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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Value Type Interaction Map description Rank Network Comparison Type Gene red green Filtered network_comparison
Results: HTML CSV LaTeX Showing element 1062 to 1111 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	621	4115.39	4633.96	1.12601	
fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [source:swissprot;acc:p07954]	2726	5332.98	5351.72	1.00351	
fuse binding protein 3 (fragment). [source:sptrembl;acc:q92946]	2093	5817.56	6138.9	1.05524	
fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [source:refseq;acc:nm_014281]	1590	6364.01	6819.38	1.07155	
fused toes homolog; likely ortholog of mouse fused toes. [source:refseq;acc:nm_022476]	1820	5633.44	5997	1.06454	
fyve-finger-containing rab5 effector protein rabenosyn-5. [source:refseq;acc:nm_022340]	2998	0.00001	0.00001	1	
fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	733	13241.4	11864	1.1161	
g protein-coupled receptor 66. [source:refseq;acc:nm_006056]	2815	0.00001	0.00001	1	
g-rich sequence factor-1 (grsf-1). [source:swissprot;acc:q12849]	1396	5803.54	6256.54	1.07806	
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [source:swissprot;acc:p15170]	1336	6140.18	6632.24	1.08014	
g2/mitotic-specific cyclin b1. [source:swissprot;acc:p14635]	362	12786.6	10879.9	1.17525	
g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	360	12796.8	10886	1.17553	
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [source:swissprot;acc:q06546]	455	4890.51	5610.95	1.14731	
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [source:swissprot;acc:q06545]	456	4890.51	5610.95	1.14731	
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	133	23421.5	17580.4	1.33225	
gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	134	21785.2	16426.1	1.32626	
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	517	4910.6	5600.61	1.14051	
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [source:swissprot;acc:p56470]	966	7817.9	8575.12	1.09686	
galectin-9 (hom-hd-21) (ecalectin). [source:swissprot;acc:o00182]	973	7810.11	8566.29	1.09682	
gamma adducin (adducin-like protein 70). [source:swissprot;acc:q9uey8]	1365	5799.14	6255.04	1.07862	
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [source:swissprot;acc:p09104]	943	6597.98	7241	1.09746	
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	587	6739.83	7644.63	1.13425	
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	580	6739.83	7644.63	1.13425	
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	588	6739.83	7644.63	1.13425	
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	584	6739.82	7644.63	1.13425	
gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	581	6739.82	7644.63	1.13425	
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	585	6739.82	7644.63	1.13425	
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	579	6739.82	7644.62	1.13425	
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	582	6739.82	7644.62	1.13425	
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	577	6739.81	7644.62	1.13425	
gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [source:swissprot;acc:o75936]	1348	6153.36	6640.77	1.07921	
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]	741	5768.32	6434.78	1.11554	
gamma-snap-associated factor 1; rab11-interacting protein. [source:refseq;acc:nm_015470]	1450	5602.01	6031.05	1.07659	
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	500	4682.87	4093.05	1.1441	
ganglioside-induced differentiation-associated protein 1-like 1. [source:refseq;acc:nm_024034]	776	5874.76	6533.36	1.11211	
ganglioside-induced differentiation-associated protein 1. [source:refseq;acc:nm_018972]	779	5874.76	6533.36	1.11211	
gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [source:swissprot;acc:p20142]	1188	4392.63	4776.19	1.08732	
gbp protein isoform a. [source:refseq;acc:nm_017870]	23	699.76	1894.39	2.7072	
gc-rich sequence dna-binding factor homolog. [source:swissprot;acc:q9y5b6]	1685	6088.07	6508.45	1.06905	
gcn5-like protein 1 (rt14 protein). [source:swissprot;acc:p78537]	2432	8154.48	8453.84	1.03671	
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]	1520	5283.8	5673.81	1.07381	
gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [source:refseq;acc:nm_013334]	1519	5283.8	5673.81	1.07381	
general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [source:swissprot;acc:q92830]	1944	7210.64	7648.94	1.06079	
general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [source:swissprot;acc:o60763]	2156	5701.81	6000.03	1.0523	
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]	1203	4322.65	4696.04	1.08638	
geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [source:swissprot;acc:p53609]	2366	5265.95	5492.28	1.04298	
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]	2096	6682.05	7051.02	1.05522	

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/