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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 7836 to 7885 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
980 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Squared Subtracted 15034.5 18552.2 3517.7
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Ranked 211.987 204.964 7.023
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Measured 5887.52 6434.32 546.8
solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] Squared Divided 27403.6 31533.6 1.15071
vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Measured 6654.42 7296.51 1.09649
981 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Rooted 61.9129 65.3733 1.05589
cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] Measured 6654.42 7296.51 1.09649
exocyst complex component sec6. [swissprot;acc:o60645] Ranked 207.186 200.398 1.03387
loh1cr12. [refseq;acc:nm_058169] Measured Subtracted 5195.48 5741.63 546.15
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Rooted 56.7817 60.2368 3.4551
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Squared Divided 27403.1 31533 1.15071
tbc1 domain family member 5. [swissprot;acc:q92609] Ranked Subtracted 211.987 204.964 7.023
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Squared 22626.3 26143 3516.7
982 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Measured Divided 6654.42 7296.51 1.09649
atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] Rooted Subtracted 56.7818 60.2369 3.4551
bystin. [swissprot;acc:q13895] Divided 53.1515 56.1209 1.05587
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Ranked 243.312 235.351 1.03383
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Squared 30999.6 35666.3 1.15054
rna-binding protein. [refseq;acc:nm_019027] Subtracted 15043.7 18560.1 3516.4
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Ranked 211.987 204.964 7.023
unr protein. [swissprot;acc:o75534] Measured 5195.48 5741.63 546.15
983 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Squared 15043.7 18560.1 3516.4
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Rooted Divided 56.1832 53.2244 1.05559
pbk1 protein. [sptrembl;acc:o76021] Ranked 243.312 235.353 1.03382
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Rooted Subtracted 56.7818 60.2369 3.4551
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Squared Divided 31010.8 35677.6 1.15049
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Measured Subtracted 5350.87 5896.82 545.95
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Ranked 211.987 204.964 7.023
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Measured Divided 6654.42 7296.51 1.09649
984 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Subtracted 5568.96 6113.35 544.39
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Rooted Divided 56.1854 53.2272 1.05558
glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Subtracted 56.781 60.2344 3.4534
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Measured Divided 6362.64 6976.1 1.09642
ns1-associated protein 1. [refseq;acc:nm_006372] Squared Subtracted 15043.7 18560.1 3516.4
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Ranked 211.987 204.964 7.023
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Divided 116.71 120.654 1.03379
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Squared 59338.5 68268.3 1.15049
985 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Rooted Subtracted 62.4582 65.9096 3.4514
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Measured 3720.18 4264.46 544.28
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Squared 15043.7 18560.1 3516.4
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Measured Divided 6362.64 6976.1 1.09642
ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Squared 22569.9 25956.6 1.15005
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Ranked 233.402 225.782 1.03375
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Subtracted 211.987 204.964 7.023
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Rooted Divided 61.9502 65.389 1.05551
986 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] Measured Subtracted 6436.19 6980.13 543.94
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Rooted Divided 62.4582 65.9096 1.05526
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Squared Subtracted 15053 18568 3515
exocyst complex component sec5. [swissprot;acc:q96kp1] Ranked Divided 116.771 120.707 1.03371
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Measured 6362.64 6976.1 1.09642

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/