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 10664 to 10713 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2666 thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755] Ranked 210.136 209.911 1.00107
2667 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Rooted 72.1844 72.5201 1.00465
dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] Measured 4071.9 4099.01 1.00666
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Ranked 204.768 204.549 1.00107
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Squared 17882.8 18344.4 1.02581
2668 fuse binding protein 3 (fragment). [sptrembl;acc:q92946] Ranked 217.176 216.944 1.00107
iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] Measured 8222.61 8169.38 1.00652
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Squared 17870.6 18327.4 1.02556
sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Rooted 72.1844 72.5201 1.00465
2669 clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172]
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Measured 4336.58 4310.3 1.0061
glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] Ranked 214.575 214.354 1.00103
myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] Squared 54033.8 55375.5 1.02483
2670 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]
atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] Rooted 72.1844 72.5201 1.00465
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Measured 4336.62 4310.35 1.00609
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Ranked 144.391 144.538 1.00102
2671 lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754] Rooted 72.1844 72.5201 1.00465
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Measured 4338.79 4313.52 1.00586
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] Ranked 216.288 216.067 1.00102
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Squared 54033.8 55375.5 1.02483
2672 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Ranked 210.957 210.741 1.00102
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Squared 54033.8 55375.5 1.02483
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Rooted 72.1844 72.5201 1.00465
ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] Measured 7350.69 7390.45 1.00541
2673 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 7780.98 7741.14 1.00515
rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] Ranked 216.372 216.588 1.001
testis-specific protein tex28. [swissprot;acc:o15482] Squared 24123.5 24679.6 1.02305
tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] Rooted 66.0562 65.755 1.00458
2674 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Ranked 203.151 202.948 1.001
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Squared 24123.5 24679.6 1.02305
sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Measured 7780.98 7741.14 1.00515
tumor protein d52 (n8 protein). [swissprot;acc:p55327] Rooted 66.0578 65.7588 1.00455
2675 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] Ranked 214.893 215.108 1.001
a kindred of iglon. [refseq;acc:nm_173808] Squared 24123.5 24679.6 1.02305
arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] Rooted 62.4892 62.7542 1.00424
clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] Measured 7780.98 7741.14 1.00515
2676 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Squared 24123.5 24679.6 1.02305
atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] Measured 7780.98 7741.14 1.00515
enhancer of rudimentary homolog. [swissprot;acc:q14259] Ranked 214.893 215.108 1.001
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Rooted 56.3861 56.1514 1.00418
2677 inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Squared 24123.5 24679.6 1.02305
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Ranked 144.412 144.553 1.00098
lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754] Measured 7780.98 7741.14 1.00515
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] Rooted 44.8462 45.0224 1.00393
2678 palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Squared 24123.5 24679.6 1.02305
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Ranked 144.411 144.552 1.00098
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Measured 7780.98 7741.14 1.00515
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] Rooted 44.8383 45.0098 1.00382
2679 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Ranked 190.142 189.959 1.00096

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/