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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3408 to 3457 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
426 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Squared Divided 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
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Measured Subtracted 6739.81 7644.62 904.81
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Rooted 66.0817 71.6545 5.5728
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Divided 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
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Subtracted 33104 38818.5 5714.5
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Ranked 212.547 229.411 16.864
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Measured Divided 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
carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] Squared Subtracted 33104 38818.5 5714.5
gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Measured 6739.82 7644.63 904.81
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Rooted 66.0817 71.6543 5.5726
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Measured Divided 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
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Ranked Subtracted 227.748 210.888 16.86
429 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Rooted Divided 54.4927 49.6125 1.09837
cpz gene product. [refseq;acc:nm_003652] Squared Subtracted 33104 38818.5 5714.5
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Rooted 66.0818 71.6537 5.5719
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Measured 6739.81 7644.62 904.81
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Ranked Divided 239.709 259.038 1.08064
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Subtracted 251.344 234.514 16.83
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Squared Divided 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
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Subtracted 33104 38818.5 5714.5
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Measured 6739.82 7644.63 904.81
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Rooted 66.082 71.6526 5.5706
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Divided 54.4927 49.6125 1.09837
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Ranked Subtracted 250.938 234.134 16.804
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Measured Divided 3804.09 4379.37 1.15123
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Ranked 227.748 210.888 1.07995
431 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] Subtracted 233.529 216.737 16.792
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Measured Divided 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
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Subtracted 66.082 71.6526 5.5706
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Measured 6739.82 7644.63 904.81
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Squared 33104 38818.5 5714.5
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Divided 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
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Subtracted 26598.9 32283.5 5684.6
endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Ranked Divided 212.547 229.411 1.07934
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Rooted Subtracted 66.082 71.6526 5.5706
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Divided 54.4927 49.6125 1.09837
mct-1 protein. [refseq;acc:nm_014060] Ranked Subtracted 226.313 243.03 16.717
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Measured Divided 5244.71 6036.27 1.15093
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Subtracted 6739.81 7644.62 904.81
433 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Squared 26598.9 32283.5 5684.6

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/