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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1708 to 1757 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
427 Rooted neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 54.4927 49.6125 1.09837
428 Measured nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 3721.19 4288.17 1.15237
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
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
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
429 Measured vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 6272.91 7226.06 1.15195
Ranked polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 239.709 259.038 1.08064
Squared programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] 29101.9 35347 1.21459
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
430 Measured transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 3804.09 4379.37 1.15123
Ranked u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 227.748 210.888 1.07995
Squared brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 29098.8 35342.6 1.21457
Rooted leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 54.4927 49.6125 1.09837
431 Measured dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 3849.94 4431.36 1.15102
Ranked trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 236.245 255.113 1.07987
Squared sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 29096 35338.7 1.21456
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
432 Measured mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] 5244.71 6036.27 1.15093
Ranked endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 212.547 229.411 1.07934
Squared calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 29095.3 35337.6 1.21455
Rooted leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 54.4927 49.6125 1.09837
433 Measured mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] 5244.88 6036.38 1.15091
Ranked programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] 212.547 229.411 1.07934
Squared grancalcin. [swissprot;acc:p28676] 29095.7 35338.3 1.21455
Rooted laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 54.4927 49.6125 1.09837
434 Measured ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 5246.38 6037.37 1.15077
Ranked t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] 212.547 229.411 1.07934
Squared splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 18306.1 22230.6 1.21438
Rooted thymic stromal co-transporter. [refseq;acc:nm_033051] 54.4927 49.6125 1.09837
435 Measured proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 5233.86 6022.6 1.1507
Ranked polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 221.522 205.286 1.07909
Squared cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 26598.9 32283.5 1.21372
Rooted 60s ribosomal protein l19. [swissprot;acc:p14118] 50.832 46.3081 1.09769
436 Measured arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 6230.94 7168.2 1.15042
Ranked paxillin. [swissprot;acc:p49023] 221.522 205.286 1.07909
Squared cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] 26598.9 32283.5 1.21372
Rooted putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 210.928 192.165 1.09764
437 Measured suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 3779.92 4348.48 1.15042
Ranked cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 209.921 226.459 1.07878
Squared nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] 26598.9 32283.5 1.21372
Rooted zinc finger protein t86. [swissprot;acc:o00488] 51.0466 56.024 1.09751
438 Measured swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] 6252.58 7192.88 1.15039
Ranked n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 233.723 216.674 1.07869
Squared arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 28863.2 35031.5 1.21371
Rooted 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] 55.1867 60.5522 1.09722
439 Measured programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] 6252.58 7192.88 1.15039
Ranked 40s ribosomal protein s9. [swissprot;acc:p46781] 238.986 257.784 1.07866
Squared cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 51616.7 42588.9 1.21198
Rooted dok-like protein. [refseq;acc:nm_024872] 63.2134 69.352 1.09711
440 Measured calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 6251.91 7192.08 1.15038

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/