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 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
489 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Squared 0 21555.6 21619.8 1.00298
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Ranked 8854.04 8811.09 1.00487
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 1 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 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Rooted 0 24.4309 24.4079 1.00094
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Ranked 10388.7 10338.7 1.00484
Squared 3228.32 3221.55 1.0021
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 1 5301.97 6377.93 1.20294
high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] Measured 0 22940.1 22888.8 1.00224
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Rooted 1 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 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Rooted 0 42.6139 42.6315 1.00041
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Squared 1 5302.25 6378.24 1.20293
high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] Measured 0 22962 22910.9 1.00223
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] 1 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
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Squared 0 2871.07 2873.96 1.00101
rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] Ranked 21970 21880 1.00411
492 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] Measured 5038.33 5046.33 1.00159
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Squared 6791.15 6792.32 1.00017
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 1 5313 6389.9 1.20269
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Rooted 55.1759 60.2621 1.09218
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 0 62.8936 62.8986 1.00008
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Measured 1 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
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] 0 6802.96 6829.74 1.00394
493 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] Squared 17901.1 17901.1 1
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Rooted 1 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
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 0 11999.1 12041.7 1.00355
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Rooted 62.8936 62.8986 1.00008
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Measured 1 5979.95 6842.78 1.14429
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] 0 2410.35 2411.78 1.00059
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Squared 1 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
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261] Measured 0 0.00001 0.00001 1
Squared
Rooted
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 1 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
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 0 11985.5 11959.4 1.00218
495 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 11725.2 11748.1 1.00195
60s ribosomal protein l8. [swissprot;acc:p25120] Rooted 1 55.1759 60.2621 1.09218
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001] Measured 0 0.00001 0.00001 1
Squared
Rooted

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/