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 2708 to 2757 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
677 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Ranked 228.944 216.745 1.05628
678 myelin gene expression factor 2. [refseq;acc:nm_016132] Rooted 56.8369 52.8585 1.07527
sorting nexin 5. [swissprot;acc:q9y5x3] Ranked 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
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Rooted 61.5558 66.1861 1.07522
680 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Measured 6503.03 7282.5 1.11986
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Ranked 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
t54 protein. [swissprot;acc:q92917] Rooted 61.5558 66.1861 1.07522
681 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Squared 22335.8 26232.2 1.17445
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Ranked 132.413 125.389 1.05602
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Rooted 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
682 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Ranked 132.413 125.389 1.05602
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Squared 22335.8 26232.2 1.17445
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Rooted 86.5959 93.0684 1.07474
syntaxin 12. [refseq;acc:nm_177424] Measured 5552.92 6217.59 1.1197
683 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Ranked 132.413 125.389 1.05602
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Measured 7139.5 7994.06 1.11969
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Rooted 72.8809 78.3254 1.0747
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Squared 22328.1 26222.3 1.17441
684 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Measured 4359.82 4880.99 1.11954
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Ranked 132.413 125.389 1.05602
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Rooted 72.9862 78.4342 1.07464
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Squared 22328.2 26222.4 1.17441
685 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Rooted 57.4644 61.7491 1.07456
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Ranked 132.413 125.389 1.05602
metaxin 1. [swissprot;acc:q13505] Measured 9327.58 10442.2 1.1195
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Squared 42363.8 36083.8 1.17404
686 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Measured 6920.69 7747.63 1.11949
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Rooted 86.4264 92.8635 1.07448
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Ranked 132.413 125.389 1.05602
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Squared 28982.3 34012.8 1.17357
687 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Measured 6920.71 7747.65 1.11949
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Squared 24633.6 28893.6 1.17293
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Rooted 57.6308 61.9165 1.07436
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Ranked 132.413 125.389 1.05602
688 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Measured 6920.67 7747.6 1.11949
adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Squared 22245.5 26087.5 1.17271
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Rooted 60.7997 65.3199 1.07435
dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Ranked 237.554 250.823 1.05586
689 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Measured 6920.69 7747.63 1.11949
dendritic cell protein. [refseq;acc:nm_006360] Squared 33104 38818.5 1.17262
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted 100.684 108.135 1.074
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Ranked 135.379 128.225 1.05579
690 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Measured 6920.69 7747.63 1.11949

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/