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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2551 to 2600 of 29840 in total 
Interaction Map	High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison	
160	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [source:swissprot;acc:p14061]	Squared	Subtracted	0	14907.5	15522.7	615.2	
160	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [source:swissprot;acc:q07075]	Squared	Divided	0	6123.28	3763.18	1.62716	
160	guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471]	Ranked	Divided	1	249.663	298.263	1.19466	
160	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Squared	Divided	1	173408	242989	1.40126	
160	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Measured	Divided	0	1653.74	1296.38	1.27566	
160	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Rooted	Subtracted	1	43.4291	31.7159	11.7132	
160	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Measured	Divided	1	23693.7	18263	1.29736	
160	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Ranked	Subtracted	1	312	284	28	
160	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Ranked	Subtracted	0	10060.2	11616.4	1556.2	
160	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	Squared	Subtracted	1	42788.3	60162.6	17374.3	
161	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [source:swissprot;acc:p35268]	Rooted	Subtracted	0	19.3128	16.0484	3.2644	
161	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	Squared	Subtracted	0	50.7031	647.816	597.113	
161	adp-ribosylation factor 3. [source:swissprot;acc:p16587]	Rooted	Divided	0	14.8377	17.2252	1.16091	
161	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Ranked	Divided	0	5781.93	6660.63	1.15197	
161	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [source:swissprot;acc:p15104]	Measured	Subtracted	0	1230.54	1026.18	204.36	
161	glycine cleavage system h protein, mitochondrial precursor. [source:swissprot;acc:p23434]	Measured	Divided	0	903.767	1152.06	1.27473	
161	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Squared	Divided	1	173408	242989	1.40126	
161	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Measured	Divided	1	23693.7	18263	1.29736	
161	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Measured	Subtracted	1	9035	7279.6	1755.4	
161	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Ranked	Subtracted	1	312	284	28	
161	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Rooted	Divided	1	52.7642	61.9019	1.17318	
161	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Rooted	Subtracted	1	43.4519	31.7522	11.6997	
161	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Ranked	Subtracted	0	15245.4	16788.5	1543.1	
161	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	Ranked	Divided	1	249.663	298.263	1.19466	
161	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	Squared	Subtracted	1	52591.3	69845.1	17253.8	
161	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [source:swissprot;acc:p36537]	Squared	Divided	0	6123.28	3763.18	1.62716	
162	60s ribosomal protein l23 (l17). [source:swissprot;acc:p23131]	Measured	Subtracted	0	1753.85	1956.36	202.51	
162	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	Rooted	Subtracted	0	21.0926	17.849	3.2436	
162	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [source:swissprot;acc:o43681]	Squared	Subtracted	0	1662.68	2253.78	591.1	
162	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Ranked	Subtracted	1	142	170	28	
162	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Measured	Divided	0	5734.28	7252.02	1.26468	
162	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Ranked	Subtracted	0	13068	11528	1540	
162	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Rooted	Divided	1	52.7642	61.9019	1.17318	
162	high-mobility group 20a. [source:refseq;acc:nm_018200]	Measured	Subtracted	1	5140.14	6893.53	1753.39	
162	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Squared	Divided	1	173408	242989	1.40126	
162	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]	Rooted	Subtracted	1	43.4554	31.7576	11.6978	
162	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Rooted	Divided	0	9.27362	8	1.1592	
162	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Measured	Divided	1	23693.7	18263	1.29736	
162	nostrin. [source:refseq;acc:nm_052946]	Ranked	Divided	1	209.299	249.187	1.19058	
162	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Ranked	Divided	0	12301.4	10680.5	1.15176	
162	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	Squared	Subtracted	1	59704	76460.4	16756.4	
162	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [source:swissprot;acc:p54855]	Squared	Divided	0	6123.28	3763.18	1.62716	
163	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Rooted	Subtracted	1	54.935	66.6101	11.6751	
163	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Ranked	Subtracted	1	133	105	28	
163	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	Squared	Subtracted	1	59464	76120.8	16656.8	
163	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Rooted	Subtracted	0	57.5016	60.7262	3.2246	
163	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Ranked	Divided	1	209.299	249.187	1.19058	
163	elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [source:swissprot;acc:p43897]	Squared	Subtracted	0	328.83	917.917	589.087	
163	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Rooted	Divided	1	52.7702	61.8915	1.17285	
163	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Squared	Divided	1	173408	242989	1.40126	

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/