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 [...,...].
    Network Comparison Type Rank Gene Value Type description Hugo Interaction Map network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 1201 to 1250 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    151 Measured cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] CTSZ Low confidence 1.08628 7136.14 7751.87
    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] SH2D3C High confidence 1.29746 4578.09 5939.91
    Ranked cathepsin z precursor (ec 3.4.22.-) (cathepsin x) (cathepsin p). [swissprot;acc:q9ubr2] CTSZ Low confidence 1.06148 206.516 194.554
    myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C High confidence 1.19565 55 46
    Squared deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] DNASE2B 1.41786 250303 354894
    spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] ABI1 Low confidence 1.12421 53603.3 47680.8
    Rooted chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] CHRAC1 High confidence 1.1977 38.8223 46.4975
    homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 Low confidence 1.06862 101.348 108.302
    152 Measured melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] MAGED4 High confidence 1.29736 23693.7 18263
    nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS Low confidence 1.08627 5538.35 6016.13
    Ranked high-mobility group 20a. [refseq;acc:nm_018200] HMG20A 1.06144 202.934 191.187
    myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] no value High confidence 1.19565 55 46
    Squared 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (6pf-2-k/fru- 2,6-p2ase brain/placenta-type isozyme) (ipfk-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:q16875] PFKFB3 Low confidence 1.12404 53380.6 47490
    septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] SEPT8 High confidence 1.4069 90226 126939
    Rooted homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value Low confidence 1.06862 101.348 108.302
    luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] LUC7L2 High confidence 1.19251 55.2859 65.9288
    153 Measured hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2 1.29736 23693.7 18263
    nipsnap1 protein. [swissprot;acc:q9bpw8] NIPSNAP1 Low confidence 1.08611 5544.97 6022.42
    Ranked chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] RBM15B High confidence 1.19466 249.663 298.263
    rab11-family interacting protein 4. [refseq;acc:nm_032932] RAB11FIP4 Low confidence 1.06119 183.27 172.702
    Squared 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (6pf-2-k/fru- 2,6-p2ase liver isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:p16118] PFKFB1 1.12404 53380.6 47490
    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] no value High confidence 1.40632 70011 49783
    Rooted homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Low confidence 1.06862 101.348 108.302
    luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] LUC7L High confidence 1.19217 55.297 65.9236
    154 Measured melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] no value 1.29736 23693.7 18263
    monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021] SLC16A2 Low confidence 1.08517 10553.9 11452.8
    Ranked eferin. [swissprot;acc:o75154] RAB11FIP3 1.06119 183.27 172.702
    regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] RGS19 High confidence 1.19466 249.663 298.263
    Squared cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] DYNLT1 Low confidence 1.12404 53380.6 47490
    t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] CCT3 High confidence 1.40605 42788.3 60162.6
    Rooted eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] EIF5 1.18369 43.5479 51.5473
    homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Low confidence 1.06862 101.348 108.302
    155 Measured melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] MAGEA11 High confidence 1.29736 23693.7 18263
    solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] SLC16A10 Low confidence 1.08517 10553.7 11452.6
    Ranked cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] CTSL2 1.0605 211.818 199.734
    putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] RBM15 High confidence 1.19466 249.663 298.263
    Squared 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (6pf-2-k/fru- 2,6-p2ase heart-type isozyme) (pfk-2/fbpase-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:o60825] PFKFB2 Low confidence 1.12404 53380.6 47490
    cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] CSTF2 High confidence 1.40546 126408 89940.5
    Rooted homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Low confidence 1.06862 101.348 108.302
    small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] SNRPD2 High confidence 1.17835 55.7423 65.6839
    156 Measured melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] MAGEA2B 1.29736 23693.7 18263
    tho complex 3. [refseq;acc:nm_032361] no value Low confidence 1.08467 7401.51 8028.16
    Ranked cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] CTSL1 1.06031 211.808 199.761
    regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] RGS20 High confidence 1.19466 249.663 298.263
    Squared 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (6pf-2-k/fru- 2,6-p2ase testis-type isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:q16877] PFKFB4 Low confidence 1.12404 53380.6 47490
    septin 10 isoform 1. [refseq;acc:nm_144710] SEPT10 High confidence 1.40528 89578.7 125883
    Rooted homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value Low confidence 1.06862 101.348 108.302
    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] SH2D3C High confidence 1.17356 56.3447 66.124
    157 Measured hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] no value 1.29736 23693.7 18263
    vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754] VPS41 Low confidence 1.08462 7497.17 8131.56

    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/