared	Divided	110342	184298	1.67024	
76	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [source:swissprot;acc:p30154]	Measured	Divided	4599.26	3058.57	1.50373	
76	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [source:swissprot;acc:o60359]	Ranked	Subtracted	254.693	202.668	52.025	
77	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Measured	Subtracted	20446.1	24136.4	3690.3	
77	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Rooted	Subtracted	27.7254	44.0299	16.3045	
77	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Squared	Divided	110342	184298	1.67024	
77	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	Rooted	Divided	39.9725	52.9973	1.32584	

Legend:
- Rank is the rank after comparing the two networks
- 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/