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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 354 to 403 of 502 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 0
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    354 MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 16321 15577 1.04776
    355 MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
    356 no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
    357 MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
    358 MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
    359 MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
    360 MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
    361 no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
    362 MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
    363 MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
    364 MAGED2 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
    365 E2F2 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 7769.96 8139.71 1.04759
    366 no value glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] 8614.89 9017.27 1.04671
    367 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 13801.7 13185.9 1.0467
    368 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 16679.2 15940.6 1.04633
    369 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 18849.7 19704.7 1.04536
    370 PDHA2 pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] 13652.7 13061 1.0453
    371 SMARCC2 swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] 13247.9 12674.2 1.04527
    372 no value dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] 11869.9 12402.7 1.04489
    373 mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] 10598.2 11061.5 1.04371
    374 CAPS calcyphosine. [swissprot;acc:q13938] 9874.54 9478.1 1.04183
    375 TAF9B tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] 14247.6 13686.9 1.04097
    376 UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 10284.9 10695.6 1.03993
    377 ITGB3 integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] 14512.3 13958.2 1.0397
    378 DCHS1 protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] 19713.5 18962.5 1.0396
    379 PSMD10 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 11228.4 10806 1.03909
    380 no value 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 9566.15 9936.37 1.0387
    381 RPS27L ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 9565.54 9935.19 1.03864
    382 ACTG1 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 10449 10061.8 1.03848
    383 CDYL2 chromodomain y-like protein 2. [refseq;acc:nm_152342] 10273.1 10665.1 1.03816
    384 BYSL bystin. [swissprot;acc:q13895] 10833.3 11244.5 1.03796
    385 CDY2B testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 10302.7 10686.7 1.03727
    386 CDY1B testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 10303.7 10687.4 1.03724
    387 DTYMK thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] 10481.8 10869.5 1.03699
    388 no value peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 9953.39 10320.9 1.03692
    389 HOMER1 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 11794.7 11375.4 1.03686
    390 no value alpha-nac protein. [sptrembl;acc:q9h009] 14204.4 14724.5 1.03662
    391 nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 14223.9 14738.5 1.03618
    392 seven in absentia homolog 1. [refseq;acc:nm_003031] 9854.67 10201.4 1.03518
    393 transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] 12576 13010 1.03451
    394 60s ribosomal protein l12. [swissprot;acc:p30050] 10196.9 9857.79 1.0344
    395 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 10195.5 9856.7 1.03437
    396 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 10194.8 9856.12 1.03436
    397 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 10006.9 9676.53 1.03414
    398 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] 16699.2 17267.9 1.03406
    399 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] 16703.1 17271.4 1.03402
    400 glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] 16711 17278.4 1.03395
    401 transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 12305.9 11904.9 1.03368
    402 AP1M2 adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] 10562.4 10918 1.03367
    403 no value udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] 9783.63 10111.2 1.03348

    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
    - Hugo is the HGNC identifier if it exists
    - 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/