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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3658 to 3707 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
458 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Rooted 1 50.2954 45.9216 1.09524
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Measured 4890.55 5610.96 1.14731
far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Squared 0 246.531 241.387 1.02131
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 1 10950.4 13235.9 1.20871
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Measured 0 2633.61 2668.56 1.01327
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Ranked 1 235.922 218.925 1.07764
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] 0 16416.1 16721.6 1.01861
459 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] 1 233.529 216.737 1.07748
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Measured 0 3774.08 3821.87 1.01266
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 1 4892.16 5611.48 1.14704
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Squared 27096.7 32743.5 1.20839
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Rooted 0 30.9876 30.5384 1.01471
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Squared 18485.5 18144.8 1.01878
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Ranked 20875 20495 1.01854
vav proto-oncogene. [swissprot;acc:p15498] Rooted 1 66.0892 72.3741 1.0951
460 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 0 16.2959 16.5202 1.01376
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Measured 3693.07 3739.55 1.01259
mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] Ranked 20914 20558 1.01732
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Measured 1 3790.11 4346.98 1.14693
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Rooted 50.6156 46.2239 1.09501
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Ranked 223.648 207.62 1.0772
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Squared 0 18489.4 18148.7 1.01877
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 1 29547.4 35683.5 1.20767
461 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Rooted 50.6156 46.2239 1.09501
chromodomain y-like protein 2. [refseq;acc:nm_152342] Squared 0 18606.3 18263.6 1.01876
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Measured 1915.69 1892.44 1.01229
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Rooted 62.6706 61.8357 1.0135
grb2-related adaptor protein. [swissprot;acc:q13588] Measured 1 5986.65 6865.68 1.14683
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Ranked 223.648 207.62 1.0772
scratch; scratch 1. [refseq;acc:nm_031309] 0 12164.9 12358.1 1.01588
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Squared 1 29544.1 35678.3 1.20763
462 40s ribosomal protein s3. [swissprot;acc:p23396] Rooted 50.6274 46.236 1.09498
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Ranked 0 12189.6 12378.3 1.01548
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Squared 2400.71 2356.66 1.01869
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Measured 11170.7 11305 1.01202
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Ranked 1 254.434 236.224 1.07709
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Measured 11383.2 9926.61 1.14674
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Rooted 0 18.5298 18.2858 1.01334
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Squared 1 29540.4 35672.6 1.20759
463 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Measured 3720.18 4264.46 1.1463
calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Squared 25533.3 30810.8 1.20669
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Measured 0 1262.65 1248.14 1.01163
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Ranked 5558.06 5473.99 1.01536
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Squared 2403.2 2359.13 1.01868
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Ranked 1 238.921 257.327 1.07704
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Rooted 50.2317 55.0025 1.09498
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 0 35.7784 35.3221 1.01292
464 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] 30.3413 30.7252 1.01265
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Ranked 1 210.578 226.764 1.07686
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 0 10076.4 9928.08 1.01494

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/