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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 9036 to 9085 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2259 ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] Measured 6486.84 6786.23 1.04615
2260 block 23. [sptrembl;acc:q8nhw5] 5150.14 5387.84
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Squared 22323.5 24140.5 1.08139
leng5 protein. [refseq;acc:nm_024075] Ranked 221.599 220.351 1.00566
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Rooted 71.6125 73.1078 1.02088
2261 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] Measured 6486.84 6786.23 1.04615
chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] Rooted 71.6125 73.1078 1.02088
heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Squared 22323.5 24140.5 1.08139
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Ranked 221.599 220.351 1.00566
2262 fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] Squared 22323.5 24140.5 1.08139
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Ranked 221.599 220.351 1.00566
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Measured 5148.88 5386.34 1.04612
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Rooted 71.6125 73.108 1.02088
2263 40s ribosomal protein s3a. [swissprot;acc:p49241] Measured 4918.64 5145.39 1.0461
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Rooted 60.1456 61.4009 1.02087
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Ranked 221.599 220.351 1.00566
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Squared 22323.5 24140.5 1.08139
2264 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Measured 3633.74 3473.68 1.04608
cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Rooted 60.3644 61.6167 1.02075
elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] Squared 22323.5 24140.5 1.08139
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Ranked 221.599 220.351 1.00566
2265 mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] 211.597 210.416 1.00561
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Measured 3612.45 3453.39 1.04606
rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Squared 22323.5 24140.5 1.08139
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Rooted 86.2704 84.5258 1.02064
2266 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] 62.7034 61.44 1.02056
guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] Squared 24025.5 25976.9 1.08122
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Ranked 211.597 210.416 1.00561
transcription factor iib. [refseq;acc:nm_013242] Measured 9146.11 8743.98 1.04599
2267 cab2. [refseq;acc:nm_033419] Rooted 62.7034 61.44 1.02056
cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] Squared 26297.5 28426.6 1.08096
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Measured 9146.11 8743.98 1.04599
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Ranked 211.597 210.416 1.00561
2268 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] Rooted 62.7034 61.44 1.02056
eyes absent homolog 1. [swissprot;acc:q99502] Measured 5785.08 6051.03 1.04597
tripartite motif protein 2. [swissprot;acc:q9c040] Ranked 202.312 203.437 1.00556
tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382] Squared 44103.2 40803.3 1.08087
2269 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] Ranked 217.419 218.627 1.00556
dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Rooted 62.7034 61.44 1.02056
lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] Squared 27641.2 29861.7 1.08033
upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Measured 6373.94 6666.87 1.04596
2270 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 6568.41 6869.9 1.0459
eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Rooted 62.7034 61.44 1.02056
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Ranked 207.54 208.69 1.00554
tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Squared 27641.2 29861.7 1.08033
2271 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Measured 6568.51 6869.97 1.04589
defender against cell death 1 (dad-1). [swissprot;acc:p46966] Squared 27641.2 29861.7 1.08033
dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Ranked 216.622 215.436 1.00551
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Rooted 62.7034 61.44 1.02056
2272 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Measured 6568.51 6869.97 1.04589

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/