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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 110 to 159 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
55	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Subtracted	23303.1	19279.5	4023.6	
56	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Subtracted	20911	24908.5	3997.5	
56	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]	Divided	1631.67	2664.55	1.63302	
57	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Divided	1631.67	2664.55	1.63302	
57	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Subtracted	20911	24908.5	3997.5	
58	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Divided	1631.67	2664.55	1.63302	
58	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Subtracted	20911	24908.5	3997.5	
59	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Subtracted	20911	24908.5	3997.5	
59	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Divided	1631.67	2664.55	1.63302	
60	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Divided	4489.19	2765.82	1.6231	
60	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Subtracted	16771.5	12889.1	3882.4	
61	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Subtracted	6475.5	10307.5	3832	
61	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Divided	4489.19	2765.82	1.6231	
62	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Subtracted	6475.5	10307.5	3832	
62	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Divided	4489.19	2765.82	1.6231	
63	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Divided	4489.19	2765.82	1.6231	
63	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Subtracted	6475.5	10307.5	3832	
64	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Subtracted	6475.5	10307.5	3832	
64	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Divided	4489.19	2765.82	1.6231	
65	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Subtracted	22515.5	18702.6	3812.9	
65	neuralized-like. [source:refseq;acc:nm_004210]	Divided	1657.68	2690.25	1.6229	
66	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Subtracted	17757.5	14008	3749.5	
66	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Divided	1991.03	3221.38	1.61795	
67	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Divided	6475.5	10307.5	1.59177	
67	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Subtracted	17756.5	14007.3	3749.2	
68	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Divided	6475.5	10307.5	1.59177	
68	cyclin g2. [source:swissprot;acc:q16589]	Subtracted	17738.6	13995.7	3742.9	
69	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	Subtracted	17738.5	13995.6	3742.9	
69	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Divided	6475.5	10307.5	1.59177	
70	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Divided	6475.5	10307.5	1.59177	
70	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). [source:swissprot;acc:q16537]	Subtracted	17738.5	13995.7	3742.8	
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]	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]	Subtracted	17738.5	13995.7	3742.8	
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]	Subtracted	17710.9	13977.7	3733.2	
72	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Divided	4556.79	2945.28	1.54715	
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]	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]	Subtracted	22268.8	18560.4	3708.4	
74	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Subtracted	20446.1	24136.4	3690.3	
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]	Divided	4556.99	2945.8	1.54694	
75	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Subtracted	20446.1	24136.4	3690.3	
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]	Divided	1920.75	2907.43	1.5137	
76	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Subtracted	20446.1	24136.4	3690.3	
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]	Divided	4599.26	3058.57	1.50373	
77	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Subtracted	20446.1	24136.4	3690.3	
77	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]	Divided	4612.39	3093.6	1.49095	
78	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Divided	4800.81	7132.71	1.48573	
78	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Subtracted	20446.1	24136.4	3690.3	
79	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Subtracted	20446.1	24136.4	3690.3	
79	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Divided	3074.57	4567.51	1.48558	
80	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Subtracted	20446.1	24136.4	3690.3	

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/