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 7191 to 7240 of 8289 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		red
    		green
    		network_comparison
    3963 TLX1 t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] 204.615 202.171 1.01209
    3964 ACTA2 actin, aortic smooth muscle (alpha-actin 2). [swissprot;acc:p03996] 200.877 198.477
    3965 TLX2 t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] 204.614 202.172 1.01208
    3966 PARD6G partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 201.922 199.513 1.01207
    3967 PEX13 peroxisomal membrane protein pex13 (peroxin-13). [swissprot;acc:q92968] 202.356 199.945 1.01206
    3968 PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]
    3969 NCBP1 80 kda nuclear cap binding protein (ncbp 80 kda subunit) (cbp80). [swissprot;acc:q09161]
    3970 NFX1 transcriptional repressor nf-x1 (ec 6.3.2.-) (nuclear transcription factor, x box-binding, 1). [swissprot;acc:q12986] 207.269 204.799
    3971 RPS6KA6 ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32] 199.95 197.568
    3972 CMPK ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 210.066 212.598 1.01205
    3973 TUSC4 homologous to yeast nitrogen permease (candidate tumor suppressor). [refseq;acc:nm_006545] 201.99 204.416 1.01201
    3974 PGM3 phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] 196.483 194.152
    3975 TTN titin isoform novex-3; connectin; cmh9, included; cardiomyopathy, dilated 1g (autosomal dominant). [refseq;acc:nm_133379] 205.357 202.923 1.01199
    3976 CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] 192.47 190.192 1.01198
    3977 CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 192.473 190.194
    3978 CPB2 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 192.466 190.19 1.01197
    3979 RPS6KA2 ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [swissprot;acc:q15349] 199.946 197.582 1.01196
    3980 MLH1 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 201.031 198.658 1.01195
    3981 no value 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 203.072 200.675 1.01194
    3982 RPS27L ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 203.038 200.645 1.01193
    3983 TRIO triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] 203.287 200.891
    3984 CDC2L5 cell division cycle 2-like protein kinase 5 (ec 2.7.1.-) (cholinesterase-related cell division controller) (cdc2-related protein kinase 5). [swissprot;acc:q14004] 202.774 200.388 1.01191
    3985 PACSIN3 protein kinase c and casein kinase substrate in neurons protein 3 (sh3 domain-containing protein 6511) (endophilin i). [swissprot;acc:q9uks6] 201.469 199.1 1.0119
    3986 PACSIN1 protein kinase c and casein kinase substrate in neurons protein 1. [swissprot;acc:q9by11]
    3987 POFUT1 gdp-fucose protein o-fucosyltransferase 1 precursor (ec 2.4.1.221) (peptide o-fucosyltransferase) (o-fuct-1). [swissprot;acc:q9h488]
    3988 PACSIN2 protein kinase c and casein kinase substrate in neurons protein 2. [swissprot;acc:q9unf0]
    3989 RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] 206.934 209.395 1.01189
    3990 AGXT2 alanine--glyoxylate aminotransferase 2, mitochondrial precursor (ec 2.6.1.44) (agt 2) (beta-alanine-pyruvate aminotransferase) (beta- alaat ii). [swissprot;acc:q9byv1]
    3991 no value cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] 203.948 206.371 1.01188
    3992 C2orf33 gl004 protein. [refseq;acc:nm_020194] 200.847 198.494 1.01185
    3993 DACH1 dachshund homolog isoform a. [refseq;acc:nm_080759] 202.446 200.075
    3994 SET set protein (hla-dr associated protein ii) (phapii) (phosphatase 2a inhibitor i2pp2a). [swissprot;acc:q01105]
    3995 TRUB1 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 209.294 211.763 1.0118
    3996 no value huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] 203.287 200.918 1.01179
    3997 FOXG1 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 206.776 204.371 1.01177
    3998 UQCRC1 ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 201.446 199.107 1.01175
    3999 LIMS2 lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980] 203.893 201.528 1.01174
    4000 SPHK2 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 204.262 201.891
    4001 HSPB8 alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 205.873 203.49 1.01171
    4002 GPR84 inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] 202.911 200.564 1.0117
    4003 CRKRS cell division cycle 2-related protein kinase 7 (ec 2.7.1.-) (cdc2- related protein kinase 7) (crkrs). [swissprot;acc:q9nyv4] 202.807 200.463 1.01169
    4004 HSPB1 heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792] 205.901 203.522
    4005 ACLY atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] 201.572 199.244 1.01168
    4006 ATP5G1 atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p1) (atpase protein 9) (atpase subunit c). [swissprot;acc:p05496] 201.708 199.381 1.01167
    4007 FIP1L1 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 196.45 194.183
    4008 TUBA1C tubulin alpha-6 chain (alpha-tubulin 6). [swissprot;acc:q9bqe3] 200.479 198.173 1.01164
    4009 CANT1 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 199.575 197.281 1.01163
    4010 CSNK1G1 casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] 196.478 194.223 1.01161
    4011 OPN4 opsin 4 (melanopsin). [swissprot;acc:q9uhm6] 205.753 203.392
    4012 HECTD1 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]

    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/