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 network_comparison green
    Results: HTML CSV LaTeX Showing element 1632 to 1681 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    408 JPH4 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Divided Low confidence 207.558 1.03591 200.363
    409 no value metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Subtracted 203.081 7.081 196
    NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Divided 149.423 1.03582 144.256
    POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] High confidence 241.045 1.08641 261.874
    RUNX2 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Subtracted 237.109 17.558 254.667
    410 no value tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Divided 233.376 1.0864 253.539
    ACTR3B similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Subtracted Low confidence 205.594 7.04 198.554
    HNRPUL1 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] High confidence 237.109 17.558 254.667
    LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Divided Low confidence 202.074 1.03576 195.097
    411 C19orf29 ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] Subtracted 210.727 7.034 203.693
    EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Divided 214.628 1.03575 222.301
    GTF2H1 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] High confidence 233.376 1.0864 253.539
    RPL18 60s ribosomal protein l18. [swissprot;acc:q07020] Subtracted 237.109 17.558 254.667
    412 LIMCH1 similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Low confidence 210.594 7.033 203.561
    NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] High confidence 251.926 17.379 234.547
    SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Divided Low confidence 201.711 1.03555 194.787
    UQCRFSL1 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] High confidence 240.788 1.08567 261.416
    413 CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Subtracted Low confidence 210.252 7.012 203.24
    KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Divided 201.711 1.03555 194.787
    POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] High confidence 240.913 1.08525 261.45
    TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Subtracted 223.202 17.302 205.9
    414 ACTR3B similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Divided Low confidence 205.594 1.03546 198.554
    CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Subtracted 210.251 7.01 203.241
    KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] Divided High confidence 232.431 1.08522 252.238
    MAX max protein. [swissprot;acc:p25912] Subtracted 227.828 17.267 210.561
    415 CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Low confidence 210.251 7.01 203.241
    KATNB1 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Divided High confidence 232.382 1.08514 252.166
    PPP2R5A serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Low confidence 203.463 1.03546 196.495
    TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Subtracted High confidence 200.586 17.163 183.423
    416 AP1G1 adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] Divided Low confidence 207.442 1.03545 200.339
    CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Subtracted 210.251 7.01 203.241
    POLR1B dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Divided High confidence 240.6 1.08496 261.041
    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] Subtracted 200.791 17.131 183.66
    417 no value tho complex 3. [refseq;acc:nm_032361] Low confidence 186.383 7.009 179.374
    OXA1L cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Divided 211.182 1.03525 203.991
    SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] High confidence 233.539 1.08417 253.197
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Subtracted 235.94 17.103 218.837
    418 ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 233.723 17.049 216.674
    CLEC4M cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Divided 233.539 1.08417 253.197
    LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Subtracted Low confidence 201.095 6.996 194.099
    PPP2R5E serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Divided 203.448 1.03523 196.524
    419 BCKDK [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] 202.714 1.03518 195.825
    FCER2 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] High confidence 233.539 1.08417 253.197
    LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Subtracted Low confidence 201.123 6.996 194.127
    SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence 235.922 16.997 218.925
    420 CD209 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Divided 233.539 1.08417 253.197
    CYC1 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Subtracted 238.704 16.976 255.68
    NMNAT3 nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Low confidence 206.507 6.992 199.515
    SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Divided 201.134 1.03516 194.302
    421 AP2B1 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] Subtracted 207.064 6.988 200.076

    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/