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 description Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 3101 to 3150 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    388 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] HTRA3 Ranked Low confidence 200.049 192.942 1.03683
    pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] HDGFL1 Measured High confidence 4533.74 5279.4 1.16447
    serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] SRR Rooted 50.3345 45.6718 1.10209
    small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] no value Ranked 227.575 208.756 1.09015
    389 60s ribosomal protein l34. [swissprot;acc:p49207] RPL34 Rooted 50.3345 45.6718 1.10209
    arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] RARS2 Squared 31819.7 39222.2 1.23264
    homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] CUTL2 Measured Low confidence 8159.97 8595.12 1.05333
    nocturnin (ccr4 protein homolog). [swissprot;acc:q9uk39] CCRN4L Rooted 69.1568 72.4882 1.04817
    probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] DDX6 Measured High confidence 4533.74 5279.4 1.16447
    probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] HTRA4 Ranked Low confidence 200.049 192.942 1.03683
    rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] RACGAP1 Squared 45959.5 42968.2 1.06962
    small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] SNRPF Ranked High confidence 227.575 208.756 1.09015
    390 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] MRPL13 241.828 263.62 1.09011
    heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] HS6ST1 Squared Low confidence 47629.9 44535.1 1.06949
    monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] SLC16A7 Rooted 82.9732 86.9699 1.04817
    nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] no value Squared High confidence 28895.6 35572.8 1.23108
    protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] SEC61A2 Rooted 50.3345 45.6718 1.10209
    rw1 protein (fragment). [swissprot;acc:q92545] TMEM131 Measured 4533.74 5279.4 1.16447
    solute carrier family 35, member e2. [refseq;acc:nm_182838] no value Ranked Low confidence 203.647 211.144 1.03681
    toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] TLR2 Measured 6983.51 7354.87 1.05318
    391 40s ribosomal protein s16. [swissprot;acc:p17008] RPS16 Ranked High confidence 241.828 263.62 1.09011
    importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] KPNB1 Squared 28895.6 35572.8 1.23108
    kidney and liver proline oxidase 1. [refseq;acc:nm_021232] PRODH2 Low confidence 50781.5 47483.2 1.06946
    monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907] SLC16A8 Rooted 82.9474 86.9421 1.04816
    protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] SEC61A1 High confidence 50.3345 45.6718 1.10209
    serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] HTRA2 Ranked Low confidence 200.046 192.943 1.03681
    tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] TARDBP Measured High confidence 3658.76 3144.39 1.16358
    vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] ATP6V0A1 Low confidence 8552.2 9004.53 1.05289
    392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] RPL13A Ranked High confidence 241.83 263.615 1.09008
    60s ribosomal protein l3-like. [swissprot;acc:q92901] RPL3L Rooted 50.3313 45.6913 1.10155
    atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] DDX54 Measured 3641.89 4236.95 1.16339
    lim domains containing 1. [refseq;acc:nm_014240] LIMD1 Rooted Low confidence 70.7384 74.1429 1.04813
    nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 Ranked 200.894 193.766 1.03679
    ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] RRS1 Squared 49539.3 46326.1 1.06936
    small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] SNRPD2 Measured 7781.34 8192.41 1.05283
    transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] TBL1X Squared High confidence 28895.6 35572.8 1.23108
    393 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] AK2 Low confidence 47766.3 44669.1 1.06934
    cryptochrome 1 (photolyase-like). [refseq;acc:nm_004075] CRY1 Measured 8673.83 9132.05 1.05283
    dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] POLR2A Rooted High confidence 49.8842 45.2875 1.1015
    eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] EIF4E Measured 4490.28 5222.25 1.16301
    monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427] SLC16A3 Rooted Low confidence 82.865 86.8534 1.04813
    small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] no value Ranked 201.334 194.242 1.03651
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] TXNL4A High confidence 225.719 207.072 1.09005
    transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] TBL1Y Squared 28895.6 35572.8 1.23108
    394 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] BAIAP3 Measured 4490.28 5222.25 1.16301
    crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] CRNKL1 Ranked Low confidence 204.815 197.606 1.03648
    dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] DPP9 High confidence 218.827 238.407 1.08948
    mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Squared 17248.4 21214 1.22991
    pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] CLP1 Low confidence 48577.7 45429.7 1.06929
    pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] CDC40 Rooted High confidence 58.6533 64.5958 1.10132

    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/