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 Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2525 to 2574 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    632 no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Divided Low confidence 204.242 1.0292 198.448
    large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Subtracted 207.662 5.786 201.876
    ECH1 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] High confidence 229.072 12.496 216.576
    HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Divided 214.254 1.05979 202.166
    633 no value dolichyl-p-man:man(5)glcnac(2)-pp-dolichyl mannosyltransferase (ec 2.4.1.-) (dol-p-man dependent alpha(1-3)-mannosyltransferase) (not56-like protein). [swissprot;acc:q92685] Subtracted Low confidence 200.085 5.784 194.301
    AARS alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Divided High confidence 234.106 1.05979 248.104
    ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Subtracted 229.072 12.496 216.576
    TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Divided Low confidence 203.734 1.02919 197.956
    634 no value dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] High confidence 226.523 1.05958 213.786
    SYN1 synapsin i (brain protein 4.1). [swissprot;acc:p17600] Subtracted 229.072 12.496 216.576
    TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Low confidence 203.734 5.778 197.956
    TSC22D4 tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Divided 203.726 1.02915 197.955
    635 BBS7 bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] 207.763 1.02913 201.882
    MVK mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Subtracted High confidence 235.296 12.377 247.673
    RPL37 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] Divided 228.639 1.05957 242.258
    TSC22D4 tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Subtracted Low confidence 203.726 5.771 197.955
    636 N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] 204.933 5.769 199.164
    RBM19 probable rna-binding protein kiaa0682. [swissprot;acc:q9y4c8] Divided 206.001 1.02901 200.193
    SFRS1 splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] High confidence 228.639 1.05957 242.258
    VAV1 vav proto-oncogene. [swissprot;acc:p15498] Subtracted 212.2 12.351 199.849
    637 AGPAT3 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Divided Low confidence 192.166 1.029 186.751
    PPAT amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] High confidence 228.639 1.05957 242.258
    RNF144B ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] Subtracted Low confidence 208.62 5.765 202.855
    VAV3 vav-3 protein. [swissprot;acc:q9ukw4] High confidence 212.253 12.345 199.908
    638 NUFIP1 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Divided Low confidence 203.825 1.029 198.081
    SNX17 sorting nexin 17. [swissprot;acc:q15036] High confidence 228.639 1.05957 242.258
    SURF1 surfeit locus protein 1. [swissprot;acc:q15526] Subtracted Low confidence 201.211 5.752 195.459
    VAV2 vav-2 protein. [swissprot;acc:p52735] High confidence 212.526 12.314 200.212
    639 HRB nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Divided 217.67 1.05938 230.596
    N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Low confidence 204.933 1.02897 199.164
    NOVA1 rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Subtracted High confidence 222.554 12.293 234.847
    ZFAND5 zinc finger protein 216. [swissprot;acc:o76080] Low confidence 184.361 5.748 178.613
    640 no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] High confidence 244.842 12.265 232.577
    intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Divided 217.67 1.05938 230.596
    MEGF6 megf6 (fragment). [sptrembl;acc:o75095] Low confidence 207.235 1.02896 201.402
    ZFAND6 protein associated with prk1. [refseq;acc:nm_019006] Subtracted 184.361 5.748 178.613
    641 no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] High confidence 244.842 12.265 232.577
    NUFIP1 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Low confidence 203.825 5.744 198.081
    PRAM1 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Divided High confidence 217.67 1.05938 230.596
    RABEP1 rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Low confidence 198.493 1.02896 192.907
    642 no value intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] High confidence 217.67 1.05938 230.596
    CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Low confidence 203.883 1.02894 198.148
    Subtracted 5.735
    LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] High confidence 228.944 12.199 216.745
    643 HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Divided Low confidence 203.104 1.0289 197.399
    HRBL hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] High confidence 217.67 1.05938 230.596
    MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Subtracted 218.227 12.149 206.078
    ZNF593 zinc finger protein t86. [swissprot;acc:o00488] Low confidence 205.897 5.734 200.163
    644 C16orf35 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Divided High confidence 217.67 1.05938 230.596
    CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Subtracted 226.497 12.142 214.355

    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/