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 1001 to 1050 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked 1 94 114 1.21277
calcyphosine. [swissprot;acc:q13938] Measured 0 472.524 635.875 1.3457
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 1 24250 18164.9 1.33499
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Squared 0 118.204 219.216 1.85456
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Rooted 21.3244 25.9172 1.21538
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 1 60.9342 75.1387 1.23311
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] Ranked 0 9722.71 11493.8 1.18216
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Squared 1 189976 124480 1.52616
127 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 88432.6 58423.3 1.51365
high-mobility group 20a. [refseq;acc:nm_018200] Rooted 60.9353 75.094 1.23236
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Measured 0 86 64 1.34375
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Ranked 1 94 114 1.21277
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Rooted 0 37.9737 31.257 1.21489
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Squared 799.337 432.882 1.84655
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Ranked 9411.34 11119.7 1.18152
transcription factor jun-d. [swissprot;acc:p17535] Measured 1 5638.2 7523.39 1.33436
128 60s ribosomal protein l39. [swissprot;acc:p02404] Ranked 0 11564.4 9794.29 1.18073
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 1 94 114 1.21277
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Squared 0 166.774 90.363 1.8456
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Measured 1 4355.61 5810.82 1.3341
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 0 81.504 60.8613 1.33918
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] Rooted 37.9737 31.257 1.21489
pnas-18. [sptrembl;acc:q9bzu3] Squared 1 87787.3 58155.8 1.50952
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 39.0445 1.23069
129 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Squared 0 21723.1 39570.4 1.82158
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted 1 54.2343 66.7323 1.23044
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Ranked 0 14222.5 12058.6 1.17945
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Measured 1 4358.13 5811.49 1.33348
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Ranked 94 114 1.21277
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Rooted 0 27.8028 22.9122 1.21345
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Squared 1 178263 118639 1.50257
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Measured 0 606.485 454.837 1.33341
130 44050 protein. [refseq;acc:nm_178832] Squared 1 148058 99628.4 1.4861
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 0 21165.1 38499.2 1.81899
enigma protein; lim domain protein. [refseq;acc:nm_005451] Ranked 14476.2 17069.5 1.17914
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Measured 1 2234.68 2978.53 1.33287
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Rooted 55.1026 67.5701 1.22626
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Measured 0 42 56 1.33333
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Ranked 1 94 114 1.21277
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Rooted 0 12.7347 10.4997 1.21286
131 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 19.3128 16.0484 1.20341
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Ranked 8375.43 9873.58 1.17887
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Measured 1 2234.73 2978.57 1.33285
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Rooted 55.1113 67.5537 1.22577
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 148058 99628.4 1.4861
serpin b11. [swissprot;acc:q96p15] Measured 0 42 56 1.33333
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Ranked 1 294.053 242.562 1.21228
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Squared 0 451.156 817.981 1.81308
132 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 1 36359.2 24466.8 1.48606
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Rooted 0 23.9003 19.8655 1.20311

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/