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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5958 to 6007 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
745 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Measured Divided 4086.6 4557.68 1.11527
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Ranked 214.679 225.568 1.05072
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Rooted 67.0475 71.5566 1.06725
746 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Subtracted 61.0098 65.3071 4.2973
eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Ranked Divided 250.465 238.38 1.0507
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Squared 31406.6 36662.8 1.16736
katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Rooted 54.5195 51.084 1.06725
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Measured Subtracted 9899.73 9251.16 648.57
protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Ranked 213.804 224.226 10.422
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Squared 31558.8 35722 4163.2
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Measured Divided 4086.6 4557.68 1.11527
747 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Subtracted 9899.73 9251.16 648.57
down-regulated in metastasis. [refseq;acc:nm_014503] Divided 4086.6 4557.68 1.11527
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Rooted Subtracted 61.0111 65.3081 4.297
inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] Squared 25560.1 29720.6 4160.5
rho interacting protein 3. [refseq;acc:nm_015134] Ranked 213.803 224.224 10.421
sr rich protein. [refseq;acc:nm_032870] Rooted Divided 61.4809 65.6088 1.06714
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Squared 31401.8 36655.7 1.16731
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Ranked 250.465 238.38 1.0507
748 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Squared 23148.8 27021.5 1.1673
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Measured 12503.3 11212 1.11517
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Ranked 245.246 233.483 1.05038
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Rooted Subtracted 51.7204 56.0156 4.2952
inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Squared 25555.4 29715.4 4160
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Rooted Divided 60.4376 64.4898 1.06705
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Ranked Subtracted 222.082 211.707 10.375
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Measured 9899.73 9251.16 648.57
749 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Rooted Divided 66.9737 71.4637 1.06704
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Measured Subtracted 3432.96 4081.21 648.25
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Squared Divided 23148.8 27021.5 1.1673
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Subtracted 24644.9 28800.7 4155.8
dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] Ranked 210.946 221.225 10.279
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Measured Divided 4565.34 5085.92 1.11403
exocyst complex component sec15b. [swissprot;acc:q9y2d4] Ranked 221.968 211.326 1.05036
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Rooted Subtracted 57.6308 61.9165 4.2857
750 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] Squared 27478.1 31623.7 4145.6
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Measured 9895.77 9248.18 647.59
cab2. [refseq;acc:nm_033419] Ranked 210.946 221.225 10.279
exocyst complex component sec15a. [swissprot;acc:q8tag9] Divided 222.138 211.503 1.05028
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Rooted Subtracted 57.4644 61.7491 4.2847
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Divided 60.4385 64.49 1.06704
myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] Measured 4565.34 5085.92 1.11403
n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2] Squared 21678.4 25303.3 1.16721
751 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Rooted 66.9738 71.4638 1.06704
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Squared 20305.9 23689.4 1.16663
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Measured Subtracted 6513.45 7161 647.55
dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] Ranked 210.946 221.225 10.279
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Rooted 51.5667 55.8498 4.2831
huntingtin interacting protein c. [refseq;acc:nm_012272] Squared 16203.4 20339.9 4136.5
myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Measured Divided 4565.34 5085.92 1.11403

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/