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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1975 to 2024 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
494 Squared electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 31583 37925.6 1.20082
Rooted pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 55.1759 60.2621 1.09218
495 Measured tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 10804.7 12363.6 1.14428
Ranked serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 220.171 235.979 1.0718
Squared partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 30286.5 36362 1.2006
Rooted 60s ribosomal protein l8. [swissprot;acc:p25120] 55.1759 60.2621 1.09218
496 Measured nostrin. [refseq;acc:nm_052946] 4682.87 4093.05 1.1441
Ranked suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 250.938 234.134 1.07177
Squared tubby protein homolog. [swissprot;acc:p50607] 30286.5 36362 1.2006
Rooted hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] 55.1759 60.2621 1.09218
497 Measured eap30 subunit of ell complex. [refseq;acc:nm_007241] 4682.87 4093.05 1.1441
Ranked probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 251.344 234.514 1.07177
Squared protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] 30286.5 36362 1.2006
Rooted pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] 55.1759 60.2621 1.09218
498 Measured liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 4682.87 4093.05 1.1441
Ranked rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] 220.161 235.95 1.07172
Squared numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] 30286.5 36362 1.2006
Rooted probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 55.1759 60.2621 1.09218
499 Measured glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 4682.87 4093.05 1.1441
Ranked triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] 231.496 248.048 1.0715
Squared tbc1 domain family member 5. [swissprot;acc:q92609] 30286.5 36362 1.2006
Rooted rw1 protein (fragment). [swissprot;acc:q92545] 55.1759 60.2621 1.09218
500 Measured gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 4682.87 4093.05 1.1441
Ranked inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 224.662 240.673 1.07127
Squared tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] 30286.5 36362 1.2006
Rooted 60s ribosomal protein l7. [swissprot;acc:p18124] 52.6483 48.2135 1.09198
501 Measured glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 4682.87 4093.05 1.1441
Ranked cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] 238.704 255.68 1.07112
Squared vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] 30286.5 36362 1.2006
Rooted dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 50.4253 46.1792 1.09195
502 Measured ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 6913.6 7907.05 1.1437
Ranked oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] 238.704 255.68 1.07112
Squared numb-like protein (numb-r). [swissprot;acc:q9y6r0] 30286.5 36362 1.2006
Rooted 60s ribosomal protein l30. [swissprot;acc:p04645] 50.4616 46.2257 1.09164
503 Measured tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] 15182.5 13277.9 1.14344
Ranked senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] 238.704 255.68 1.07112
Squared tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] 30286.5 36362 1.2006
Rooted nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 177.987 194.29 1.0916
504 Measured 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
Ranked oligophrenin 1. [swissprot;acc:o60890] 238.704 255.68 1.07112
Squared vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] 30286.5 36362 1.2006
Rooted ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 144.606 157.824 1.09141
505 Measured signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 6856.71 7838.3 1.14316
Ranked ad24 protein. [refseq;acc:nm_022451] 251.334 234.672 1.071
Squared protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] 30286.5 36362 1.2006
Rooted ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 144.606 157.824 1.09141
506 Measured 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
Ranked inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] 224.535 240.476 1.071
Squared vav-2 protein. [swissprot;acc:p52735] 31377.3 37670.1 1.20055
Rooted ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 144.606 157.824 1.09141

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/