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 1951 to 2000 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
488 secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Squared 26866.1 32333.2 1.20349
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Ranked 225.026 209.798 1.07258
489 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Rooted 50.5505 46.2797 1.09228
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] Squared 26859 32321.2 1.20337
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Ranked 231.276 215.627 1.07257
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Measured 5281.11 6044.61 1.14457
490 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Squared 5301.97 6377.93 1.20294
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Rooted 50.5505 46.2797 1.09228
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Measured 15274.9 13346.9 1.14445
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Ranked 220.183 236.015 1.0719
491 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Squared 5302.25 6378.24 1.20293
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Measured 5980.15 6843.48 1.14437
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Ranked 251.83 234.951 1.07184
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Rooted 55.1759 60.2621 1.09218
492 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Squared 5313 6389.9 1.20269
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Rooted 55.1759 60.2621 1.09218
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Measured 5979.94 6842.76 1.14429
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] Ranked 220.171 235.979 1.0718
493 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Rooted 55.1759 60.2621 1.09218
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Ranked 220.172 235.98 1.0718
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Measured 5979.95 6842.78 1.14429
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Squared 28408.7 34148.5 1.20204
494 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Measured 5979.93 6842.72 1.14428
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Squared 31583 37925.6 1.20082
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Rooted 55.1759 60.2621 1.09218
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Ranked 220.172 235.98 1.0718
495 60s ribosomal protein l8. [swissprot;acc:p25120] Rooted 55.1759 60.2621 1.09218
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Squared 30286.5 36362 1.2006
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Ranked 220.171 235.979 1.0718
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

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/