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 4408 to 4457 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
276 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Squared Divided 0 14470.6 11676.7 1.23927
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Ranked Subtracted 12228.2 11367.3 860.9
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Rooted 9.7842 7.75282 2.03138
gbp protein isoform a. [refseq;acc:nm_017870] Measured 1 699.76 1894.39 1194.63
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Rooted Divided 66.1046 74.0964 1.1209
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Squared 16120.1 20665.7 1.28198
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Measured 3119.98 2579.49 1.20953
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Squared Subtracted 33100.3 41520.6 8420.3
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] Measured 0 465.37 562.085 96.715
277 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] Ranked 18849.7 19704.7 855
40s ribosomal protein s29. [swissprot;acc:p30054] Divided 1 241.849 267.642 1.10665
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 0 11096.8 10251.6 1.08245
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Subtracted 1 239.277 262.434 23.157
adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Rooted Divided 0 24.1033 22.0791 1.09168
cerebral cell adhesion molecule. [refseq;acc:nm_016174] Squared Subtracted 1 62198.5 70599.4 8400.9
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Measured Divided 0 870.93 975.647 1.12024
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Subtracted 143 47 96
importin 9. [refseq;acc:nm_018085] Squared 1062.18 952.74 109.44
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Rooted 21.1331 19.1063 2.0268
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Measured 1 8600.02 9792.49 1192.47
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Squared Divided 0 21885.1 17682.1 1.2377
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Measured 1 3119.98 2579.49 1.20953
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Rooted 65.9938 73.9449 1.12048
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted 104.459 113.143 8.684
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Squared Divided 16120.1 20665.7 1.28198
278 40s ribosomal protein s11. [swissprot;acc:p04643] Ranked 241.399 267.088 1.10642
adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Rooted Subtracted 0 24.1033 22.0791 2.0242
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked Divided 11644 10763.4 1.08181
bystin. [swissprot;acc:q13895] Squared 26569.7 32857.7 1.23666
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Rooted 34.0153 31.1803 1.09092
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Squared 1 16120.1 20665.7 1.28198
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Subtracted 34018.3 42373 8354.7
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Ranked 0 11107.1 11959.2 852.1
myelin gene expression factor 2. [refseq;acc:nm_016132] 1 235.383 258.476 23.093
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Squared 0 1062.18 952.74 109.44
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Measured 1 8600.02 9792.49 1192.47
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Rooted Divided 65.9938 73.9449 1.12048
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Measured 0 2162.33 1932 1.11922
seven in absentia homolog 1. [refseq;acc:nm_003031] Subtracted 2221.04 2316.94 95.9
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Rooted 1 57.3527 65.7973 8.4446
transcription factor lbx1. [swissprot;acc:p52954] Measured Divided 3119.98 2579.49 1.20953
279 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Squared Subtracted 30596.2 38919.9 8323.7
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 0 3778.75 3670.49 108.26
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Ranked Divided 10614.2 9812.39 1.08171
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] Measured 545.902 610.424 1.11819
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Rooted Subtracted 10 12 2
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Divided 33.1655 30.4161 1.09039
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Squared 229.508 283.721 1.23621
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Rooted Subtracted 1 42.0574 50.4237 8.3663
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Ranked Divided 252.644 228.42 1.10605

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/