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 12214 to 12263 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2552 phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Squared 16926 17789.2 1.051
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Measured 4884.35 4985.78 1.02077
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Ranked 193.12 193.467 1.0018
2553 chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]
histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] Rooted 58.0778 58.6154 1.00926
pp3111 protein. [refseq;acc:nm_022156] Squared 16926 17789.2 1.051
ras-related protein rab-37. [swissprot;acc:q96ax2] Measured 3852.99 3775.86 1.02043
2554 lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] Rooted 66.145 66.7577 1.00926
ras-related protein rab-26. [swissprot;acc:q9ulw5] Measured 3852.99 3775.86 1.02043
syntaxin 18. [swissprot;acc:q9p2w9] Squared 16926 17789.2 1.051
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Ranked 193.12 193.467 1.0018
2555 dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Measured 3852.99 3775.86 1.02043
eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] Rooted 58.0778 58.6154 1.00926
rd protein. [swissprot;acc:p18615] Squared 16926 17789.2 1.051
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Ranked 212.953 212.572 1.00179
2556 chromodomain y-like protein 2. [refseq;acc:nm_152342] 193.119 193.46 1.00177
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Squared 16926 17789.2 1.051
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Measured 4883.73 4982.88 1.0203
tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Rooted 66.145 66.7577 1.00926
2557 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Squared 16926 17789.2 1.051
defender against cell death 1 (dad-1). [swissprot;acc:p46966] Rooted 66.145 66.7577 1.00926
elongation factor 2 (ef-2). [swissprot;acc:p13639] Ranked 222.658 223.047 1.00175
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Measured 5291.65 5187.78 1.02002
2558 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Squared 16926 17789.2 1.051
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Measured 5291.65 5187.78 1.02002
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Ranked 222.658 223.047 1.00175
t-complex 11. [refseq;acc:nm_018679] Rooted 66.145 66.7577 1.00926
2559 histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] 58.0778 58.6154
j domain containing protein 1. [swissprot;acc:q9ukb3] Squared 16926 17789.2 1.051
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Ranked 222.658 223.047 1.00175
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Measured 5291.65 5187.78 1.02002
2560 intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Ranked 202.395 202.042 1.00175
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Squared 16926 17789.2 1.051
tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3] Rooted 66.145 66.7577 1.00926
2561 alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 60.5625 61.1201 1.00921
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Squared 16926 17789.2 1.051
fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Ranked 209.825 210.18 1.00169
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Measured 5291.65 5187.78 1.02002
2562 cgthba protein (-14 gene protein). [swissprot;acc:q12980]
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Ranked 208.429 208.779 1.00168
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Squared 3269.52 3111.31 1.05085
heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792] Rooted 60.556 61.109 1.00913
2563 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] 71.8443 72.4984 1.0091
adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263] Ranked 208.429 208.779 1.00168
cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] Squared 37419.3 39316.7 1.05071
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Measured 5291.65 5187.78 1.02002
2564 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Rooted 56.832 56.3214 1.00907
dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] Squared 27109 28479.5 1.05056
protein x 0001. [refseq;acc:nm_016302] Ranked 208.429 208.779 1.00168

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/