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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Gene description Rank Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1077 to 1126 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

description	Rank	red	green	network_comparison	
gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	168	82.5916	98.0548	1.18722	
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	1337	215.162	210.412	1.02257	
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [source:swissprot;acc:p56470]	2158	206.401	207.796	1.00676	
galectin-9 (hom-hd-21) (ecalectin). [source:swissprot;acc:o00182]	2122	206.473	207.911	1.00696	
gamma adducin (adducin-like protein 70). [source:swissprot;acc:q9uey8]	1934	224.264	222.055	1.00995	
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [source:swissprot;acc:p09104]	2360	207.186	208.046	1.00415	
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	628	214.256	202.14	1.05994	
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	621	214.256	202.14	1.05994	
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	629	214.256	202.14	1.05994	
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	625	214.256	202.14	1.05994	
gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	622	214.256	202.14	1.05994	
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	626	214.256	202.14	1.05994	
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	620	214.256	202.14	1.05994	
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	623	214.256	202.14	1.05994	
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	618	214.256	202.139	1.05994	
gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [source:swissprot;acc:o75936]	1842	212.455	210.113	1.01115	
gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [source:swissprot;acc:p13284]	3101	0.00001	0.00001	1	
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q13326]	1181	218.186	212.672	1.02593	
gamma-snap-associated factor 1; rab11-interacting protein. [source:refseq;acc:nm_015470]	1817	220.462	217.926	1.01164	
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	166	209.299	249.187	1.19058	
ganglioside-induced differentiation-associated protein 1-like 1. [source:refseq;acc:nm_024034]	1139	218.484	212.675	1.02731	
ganglioside-induced differentiation-associated protein 1. [source:refseq;acc:nm_018972]	1141	218.484	212.675	1.02731	
gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [source:swissprot;acc:p20142]	2470	235.812	235.088	1.00308	
gbp protein isoform a. [source:refseq;acc:nm_017870]	47	325.586	256.492	1.26938	
gc-rich sequence dna-binding factor homolog. [source:swissprot;acc:q9y5b6]	2539	217.144	216.699	1.00205	
gcn5-like protein 1 (rt14 protein). [source:swissprot;acc:p78537]	979	202.027	195.386	1.03399	
gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [source:swissprot;acc:q9h488]	3125	0.00001	0.00001	1	
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [source:refseq;acc:nm_013335]	1894	222.842	225.17	1.01045	
gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [source:refseq;acc:nm_013334]	1893	222.842	225.17	1.01045	
general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [source:swissprot;acc:q92830]	2732	202.233	202.175	1.00029	
general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [source:swissprot;acc:o60763]	1923	220.659	218.452	1.0101	
geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [source:swissprot;acc:o95749]	2536	236.51	236.008	1.00213	
geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [source:swissprot;acc:p53609]	1438	225.039	229.573	1.02015	
geranylgeranyl transferase type ii beta subunit (ec 2.5.1.-) (rab geranylgeranyltransferase beta subunit) (rab geranyl- geranyltransferase beta subunit) (rab gg transferase beta) (rab ggtase beta). [source:swissprot;acc:p53611]	2963	0.00001	0.00001	1	
germ cell specific y-box binding protein; contrin. [source:refseq;acc:nm_015982]	2685	208.438	208.635	1.00095	
germ cell-less. [source:refseq;acc:nm_022471]	1780	206.335	203.877	1.01206	
gk001 protein. [source:refseq;acc:nm_020198]	2704	188.435	188.311	1.00066	
glia maturation factor gamma (gmf-gamma). [source:swissprot;acc:o60234]	1373	216.542	211.908	1.02187	
glioma pathogenesis-related protein (glipr) (rtvp-1 protein). [source:swissprot;acc:p48060]	2953	0.00001	0.00001	1	
glioma tumor suppressor candidate region gene 2 protein (p60). [source:swissprot;acc:q9nzm5]	3104	0.00001	0.00001	1	
glioma-amplified sequence-41; numa binding protein 1. [source:refseq;acc:nm_006530]	3007	0.00001	0.00001	1	
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [source:swissprot;acc:q06210]	2084	222.548	224.293	1.00784	
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [source:swissprot;acc:o94808]	2090	222.609	224.344	1.00779	
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [source:swissprot;acc:p46926]	3058	0.00001	0.00001	1	
glucosamine-6-phosphate isomerase. [source:refseq;acc:nm_138335]	2861	0.00001	0.00001	1	
glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [source:swissprot;acc:p11413]	1701	216.079	219.024	1.01363	
glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [source:swissprot;acc:p06744]	1491	217.704	221.839	1.01899	
glutamate carboxypeptidase-like protein 2 precursor. [source:swissprot;acc:q96kn2]	2365	208.958	209.82	1.00413	
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	165	209.299	249.187	1.19058	
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	167	209.299	249.187	1.19058	

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/