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 5458 to 5507 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
342 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Ranked Subtracted 0 11563.7 12151.8 588.1
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Rooted 27.5221 28.7585 1.2364
dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Ranked 1 240.913 261.45 20.537
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided 0 10074 10609 1.05311
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Measured 3691.15 3952.59 1.07083
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] Subtracted 0 59 59
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Squared Divided 1 70830.5 56822 1.24653
histone h2b. [refseq;acc:nm_175055] Rooted 0 29.6319 31.1848 1.05241
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Measured 1 20446.1 24136.4 1.18049
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Squared Subtracted 0 237.082 277.442 40.36
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Rooted Divided 1 49.2715 54.5757 1.10765
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Squared Subtracted 31620.5 38250.7 6630.2
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Divided 0 3679.95 3222.24 1.14205
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Measured Subtracted 1 10230.1 11256.2 1026.1
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Rooted 46.0352 53.0192 6.984
343 40s ribosomal protein s3a. [swissprot;acc:p49241] Ranked 0 10405.1 10992.4 587.3
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Rooted 27.5242 28.7604 1.2362
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 1 50.3169 45.4333 1.10749
bystin. [swissprot;acc:q13895] Measured 0 2930.88 3135.76 1.0699
casein kinase i alpha s-like. [refseq;acc:nm_145203] Ranked 8356.31 8788.62 1.05173
conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Squared 1 70830.5 56822 1.24653
espin. [refseq;acc:nm_031475] 0 3679.78 3222.11 1.14204
histone h2b.e (h2b/e). [swissprot;acc:q99879] Rooted 29.632 31.1848 1.0524
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured 1 20446.1 24136.4 1.18049
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Subtracted 0 304 363 59
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Ranked Divided 1 241.625 265.136 1.0973
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Subtracted 231.73 211.252 20.478
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Squared 31620.5 38250.7 6630.2
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Rooted 46.0352 53.0192 6.984
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Measured 4991.48 6014.08 1022.6
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Squared 0 43.8625 5.33358 38.5289
344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Ranked Divided 1 241.625 265.136 1.0973
acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] Squared Subtracted 31597.8 38216.9 6619.1
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Rooted 57.9068 64.8562 6.9494
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Measured 9921.43 10941.2 1019.77
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Ranked Divided 0 10540.6 10027.6 1.05116
dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Subtracted 1 240.6 261.041 20.441
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 0 9328.78 8741.55 587.23
histone h2b.c (h2b/c). [swissprot;acc:q99880] Rooted Divided 29.633 31.1851 1.05238
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Measured 1 20446.1 24136.4 1.18049
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 0 2075.64 2220.68 1.06988
isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Squared 1 37226.9 46400.1 1.24641
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 0 3665.1 3211.04 1.14141
protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] Measured Subtracted 2331 2390 59
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted 30.3054 31.5389 1.2335
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Divided 1 49.4233 54.7327 1.10743
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Squared Subtracted 0 208.691 170.202 38.489
345 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Ranked Divided 11563.7 12151.8 1.05086
collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Measured 2113.27 2255.28 1.0672
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Ranked Subtracted 11372.3 10792.3 580

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/