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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1677 to 1726 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
420 CD209 Ranked cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 233.539 253.197 1.08417
HPRT1 Measured hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 10235.2 11830.8 1.15589
POLE Rooted dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 51.7959 56.9253 1.09903
RPL24 Squared 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 30924.3 37652.3 1.21756
421 no value Rooted c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 50.4666 45.9317 1.09873
CBL Squared cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 36933 44953.6 1.21717
TFIP11 Ranked tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 223.202 205.9 1.08403
VAV2 Measured vav-2 protein. [swissprot;acc:p52735] 6660.02 7697.78 1.15582
422 MLH3 Squared dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 25860 31475.4 1.21715
NXF5 Measured nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 5206.9 6010.04 1.15425
RAB37 Ranked ras-related protein rab-37. [swissprot;acc:q96ax2] 240.287 260.193 1.08284
RPL5 Rooted 60s ribosomal protein l5. [swissprot;acc:p46777] 50.4641 45.9293 1.09873
423 CBLB Squared signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 36735.7 44689.6 1.21652
CDH1 Rooted epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 50.4663 45.9313 1.09873
NXF3 Measured nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 5207.03 6010.1 1.15423
RAB26 Ranked ras-related protein rab-26. [swissprot;acc:q9ulw5] 240.287 260.193 1.08284
424 no value Rooted 60s ribosomal protein l23a. [swissprot;acc:p29316] 50.4703 45.9373 1.09868
NXF1 Measured nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 5207.78 6010.45 1.15413
PMPCA Squared mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] 20259.5 24635.7 1.21601
POLR2C Ranked dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] 240.287 260.193 1.08284
425 MAX max protein. [swissprot;acc:p25912] 227.828 210.561 1.082
NIP7 Measured saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 3729.02 4301.58 1.15354
PMPCB Squared mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] 20258.6 24634.7 1.21601
RPS20 Rooted 40s ribosomal protein s20. [swissprot;acc:p17075] 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 Ranked dynactin 4. [refseq;acc:nm_032486] 233.142 252.253 1.08197
PEF1 Measured pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 5942.49 6853.15 1.15325
UQCRC1 Squared ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 20267.8 24644.8 1.21596
427 CHRNA7 Rooted neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 54.4927 49.6125 1.09837
PMS2 Squared pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 25380.3 30835.9 1.21495
POLR2E Ranked dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 239.977 259.525 1.08146
TRMU Measured trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 11736.6 13531.9 1.15297
428 ADCY6 Rooted adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 54.4927 49.6125 1.09837
ARID1A Squared swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] 29101.9 35347 1.21459
DDX54 Ranked atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 253.852 234.808 1.0811
GTPBP4 Measured nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 3721.19 4288.17 1.15237
429 ADCY5 Rooted adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 54.4927 49.6125 1.09837
PDCD6 Squared programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] 29101.9 35347 1.21459
POLR3G Ranked polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 239.709 259.038 1.08064
SORBS3 Measured vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 6272.91 7226.06 1.15195
430 ARID1B Squared brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 29098.8 35342.6 1.21457
LRRC15 Rooted leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 54.4927 49.6125 1.09837
LSM5 Ranked u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 227.748 210.888 1.07995
TFDP2 Measured transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 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 Rooted fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 54.4927 49.6125 1.09837
SRI Squared sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 29096 35338.7 1.21456
TRUB1 Ranked trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 236.245 255.113 1.07987
432 CAPNS1 Squared calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 29095.3 35337.6 1.21455
ENDOG Ranked endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 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/