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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Network Comparison Type Value Type Gene description Rank Filtered Interaction Map network_comparison red green
Results: HTML CSV LaTeX Showing element 2100 to 2149 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
red
green
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] 977 1.03402 228.953 221.421
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] 978
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 574 1.06503 221.807 208.264
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 211 1.13261 285.684 252.234
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 207
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 3100 1 0.00001 0.00001
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 736 1.0513 232.601 244.534
presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] 734
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] 1841 1.01115 212.455 210.113
presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352] 2658 1.00108 216.933 216.7
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 216.937 216.704
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] 913 1.03801 210.863 218.878
prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5] 3143 1 0.00001 0.00001
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 376 1.09395 257.017 234.945
probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] 2645 1.00119 194.097 194.328
probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6] 1675 1.01415 228.496 231.729
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 837 1.0428 231.734 222.222
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 1097 1.02911 209.123 203.208
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] 2266 1.00561 211.597 210.416
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] 1321 1.023 226.347 221.259
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 1.025 211.959 217.258
probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 1737 1.01296 218.99 216.189
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] 1031 1.03167 242.978 235.518
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 497 1.07177 251.344 234.514
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 989 1.03367 218.462 211.345
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 988 1.03368 218.461 211.343
probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] 727 1.05188 208.873 219.71
programmed cell death 10; apoptosis-related protein 15. [refseq;acc:nm_007217] 3052 1 0.00001 0.00001
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] 985 1.03375 233.402 225.782
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] 944 1.03586 212.437 205.083
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] 433 1.07934 212.547 229.411
prohibitin. [swissprot;acc:p35232] 1351 1.02209 211.513 206.941
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] 2066 1.00829 229.102 231.001
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 511 1.06986 250.053 233.725
proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] 1130 1.02732 221.285 215.4
proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] 1297 1.02394 209.062 204.174
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 1159 1.02641 170.28 165.898
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 1.00662 209.54 208.162
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 1.03168 222.364 215.535
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 1.04184 147.211 153.371
prostate tumor overexpressed gene 1; prostate tumor over expressed gene 1. [refseq;acc:nm_017432] 3106 1 0.00001 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 1.00012 215.338 215.312
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 1.00352 213.048 212.3
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 1.00357 212.374 211.618
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 1.0034 214.049 213.323
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 1.03087 207.04 200.84

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/