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 1132 to 1181 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
71 serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Measured Subtracted 1 17738.5 13995.7 3742.8
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Rooted Divided 0 22.1933 16.1491 1.37427
tubby protein homolog. [swissprot;acc:p50607] Measured Subtracted 3797.57 4228.27 430.7
ubiquitin protein ligase. [refseq;acc:nm_130466] Divided 620 352.75 1.75762
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] Squared Subtracted 6123.28 3763.18 2360.1
72 44050 protein. [refseq;acc:nm_178832] 1 148058 99628.4 48429.6
60s ribosomal protein l21. [swissprot;acc:p46778] Measured Divided 0 572 992.083 1.73441
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Subtracted 1 17710.9 13977.7 3733.2
deltex 2. [refseq;acc:nm_020892] Rooted 27.634 43.9629 16.3289
fos-related antigen 2. [swissprot;acc:p15408] Squared Divided 0 6691.06 2188.28 3.05768
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Ranked 1 267.144 336.073 1.25802
importin 9. [refseq;acc:nm_018085] Rooted 0 21.8651 29.828 1.36418
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Squared 1 219048 129762 1.68808
metaxin 1. [swissprot;acc:q13505] Ranked Subtracted 0 13761.3 16422.1 2660.8
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Rooted Divided 1 27.9136 37.2872 1.33581
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Ranked Subtracted 265.639 319.546 53.907
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Divided 0 4119 5397 1.31027
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] Measured Subtracted 679.449 1106.88 427.431
syntaxin 10 (syn10). [swissprot;acc:o60499] Rooted 9.62443 3.64637 5.97806
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] Squared 6123.28 3763.18 2360.1
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Measured Divided 1 4556.79 2945.28 1.54715
73 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Rooted Subtracted 27.7078 44.017 16.3092
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 0 8.79142 14.7392 5.94778
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] Ranked Divided 1 288 362 1.25694
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Subtracted 265.632 319.531 53.899
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Squared Divided 219048 129762 1.68808
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Rooted 27.9136 37.2872 1.33581
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Squared Subtracted 148058 99628.4 48429.6
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Ranked 0 9465.55 12106.5 2640.95
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Rooted Divided 21.8651 29.828 1.36418
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Squared 1495.1 509.542 2.9342
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Ranked 4119 5397 1.31027
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Measured 65.2968 37.693 1.73233
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] Squared Subtracted 10596.4 8278.87 2317.53
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Measured 1965.47 2389.69 424.22
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Divided 1 4556.83 2945.38 1.54711
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Subtracted 22268.8 18560.4 3708.4
74 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared 117858 70570.1 47287.9
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Ranked Divided 0 6742.5 8759.5 1.29915
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] Measured 501.151 859.34 1.71473
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Squared Subtracted 18585 20796.3 2211.3
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Ranked 14548.5 11915.2 2633.3
dok-like protein. [refseq;acc:nm_024872] Rooted 5.91608 0 5.91608
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Measured 14267.5 14688.8 421.3
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] Rooted Divided 5.01247 6.80523 1.35766
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured Subtracted 1 20446.1 24136.4 3690.3
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Ranked Divided 288 362 1.25694
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Rooted 27.9136 37.2872 1.33581
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] Squared 0 0.092781 0.0318343 2.9145
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Measured 1 4556.99 2945.8 1.54694

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/