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 Value Type Network Comparison Type description Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1925 to 1974 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
green
network_comparison
963 Divided cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 11773 10733.2 1.09688
Subtracted annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] 5778.65 6328.56 549.91
964 Divided cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 11773 10733.2 1.09688
Subtracted synapsin iii. [swissprot;acc:o14994] 5791.82 6340.86 549.04
965 Divided protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] 11773.7 10733.8 1.09688
Subtracted aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 5791.82 6340.86 549.04
966 Divided galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 7817.9 8575.12 1.09686
Subtracted hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] 5791.82 6340.86 549.04
967 Divided protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] 7813.35 8569.96 1.09684
Subtracted actin binding lim protein 2. [refseq;acc:nm_032432] 5791.82 6340.86 549.04
968 Divided spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] 7813.48 8570.11 1.09684
Subtracted hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] 5791.82 6340.86 549.04
969 Divided band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 7813.34 8569.95 1.09684
Subtracted synapsin ii. [swissprot;acc:q92777] 5791.82 6340.86 549.04
970 Divided band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] 7813.45 8570.07 1.09684
Subtracted mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] 5791.82 6340.86 549.04
971 Divided band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] 7813.36 8569.97 1.09684
Subtracted peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 5791.82 6340.86 549.04
972 Divided 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] 7813.48 8570.11 1.09684
Subtracted hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] 5791.82 6340.86 549.04
973 Divided galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] 7810.11 8566.29 1.09682
Subtracted transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 5791.82 6340.86 549.04
974 Divided dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] 5365.06 5884.52 1.09682
Subtracted delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] 5791.82 6340.86 549.04
975 Divided dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] 5365.14 5884.43 1.09679
Subtracted actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 5791.82 6340.86 549.04
976 Divided dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] 5365.22 5884.32 1.09675
Subtracted synapsin i (brain protein 4.1). [swissprot;acc:p17600] 5791.82 6340.86 549.04
977 Divided u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 4115.9 4513.14 1.09651
Subtracted annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] 5780.34 6329.3 548.96
978 Divided vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] 6654.42 7296.51 1.09649
Subtracted lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] 5385.04 5933.65 548.61
979 Divided vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] 6654.42 7296.51 1.09649
Subtracted transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 3890.53 4439.07 548.54
980 Divided vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] 6654.42 7296.51 1.09649
Subtracted similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] 5887.52 6434.32 546.8
981 Divided cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] 6654.42 7296.51 1.09649
Subtracted loh1cr12. [refseq;acc:nm_058169] 5195.48 5741.63 546.15
982 Divided 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] 6654.42 7296.51 1.09649
Subtracted unr protein. [swissprot;acc:o75534] 5195.48 5741.63 546.15
983 Divided vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] 6654.42 7296.51 1.09649
Subtracted tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] 5350.87 5896.82 545.95
984 Divided integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] 6362.64 6976.1 1.09642
Subtracted adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 5568.96 6113.35 544.39
985 Divided integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] 6362.64 6976.1 1.09642
Subtracted atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 3720.18 4264.46 544.28
986 Divided integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] 6362.64 6976.1 1.09642
Subtracted 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] 6436.19 6980.13 543.94
987 Divided maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] 6660.04 7301.81 1.09636
Subtracted tubulin-tyrosine ligase. [refseq;acc:nm_153712] 5511.2 6054.71 543.51

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/