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 Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1330 to 1379 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
665 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Subtracted 202.166 214.254 12.088
666 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 238.38 250.465 12.085
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Divided 216.576 229.072 1.0577
667 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted 238.38 250.465 12.085
668 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Divided 216.576 229.072 1.0577
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Subtracted 232.419 244.495 12.076
669 presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] 244.534 232.601 11.933
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Divided 216.576 229.072 1.0577
670 autoantigen ngp-1. [swissprot;acc:q13823] 236.817 250.302 1.05694
gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Subtracted 244.534 232.601 11.933
671 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Divided 199.398 210.739 1.05688
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Subtracted 244.534 232.601 11.933
672 dok-like protein. [refseq;acc:nm_024872] 204.622 216.504 11.882
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Divided 199.398 210.739 1.05688
673 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Subtracted 204.622 216.504 11.882
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Divided 214.355 226.497 1.05664
674 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Subtracted 204.622 216.504 11.882
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Divided 214.355 226.497 1.05664
675 single-minded homolog 1. [swissprot;acc:p81133]
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Subtracted 204.622 216.504 11.882
676 dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Divided 245.613 232.469 1.05654
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Subtracted 257.636 245.84 11.796
677 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 233.483 245.246 11.763
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Divided 216.745 228.944 1.05628
678 peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Subtracted 214.405 226.135 11.73
sorting nexin 5. [swissprot;acc:q9y5x3] Divided 220.175 208.482 1.05609
679 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 125.389 132.413 1.05602
sorting nexin 5. [swissprot;acc:q9y5x3] Subtracted 220.175 208.482 11.693
680 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided 125.389 132.413 1.05602
sr rich protein. [refseq;acc:nm_032870] Subtracted 213.64 225.293 11.653
681 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Divided 125.389 132.413 1.05602
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Subtracted 208.987 220.593 11.606
682 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 125.389 132.413 1.05602
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Subtracted 234.458 246.055 11.597
683 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Divided 125.389 132.413 1.05602
osteoclast stimulating factor 1. [swissprot;acc:q92882] Subtracted 243.289 231.809 11.48
684 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Divided 125.389 132.413 1.05602
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Subtracted 235.027 223.58 11.447
685 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Divided 125.389 132.413 1.05602
686 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Subtracted 235.027 223.58 11.447
687 dendritic cell protein. [refseq;acc:nm_006360] 211.685 223.121 11.436
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Divided 125.389 132.413 1.05602
688 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 250.823 237.554 1.05586
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Subtracted 211.685 223.121 11.436
689 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Divided 128.225 135.379 1.05579
690 cpz gene product. [refseq;acc:nm_003652] Subtracted 211.685 223.121 11.436

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/