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 description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1975 to 2024 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
network_comparison
green
494 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Rooted 55.1759 1.09218 60.2621
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Ranked 220.172 1.0718 235.98
495 60s ribosomal protein l8. [swissprot;acc:p25120] Rooted 55.1759 1.09218 60.2621
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Squared 30286.5 1.2006 36362
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Ranked 220.171 1.0718 235.979
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Measured 10804.7 1.14428 12363.6
496 hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Rooted 55.1759 1.09218 60.2621
nostrin. [refseq;acc:nm_052946] Measured 4682.87 1.1441 4093.05
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Ranked 250.938 1.07177 234.134
tubby protein homolog. [swissprot;acc:p50607] Squared 30286.5 1.2006 36362
497 eap30 subunit of ell complex. [refseq;acc:nm_007241] Measured 4682.87 1.1441 4093.05
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Ranked 251.344 1.07177 234.514
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 1.2006 36362
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Rooted 55.1759 1.09218 60.2621
498 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Measured 4682.87 1.1441 4093.05
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Squared 30286.5 1.2006 36362
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Rooted 55.1759 1.09218 60.2621
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Ranked 220.161 1.07172 235.95
499 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Measured 4682.87 1.1441 4093.05
rw1 protein (fragment). [swissprot;acc:q92545] Rooted 55.1759 1.09218 60.2621
tbc1 domain family member 5. [swissprot;acc:q92609] Squared 30286.5 1.2006 36362
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Ranked 231.496 1.0715 248.048
500 60s ribosomal protein l7. [swissprot;acc:p18124] Rooted 52.6483 1.09198 48.2135
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Measured 4682.87 1.1441 4093.05
inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Ranked 224.662 1.07127 240.673
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Squared 30286.5 1.2006 36362
501 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Ranked 238.704 1.07112 255.68
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 1.09195 46.1792
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Measured 4682.87 1.1441 4093.05
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Squared 30286.5 1.2006 36362
502 60s ribosomal protein l30. [swissprot;acc:p04645] Rooted 50.4616 1.09164 46.2257
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Squared 30286.5 1.2006 36362
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Ranked 238.704 1.07112 255.68
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Measured 6913.6 1.1437 7907.05
503 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Rooted 177.987 1.0916 194.29
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Ranked 238.704 1.07112 255.68
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Squared 30286.5 1.2006 36362
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Measured 15182.5 1.14344 13277.9
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 1.14334 11511
oligophrenin 1. [swissprot;acc:o60890] Ranked 238.704 1.07112 255.68
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Rooted 144.606 1.09141 157.824
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Squared 30286.5 1.2006 36362
505 ad24 protein. [refseq;acc:nm_022451] Ranked 251.334 1.071 234.672
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Squared 30286.5 1.2006 36362
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Rooted 144.606 1.09141 157.824
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Measured 6856.71 1.14316 7838.3
506 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 3893.85 1.14308 4450.98
inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] Ranked 224.535 1.071 240.476
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Rooted 144.606 1.09141 157.824
vav-2 protein. [swissprot;acc:p52735] Squared 31377.3 1.20055 37670.1

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/