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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 1077 to 1126 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	red	green	network_comparison	
1077	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [source:swissprot;acc:p48444]	174.387	179.697	1.03045	
1078	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [source:swissprot;acc:q9unp9]	174.387	179.697	1.03045	
1079	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	174.387	179.697	1.03045	
1080	zinc finger protein 444; endothelial zinc finger protein 2. [source:refseq;acc:nm_018337]	269.896	278.093	1.03037	
1081	40s ribosomal protein s30. [source:swissprot;acc:q05472]	223.44	216.875	1.03027	
1082	phafin 2; ph and fyve domain-containing protein 2. [source:refseq;acc:nm_024613]	220.118	213.685	1.03011	
1083	3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [source:swissprot;acc:p18405]	220.118	213.685	1.03011	
1084	3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [source:swissprot;acc:p31213]	220.118	213.685	1.03011	
1085	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	231.007	237.864	1.02968	
1086	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	236.679	243.679	1.02958	
1087	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	236.679	243.679	1.02958	
1088	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [source:swissprot;acc:p50995]	219.673	213.378	1.0295	
1089	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	121.428	125.004	1.02945	
1090	similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	226.218	232.88	1.02945	
1091	block 23. [source:sptrembl;acc:q8nhw5]	226.205	232.858	1.02941	
1092	60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	226.203	232.855	1.02941	
1093	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	177.432	182.647	1.02939	
1094	annexin a7 (annexin vii) (synexin). [source:swissprot;acc:p20073]	219.655	213.385	1.02938	
1095	mitochondrial gtp binding protein isoform v. [source:refseq;acc:nm_032620]	213.552	207.463	1.02935	
1096	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [source:swissprot;acc:q9y6m9]	212.345	206.339	1.02911	
1097	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	209.123	203.208	1.02911	
1098	adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [source:swissprot;acc:q9y2t2]	217.323	211.185	1.02906	
1099	adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [source:swissprot;acc:p53677]	217.315	211.183	1.02904	
1100	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [source:swissprot;acc:p98194]	209.052	203.183	1.02889	
1101	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [source:swissprot;acc:q15046]	220.291	226.584	1.02857	
1102	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	229.442	235.974	1.02847	
1103	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [source:refseq;acc:nm_015920]	229.441	235.972	1.02846	
1104	hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [source:swissprot;acc:q9ujm8]	231.922	238.486	1.0283	
1105	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	191.139	185.882	1.02828	
1106	pxr2b protein. [source:refseq;acc:nm_016559]	212.945	207.109	1.02818	
1107	serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [source:swissprot;acc:o15270]	204.603	210.324	1.02796	
1108	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	218.006	212.119	1.02775	
1109	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	218.098	212.209	1.02775	
1110	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [source:swissprot;acc:q14161]	216.78	222.782	1.02769	
1111	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	217.99	212.123	1.02766	
1112	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [source:swissprot;acc:q14541]	251.863	258.829	1.02766	
1113	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [source:swissprot;acc:o95257]	251.863	258.829	1.02766	
1114	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [source:swissprot;acc:p24522]	251.863	258.829	1.02766	
1115	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [source:swissprot;acc:p41235]	251.863	258.829	1.02766	
1116	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [source:swissprot;acc:o75293]	251.863	258.829	1.02766	
1117	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	168.989	164.46	1.02754	
1118	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5]	168.995	164.467	1.02753	
1119	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [source:swissprot;acc:q9y487]	218.528	212.676	1.02752	
1120	atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [source:refseq;acc:nm_020632]	218.528	212.676	1.02752	
1121	vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [source:swissprot;acc:q93050]	218.529	212.676	1.02752	
1122	vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [source:swissprot;acc:q13488]	218.527	212.676	1.02751	
1123	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [source:swissprot;acc:q9ubu9]	169.031	164.507	1.0275	
1124	peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [source:swissprot;acc:p30044]	207.553	213.256	1.02748	
1125	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [source:sptrembl;acc:q9ugb5]	204.404	210.022	1.02748	
1126	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	218.487	212.656	1.02742	

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/