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.


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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 1701 to 1750 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
426 dynactin 4. [refseq;acc:nm_032486] Ranked 233.142 252.253 1.08197
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Rooted 55.1073 60.5285 1.09838
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Measured 5942.49 6853.15 1.15325
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 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
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Rooted 54.4927 49.6125 1.09837
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Squared 25380.3 30835.9 1.21495
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Measured 11736.6 13531.9 1.15297
428 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
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
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Measured 3721.19 4288.17 1.15237
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
429 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
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Ranked 239.709 259.038 1.08064
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Squared 29101.9 35347 1.21459
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Measured 6272.91 7226.06 1.15195
430 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Squared 29098.8 35342.6 1.21457
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Rooted 54.4927 49.6125 1.09837
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Measured 3804.09 4379.37 1.15123
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Ranked 227.748 210.888 1.07995
431 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Measured 3849.94 4431.36 1.15102
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
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Squared 29096 35338.7 1.21456
trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Ranked 236.245 255.113 1.07987
432 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Squared 29095.3 35337.6 1.21455
endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Ranked 212.547 229.411 1.07934
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Rooted 54.4927 49.6125 1.09837
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 grancalcin. [swissprot;acc:p28676] Squared 29095.7 35338.3 1.21455
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Rooted 54.4927 49.6125 1.09837
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Measured 5244.88 6036.38 1.15091
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Ranked 212.547 229.411 1.07934
434 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Squared 18306.1 22230.6 1.21438
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Ranked 212.547 229.411 1.07934
thymic stromal co-transporter. [refseq;acc:nm_033051] Rooted 54.4927 49.6125 1.09837
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Measured 5246.38 6037.37 1.15077
435 60s ribosomal protein l19. [swissprot;acc:p14118] Rooted 50.832 46.3081 1.09769
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Squared 26598.9 32283.5 1.21372
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Ranked 221.522 205.286 1.07909
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Measured 5233.86 6022.6 1.1507
436 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 6230.94 7168.2 1.15042
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Squared 26598.9 32283.5 1.21372
paxillin. [swissprot;acc:p49023] Ranked 221.522 205.286 1.07909
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Rooted 210.928 192.165 1.09764
437 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Ranked 209.921 226.459 1.07878
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Squared 26598.9 32283.5 1.21372
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Measured 3779.92 4348.48 1.15042
zinc finger protein t86. [swissprot;acc:o00488] Rooted 51.0466 56.024 1.09751
438 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Squared 28863.2 35031.5 1.21371
bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Rooted 55.1867 60.5522 1.09722

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/