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 Network Comparison Type Gene description Rank Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 2451 to 2500 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence
description
Rank
red
green
network_comparison
schwannomin interacting protein 1. [refseq;acc:nm_014575] 2900 0.00001 0.00001 1
scratch; scratch 1. [refseq;acc:nm_031309] 1873 210.55 208.305 1.01078
scribble. [refseq;acc:nm_015356] 2528 221.782 222.291 1.0023
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] 1575 222.585 218.982 1.01645
sec13-related protein. [swissprot;acc:p55735] 1133 218.484 212.675 1.02731
sec23-interacting protein p125; phospholipase. [refseq;acc:nm_007190] 3097 0.00001 0.00001 1
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 1644 217.256 214.149 1.01451
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] 1646
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] 2453 204.688 205.332 1.00315
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] 2451 205.333
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] 2452
secretory pathway component sec31b-1. [refseq;acc:nm_015490] 1143 218.484 212.675 1.02731
sedlin. [swissprot;acc:o14582] 565 129.219 121.261 1.06563
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 513 218.596 204.344 1.06975
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 514 218.613 204.382 1.06963
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 519 218.702 204.582 1.06902
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] 543 222.156 208.201 1.06703
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 540
semaphorin 6b precursor (semaphorin z) (sema z). [swissprot;acc:q9h3t3] 2832 0.00001 0.00001 1
semaphorin 6c precursor (semaphorin y) (sema y). [swissprot;acc:q9h3t2] 2933
semaphorin 6d isoform 3 precursor. [refseq;acc:nm_153617] 2964
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] 503 238.704 255.68 1.07112
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] 2843 0.00001 0.00001 1
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] 1517 213.267 209.511 1.01793
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 909 142.077 136.846 1.03823
septin 10 isoform 1. [refseq;acc:nm_144710] 737 125.526 119.402 1.05129
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 829 135.844 130.259 1.04288
septin 6. [swissprot;acc:q14141] 744 126.604 120.463 1.05098
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 743 126.215 120.078 1.05111
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 732 124.434 118.318 1.05169
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] 799 221.965 212.404 1.04501
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] 1617 221.045 217.699 1.01537
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] 1638 220.686 217.481 1.01474
serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] 1775 207.757 210.274 1.01212
serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] 1107 204.603 210.324 1.02796
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 992 218.468 211.357 1.03364
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] 987 218.459 211.338 1.03369
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] 307 242.153 266.673 1.10126
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] 2753 208.859 208.846 1.00006
serine/threonine kinase 38 like. [refseq;acc:nm_015000] 2897 0.00001 0.00001 1
serine/threonine kinase 38; serine threonine protein kinase. [refseq;acc:nm_007271] 3071
serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965] 2569 219.907 220.267 1.00164
serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4] 2566
serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9] 2568
serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] 1678 216.899 213.889 1.01407
serine/threonine protein kinase 24 (ec 2.7.1.37) (ste20-like kinase mst3) (mst-3) (mammalian ste20-like protein kinase 3). [swissprot;acc:q9y6e0] 3115 0.00001 0.00001 1
serine/threonine protein kinase 25 (ec 2.7.1.37) (sterile 20/oxidant stress-response kinase 1) (ste20/oxidant stress response kinase-1) (sok-1) (ste20-like kinase). [swissprot;acc:o00506] 3048
serine/threonine protein kinase 3 (ec 2.7.1.37) (ste20-like kinase mst2) (mst-2) (mammalian ste20-like protein kinase 2) (serine/threonine protein kinase krs-1). [swissprot;acc:q13188] 3111
serine/threonine protein kinase mask; ste20-like kinase mst4. [refseq;acc:nm_016542] 2982
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 30 187.457 243.678 1.29991

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/