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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1962 to 2011 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
491 Ranked nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 251.83 234.951 1.07184
Squared forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 5302.25 6378.24 1.20293
Rooted parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 55.1759 60.2621 1.09218
492 Measured neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 5979.94 6842.76 1.14429
Ranked serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] 220.171 235.979 1.0718
Squared forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 5313 6389.9 1.20269
Rooted hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] 55.1759 60.2621 1.09218
493 Measured neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 5979.95 6842.78 1.14429
Ranked conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] 220.172 235.98 1.0718
Squared serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] 28408.7 34148.5 1.20204
Rooted cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] 55.1759 60.2621 1.09218
494 Measured e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 5979.93 6842.72 1.14428
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
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

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/