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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Value Type Gene description Rank Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2130 to 2179 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
red
green
network_comparison
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] 944 212.437 205.083 1.03586
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] 433 212.547 229.411 1.07934
prohibitin. [swissprot;acc:p35232] 1351 211.513 206.941 1.02209
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] 2066 229.102 231.001 1.00829
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 511 250.053 233.725 1.06986
proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] 1130 221.285 215.4 1.02732
proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] 1297 209.062 204.174 1.02394
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 1159 170.28 165.898 1.02641
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 209.54 208.162 1.00662
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 222.364 215.535 1.03168
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] 849 147.211 153.371 1.04184
prostate tumor overexpressed gene 1; prostate tumor over expressed gene 1. [refseq;acc:nm_017432] 3106 0.00001 0.00001 1
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 215.338 215.312 1.00012
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 213.048 212.3 1.00352
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 212.374 211.618 1.00357
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 214.049 213.323 1.0034
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 207.04 200.84 1.03087
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 214.605 214.287 1.00148
proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] 2280 212.793 211.657 1.00537
proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] 2283 212.81 211.676 1.00536
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 212.129 211.129 1.00474
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 216.201 214.245 1.00913
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 215.497 215.799 1.0014
proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] 2407 214.234 213.456 1.00364
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 218.167 215.034 1.01457
proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] 2387 211.301 210.475 1.00392
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] 2450 213.85 213.177 1.00316
proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] 2686 219.829 219.629 1.00091
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] 2530 212.464 211.99 1.00224
proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] 2545 213.494 213.088 1.00191
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 352 242.14 265.696 1.09728
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] 2142 206.443 207.864 1.00688
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] 1505 216.158 212.316 1.0181
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 188 226.582 198.444 1.14179
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 343 241.625 265.136 1.0973
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 189 226.582 198.444 1.14179
protein bap28. [swissprot;acc:q9h583] 1013 244.312 236.647 1.03239
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] 1819 220.462 217.926 1.01164
protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8] 3131 0.00001 0.00001 1
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] 1587 220.129 216.598 1.0163
protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] 3206 0.00001 0.00001 1
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] 1570 221.128 224.767 1.01646
protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [swissprot;acc:o43822] 2874 0.00001 0.00001 1
protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79] 3219
protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260] 1357 228.409 223.475 1.02208
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 13 288.754 212.554 1.3585
protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] 3102 0.00001 0.00001 1

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/