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.


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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 5108 to 5157 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
639 ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Measured Subtracted 4890.51 5610.95 720.44
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Ranked Divided 217.67 230.596 1.05938
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Measured 7753.59 8728.13 1.12569
paxillin. [swissprot;acc:p49023] Squared Subtracted 22387.1 26827.3 4440.2
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Ranked 222.554 234.847 12.293
640 60s ribosomal protein l35. [swissprot;acc:p42766] Rooted 50.2545 45.5637 4.6908
actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Divided 60.0129 64.7371 1.07872
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Measured Subtracted 4890.51 5610.95 720.44
glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] Squared 34742.2 30305.8 4436.4
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Measured Divided 4811.02 5414.64 1.12547
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Ranked Subtracted 244.842 232.577 12.265
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Divided 217.67 230.596 1.05938
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Squared 22848.5 26941.5 1.17914
641 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Ranked Subtracted 244.842 232.577 12.265
glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506] Squared 34742.2 30305.8 4436.4
histone h2b.c (h2b/c). [swissprot;acc:q99880] Rooted 50.6084 55.2961 4.6877
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Measured 4890.51 5610.95 720.44
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Divided 4810.85 5414.21 1.12542
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Ranked 217.67 230.596 1.05938
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Rooted 60.0129 64.7371 1.07872
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Squared 18364.9 21653.8 1.17909
642 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 16123.9 19009.7 1.17898
atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] Measured 4810.85 5414.23 1.12542
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Squared Subtracted 58316.6 53884.7 4431.9
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Measured 4890.55 5610.96 720.41
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Rooted 50.6084 55.2961 4.6877
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Ranked Divided 217.67 230.596 1.05938
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Rooted 64.4857 69.5606 1.0787
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Ranked Subtracted 228.944 216.745 12.199
643 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] Squared Divided 16126.5 19012.6 1.17897
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Rooted 87.4586 81.0798 1.07867
creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Squared Subtracted 58381 53950.3 4430.7
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Rooted 50.6084 55.2961 4.6877
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Ranked Divided 217.67 230.596 1.05938
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Subtracted 218.227 206.078 12.149
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Measured Divided 4810.85 5414.23 1.12542
scratch; scratch 1. [refseq;acc:nm_031309] Subtracted 7281.6 8001.64 720.04
644 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Squared Divided 16156.3 19046 1.17886
cgthba protein (-14 gene protein). [swissprot;acc:q12980] Ranked 217.67 230.596 1.05938
cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Measured 4810.85 5414.22 1.12542
histone h2b. [refseq;acc:nm_175055] Rooted Subtracted 50.6084 55.2961 4.6877
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Squared 29907.6 34337 4429.4
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Ranked 226.497 214.355 12.142
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Measured 5713.41 6432.92 719.51
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Rooted Divided 51.1896 47.4617 1.07855
645 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Measured 4810.71 5413.89 1.12538
histone h2b.s (h2b/s). [swissprot;acc:p57053] Rooted Subtracted 50.6084 55.2961 4.6877
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Ranked Divided 217.67 230.596 1.05938
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Subtracted 226.497 214.355 12.142
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Measured 4892.16 5611.48 719.32

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/