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 5408 to 5457 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
676 vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] Squared Subtracted 25904.2 30273.7 4369.5
677 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Divided 22335.8 26232.2 1.17445
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Measured Subtracted 4024.4 4719.35 694.95
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Ranked 245.246 233.483 11.763
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Rooted 57.2007 61.7615 4.5608
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Divided 59.2629 63.7418 1.07558
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Squared Subtracted 24614 28973.4 4359.4
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Measured Divided 5549.2 6215.42 1.12006
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Ranked 228.944 216.745 1.05628
678 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Measured Subtracted 6784.67 7475.48 690.81
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Rooted 57.2007 61.7615 4.5608
importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] Squared 23534.9 27890.2 4355.3
myelin gene expression factor 2. [refseq;acc:nm_016132] Rooted Divided 56.8369 52.8585 1.07527
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Ranked Subtracted 226.135 214.405 11.73
sorting nexin 5. [swissprot;acc:q9y5x3] Divided 208.482 220.175 1.05609
surfeit locus protein 1. [swissprot;acc:q15526] Squared 22335.8 26232.2 1.17445
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Measured 6938.22 7770.65 1.11998
679 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 6503.1 7282.94 1.11992
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Squared 22337.3 26234.1 1.17445
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Ranked 132.413 125.389 1.05602
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Measured Subtracted 4910.6 5600.61 690.01
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Rooted 57.2007 61.7615 4.5608
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Divided 61.5558 66.1861 1.07522
sorting nexin 5. [swissprot;acc:q9y5x3] Ranked Subtracted 208.482 220.175 11.693
voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448] Squared 23526.4 27879.4 4353
680 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Measured Divided 6503.03 7282.5 1.11986
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Rooted Subtracted 57.2008 61.7614 4.5606
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Measured 4910.6 5600.61 690.01
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Ranked Divided 132.413 125.389 1.05602
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Squared 22336.8 26233.5 1.17445
sr rich protein. [refseq;acc:nm_032870] Ranked Subtracted 225.293 213.64 11.653
t54 protein. [swissprot;acc:q92917] Rooted Divided 61.5558 66.1861 1.07522
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470] Squared Subtracted 23526.4 27879.3 4352.9
681 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Divided 22335.8 26232.2 1.17445
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Ranked 132.413 125.389 1.05602
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Rooted Subtracted 57.208 61.7592 4.5512
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Ranked 220.593 208.987 11.606
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Rooted Divided 80.2562 86.277 1.07502
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Measured 7170.83 8029.64 1.11976
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Subtracted 4910.6 5600.61 690.01
voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722] Squared 23526.4 27879.3 4352.9
682 60s ribosomal protein l12. [swissprot;acc:p30050] Rooted 49.9858 45.4433 4.5425
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Ranked Divided 132.413 125.389 1.05602
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Measured Subtracted 5560.06 6248.27 688.21
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Squared Divided 22335.8 26232.2 1.17445
similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557] Subtracted 23526.4 27879.3 4352.9
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Rooted Divided 86.5959 93.0684 1.07474
syntaxin 12. [refseq;acc:nm_177424] Measured 5552.92 6217.59 1.1197
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Ranked Subtracted 246.055 234.458 11.597
683 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Rooted 49.9856 45.4431 4.5425

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/