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 3791 to 3840 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
948 vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Rooted 62.4102 66.0829 1.05885
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] Squared 25295.5 29197.3 1.15425
949 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] Measured 4633.48 5084.24 1.09728
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Rooted 82.2821 87.1197 1.05879
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] Ranked 217.253 209.826 1.0354
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Squared 27084.5 31257.9 1.15409
950 bystin. [swissprot;acc:q13895] Measured 4280.99 4697.02 1.09718
dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] Ranked 252.873 261.821 1.03539
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Rooted 82.2706 87.1037 1.05875
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Squared 16129.2 18614.3 1.15407
951 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Measured 5364.3 5885.48 1.09716
gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] Squared 19634.1 22653.4 1.15378
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Rooted 56.264 59.5672 1.05871
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] Ranked 217.253 209.827 1.03539
952 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Rooted 56.264 59.5672 1.05871
my016 protein. [sptrembl;acc:q9h3k6] Squared 18239.4 21037.9 1.15343
putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Measured 5364.3 5885.48 1.09716
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Ranked 217.252 209.83 1.03537
953 casein kinase i alpha s-like. [refseq;acc:nm_145203] Measured 4906.33 5382.5 1.09705
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Rooted 93.6481 88.4638 1.0586
eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Squared 16131.6 18602.2 1.15315
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] Ranked 198.494 205.466 1.03512
954 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Measured 4906.33 5382.5 1.09705
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Squared 16131.6 18602.2 1.15315
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Rooted 93.6382 88.4565 1.05858
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Ranked 267.447 276.773 1.03487
955 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Rooted 93.5947 88.4244 1.05847
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Squared 24856.2 28661.3 1.15308
mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Ranked 231.163 239.205 1.03479
uridine kinase-like 1. [swissprot;acc:q9nwz5] Measured 5548.78 6086.89 1.09698
956 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 5364.77 5884.89 1.09695
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Rooted 93.5901 88.4209 1.05846
serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] Squared 24804.6 28595.4 1.15283
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Ranked 211.812 204.732 1.03458
957 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 129.913 134.399 1.03453
asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] Squared 26822.8 30911.4 1.15243
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Rooted 93.5619 88.4001 1.05839
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Measured 4483.26 4917.77 1.09692
958 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Ranked 129.921 134.406 1.03452
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Squared 29830.2 34375.9 1.15239
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Rooted 82.1645 86.9566 1.05832
959 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Squared 29830.2 34375.9 1.15239
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] Ranked 237.558 229.677 1.03431
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Measured 4379.28 4803.59 1.09689
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Rooted 62.1275 65.7481 1.05828
960 inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Squared 29830.2 34375.9 1.15239
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Rooted 66.4035 70.2633 1.05813
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Measured 11773 10733.2 1.09688
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Ranked 237.558 229.677 1.03431

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/