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 3351 to 3400 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1676 indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Divided 5791.14 6193.02 1.0694
transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Subtracted 7088.08 7492.23 404.15
1677 40s ribosomal protein s13. [swissprot;acc:q02546] 5414.98 5818.7 403.72
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Divided 6075.19 6496.61 1.06937
1678 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Subtracted 5782.92 6186.39 403.47
cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] Divided 5763.25 6162.98 1.06936
1679 40s ribosomal protein s7 (s8). [swissprot;acc:p23821] Subtracted 5782.92 6186.39 403.47
proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] Divided 6180.24 6608.11 1.06923
1680 26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805] Subtracted 5782.92 6186.39 403.47
methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Divided 6436.73 6882.16 1.0692
1681 apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114] Subtracted 5782.92 6186.39 403.47
f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] Divided 6304.74 6740.66 1.06914
1682 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] Subtracted 6011.57 6414.98 403.41
f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] Divided 6304.74 6740.66 1.06914
1683 leng5 protein. [refseq;acc:nm_024075] Subtracted 5372.25 5775.21 402.96
ring finger protein 20. [refseq;acc:nm_019592] Divided 5419.54 5793.94 1.06908
1684 ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771]
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Subtracted 5372.25 5775.21 402.96
1685 gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Divided 6088.07 6508.45 1.06905
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Subtracted 5372.25 5775.21 402.96
1686 toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Divided 6088.07 6508.45 1.06905
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Subtracted 5372.25 5775.21 402.96
1687 serpin b12. [swissprot;acc:q96p63] Divided 5767.69 6165.87 1.06904
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Subtracted 5372.25 5775.21 402.96
1688 megsin (tp55) (serpin b7). [swissprot;acc:o75635] Divided 5767.69 6165.87 1.06904
transcription factor iib. [refseq;acc:nm_013242] Subtracted 9146.11 8743.98 402.13
1689 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Divided 5767.69 6165.87 1.06904
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Subtracted 9146.11 8743.98 402.13
1690 fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] 5791.14 6193.02 401.88
oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] Divided 5767.69 6165.87 1.06904
1691 fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469] Subtracted 5791.14 6193.02 401.88
upf0183 protein. [swissprot;acc:q9bsu1] Divided 5767.69 6165.87 1.06904
1692 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Subtracted 5791.14 6193.02 401.88
1693 translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Divided 5767.69 6165.87 1.06904
wd-repeat protein 4. [swissprot;acc:p57081] Subtracted 5791.14 6193.02 401.88
1694 myelin p2 protein. [swissprot;acc:p02689]
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Divided 5767.69 6165.87 1.06904
1695 kelch-like protein 8. [swissprot;acc:q9p2g9] Subtracted 5791.14 6193.02 401.88
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Divided 5767.69 6165.87 1.06904
1696 phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Subtracted 5791.14 6193.02 401.88
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] Divided 6304.22 6738.77 1.06893
1697 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Subtracted 5791.14 6193.02 401.88
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Divided 6304.21 6738.77 1.06893
1698 beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] Subtracted 5791.14 6193.02 401.88
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558] Divided 6304.22 6738.77 1.06893
1699 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Subtracted 5791.14 6193.02 401.88
rest corepressor. [refseq;acc:nm_015156] Divided 6304.21 6738.77 1.06893
1700 phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] 6326.24 6762.27 1.06892
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] Subtracted 5791.14 6193.02 401.88

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/