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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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 [...,...].
Network Comparison Type Value Type Gene description Rank green network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 2108 to 2157 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
green
network_comparison
red
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 1841 210.113 1.01115 212.455
presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352] 2658 216.7 1.00108 216.933
presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796] 2659
presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] 2660 216.704 216.937
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] 913 218.878 1.03801 210.863
prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5] 3143 0.00001 1 0.00001
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 376 234.945 1.09395 257.017
probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] 2645 194.328 1.00119 194.097
probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6] 1675 231.729 1.01415 228.496
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 837 222.222 1.0428 231.734
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 1097 203.208 1.02911 209.123
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] 2266 210.416 1.00561 211.597
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] 1321 221.259 1.023 226.347
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] 1221 217.258 1.025 211.959
probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 1737 216.189 1.01296 218.99
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] 1031 235.518 1.03167 242.978
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 497 234.514 1.07177 251.344
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 989 211.345 1.03367 218.462
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 988 211.343 1.03368 218.461
probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] 727 219.71 1.05188 208.873
programmed cell death 10; apoptosis-related protein 15. [refseq;acc:nm_007217] 3052 0.00001 1 0.00001
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] 985 225.782 1.03375 233.402
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] 944 205.083 1.03586 212.437
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] 433 229.411 1.07934 212.547
prohibitin. [swissprot;acc:p35232] 1351 206.941 1.02209 211.513
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] 2066 231.001 1.00829 229.102
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 511 233.725 1.06986 250.053
proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] 1130 215.4 1.02732 221.285
proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] 1297 204.174 1.02394 209.062
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 1159 165.898 1.02641 170.28
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). [swissprot;acc:p13674] 2193 208.162 1.00662 209.54
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). [swissprot;acc:o15460] 2196
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] 1030 215.535 1.03168 222.364
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] 849 153.371 1.04184 147.211
prostate tumor overexpressed gene 1; prostate tumor over expressed gene 1. [refseq;acc:nm_017432] 3106 0.00001 1 0.00001
protease inhibitor 15 preproprotein; 25 kda trypsin inhibitor. [refseq;acc:nm_015886] 2966
proteasome activator complex subunit 3 (proteasome activator 28-gamma subunit) (pa28gamma) (pa28g) (activator of multicatalytic protease subunit 3) (11s regulator complex gamma subunit) (reg-gamma) (ki nuclear autoantigen). [swissprot;acc:q12920] 2997
proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786] 2751 215.312 1.00012 215.338
proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] 2431 212.3 1.00352 213.048
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] 2427 211.618 1.00357 212.374
proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] 2438 213.323 1.0034 214.049
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] 1053 200.84 1.03087 207.04
proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] 2590 214.287 1.00148 214.605
proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] 2280 211.657 1.00537 212.793
proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] 2283 211.676 1.00536 212.81
proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618] 2324 211.129 1.00474 212.129
proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] 2009 214.245 1.00913 216.201
proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721] 2612 215.799 1.0014 215.497
proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] 2407 213.456 1.00364 214.234
proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] 1641 215.034 1.01457 218.167

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/