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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Value Type green Interaction Map Gene Rank description Filtered Network Comparison Type red network_comparison
Results: HTML CSV LaTeX Showing element 832 to 881 of 3228 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided
green
Rank
description
red
network_comparison
4492.98 837 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] 4063.64 1.10565
4493.36 838 pbk1 protein. [sptrembl;acc:o76021] 4064.23 1.10559
4497.74 862 probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] 4076.72 1.10327
4499.52 2737 tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 4486.83 1.00283
2738 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]
4502.32 853 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 4078.45 1.10393
4513.14 977 u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 4115.9 1.09651
4517.54 2606 tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] 4450.84 1.01499
4521.87 2752 set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 4521.42 1.0001
2753 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]
2754 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]
2755 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]
4522.61 646 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 4019.88 1.12506
4539.34 2400 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 4368.44 1.03912
4545.01 755 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] 4079.81 1.11402
4557.68 745 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 4086.6 1.11527
746 rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555]
747 down-regulated in metastasis. [refseq;acc:nm_014503]
4567.51 79 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 3074.57 1.48558
4576.35 2663 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] 4608.54 1.00703
4576.78 2664 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] 4608.91 1.00702
4577.5 206 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 5720.25 1.24965
4593.43 654 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 4088.63 1.12346
655 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
4594.43 647 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 5167.88 1.12481
4594.87 2388 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] 4418.21 1.03998
4597.44 651 ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 5168.43 1.1242
652 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
4607.9 742 eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 4131.04 1.11543
743 eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152]
4612.54 546 zinc finger protein t86. [swissprot;acc:o00488] 4052.77 1.13812
4621.88 2666 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 4591.08 1.00671
4624.15 305 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 3856.29 1.19912
4633.96 621 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 4115.39 1.12601
4642.72 2382 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] 4457.6 1.04153
4642.93 1989 m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] 4383.34 1.05922
4649.17 2629 dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] 4582.38 1.01458
4654.97 2581 dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] 4570.81 1.01841
4669.27 272 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 3858.52 1.21012
4691.24 568 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] 4134.77 1.13458
569 grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]
570 swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]
571 swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]
572 swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]
4696.04 1203 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] 4322.65 1.08638
4697.02 950 bystin. [swissprot;acc:q13895] 4280.99 1.09718
4700.91 1224 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] 4331.35 1.08532
4702.58 2747 putatative 28 kda protein. [refseq;acc:nm_020143] 4708.68 1.0013
4719.35 367 dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 4024.4 1.17268
4721.37 1940 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] 4450.17 1.06094

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/