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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3358 to 3407 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
210 transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Squared Divided 0 177.23 126.355 1.40264
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Measured 1053.33 887.413 1.18697
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 1 4068.82 5082.21 1.24906
211 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Ranked Subtracted 237.302 212.41 24.892
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Measured Divided 0 2464 2076.5 1.18661
Rooted 48.2208 42.3517 1.13858
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared Subtracted 1 28994.2 17134.8 11859.4
guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] 0 668.421 962.098 293.677
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Rooted 1 121.695 131.815 10.12
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Measured 0 2713.5 2864.68 151.18
lamin b2. [swissprot;acc:q03252] Rooted 17.4452 14.7595 2.6857
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured 1 4358.13 5811.49 1453.36
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Rooted Divided 88.4361 77.5112 1.14095
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Squared 0 98.1677 70.141 1.39958
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 1 14668.3 19547 1.3326
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Ranked 285.684 252.234 1.13261
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 0 10367 9320.25 1.11231
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Subtracted 12364.8 11207.9 1156.9
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Measured Divided 1 4068.91 5082.27 1.24905
212 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Subtracted 0 1621.1 1771.04 149.94
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Rooted Divided 1 88.4266 77.5047 1.14092
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Ranked 285.684 252.234 1.13261
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

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/