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 6258 to 6307 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
392 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Measured Divided 0 229.211 219.891 1.04238
60s ribosomal protein l3-like. [swissprot;acc:q92901] Rooted 1 50.3313 45.6913 1.10155
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Measured 3641.89 4236.95 1.16339
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Subtracted 6251.91 7192.08 940.17
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Squared 0 61.898 74.2593 12.3613
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 1 26157.6 20236.2 5921.4
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Measured 0 6428 6396.8 31.2
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Ranked 1 239.092 257.705 18.613
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Squared Divided 0 94.678 87.5656 1.08122
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Rooted Subtracted 8.05424 8.90701 0.85277
seven in absentia homolog 1. [refseq;acc:nm_003031] Ranked Divided 9854.67 10201.4 1.03518
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Subtracted 10303.7 10687.4 383.7
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Squared Divided 1 28895.6 35572.8 1.23108
vav-3 protein. [swissprot;acc:q9ukw4] Rooted Subtracted 66.089 72.3555 6.2665
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Divided 0 7.21166 7.46223 1.03475
393 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Squared Subtracted 1 26157.6 20236.2 5921.4
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Divided 0 9.11845 8.43969 1.08042
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Rooted 1 49.8842 45.2875 1.1015
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Ranked Subtracted 238.921 257.327 18.406
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Measured Divided 4490.28 5222.25 1.16301
grancalcin. [swissprot;acc:p28676] Subtracted 6251.96 7192.13 940.17
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Divided 0 2131.42 2218.51 1.04086
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Rooted Subtracted 8.05424 8.90701 0.85277
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] Squared 15.4957 3.83288 11.6628
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Measured 3855.78 3825.73 30.05
Rooted Divided 33.8811 32.7487 1.03458
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Ranked 1 225.719 207.072 1.09005
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 0 12576 13010 1.03451
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Squared 1 28895.6 35572.8 1.23108
vav-2 protein. [swissprot;acc:p52735] Rooted Subtracted 66.088 72.2597 6.1717
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Ranked 0 5540 5921 381
394 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 10196.9 9857.79 1.0344
adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] Squared 70.823 65.5835 1.07989
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Subtracted 1 26157.6 20236.2 5921.4
bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Measured Divided 4490.28 5222.25 1.16301
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Squared Subtracted 0 15.0305 26.5621 11.5316
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Ranked 1 207.889 226.226 18.337
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Divided 218.827 238.407 1.08948
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Rooted Subtracted 58.0752 64.23 6.1548
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] 0 62.6706 61.8357 0.8349
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Measured 1 1834.33 895.134 939.196
histone h2b.d (h2b/d). [swissprot;acc:q99877] Divided 0 2131.52 2218.58 1.04084
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Subtracted 3889.5 3919.25 29.75
mad protein (max dimerizer). [swissprot;acc:q05195] Squared Divided 1 17248.4 21214 1.22991
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Rooted 58.6533 64.5958 1.10132
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] 0 13.4343 13.8963 1.03439
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Ranked Subtracted 20875 20495 380
395 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 9566.15 9936.37 370.22
Rooted Divided 32.0326 30.9731 1.03421
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Squared Subtracted 202.436 212.386 9.95

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/