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 Network Comparison Type Value Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1658 to 1707 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		Value Type
    		description
    		red
    		green
    		network_comparison
    208 BHLHB4 Subtracted Squared ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 62783.5 50784.1 11999.4
    CACNG8 Divided Measured voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 4068.78 5082.18 1.24907
    CKS2 Squared cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] 70525.9 52678.7 1.33879
    CLSTN3 Subtracted Measured calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 10599.9 12064.7 1464.8
    DDX24 Divided Rooted atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 46.901 53.624 1.14334
    SEPT10 Subtracted septin 10 isoform 1. [refseq;acc:nm_144710] 113.733 123.871 10.138
    SKP1A Divided Ranked s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] 285.684 252.234 1.13261
    209 no value Subtracted Measured ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 11383.2 9926.61 1456.59
    Rooted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 121.695 131.815 10.12
    BCCIP Ranked brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] 240.782 265.717 24.935
    BHLHB5 Squared basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 62757.7 50767.8 11989.9
    CACNG3 Divided Measured voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 4068.78 5082.18 1.24907
    CAPN2 Rooted calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] 46.8525 53.5324 1.14257
    CTNNAL1 Squared catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 70525.9 52678.7 1.33879
    FBXW7 Ranked f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] 285.684 252.234 1.13261
    210 no value Subtracted rna-binding protein. [refseq;acc:nm_019027] 237.302 212.41 24.892
    ATG5 Squared autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 36359.2 24466.8 11892.4
    CACNG2 Divided Measured voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 4068.82 5082.21 1.24906
    CAPN1 Rooted calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 46.8525 53.5316 1.14256
    CUL2 Ranked cullin homolog 2 (cul-2). [swissprot;acc:q13617] 285.684 252.234 1.13261
    HOXB4 Subtracted Rooted homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 121.695 131.815 10.12
    LUC7L2 Measured luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 4355.61 5810.82 1455.21
    SGTA Divided Squared small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] 69549 92953.5 1.33652
    211 no value Subtracted Ranked apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 237.302 212.41 24.892
    CACNG4 Divided Measured voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 4068.91 5082.27 1.24905
    HOXC5 Subtracted Rooted homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 121.695 131.815 10.12
    LUC7L Measured luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 4358.13 5811.49 1453.36
    PITRM1 Divided Rooted metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 88.4361 77.5112 1.14095
    PSEN1 Ranked presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 285.684 252.234 1.13261
    STAMBPL1 Subtracted Squared associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 28994.2 17134.8 11859.4
    TIA1 Divided nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 14668.3 19547 1.3326
    212 no value Subtracted Rooted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 121.695 131.815 10.12
    ALG1 Divided beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 88.4266 77.5047 1.14092
    BRF1 Measured transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 4446.72 5553.79 1.24896
    CHMP2A Subtracted Squared putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 28994.2 17134.8 11859.4
    CUL1 Divided Ranked cullin homolog 1 (cul-1). [swissprot;acc:q13616] 285.684 252.234 1.13261
    SYNCRIP Subtracted ns1-associated protein 1. [refseq;acc:nm_006372] 237.302 212.41 24.892
    TIAL1 Divided Squared nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 14690.3 19560.2 1.3315
    WAS Subtracted Measured wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 6416.68 7865.15 1448.47
    213 CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] 7711.38 6265.8 1445.58
    HNRNPR Ranked heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 237.302 212.41 24.892
    HOXD4 Rooted homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 121.695 131.815 10.12
    NOLA1 Divided Measured nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 4446.72 5553.79 1.24896
    PLDN Ranked pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 210.693 186.95 1.127
    STAM Squared signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] 86861.5 65369.7 1.32877
    STAMBP Subtracted associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 28994.2 17134.8 11859.4
    STAMBPL1 Divided Rooted associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 105.205 92.2415 1.14054
    214 CACNG5 Measured voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 4074.83 5086.49 1.24827
    CHMP2A Rooted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 105.205 92.2415 1.14054
    CPA3 Subtracted Measured mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 7711.36 6265.79 1445.57

    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/