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 5208 to 5257 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1302 zinc finger-like protein 9. [refseq;acc:nm_033414] Squared 14381.7 16243.1 1.12943
1303 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] Ranked 269.157 275.531 1.02368
cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Measured 6334.15 6852.61 1.08185
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Squared 14381.7 16243.1 1.12943
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Rooted 61.4805 64.1473 1.04338
1304 fibulin-1 precursor. [swissprot;acc:p23142] Measured 8550.79 9248.06 1.08154
glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] Ranked 207.387 212.275 1.02357
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Squared 14381.7 16243.1 1.12943
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Rooted 65.6542 68.5013 1.04337
1305 ad24 protein. [refseq;acc:nm_022451] Squared 14354.8 16210.8 1.12929
glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] Measured 5500.92 5949.26 1.0815
serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209] Ranked 218.439 213.436 1.02344
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Rooted 61.3044 63.9578 1.04328
1306 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Squared 14517.9 16388.6 1.12885
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Rooted 56.7289 59.1831 1.04326
serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] Ranked 218.441 213.441 1.02343
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623] Measured 5500.92 5949.26 1.0815
1307 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Rooted 63.0056 65.7244 1.04315
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] Measured 5500.92 5949.26 1.0815
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Squared 14392.1 16246.1 1.12882
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] Ranked 218.44 213.44 1.02343
1308 glutamyl trna synthetase. [sptrembl;acc:o14563] Measured 5500.92 5949.26 1.0815
nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] Rooted 59.3482 61.9083 1.04314
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] Ranked 218.44 213.439 1.02343
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Squared 14868.3 16782.3 1.12873
1309 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Ranked 226.439 221.26 1.02341
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Measured 6110.09 6607.81 1.08146
transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] Rooted 59.3482 61.9083 1.04314
trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Squared 15397.3 17378.3 1.12866
1310 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] 17064.6 19258.7 1.12858
mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] Measured 6051.23 6544.17 1.08146
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Ranked 226.439 221.26 1.02341
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Rooted 66.2263 69.0756 1.04302
1311 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Squared 24923.6 28122.8 1.12836
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Rooted 53.9101 51.6896 1.04296
exocyst complex component sec8. [swissprot;acc:q96a65] Measured 6221.22 6727.77 1.08142
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Ranked 226.439 221.26 1.02341
1312 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Squared 24923.6 28122.8 1.12836
rad50 homolog isoform 1. [refseq;acc:nm_005732] Ranked 199.739 204.407 1.02337
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Rooted 87.3823 83.7932 1.04283
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Measured 5675.96 6136.47 1.08113
1313 60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] 5457.14 5899.85 1.08112
aarf domain containing kinase 4. [refseq;acc:nm_024876] Squared 24923.6 28122.8 1.12836
hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Rooted 62.0983 64.7441 1.04261
signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] Ranked 222.573 227.75 1.02326
1314 aarf domain containing kinase 1. [refseq;acc:nm_020421] Squared 24923.6 28122.8 1.12836
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Rooted 62.6357 65.2949 1.04246
signal transducer and activator of transcription 4. [swissprot;acc:q14765] Ranked 222.573 227.751 1.02326
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Measured 5401.39 5838.63 1.08095
1315 dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 5685.77 6145.43 1.08084

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/