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 3208 to 3257 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
201 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Rooted Divided 1 61.2893 70.3856 1.14842
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 0 23.8722 20.9336 1.14038
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Ranked 16853 15123 1.1144
mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] Squared Subtracted 1 42411.6 55802.1 13390.5
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Measured 0 6699.82 6856.28 156.46
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Ranked Divided 1 240.133 211.382 1.13601
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] Measured 0 6804.88 5690.63 1.1958
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 1 4810.22 6075.04 1.26294
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Subtracted 10603.5 12069.5 1466
202 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked 240.758 266.079 25.321
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Rooted 0 10.9038 8.12243 2.78137
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] Measured 2039.07 2194.52 155.45
calsyntenin-1 precursor. [swissprot;acc:o94985] 1 10603.5 12069.5 1466
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared Divided 71030.1 95434.8 1.34358
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured 0 606.049 723.75 1.19421
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Squared 3339.18 2360.97 1.41433
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Measured 1 4812.01 6076.09 1.26269
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Rooted 0 23.8722 20.9336 1.14038
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared Subtracted 1 42411.6 55802.1 13390.5
serpin b11. [swissprot;acc:q96p15] Ranked Divided 0 16853 15123 1.1144
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 1 201.478 228.784 1.13553
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Rooted 57.3527 65.7973 1.14724
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Squared Subtracted 0 631.532 280.389 351.143
trs85 homolog. [swissprot;acc:q9y2l5] Rooted 1 138.375 127.926 10.449
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Ranked 0 8214.41 7026.41 1188
203 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 1 240.758 266.078 25.32
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Measured Divided 11757.8 9352.11 1.25723
chromodomain y-like protein 2. [refseq;acc:nm_152342] Squared Subtracted 0 18606.3 18263.6 342.7
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Ranked Divided 16853 15123 1.1144
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 1 201.515 228.752 1.13516
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Squared 0 93.5732 66.2405 1.41263
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 1 20988.2 15632.1 1.34263
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Measured 0 304 363 1.19408
my016 protein. [sptrembl;acc:q9h3k6] Subtracted 1770.21 1615.47 154.74
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Squared 1 42411.6 55802.1 13390.5
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Rooted Divided 0 22.1344 25.2414 1.14037
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Measured Subtracted 1 10603.5 12069.5 1466
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Ranked 0 12196.2 11009.7 1186.5
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Rooted 32.8979 30.1206 2.7773
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Divided 1 46.3291 53.1063 1.14628
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Subtracted 138.032 127.651 10.381
204 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Ranked 268.632 243.588 25.044
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Rooted 138.032 127.651 10.381
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Ranked Divided 0 15081.8 16802.1 1.11406
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Measured Subtracted 1370.82 1525.56 154.74
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Squared Divided 94.1723 66.6659 1.4126
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Rooted 23.8722 20.9337 1.14037
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Ranked Subtracted 10559.7 11732 1172.3
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Measured 1 10603.5 12069.4 1465.9
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Ranked Divided 201.515 228.752 1.13516

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/