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 1130 to 1179 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
red
green
network_comparison
glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] 1228 213.079 218.325 1.02462
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 2674 203.151 202.948 1.001
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 1217 211.959 217.258 1.025
glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] 1470 221.412 217.199 1.0194
glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075] 2957 0.00001 0.00001 1
glutamyl trna synthetase. [sptrembl;acc:o14563] 1473 221.412 217.199 1.0194
glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] 2167 215.925 214.481 1.00673
glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] 1304 207.387 212.275 1.02357
glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211] 1677 218.654 221.732 1.01408
glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 1371 228.646 223.744 1.02191
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 1359 228.642 223.726 1.02197
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 239 227.357 254.15 1.11785
glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] 2348 217.057 218.03 1.00448
glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] 2549 206.902 206.519 1.00185
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] 2548 206.899 206.516
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] 2547 206.894 206.51 1.00186
glycerol-3-phosphate acyltransferase, mitochondrial precursor (ec 2.3.1.15) (gpat). [swissprot;acc:q9hcl2] 3033 0.00001 0.00001 1
glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] 2669 214.575 214.354 1.00103
glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] 2534 208 207.555 1.00214
glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] 1296 209.062 204.174 1.02394
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 2343 212.222 211.27 1.00451
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] 2448 212.446 211.766 1.00321
glycine receptor alpha-1 chain precursor (glycine receptor 48 kda subunit) (strychnine binding subunit). [swissprot;acc:p23415] 2919 0.00001 0.00001 1
glycine receptor alpha-2 chain precursor. [swissprot;acc:p23416] 3121
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] 2920
glycine receptor beta chain precursor (glycine receptor 58 kda subunit). [swissprot;acc:p48167] 3083
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 19 185.678 245.247 1.32082
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 20
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 22
glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] 2186 211.713 210.318 1.00663
glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] 2187
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 1324 159.993 156.421 1.02284
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 1319 159.75 156.153 1.02304
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] 2562 208.429 208.779 1.00168
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] 2565
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] 1472 221.412 217.199 1.0194
gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] 1694 218.937 215.971 1.01373
golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] 1177 218.186 212.672 1.02593
golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] 1960 211.633 213.703 1.00978
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 1835 194.573 192.396 1.01132
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] 1994 189.011 190.787 1.0094
gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [swissprot;acc:q96s52] 3165 0.00001 0.00001 1
grancalcin. [swissprot;acc:p28676] 942 212.442 205.088 1.03586
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] 551 207.261 194.347 1.06645
grb2-related adaptor protein. [swissprot;acc:q13588] 441 223.457 207.222 1.07835
growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] 1114 251.863 258.829 1.02766
growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] 1116
growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] 1113
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 446 224.049 207.785 1.07827
growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] 1395 218.47 213.876 1.02148

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/