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 1813 to 1862 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
454 40s ribosomal protein s26. [swissprot;acc:p02383] Divided 1 210.224 226.578 1.07779
grb2-related adaptor protein. [swissprot;acc:q13588] Subtracted 223.457 207.222 16.235
lats homolog 1. [refseq;acc:nm_004690] Divided 0 13933.5 14204.8 1.01947
scratch; scratch 1. [refseq;acc:nm_031309] Subtracted 12164.9 12358.1 193.2
455 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 1 224.161 207.972 16.189
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 0 12189.6 12378.3 188.7
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Divided 1 210.225 226.578 1.07779
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] 0 13933.5 14204.8 1.01947
456 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] 1 210.225 226.578 1.07779
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Subtracted 0 7965.06 7790.78 174.28
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 1 224.161 207.972 16.189
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Divided 0 16416.1 16721.6 1.01861
457 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Subtracted 1 210.578 226.764 16.186
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 0 7965.06 7790.78 174.28
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Divided 1 210.225 226.578 1.07779
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] 0 16416.1 16721.6 1.01861
458 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Subtracted 1 251.653 235.506 16.147
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 0 7759.36 7586.42 172.94
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 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
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Subtracted 0 5905 6073 168
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] 1 250.538 234.401 16.137
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Divided 0 20875 20495 1.01854
460 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Subtracted 18667 18500 167
mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] Divided 20914 20558 1.01732
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Subtracted 1 186.52 170.42 16.1
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Divided 223.648 207.62 1.0772
461 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]
protein cgi-147. [swissprot;acc:q9y3e5] Subtracted 0 5135.25 5298.12 162.87
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 1 186.52 170.42 16.1
scratch; scratch 1. [refseq;acc:nm_031309] Divided 0 12164.9 12358.1 1.01588
462 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Subtracted 10076.4 9928.08 148.32
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Divided 12189.6 12378.3 1.01548
dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Subtracted 1 236.662 252.708 16.046
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Divided 254.434 236.224 1.07709
463 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 0 5558.06 5473.99 1.01536
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 1 238.921 257.327 1.07704
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Subtracted 0 11319.2 11463 143.8
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 1 223.648 207.62 16.028
464 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Divided 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
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] Subtracted 1 223.648 207.62 16.028
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 0 15920 15780.2 139.8
465 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 1 224.662 240.673 16.011
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Divided 248.152 267.226 1.07686
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 0 9482.68 9620.66 1.01455
Subtracted 137.98
466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Divided 1 248.152 267.226 1.07686
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Subtracted 0 15155.8 15031.7 124.1

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/