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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7412 to 7461 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
927 microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Ranked Divided 217.942 210.139 1.03713
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Subtracted 220.246 212.618 7.628
swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] Measured 4134.77 4691.24 556.47
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] Squared Divided 24049.1 27802.5 1.15607
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Rooted 62.0422 65.7019 1.05899
928 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Measured 5638.46 6194.04 1.09853
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Rooted 62.0422 65.7019 1.05899
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Subtracted 62.3618 66.0328 3.671
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Ranked Divided 225.976 218.017 1.03651
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] Squared Subtracted 25151.8 28800.9 3649.1
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Ranked 220.246 212.618 7.628
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Squared Divided 20685.1 23904.8 1.15565
swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078] Measured Subtracted 4134.77 4691.24 556.47
929 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Ranked 243.045 235.422 7.623
argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] Squared 24976.9 28625.4 3648.5
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Ranked Divided 225.955 218.015 1.03642
surfeit locus protein 1. [swissprot;acc:q15526] Measured 5638.46 6194.04 1.09853
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] Subtracted 4134.77 4691.24 556.47
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Squared Divided 22626.3 26143 1.15543
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Rooted Subtracted 62.3618 66.0328 3.671
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Divided 62.3617 66.0327 1.05887
930 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Measured 5638.65 6194.23 1.09853
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Subtracted 6281.21 6837.61 556.4
homolog of yeast maf1. [refseq;acc:nm_032272] Squared Divided 26029.5 30074.5 1.1554
phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] Subtracted 25180.2 28821.7 3641.5
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Ranked 233.402 225.782 7.62
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Divided 231.357 239.778 1.0364
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Rooted Subtracted 62.3618 66.0328 3.671
931 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Ranked Divided 159.13 164.917 1.03637
cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Measured Subtracted 6281.21 6837.61 556.4
kinesin family member c3. [refseq;acc:nm_005550] Squared 26958 30597.1 3639.1
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Ranked 228.953 221.421 7.532
sec13-related protein. [swissprot;acc:p55735] Rooted Divided 62.3618 66.0328 1.05887
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Measured 5638.59 6194.17 1.09853
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Squared 26029.5 30074.5 1.1554
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Rooted Subtracted 62.3617 66.0327 3.671
932 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Measured 6281.21 6837.61 556.4
cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Divided 5638.46 6194.04 1.09853
mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Ranked 225.939 218.013 1.03636
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Subtracted 228.953 221.421 7.532
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Squared Divided 26029.5 30074.5 1.1554
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Subtracted 28010 31646.5 3636.5
vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] Rooted 62.3588 66.0297 3.6709
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Divided 62.3617 66.0327 1.05887
933 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Ranked 159.165 164.951 1.03635
cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Measured Subtracted 6281.21 6837.61 556.4
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Ranked 242.978 235.518 7.46
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Measured Divided 5638.46 6194.04 1.09853
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Squared Subtracted 28010 31646.5 3636.5

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
- 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/