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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 773 to 822 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
97 microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Ranked 0 8335.82 10228.3 1.22703
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Squared 10489.8 23426.5 2.23326
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Rooted 1 47.6504 36.9304 1.29028
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] 0 13.2903 17.4395 1.3122
98 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Ranked 1 88.2482 110.265 1.24949
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] 0 7234.6 8858.94 1.22452
pp3111 protein. [refseq;acc:nm_022156] Measured 789 530 1.48868
Squared 147.342 66.4852 2.21616
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured 1 2353.63 3225.65 1.3705
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Rooted 0 13.2903 17.4395 1.3122
transcription factor lbx1. [swissprot;acc:p52954] 1 47.6504 36.9304 1.29028
trs85 homolog. [swissprot;acc:q9y2l5] Squared 227160 146079 1.55505
99 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Ranked 88.2482 110.265 1.24949
mosaic protein lgn. [swissprot;acc:p81274] Rooted 47.6504 36.9304 1.29028
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked 0 12787.8 10454.7 1.22316
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Squared 492.157 225.924 2.17842
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 31.495 24.0263 1.31086
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Measured 1 2353.63 3225.65 1.3705
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] 0 817.81 551.434 1.48306
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Squared 1 226186 145568 1.55382
100 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] Measured 0 594 402 1.47761
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Squared 1 226186 145568 1.55382
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Ranked 0 9183.49 11217.7 1.22151
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Measured 1 2353.63 3225.65 1.3705
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] Rooted 0 20.0501 15.3244 1.30838
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Ranked 1 88.2482 110.265 1.24949
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Squared 0 492.157 225.924 2.17842
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 1 47.6504 36.9304 1.29028
101 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Squared 222655 143584 1.5507
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured 2353.63 3225.65 1.3705
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Ranked 0 14548.5 11915.2 1.221
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Rooted 1 47.6504 36.9304 1.29028
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 0 12.6886 9.74679 1.30182
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Ranked 1 88.2482 110.265 1.24949
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Measured 0 1442 977 1.47595
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Squared 956.375 441.285 2.16725
102 60s ribosomal protein l18a. [swissprot;acc:q02543] Ranked 12738.7 10437.1 1.22052
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared 1 214143 138337 1.54798
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Ranked 88.2482 110.265 1.24949
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Measured 0 1442 977 1.47595
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 1 2353.63 3225.65 1.3705
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted 47.6504 36.9304 1.29028
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Squared 0 61.6678 132.922 2.15545
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Rooted 12.0669 15.6768 1.29916
103 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured 1 2353.63 3225.65 1.3705
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Ranked 0 7495.26 9130.38 1.21815
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Squared 1 407289 263351 1.54656
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Rooted 0 17.1172 22.2036 1.29715
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 1 60.8365 77.7233 1.27758
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Squared 0 61.6678 132.922 2.15545

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/