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 2150 to 2199 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1075	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [source:swissprot;acc:q9y678]	Divided	174.387	179.697	1.03045	
1076	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [source:swissprot;acc:q9y3c3]	Divided	174.387	179.697	1.03045	
1076	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Subtracted	209.123	203.208	5.915	
1077	coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [source:swissprot;acc:p48444]	Divided	174.387	179.697	1.03045	
1077	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	Subtracted	218.098	212.209	5.889	
1078	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	Subtracted	218.006	212.119	5.887	
1078	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [source:swissprot;acc:q9unp9]	Divided	174.387	179.697	1.03045	
1079	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	Divided	174.387	179.697	1.03045	
1079	homeobox protein six1 (sine oculis homeobox homolog 1). [source:swissprot;acc:q15475]	Subtracted	221.286	215.399	5.887	
1080	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [source:swissprot;acc:q9uq80]	Subtracted	221.285	215.4	5.885	
1080	zinc finger protein 444; endothelial zinc finger protein 2. [source:refseq;acc:nm_018337]	Divided	269.896	278.093	1.03037	
1081	40s ribosomal protein s30. [source:swissprot;acc:q05472]	Divided	223.44	216.875	1.03027	
1081	homeobox protein six2 (sine oculis homeobox homolog 2). [source:swissprot;acc:q9npc8]	Subtracted	221.285	215.401	5.884	
1082	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]	Subtracted	209.052	203.183	5.869	
1082	phafin 2; ph and fyve domain-containing protein 2. [source:refseq;acc:nm_024613]	Divided	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]	Divided	220.118	213.685	1.03011	
1083	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	Subtracted	217.99	212.123	5.867	
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]	Divided	220.118	213.685	1.03011	
1084	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]	Subtracted	218.529	212.676	5.853	
1085	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	Divided	231.007	237.864	1.02968	
1085	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [source:swissprot;acc:q9y487]	Subtracted	218.528	212.676	5.852	
1086	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]	Subtracted	218.528	212.676	5.852	
1086	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	Divided	236.679	243.679	1.02958	
1087	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]	Subtracted	218.527	212.676	5.851	
1087	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	Divided	236.679	243.679	1.02958	
1088	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [source:swissprot;acc:p50995]	Divided	219.673	213.378	1.0295	
1088	pxr2b protein. [source:refseq;acc:nm_016559]	Subtracted	212.945	207.109	5.836	
1089	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	Subtracted	218.487	212.656	5.831	
1089	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Divided	121.428	125.004	1.02945	
1090	neurocalcin delta. [source:swissprot;acc:p29554]	Subtracted	225.104	230.931	5.827	
1090	similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	Divided	226.218	232.88	1.02945	
1091	block 23. [source:sptrembl;acc:q8nhw5]	Divided	226.205	232.858	1.02941	
1091	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [source:swissprot;acc:p32076]	Subtracted	225.103	230.928	5.825	
1092	60s acidic ribosomal protein p0 (l10e). [source:swissprot;acc:p05388]	Divided	226.203	232.855	1.02941	
1092	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [source:swissprot;acc:p37235]	Subtracted	225.094	230.913	5.819	
1093	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	Divided	177.432	182.647	1.02939	
1093	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	Subtracted	218.484	212.675	5.809	
1094	annexin a7 (annexin vii) (synexin). [source:swissprot;acc:p20073]	Divided	219.655	213.385	1.02938	
1094	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [source:refseq;acc:nm_006595]	Subtracted	218.484	212.675	5.809	
1095	mitochondrial gtp binding protein isoform v. [source:refseq;acc:nm_032620]	Divided	213.552	207.463	1.02935	
1095	sec13-related protein. [source:swissprot;acc:p55735]	Subtracted	218.484	212.675	5.809	
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]	Divided	212.345	206.339	1.02911	
1096	vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [source:swissprot;acc:q96lb4]	Subtracted	218.484	212.675	5.809	
1097	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Divided	209.123	203.208	1.02911	
1097	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [source:swissprot;acc:p21281]	Subtracted	218.484	212.675	5.809	
1098	adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [source:swissprot;acc:q9y2t2]	Divided	217.323	211.185	1.02906	
1098	yeast sec31p homolog. [source:refseq;acc:nm_014933]	Subtracted	218.484	212.675	5.809	
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]	Divided	217.315	211.183	1.02904	
1099	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [source:swissprot;acc:o75348]	Subtracted	218.484	212.675	5.809	
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]	Divided	209.052	203.183	1.02889	

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/