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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1680 to 1729 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
420 RPL24 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Squared 30924.3 37652.3 1.21756
421 no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Rooted 50.4666 45.9317 1.09873
CBL cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Squared 36933 44953.6 1.21717
TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Ranked 223.202 205.9 1.08403
VAV2 vav-2 protein. [swissprot;acc:p52735] Measured 6660.02 7697.78 1.15582
422 MLH3 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Squared 25860 31475.4 1.21715
NXF5 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Measured 5206.9 6010.04 1.15425
RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] Ranked 240.287 260.193 1.08284
RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] Rooted 50.4641 45.9293 1.09873
423 CBLB signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Squared 36735.7 44689.6 1.21652
CDH1 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Rooted 50.4663 45.9313 1.09873
NXF3 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Measured 5207.03 6010.1 1.15423
RAB26 ras-related protein rab-26. [swissprot;acc:q9ulw5] Ranked 240.287 260.193 1.08284
424 no value 60s ribosomal protein l23a. [swissprot;acc:p29316] Rooted 50.4703 45.9373 1.09868
NXF1 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Measured 5207.78 6010.45 1.15413
PMPCA mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Squared 20259.5 24635.7 1.21601
POLR2C dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Ranked 240.287 260.193 1.08284
425 MAX max protein. [swissprot;acc:p25912] 227.828 210.561 1.082
NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Measured 3729.02 4301.58 1.15354
PMPCB mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Squared 20258.6 24634.7 1.21601
RPS20 40s ribosomal protein s20. [swissprot;acc:p17075] Rooted 50.0161 45.5318 1.09849
426 ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 55.1073 60.5285 1.09838
DCTN5 dynactin 4. [refseq;acc:nm_032486] Ranked 233.142 252.253 1.08197
PEF1 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Measured 5942.49 6853.15 1.15325
UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Squared 20267.8 24644.8 1.21596
427 CHRNA7 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Rooted 54.4927 49.6125 1.09837
PMS2 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Squared 25380.3 30835.9 1.21495
POLR2E dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Ranked 239.977 259.525 1.08146
TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Measured 11736.6 13531.9 1.15297
428 ADCY6 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Rooted 54.4927 49.6125 1.09837
ARID1A swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Squared 29101.9 35347 1.21459
DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Ranked 253.852 234.808 1.0811
GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Measured 3721.19 4288.17 1.15237
429 ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Rooted 54.4927 49.6125 1.09837
PDCD6 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Squared 29101.9 35347 1.21459
POLR3G polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Ranked 239.709 259.038 1.08064
SORBS3 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Measured 6272.91 7226.06 1.15195
430 ARID1B brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Squared 29098.8 35342.6 1.21457
LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Rooted 54.4927 49.6125 1.09837
LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Ranked 227.748 210.888 1.07995
TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Measured 3804.09 4379.37 1.15123
431 DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 3849.94 4431.36 1.15102
FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Rooted 54.4927 49.6125 1.09837
SRI sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Squared 29096 35338.7 1.21456
TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Ranked 236.245 255.113 1.07987
432 CAPNS1 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Squared 29095.3 35337.6 1.21455
ENDOG endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Ranked 212.547 229.411 1.07934
LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Rooted 54.4927 49.6125 1.09837
PMPCB mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Measured 5244.71 6036.27 1.15093
433 AIFM1 programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Ranked 212.547 229.411 1.07934

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
- Hugo is the HGNC identifier if it exists
- 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/