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 4058 to 4107 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
508 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Measured Subtracted 6920.69 7747.63 826.94
autoantigen ngp-1. [swissprot;acc:q13823] Rooted Divided 49.4756 53.9896 1.09124
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] Squared 23512.2 28206.2 1.19964
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Ranked 177.698 190.24 1.07058
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Rooted Subtracted 84.6378 89.8201 5.1823
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Squared 28982.3 34012.8 5030.5
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Ranked 228.255 213.422 14.833
509 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Measured Divided 7551.8 8630.06 1.14278
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Subtracted 6920.67 7747.6 826.93
60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Rooted Divided 50.2583 46.057 1.09122
carboxypeptidase b precursor. [refseq;acc:nm_020361] Ranked 177.698 190.239 1.07057
dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Squared 23512.2 28206.2 1.19964
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Ranked Subtracted 215.237 230.07 14.833
prohibitin. [swissprot;acc:p35232] Squared 22841.8 27856.2 5014.4
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Rooted 84.6378 89.8201 5.1823
510 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Measured 7087.23 7911.25 824.02
exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Ranked 215.237 230.07 14.833
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Measured Divided 5975.11 6826.24 1.14245
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Ranked 177.699 190.24 1.07057
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Rooted 149.397 136.972 1.09071
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Squared Subtracted 22841.8 27856.2 5014.4
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Rooted 84.6378 89.8201 5.1823
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Squared Divided 17281.7 20723 1.19913
511 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] Subtracted 26048.6 31057.4 5008.8
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Measured 6912.56 7735.12 822.56
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Rooted 84.6378 89.8201 5.1823
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Squared Divided 17281.7 20723 1.19913
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Ranked 250.053 233.725 1.06986
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Measured 5975.11 6826.24 1.14245
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Ranked Subtracted 214.754 229.565 14.811
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Rooted Divided 50.5979 46.392 1.09066
512 alpha-nac protein. [sptrembl;acc:q9h009] Measured Subtracted 6912.27 7734.68 822.41
block of proliferation 1. [swissprot;acc:q14137] Ranked Divided 250.794 234.433 1.06979
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Squared 19987.6 23960.7 1.19878
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Rooted Subtracted 84.6378 89.8201 5.1823
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Divided 56.3798 61.4858 1.09056
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Ranked Subtracted 229.803 215.301 14.502
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Squared 26084.2 31084.3 5000.1
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Measured Divided 10807.4 12338.5 1.14167
513 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 7485.08 8543.66 1.14143
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Rooted 51.5881 47.3127 1.09036
keratin associated protein 9.2. [refseq;acc:nm_031961] Squared Subtracted 31100.8 36090.1 4989.3
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] Rooted 84.6378 89.8201 5.1823
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Ranked Divided 218.596 204.344 1.06975
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Measured Subtracted 6912.09 7734.41 822.32
transforming protein rhoc (h9). [swissprot;acc:p08134] Squared Divided 19987.6 23960.7 1.19878
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Ranked Subtracted 227.483 212.994 14.489
514 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Measured Divided 7477 8532.02 1.1411
di-ras2. [refseq;acc:nm_017594] Subtracted 6912.08 7734.39 822.31
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Squared 31100.2 36086.5 4986.3

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/