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 3380 to 3429 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
212 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Squared Subtracted 0 699.353 414.113 285.24
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Rooted 20.3469 17.7078 2.6391
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 1 121.695 131.815 10.12
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Ranked 0 12394.7 11240.2 1154.5
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Divided 18241.7 16405 1.11196
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Squared 98.1677 70.141 1.39958
ns1-associated protein 1. [refseq;acc:nm_006372] Ranked Subtracted 1 237.302 212.41 24.892
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Squared Divided 14690.3 19560.2 1.3315
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Subtracted 28994.2 17134.8 11859.4
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Measured Divided 4446.72 5553.79 1.24896
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] 0 2464 2076.5 1.18661
Rooted 48.2208 42.3517 1.13858
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Measured Subtracted 1 6416.68 7865.15 1448.47
213 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Divided 0 1162.21 1376.88 1.18471
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Rooted 1 105.205 92.2415 1.14054
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared Subtracted 28994.2 17134.8 11859.4
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 0 3862.64 4136.72 274.08
carboxypeptidase b precursor. [refseq;acc:nm_020361] Measured 1 7711.38 6265.8 1445.58
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Ranked 0 11867.6 13019 1151.4
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Rooted 20.3458 17.7104 2.6354
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Ranked 1 237.302 212.41 24.892
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Rooted 121.695 131.815 10.12
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Squared Divided 0 98.1677 70.141 1.39958
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Rooted 126.359 111.067 1.13768
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Measured 1 4446.72 5553.79 1.24896
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Ranked 210.693 186.95 1.127
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] 0 9379.47 8436.39 1.11179
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Measured Subtracted 1217.96 1367.88 149.92
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Squared Divided 1 86861.5 65369.7 1.32877
214 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Measured Subtracted 0 1217.92 1367.83 149.91
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Rooted 1 121.695 131.815 10.12
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked Divided 191.644 170.192 1.12605
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Measured Subtracted 7711.36 6265.79 1445.57
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Ranked 241.282 266.12 24.838
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Squared Divided 0 98.1677 70.141 1.39958
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 1 28994.2 17134.8 11859.4
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Rooted 0 34.7164 32.0874 2.629
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Ranked Divided 7621.99 8473.85 1.11176
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Rooted 1 105.205 92.2415 1.14054
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Measured 0 13174.7 15605.1 1.18447
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Squared Subtracted 634.375 361.911 272.464
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Rooted Divided 21.5042 18.9231 1.1364
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Squared 1 52591.3 69845.1 1.32807
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Ranked Subtracted 0 14898.9 16041.6 1142.7
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured Divided 1 4074.83 5086.49 1.24827
215 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Subtracted 0 1658.23 1805.52 147.29
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Rooted Divided 1 105.205 92.2415 1.14054
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 0 9.36926 8.24639 1.13617
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked Subtracted 1 237.292 212.457 24.835
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Rooted 0 24.8155 27.4116 2.5961

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/