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 5258 to 5307 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1315 orphan nuclear receptor tr2. [swissprot;acc:p13056] Rooted 62.6353 65.2935 1.04244
signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224] Ranked 222.574 227.752 1.02326
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Squared 27156.9 30637.1 1.12815
1316 ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Rooted 67.3577 70.2116 1.04237
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Measured 6105.93 6599.41 1.08082
signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226] Ranked 222.569 227.739 1.02323
tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] Squared 26403.8 29786.4 1.12811
1317 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] 25544.9 28816.9 1.12809
centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Ranked 206.773 202.105 1.0231
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Rooted 67.3352 70.1873 1.04236
orphan nuclear receptor tr2. [swissprot;acc:p13056] Measured 6105.69 6599.06 1.0808
1318 histone h2b.c (h2b/c). [swissprot;acc:q99880] Squared 15254.5 17204.9 1.12786
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Rooted 67.3368 70.189 1.04236
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Measured 5961.97 6443.07 1.08069
signal transducer and activator of transcription 5a. [swissprot;acc:p42229] Ranked 222.546 227.673 1.02304
1319 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Rooted 67.3443 70.1972 1.04236
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Ranked 159.75 156.153 1.02304
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Squared 15254.5 17204.9 1.12786
serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] Measured 5961.97 6443.07 1.08069
1320 cda11 protein. [refseq;acc:nm_032026] Rooted 63.4104 66.0956 1.04235
glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] Measured 5961.97 6443.07 1.08069
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Squared 15254.5 17204.9 1.12786
signal transducer and activator of transcription 5b. [swissprot;acc:p51692] Ranked 222.544 227.667 1.02302
1321 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Rooted 62.1531 64.7775 1.04222
histone h2b. [refseq;acc:nm_175055] Squared 15254.5 17204.9 1.12786
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] Ranked 226.347 221.259 1.023
suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Measured 6439.79 6959.21 1.08066
1322 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Ranked 159.86 156.275 1.02294
histone h2b.s (h2b/s). [swissprot;acc:p57053] Squared 15254.5 17204.9 1.12786
scratch; scratch 1. [refseq;acc:nm_031309] Rooted 67.9472 70.8115 1.04215
1323 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Ranked 205.225 200.625 1.02293
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Rooted 67.9155 70.7734 1.04208
glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Measured 6439.79 6959.21 1.08066
histone h2b.d (h2b/d). [swissprot;acc:q99877] Squared 15254.5 17204.9 1.12786
1324 glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Measured 6439.79 6959.21 1.08066
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Ranked 159.993 156.421 1.02284
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Squared 15254.5 17204.9 1.12786
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Rooted 68.9332 71.8139 1.04179
1325 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]
serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209] Measured 5656.79 6112.02 1.08047
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Squared 15254.5 17204.9 1.12786
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Ranked 217.133 212.289 1.02282
1326 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 218.509 213.648 1.02275
histone h2b.e (h2b/e). [swissprot;acc:q99879] Squared 15254.5 17204.9 1.12786
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Measured 6222.8 6723.54 1.08047
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Rooted 68.9332 71.8139 1.04179
1327 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Squared 32117.3 36220.6 1.12776
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] Measured 5656.8 6111.9 1.08045
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Rooted 68.9332 71.8139 1.04179

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/