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 1813 to 1862 of 6456 in total 
    Value Type	Ranked
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	Network Comparison Type	red	green	network_comparison	
907	junction plakoglobin (desmoplakin iii). [source:swissprot;acc:p14923]	Divided	223.906	215.653	1.03827	
907	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	Subtracted	225.976	218.017	7.959	
908	sedlin. [source:swissprot;acc:o14582]	Subtracted	129.219	121.261	7.958	
908	tax interaction protein 1. [source:refseq;acc:nm_014604]	Divided	223.906	215.653	1.03827	
909	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	Divided	142.077	136.846	1.03823	
909	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Subtracted	129.219	121.261	7.958	
910	bet3 homolog. [source:swissprot;acc:o43617]	Subtracted	129.219	121.261	7.958	
910	uba/ubx 33.3 kda protein. [source:swissprot;acc:q04323]	Divided	217.168	209.207	1.03805	
911	ero1-like. [source:refseq;acc:nm_014584]	Divided	217.168	209.207	1.03805	
911	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [source:swissprot;acc:o75352]	Subtracted	225.955	218.015	7.94	
912	mitochondrial translational release factor 1-like. [source:refseq;acc:nm_019041]	Subtracted	225.939	218.013	7.926	
912	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	Divided	243.896	234.96	1.03803	
913	atp-dependent rna helicase rok1; atp-dependent rna helicase. [source:refseq;acc:nm_007010]	Subtracted	243.297	235.373	7.924	
913	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [source:refseq;acc:nm_024831]	Divided	210.863	218.878	1.03801	
914	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [source:swissprot;acc:p25388]	Subtracted	237.558	229.677	7.881	
914	pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [source:refseq;acc:nm_020399]	Divided	210.863	218.878	1.03801	
915	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	Divided	146.036	140.692	1.03798	
915	zuotin related factor-1 (m-phase phosphoprotein 11). [source:swissprot;acc:q99543]	Subtracted	237.558	229.677	7.881	
916	histone h4. [source:swissprot;acc:p02304]	Subtracted	227.765	219.902	7.863	
916	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [source:swissprot;acc:q9nyq3]	Divided	232.512	241.288	1.03774	
917	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	Subtracted	86.7483	78.8995	7.8488	
917	parafibromin. [source:refseq;acc:nm_024529]	Divided	239.704	230.991	1.03772	
918	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	Subtracted	217.942	210.139	7.803	
918	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	Divided	212.952	205.292	1.03731	
919	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	Subtracted	217.942	210.139	7.803	
919	midasin (midas-containing protein). [source:swissprot;acc:q9nu22]	Divided	237.218	228.698	1.03725	
920	breast cancer type 1 susceptibility protein. [source:swissprot;acc:p38398]	Subtracted	216.501	224.27	7.769	
920	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [source:swissprot;acc:o75398]	Divided	236.741	245.547	1.0372	
921	rio kinase 1 isoform 1; ad034 protein. [source:refseq;acc:nm_031480]	Divided	236.741	245.547	1.0372	
921	wd-repeat protein bing4. [source:swissprot;acc:o15213]	Subtracted	243.227	235.475	7.752	
922	map/microtubule affinity-regulating kinase 1. [source:refseq;acc:nm_018650]	Divided	236.741	245.547	1.0372	
922	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	Subtracted	215.665	207.942	7.723	
923	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	Subtracted	193.114	185.412	7.702	
923	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [source:refseq;acc:nm_004954]	Divided	236.741	245.547	1.0372	
924	meiotic recombination protein spo11. [source:swissprot;acc:q9y5k1]	Divided	236.741	245.547	1.0372	
924	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	Subtracted	238.725	231.059	7.666	
925	pef protein with a long n-terminal hydrophobic domain (peflin). [source:refseq;acc:nm_012392]	Divided	215.665	207.942	1.03714	
925	protein bap28. [source:swissprot;acc:q9h583]	Subtracted	244.312	236.647	7.665	
926	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	Divided	217.942	210.139	1.03713	
926	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	Subtracted	212.952	205.292	7.66	
927	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	Divided	217.942	210.139	1.03713	
927	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	Subtracted	220.246	212.618	7.628	
928	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	Divided	225.976	218.017	1.03651	
928	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	Subtracted	220.246	212.618	7.628	
929	apoptosis antagonizing transcription factor. [source:refseq;acc:nm_012138]	Subtracted	243.045	235.422	7.623	
929	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [source:swissprot;acc:o75352]	Divided	225.955	218.015	1.03642	
930	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [source:swissprot;acc:o14737]	Subtracted	233.402	225.782	7.62	
930	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [source:swissprot;acc:p14618]	Divided	231.357	239.778	1.0364	
931	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	Divided	159.13	164.917	1.03637	
931	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [source:swissprot;acc:q99471]	Subtracted	228.953	221.421	7.532	

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/