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 10164 to 10213 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2541 tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Measured 8542.13 8740.23 1.02319
2542 cytochrome c. [swissprot;acc:p00001] Rooted 57.7168 58.2731 1.00964
osteoclast stimulating factor 1. [swissprot;acc:q92882] Measured 4708.98 4817.39 1.02302
p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Ranked 218.068 217.633 1.002
reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Squared 26743.1 28135.6 1.05207
2543 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Rooted 57.7168 58.2731 1.00964
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Squared 37601.9 35747.3 1.05188
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Measured 8565.3 8760.3 1.02277
tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Ranked 224.726 225.164 1.00195
2544 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] 212.67 212.262 1.00192
heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Rooted 57.7168 58.2731 1.00964
peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] Measured 6239.69 6378.35 1.02222
reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Squared 26754.5 28141 1.05182
2545 fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] Rooted 57.7168 58.2731 1.00964
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Squared 3136.37 2981.88 1.05181
proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] Ranked 213.494 213.088 1.00191
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] Measured 8285.65 8107.49 1.02197
2546 dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] 4763.99 4868.66
eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] Squared 26753.6 28139.4 1.0518
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] Ranked 197.138 197.507 1.00187
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Rooted 57.7168 58.2731 1.00964
2547 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Measured 3370.46 3444.18 1.02187
eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] Squared 26754.1 28139.6 1.05179
elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] Rooted 57.7168 58.2731 1.00964
glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Ranked 206.894 206.51 1.00186
2548 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] Measured 4725.79 4824.4 1.02087
eh-domain containing protein 3. [swissprot;acc:q9nzn3] Squared 26753.8 28139.5 1.05179
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Ranked 206.899 206.516 1.00185
rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Rooted 57.7168 58.2731 1.00964
2549 eh-domain containing protein 2. [swissprot;acc:q9nzn4] Squared 26754.2 28139.6 1.05178
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Rooted 86.3167 85.4951 1.00961
glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Ranked 206.902 206.519 1.00185
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] Measured 4725.79 4824.4 1.02087
2550 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] Ranked 217.587 217.988 1.00184
mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Rooted 55.7376 55.2091 1.00957
sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] Squared 26756.4 28140.5 1.05173
2551 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Ranked 209.766 210.148 1.00182
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Rooted 74.6805 75.3829 1.00941
reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] Squared 26774.7 28144.7 1.05117
sorting nexin 17. [swissprot;acc:q15036] Measured 4725.79 4824.4 1.02087
2552 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Rooted 71.2104 71.8771 1.00936
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Squared 16926 17789.2 1.051
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Measured 4884.35 4985.78 1.02077
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Ranked 193.12 193.467 1.0018
2553 chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]
histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] Rooted 58.0778 58.6154 1.00926
pp3111 protein. [refseq;acc:nm_022156] Squared 16926 17789.2 1.051
ras-related protein rab-37. [swissprot;acc:q96ax2] Measured 3852.99 3775.86 1.02043
2554 lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] Rooted 66.145 66.7577 1.00926

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/