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 Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 2664 to 2713 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
2162	calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [source:swissprot;acc:q13557]	214.481	215.925	1.00673	
2163	mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [source:swissprot;acc:o95382]	214.481	215.925	1.00673	
2164	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	214.481	215.925	1.00673	
2165	ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [source:swissprot;acc:q15418]	214.481	215.925	1.00673	
2166	atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [source:swissprot;acc:p28288]	214.481	215.925	1.00673	
2167	glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [source:swissprot;acc:q92947]	214.481	215.925	1.00673	
2168	mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [source:swissprot;acc:p28482]	214.486	215.929	1.00673	
2169	histidine ammonia-lyase (ec 4.3.1.3) (histidase). [source:swissprot;acc:p42357]	214.481	215.925	1.00673	
2170	ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [source:swissprot;acc:q9uk32]	214.481	215.925	1.00673	
2171	ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [source:swissprot;acc:q15349]	214.481	215.925	1.00673	
2172	calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [source:swissprot;acc:q9uqm7]	214.481	215.925	1.00673	
2173	calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [source:swissprot;acc:q13554]	214.481	215.925	1.00673	
2174	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [source:swissprot;acc:q99683]	214.481	215.925	1.00673	
2175	26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [source:swissprot;acc:q13200]	208.808	210.209	1.00671	
2176	serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [source:swissprot;acc:p53350]	216.64	218.089	1.00669	
2177	peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [source:swissprot;acc:q9nr77]	209.563	210.961	1.00667	
2178	heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [source:swissprot;acc:p54652]	209.563	210.961	1.00667	
2179	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	209.563	210.961	1.00667	
2180	heat shock cognate 71 kda protein. [source:swissprot;acc:p11142]	209.563	210.961	1.00667	
2181	calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [source:swissprot;acc:p27797]	225.62	227.117	1.00664	
2182	twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [source:refseq;acc:nm_021830]	216.624	218.062	1.00664	
2183	rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [source:refseq;acc:nm_004703]	216.624	218.062	1.00664	
2184	suppressor of var1, 3-like 1. [source:refseq;acc:nm_003171]	210.318	211.713	1.00663	
2185	bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [source:swissprot;acc:q99933]	210.318	211.713	1.00663	
2186	glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [source:swissprot;acc:p49840]	210.318	211.713	1.00663	
2187	glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [source:swissprot;acc:p49841]	210.318	211.713	1.00663	
2188	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [source:swissprot;acc:p07237]	208.162	209.54	1.00662	
2189	3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	208.162	209.54	1.00662	
2190	zinc finger protein-like 1; zinc-finger protein in men1 region. [source:refseq;acc:nm_006782]	208.162	209.54	1.00662	
2191	hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [source:refseq;acc:nm_004507]	208.162	209.54	1.00662	
2192	hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [source:refseq;acc:nm_014282]	208.162	209.54	1.00662	
2193	prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [source:swissprot;acc:p13674]	208.162	209.54	1.00662	
2194	homeobox prospero-like protein prox1 (prox 1). [source:swissprot;acc:q92786]	208.162	209.54	1.00662	
2195	rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [source:refseq;acc:nm_002853]	208.162	209.54	1.00662	
2196	prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [source:swissprot;acc:o15460]	208.162	209.54	1.00662	
2197	ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [source:swissprot;acc:q9y2z9]	195.064	193.787	1.00659	
2198	kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [source:refseq;acc:nm_003679]	195.064	193.787	1.00659	
2199	squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [source:swissprot;acc:q14534]	195.064	193.787	1.00659	
2200	insulin gene enhancer protein isl-2 (islet-2). [source:swissprot;acc:q96a47]	195.466	196.748	1.00656	
2201	p47 protein isoform a. [source:refseq;acc:nm_016143]	212.254	213.642	1.00654	
2202	tumor susceptibility gene 101 protein. [source:swissprot;acc:q99816]	194.7	195.97	1.00652	
2203	symplekin. [source:swissprot;acc:q92797]	163.8	162.741	1.00651	
2204	ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [source:swissprot;acc:q9y230]	220.8	219.377	1.00649	
2205	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [source:swissprot;acc:p35268]	200.413	199.129	1.00645	
2206	transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [source:swissprot;acc:p55072]	214.19	215.571	1.00645	
2207	sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [source:refseq;acc:nm_003864]	200.413	199.129	1.00645	
2208	clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [source:swissprot;acc:p20172]	200.413	199.129	1.00645	
2209	atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [source:refseq;acc:nm_033450]	200.413	199.129	1.00645	
2210	lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [source:swissprot;acc:o00754]	200.413	199.129	1.00645	
2211	rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	200.413	199.129	1.00645	

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/