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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1980 to 2029 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
495 tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Measured 10804.7 12363.6 1.14428
496 hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Rooted 55.1759 60.2621 1.09218
nostrin. [refseq;acc:nm_052946] Measured 4682.87 4093.05 1.1441
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Ranked 250.938 234.134 1.07177
tubby protein homolog. [swissprot;acc:p50607] Squared 30286.5 36362 1.2006
497 eap30 subunit of ell complex. [refseq;acc:nm_007241] Measured 4682.87 4093.05 1.1441
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Ranked 251.344 234.514 1.07177
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Squared 30286.5 36362 1.2006
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Rooted 55.1759 60.2621 1.09218
498 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Measured 4682.87 4093.05 1.1441
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Squared 30286.5 36362 1.2006
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Rooted 55.1759 60.2621 1.09218
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Ranked 220.161 235.95 1.07172
499 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Measured 4682.87 4093.05 1.1441
rw1 protein (fragment). [swissprot;acc:q92545] Rooted 55.1759 60.2621 1.09218
tbc1 domain family member 5. [swissprot;acc:q92609] Squared 30286.5 36362 1.2006
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Ranked 231.496 248.048 1.0715
500 60s ribosomal protein l7. [swissprot;acc:p18124] Rooted 52.6483 48.2135 1.09198
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Measured 4682.87 4093.05 1.1441
inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Ranked 224.662 240.673 1.07127
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Squared 30286.5 36362 1.2006
501 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Ranked 238.704 255.68 1.07112
dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Rooted 50.4253 46.1792 1.09195
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Measured 4682.87 4093.05 1.1441
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Squared 30286.5 36362 1.2006
502 60s ribosomal protein l30. [swissprot;acc:p04645] Rooted 50.4616 46.2257 1.09164
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Squared 30286.5 36362 1.2006
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Ranked 238.704 255.68 1.07112
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Measured 6913.6 7907.05 1.1437
503 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Rooted 177.987 194.29 1.0916
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Ranked 238.704 255.68 1.07112
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Squared 30286.5 36362 1.2006
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Measured 15182.5 13277.9 1.14344
504 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 10067.9 11511 1.14334
oligophrenin 1. [swissprot;acc:o60890] Ranked 238.704 255.68 1.07112
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Rooted 144.606 157.824 1.09141
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Squared 30286.5 36362 1.2006
505 ad24 protein. [refseq;acc:nm_022451] Ranked 251.334 234.672 1.071
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Squared 30286.5 36362 1.2006
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Rooted 144.606 157.824 1.09141
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Measured 6856.71 7838.3 1.14316
506 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 3893.85 4450.98 1.14308
inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] Ranked 224.535 240.476 1.071
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Rooted 144.606 157.824 1.09141
vav-2 protein. [swissprot;acc:p52735] Squared 31377.3 37670.1 1.20055
507 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Rooted 144.606 157.824 1.09141
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Measured 6875.08 7858.38 1.14302
puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] Squared 23512.2 28206.2 1.19964
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Ranked 251.299 234.729 1.07059
508 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Measured 7556.75 8636.87 1.14293

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/