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 2901 to 2950 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    363 PARL presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Measured Low confidence 9099.15 9593.54 1.05433
    PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Rooted 71.4038 74.9877 1.05019
    SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Ranked High confidence 231.481 211.131 1.09639
    TAF7L tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Squared 57579.2 46497.2 1.23834
    364 DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Rooted 50.0785 55.3215 1.1047
    DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Ranked Low confidence 212.235 204.495 1.03785
    GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Measured High confidence 5189 6088.47 1.17334
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Low confidence 7711.11 8129.27 1.05423
    MPP2 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Squared 47813.3 44628.6 1.07136
    POLR2B dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Ranked High confidence 243.208 266.617 1.09625
    SH2D3C sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Squared 17957.2 22234.1 1.23817
    SYNJ1 synaptojanin 1 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 1). [swissprot;acc:o43426] Rooted Low confidence 72.885 76.5357 1.05009
    365 no value pnas-129. [sptrembl;acc:q9bxv8] Squared 47804.5 44622.6 1.07131
    BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] High confidence 17965.8 22243 1.23807
    CAPS calcyphosine. [swissprot;acc:q13938] Measured 5189 6088.47 1.17334
    MRPL36 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Ranked 242.744 266.07 1.09609
    NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Rooted 49.7541 54.9425 1.10428
    PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Low confidence 71.3292 74.8889 1.04991
    SLC26A9 solute carrier family 26, member 9 isoform b; anion transporter/exchanger-9. [refseq;acc:nm_134325] Measured 8452.93 8910.99 1.05419
    SPAG7 sperm associated antigen 7. [refseq;acc:nm_004890] Ranked 117.525 121.959 1.03773
    366 BHLHB4 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Squared High confidence 62783.5 50784.1 1.23628
    CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured 5189 6088.47 1.17334
    MPP6 maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Squared Low confidence 47796.9 44617.4 1.07126
    POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Rooted 70.5037 74.0176 1.04984
    RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] High confidence 50.5463 45.7763 1.1042
    RPS5 40s ribosomal protein s5. [swissprot;acc:p46782] Ranked 242.473 265.756 1.09602
    SLC26A5 prestin. [swissprot;acc:p58743] Measured Low confidence 8452.93 8910.99 1.05419
    ZMIZ1 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Ranked 207.433 199.944 1.03746
    367 no value 60s ribosomal protein l21. [swissprot;acc:p46778] Measured 8452.93 8910.99 1.05419
    BHLHB5 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Squared High confidence 62757.7 50767.8 1.23617
    DDX18 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Rooted 49.0882 54.2027 1.10419
    HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Ranked 234.146 256.627 1.09601
    POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Measured 4024.4 4719.35 1.17268
    SORBS1 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Ranked Low confidence 206.945 199.503 1.0373
    SYNJ2 synaptojanin 2 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 2) (fragment). [swissprot;acc:o15056] Rooted 72.8686 76.496 1.04978
    ZNF547 sedlin. [swissprot;acc:o14582] Squared 56121.2 60110.1 1.07108
    368 CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Measured High confidence 5082.66 5959.99 1.17261
    DRAP1 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Squared 51805.2 41916.4 1.23592
    OTC ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Rooted Low confidence 85.1252 89.3577 1.04972
    PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Ranked High confidence 242.66 265.715 1.09501
    RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Rooted 49.5225 54.6817 1.10418
    RTN4IP1 reticulon 4 interacting protein 1; nogo-interacting mitochondrial protein. [refseq;acc:nm_032730] Squared Low confidence 49403.7 46150.8 1.07048
    SLC26A4 pendrin (sodium-independent chloride/iodide transporter). [swissprot;acc:o43511] Measured 8452.93 8910.99 1.05419
    SPSB4 spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] Ranked 219.655 211.763 1.03727
    369 no value solute carrier family 26 member 6 (pendrin-like protein 1) (pendrin l1). [swissprot;acc:q9bxs9] Measured 8452.93 8910.99 1.05419
    CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] High confidence 3583.56 4194.95 1.17061
    KHK ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Squared Low confidence 53052.9 49563.7 1.0704
    LGALS9 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] High confidence 45960.8 56749.6 1.23474
    METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Rooted 49.7435 45.0586 1.10397
    MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Ranked 242.159 265.104 1.09475

    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/