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 Hugo 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
Hugo
Value Type
description
red
green
network_comparison
494 PAK1 Ranked serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] 220.172 235.98 1.0718
PSIP1 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 CLEC3B Measured tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 10804.7 12363.6 1.14428
PAK3 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
PARD6G Squared partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 30286.5 36362 1.2006
RPL8 Rooted 60s ribosomal protein l8. [swissprot;acc:p25120] 55.1759 60.2621 1.09218
496 HDGF hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]
NOSTRIN Measured nostrin. [refseq;acc:nm_052946] 4682.87 4093.05 1.1441
PPAN-P2RY11 Ranked suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 250.938 234.134 1.07177
TUB Squared tubby protein homolog. [swissprot;acc:p50607] 30286.5 36362 1.2006
497 EBNA1BP2 Ranked probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 251.344 234.514 1.07177
HDGFL1 Rooted pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] 55.1759 60.2621 1.09218
PRKCI 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
SNF8 Measured eap30 subunit of ell complex. [refseq;acc:nm_007241] 4682.87 4093.05 1.1441
498 ARHGEF6 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
DDX6 Rooted probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] 55.1759 60.2621 1.09218
NUMB Squared numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] 30286.5 36362 1.2006
SLC39A6 Measured liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 4682.87 4093.05 1.1441
499 GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
TBC1D5 Squared tbc1 domain family member 5. [swissprot;acc:q92609] 30286.5 36362 1.2006
TMEM131 Rooted rw1 protein (fragment). [swissprot;acc:q92545] 55.1759 60.2621 1.09218
TPI1 Ranked triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] 231.496 248.048 1.0715
500 no value Rooted 60s ribosomal protein l7. [swissprot;acc:p18124] 52.6483 48.2135 1.09198
ING2 Ranked inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 224.662 240.673 1.07127
NAPG Measured gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 4682.87 4093.05 1.1441
TULP1 Squared tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] 30286.5 36362 1.2006
501 CYC1 Ranked cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] 238.704 255.68 1.07112
GAD1 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
POLR1A 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
VPS29 Squared vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] 30286.5 36362 1.2006
502 ARHGAP26 Ranked oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] 238.704 255.68 1.07112
NUMBL Squared numb-like protein (numb-r). [swissprot;acc:q9y6r0] 30286.5 36362 1.2006
RPL30 Rooted 60s ribosomal protein l30. [swissprot;acc:p04645] 50.4616 46.2257 1.09164
RRM1 Measured ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 6913.6 7907.05 1.1437
503 no value Rooted nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 177.987 194.29 1.0916
RGN Ranked senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] 238.704 255.68 1.07112
TP53BP2 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
TULP3 Squared tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] 30286.5 36362 1.2006
504 ECHS1 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
OPHN1 Ranked oligophrenin 1. [swissprot;acc:o60890] 238.704 255.68 1.07112
RRAGA Rooted ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 144.606 157.824 1.09141
VPS35 Squared vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] 30286.5 36362 1.2006
505 CBLB Measured signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 6856.71 7838.3 1.14316
NOC3L Ranked ad24 protein. [refseq;acc:nm_022451] 251.334 234.672 1.071
PRKCZ Squared protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] 30286.5 36362 1.2006
RRAGC Rooted ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 144.606 157.824 1.09141
506 EIF6 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
ING1 Ranked inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] 224.535 240.476 1.071
RRAGB Rooted ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 144.606 157.824 1.09141
VAV2 Squared vav-2 protein. [swissprot;acc:p52735] 31377.3 37670.1 1.20055

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
- Hugo is the HGNC identifier if it exists
- 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/