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 3330 to 3379 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
417 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Squared Subtracted 32192.8 37967.1 5774.3
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Rooted 62.574 68.4128 5.8388
j domain containing protein 1. [swissprot;acc:q9ukb3] Divided 55.5489 50.535 1.09922
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Squared 22841.8 27856.2 1.21953
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Ranked 233.539 253.197 1.08417
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Subtracted 235.94 218.837 17.103
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Measured 7725.1 8647.74 922.64
418 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Divided 5493.1 6350.19 1.15603
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Ranked 233.539 253.197 1.08417
e-1 enzyme. [refseq;acc:nm_021204] Squared 30903.8 37638.1 1.21791
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Subtracted 32192.8 37967.1 5774.3
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Measured 7725.1 8647.74 922.64
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Ranked 233.723 216.674 17.049
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Rooted Divided 55.5489 50.535 1.09922
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Subtracted 66.941 72.7546 5.8136
419 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Squared Divided 24832.1 30242.8 1.21789
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Rooted Subtracted 48.4278 54.2262 5.7984
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Divided 55.5489 50.535 1.09922
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Measured 5493.1 6350.19 1.15603
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Ranked 233.539 253.197 1.08417
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Measured Subtracted 5039.63 5961.83 922.2
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Squared 32192.5 37966.8 5774.3
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Ranked 235.922 218.925 16.997
420 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Squared Divided 30924.3 37652.3 1.21756
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Rooted Subtracted 51.6125 45.8409 5.7716
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Ranked Divided 233.539 253.197 1.08417
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Subtracted 238.704 255.68 16.976
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Rooted Divided 51.7959 56.9253 1.09903
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Squared Subtracted 32192.8 37967.1 5774.3
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Measured Divided 10235.2 11830.8 1.15589
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Subtracted 5942.49 6853.15 910.66
421 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Rooted Divided 50.4666 45.9317 1.09873
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Squared 36933 44953.6 1.21717
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Measured Subtracted 6739.43 7644.55 905.12
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Squared 32189.9 37963.6 5773.7
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Ranked 238.704 255.68 16.976
thrombospondin 3 precursor. [swissprot;acc:p49746] Rooted 51.6132 45.8422 5.771
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Ranked Divided 223.202 205.9 1.08403
vav-2 protein. [swissprot;acc:p52735] Measured 6660.02 7697.78 1.15582
422 60s ribosomal protein l5. [swissprot;acc:p46777] Rooted 50.4641 45.9293 1.09873
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Measured Subtracted 460 1365 905
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Squared Divided 25860 31475.4 1.21715
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Subtracted 32188.2 37961.6 5773.4
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Measured Divided 5206.9 6010.04 1.15425
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Rooted Subtracted 80.4069 86.1018 5.6949
ras-related protein rab-37. [swissprot;acc:q96ax2] Ranked Divided 240.287 260.193 1.08284
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Subtracted 238.704 255.68 16.976
423 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Rooted Divided 50.4663 45.9313 1.09873
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Measured Subtracted 6739.61 7644.58 904.97
Squared 32187.7 37961 5773.3

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/