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 3908 to 3957 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
489 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Rooted Subtracted 62.7424 67.9648 5.2224
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 Divided 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
vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] Squared Subtracted 27516.2 32720 5203.8
490 ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Rooted 62.7424 67.9648 5.2224
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Squared Divided 5301.97 6377.93 1.20294
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Measured Subtracted 7101.94 7949.84 847.9
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Ranked 242.531 227.136 15.395
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Rooted Divided 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
vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Squared Subtracted 27516.2 32720 5203.8
491 cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Rooted 62.7424 67.9648 5.2224
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Squared Divided 5302.25 6378.24 1.20293
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Ranked Subtracted 150.959 166.351 15.392
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 Divided 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
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Measured Subtracted 7067.46 7909.27 841.81
492 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Squared 27516.2 32720 5203.8
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Ranked 150.982 166.372 15.39
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Squared Divided 5313 6389.9 1.20269
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Rooted 55.1759 60.2621 1.09218
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Subtracted 62.7427 67.9648 5.2221
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Measured Divided 5979.94 6842.76 1.14429
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Subtracted 6167.93 7007.7 839.77
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 Divided 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
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Rooted Subtracted 62.7456 67.9646 5.219
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Measured 6167.93 7007.7 839.77
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Divided 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
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Subtracted 27516.2 32720 5203.8
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Ranked 236.751 252.038 15.287
494 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Measured Divided 5979.93 6842.72 1.14428
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Squared 31583 37925.6 1.20082
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Measured Subtracted 6167.93 7007.7 839.77
metaxin 2. [swissprot;acc:o75431] Ranked 219.537 234.793 15.256
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Rooted 49.3771 54.5905 5.2134
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Divided 55.1759 60.2621 1.09218
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Squared Subtracted 29174 34363.5 5189.5
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Ranked Divided 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
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Rooted Subtracted 68.6822 73.8955 5.2133
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Squared 29173.8 34362.7 5188.9
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Measured 6167.93 7007.7 839.77

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/