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.


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 3080 to 3129 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
193 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Measured Divided 0 23818.1 19621.3 1.21389
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Rooted 29.5635 33.7491 1.14158
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured 1 17756.5 14007.3 1.26766
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Squared Subtracted 42411.6 55802.1 13390.5
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Rooted 0 24.1656 21.3198 2.8458
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] 1 116.707 106.044 10.663
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Measured 4612.39 3093.6 1518.79
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Ranked Divided 0 10899.5 12217.4 1.12091
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Measured Subtracted 1053.33 887.413 165.917
194 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Rooted 28.4971 25.6518 2.8453
aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Squared Divided 1 71346.6 95965.1 1.34505
calcyphosine. [swissprot;acc:q13938] Measured Subtracted 0 472.524 635.875 163.351
cyclin g2. [swissprot;acc:q16589] Divided 1 17738.6 13995.7 1.26743
Rooted Subtracted 116.707 106.044 10.663
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked 0 13573.3 14801.2 1227.9
eap30 subunit of ell complex. [refseq;acc:nm_007241] Rooted Divided 1 59.6399 51.9242 1.1486
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] Squared 0 668.421 962.098 1.43936
huntingtin interacting protein c. [refseq;acc:nm_012272] Measured Subtracted 1 4300.47 5807.72 1507.25
kappa b-ras 1. [refseq;acc:nm_020345] Ranked Divided 0 12657.7 11299.1 1.12024
keratin associated protein 9.2. [refseq;acc:nm_031961] Rooted 23.871 20.9159 1.14128
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Squared Subtracted 1 42411.6 55802.1 13390.5
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Ranked 241.373 267.352 25.979
nuclear protein ukp68. [refseq;acc:nm_024824] Divided 227.491 199.458 1.14055
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Measured 0 125.5 103.5 1.21256
uridine kinase-like 1. [swissprot;acc:q9nwz5] Squared Subtracted 269.31 688.46 419.15
195 40s ribosomal protein s28. [swissprot;acc:p25112] Ranked 12967.1 14193.6 1226.5
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Measured Divided 23 19 1.21053
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Subtracted 1475.05 1312.91 162.14
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Squared Divided 479.423 335.966 1.427
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Ranked Subtracted 1 241.373 267.352 25.979
cyclin g1 (cyclin g). [swissprot;acc:p51959] Measured Divided 17738.5 13995.6 1.26743
Rooted Subtracted 116.707 106.044 10.663
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Squared 0 608.191 190.865 417.326
huntingtin interacting protein c. [refseq;acc:nm_012272] Ranked Divided 1 227.971 200.417 1.13748
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Rooted 0 23.8722 20.933 1.14041
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 1 59.6399 51.9242 1.1486
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Ranked 0 13942.8 15586.4 1.11788
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Squared Subtracted 1 42411.6 55802.1 13390.5
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Measured 3074.57 4567.51 1492.94
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] Rooted 0 16.3248 19.168 2.8432
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Squared Divided 1 71062.4 95488.9 1.34373
196 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Measured Subtracted 10640.2 12117.8 1477.6
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Squared Divided 0 479.099 335.74 1.42699
calsyntenin-1 precursor. [swissprot;acc:o94985] 1 71062.4 95488.9 1.34373
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Subtracted 0 2758.07 3161.7 403.63
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Ranked Divided 1 263.215 231.407 1.13745
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Rooted 59.6399 51.9242 1.1486
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Ranked Subtracted 0 13653.8 14874 1220.2
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 1 272.781 246.892 25.889
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Rooted Divided 0 23.8722 20.9332 1.1404

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/