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 901 to 950 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
57 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared Subtracted 1 173408 242989 69581
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Ranked Divided 0 8152.55 11134.8 1.36581
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Measured 1 1631.67 2664.55 1.63302
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 219048 129762 1.68808
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Rooted Subtracted 137.446 120.823 16.623
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked 185.678 245.247 59.569
nanos (fragment). [sptrembl;acc:q8wy41] Rooted 0 19.4165 12.2882 7.1283
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Divided 1 41.6879 28.9554 1.43973
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured Subtracted 20911 24908.5 3997.5
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Squared 0 82695.1 87060.9 4365.8
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Ranked 19048 22389 3341
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] Measured 2230.13 1729.7 500.43
58 40s ribosomal protein s26. [swissprot;acc:p02383] Divided 150.741 81.2233 1.85588
dead-box protein. [refseq;acc:nm_018665] Ranked 10628.3 14486 1.36296
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Subtracted 1 185.678 245.247 59.569
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided 266.863 336.191 1.25979
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Measured Subtracted 0 11512.3 12011.7 499.4
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Divided 1 1631.67 2664.55 1.63302
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 219048 129762 1.68808
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Rooted Subtracted 137.446 120.823 16.623
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Squared Divided 0 129.158 488.851 3.78491
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Rooted 1 41.6969 28.9696 1.43933
ptd016 protein. [refseq;acc:nm_016125] Subtracted 0 5.47723 12.5698 7.09257
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Squared 21885.1 17682.1 4203
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Measured 1 20911 24908.5 3997.5
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Squared 173408 242989 69581
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] Rooted Divided 0 11.6322 7.84538 1.48268
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Ranked Subtracted 12460.6 15781 3320.4
59 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Measured 1 20911 24908.5 3997.5
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Squared Divided 0 57.8417 218.049 3.76975
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Measured 150.673 279.24 1.85328
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Ranked 15863.6 11662.3 1.36025
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] Subtracted 9418.7 12695.6 3276.9
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Divided 1 266.863 336.19 1.25978
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 219048 129762 1.68808
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 1631.67 2664.55 1.63302
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Rooted Subtracted 137.446 120.823 16.623
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Divided 0 4.28588 6.23127 1.45391
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Measured Subtracted 11512.3 12011.7 499.4
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Rooted Divided 1 37.2205 52.2064 1.40262
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Subtracted 0 26.63 33.5888 6.9588
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked 1 269.278 327.709 58.431
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 199594 130021 69573
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 0 29631.4 32621.1 2989.7
60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Measured Divided 1 4489.19 2765.82 1.6231
60s ribosomal protein l21. [swissprot;acc:p46778] Ranked Subtracted 0 9994.33 6758.83 3235.5
adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Measured Divided 47.4756 87.5499 1.8441
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Ranked Subtracted 1 269.254 327.655 58.401
fibrillin 3. [refseq;acc:nm_032447] Squared 0 48035.2 45133.4 2901.8
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Ranked Divided 11761 15924 1.35397

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/