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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 red Interaction Map Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1844 to 1893 of 66312 in total
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
Interaction Map
green
network_comparison
116 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Rooted Subtracted 40.6302 High confidence 25.4452 15.185
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Ranked Divided 268.565 334.483 1.24545
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Measured 11285.3 Low confidence 10318.5 1.0937
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Ranked Subtracted 208.52 High confidence 171.595 36.925
Rooted 69.0515 Low confidence 74.7493 5.6978
monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] Squared 62451.1 70673.1 8222
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Divided 19321 High confidence 12542.6 1.54043
p66 alpha. [refseq;acc:nm_017660] Subtracted 81888.8 56306.5 25582.3
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Measured Divided 21185 28492 1.34491
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Rooted 66.9562 Low confidence 72.3243 1.08017
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Measured Subtracted 13261.9 High confidence 11017.8 2244.1
testican-3 precursor. [swissprot;acc:q9bq16] Ranked 220.395 Low confidence 234.389 13.994
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Divided 204.161 190.791 1.07008
117 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared 211446 High confidence 137422 1.53866
coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488] Ranked 226.395 Low confidence 211.713 1.06935
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted Subtracted 40.5691 High confidence 25.4263 15.1428
high-mobility group 20a. [refseq;acc:nm_018200] Ranked 208.588 171.778 36.81
Rooted Divided 69.2016 Low confidence 74.7475 1.08014
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured 11285.3 10318.5 1.0937
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted 9276.47 High confidence 7090.37 2186.1
monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] Squared 62413.6 Low confidence 70617.4 8203.8
natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279] Rooted 63.7749 69.4515 5.6766
neuralized-like. [refseq;acc:nm_004210] Ranked Divided 332.326 High confidence 266.948 1.24491
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Measured 21185 28492 1.34491
striated muscle activator of rho-dependent signaling. [refseq;acc:nm_139166] Ranked Subtracted 225.495 Low confidence 211.529 13.966
transcription factor jun-b. [swissprot;acc:p17275] Rooted Divided 63.4173 High confidence 79.5311 1.25409
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Squared Subtracted 81888.8 56306.5 25582.3
transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Divided 81950.4 Low confidence 93933.1 1.14622
y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Measured Subtracted 6991.78 7848.45 856.67
118 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 9275.1 High confidence 7089.65 2185.45
cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] 6991.78 Low confidence 7848.45 856.67
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Rooted Divided 50.3065 High confidence 62.9788 1.2519
monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] Squared Subtracted 62293.5 Low confidence 70439 8145.5
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Ranked Divided 284.753 High confidence 228.934 1.24382
Rooted Subtracted 37.2205 52.2064 14.9859
natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] 64.1217 Low confidence 69.7 5.5783
necdin. [swissprot;acc:q99608] Measured Divided 11285.3 10318.5 1.0937
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Ranked Subtracted 274.027 High confidence 237.79 36.237
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Measured Divided 21185 28492 1.34491
phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Squared 81950.4 Low confidence 93933.1 1.14622
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 210445 High confidence 136779 1.53858
protein-glutamine gamma-glutamyltransferase k (ec 2.3.2.13) (transglutaminase k) (tgase k) (tgk) (tg(k)) (transglutaminase 1) (epidermal tgase). [swissprot;acc:p22735] Ranked 226.395 Low confidence 211.713 1.06935
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] Rooted 67.0736 72.4478 1.08012
testican-1 precursor (spock protein). [swissprot;acc:q08629] Ranked Subtracted 220.254 234.111 13.857
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Squared 81888.8 High confidence 56306.5 25582.3
119 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Measured 12998.5 15138.2 2139.7
adiponectin receptor 2. [refseq;acc:nm_024551] Ranked 281.582 246.371 35.211
atp synthase d chain, mitochondrial (ec 3.6.3.14) (my032 protein). [swissprot;acc:o75947] Squared 59868.5 Low confidence 51759.6 8108.9
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 81606.8 High confidence 56215.8 25391
exocyst complex component sec5. [swissprot;acc:q96kp1] Divided 210335 136716 1.53848

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/