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 6641 to 6690 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1661 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Ranked 204.437 201.551 1.01432
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Measured 7433.73 7950.61 1.06953
solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415] Rooted 54.1965 56.0231 1.0337
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Squared 23451.3 25948.4 1.10648
1662 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 13992.7 15480.4 1.10632
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Rooted 54.1965 56.0231 1.0337
transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Ranked 228.477 231.747 1.01431
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] Measured 7433.73 7950.61 1.06953
1663 epsin 3. [refseq;acc:nm_017957] Squared 26657.9 29490.6 1.10626
nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494] Measured 7433.73 7950.61 1.06953
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Ranked 218.335 215.26 1.01429
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Rooted 54.1965 56.0231 1.0337
1664 nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] Measured 7433.73 7950.61 1.06953
suppressor of fused. [refseq;acc:nm_016169] Rooted 54.1965 56.0231 1.0337
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Ranked 228.484 231.74 1.01425
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Squared 16044.8 17746.5 1.10606
1665 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Ranked 204.433 201.564 1.01423
fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Measured 5791.14 6193.02 1.0694
mesoderm induction early response 1. [refseq;acc:nm_020948] Squared 29813.9 32974.4 1.10601
zinc finger protein gli3. [swissprot;acc:p10071] Rooted 54.1965 56.0231 1.0337
1666 fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469] Measured 5791.14 6193.02 1.0694
karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] Ranked 218.679 215.612 1.01422
limb region 1 protein; limb region 1. [refseq;acc:nm_022458] Rooted 54.1965 56.0231 1.0337
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Squared 29813.9 32974.4 1.10601
1667 cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Ranked 214.898 211.898 1.01416
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Measured 5791.14 6193.02 1.0694
gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142] Rooted 54.1965 56.0231 1.0337
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Squared 25005.2 27654.4 1.10595
1668 survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Ranked 228.496 231.729 1.01415
wd-repeat protein 4. [swissprot;acc:p57081] Measured 5791.14 6193.02 1.0694
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Squared 21336.3 23595.6 1.10589
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] Rooted 54.1965 56.0231 1.0337
1669 myelin p2 protein. [swissprot;acc:p02689] Measured 5791.14 6193.02 1.0694
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Rooted 98.0116 94.8261 1.03359
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Ranked 228.496 231.729 1.01415
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Squared 21336.3 23595.6 1.10589
1670 kelch-like protein 8. [swissprot;acc:q9p2g9] Measured 5791.14 6193.02 1.0694
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Squared 24949.9 27591.9 1.10589
nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] Rooted 64.4426 66.6072 1.03359
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Ranked 228.496 231.729 1.01415
1671 nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426]
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Measured 5791.14 6193.02 1.0694
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Rooted 62.1957 64.2842 1.03358
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Squared 21336.3 23595.6 1.10589
1672 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Measured 5791.14 6193.02 1.0694
proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] Rooted 64.0468 66.1922 1.0335
ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153] Ranked 228.496 231.729 1.01415
tata element modulatory factor (tmf). [swissprot;acc:p82094] Squared 23713.7 26223.8 1.10585
1673 beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] Measured 5791.14 6193.02 1.0694
dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992] Ranked 228.496 231.729 1.01415

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/