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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Filtered Gene Value Type Rank Network Comparison Type description Interaction Map network_comparison red green
Results: HTML CSV LaTeX Showing element 101 to 150 of 77072 in total
Filtered  : 0
Value Type  : Measured
Rank
Network Comparison Type
description
Interaction Map
network_comparison
red
green
26 Divided fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] High confidence 4.3268 153 662
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Low confidence 3.04255 143 47
Subtracted block 23. [sptrembl;acc:q8nhw5] 626.74 4561.13 5187.87
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] High confidence 902.5 2965.5 2063
27 Divided melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Low confidence 2.97183 105.5 35.5
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] High confidence 4.10072 570 139
Subtracted baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 894 14357.1 13463.1
candidate tumor suppressor protein. [refseq;acc:nm_020381] Low confidence 589.67 2232 2821.67
28 Divided beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] High confidence 4.10072 570 139
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Low confidence 2.97183 105.5 35.5
Subtracted spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] High confidence 874.45 5418.2 4543.75
supervillin isoform 1; membrane-associated f-actin binding protein p205; archvillin. [refseq;acc:nm_003174] Low confidence 589.67 2232 2821.67
29 Divided melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 2.97183 105.5 35.5
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 3.90833 111.278 434.911
Subtracted cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954] Low confidence 582.8 20505.7 21088.5
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] High confidence 849.19 3248.95 2399.76
30 Divided dystrophin. [swissprot;acc:p11532] 3.82335 427.217 111.739
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Low confidence 2.97183 105.5 35.5
Subtracted cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] High confidence 837.72 3265.25 4102.97
protein kinase, lysine deficient 3. [refseq;acc:nm_020922] Low confidence 579.5 125 704.5
31 Divided dok-like protein. [refseq;acc:nm_024872] High confidence 3500000 35 0.00001
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Low confidence 2.97183 105.5 35.5
Subtracted adenomatous polyposis coli like. [refseq;acc:nm_005883] 570 2544.19 3114.19
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] High confidence 804 1833 2637
32 Divided cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] 3.25 598 184
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Low confidence 2.97183 105.5 35.5
Subtracted dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 550.54 2476.1 3026.64
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 801 859 58
33 Divided lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 3.15402 12.6208 39.8063
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Low confidence 2.97183 105.5 35.5
Subtracted protein cgi-147. [swissprot;acc:q9y3e5] High confidence 796.26 8396.12 9192.38
scribble. [refseq;acc:nm_015356] Low confidence 547.36 3697.8 4245.16
34 Divided glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] High confidence 3.04255 143 47
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Low confidence 2.97183 105.5 35.5
Subtracted acrc protein; putative nuclear protein. [refseq;acc:nm_052957] High confidence 791.03 4131.06 3340.03
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Low confidence 521.18 840.74 1361.92
35 Divided adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] High confidence 2.99674 459.5 1377
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Low confidence 2.97183 105.5 35.5
Subtracted fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] 509 153 662
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] High confidence 705 1603 898
36 Divided heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 2.80357 157 56
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Low confidence 2.97183 105.5 35.5
Subtracted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence 660.772 1586.07 925.298
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Low confidence 484.19 1763.83 1279.64
37 Divided 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 2.79409 334.401 934.348
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Low confidence 2.97183 105.5 35.5
Subtracted glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 478.72 5931.43 5452.71
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] High confidence 652.25 5202.89 4550.64
38 Divided melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Low confidence 2.97183 105.5 35.5
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] High confidence 2.65727 320.012 120.429

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/