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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5908 to 5957 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
739 phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Ranked Divided 223.58 235.027 1.0512
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Squared 25727.7 30046.7 1.16787
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Rooted Subtracted 60.6572 64.9858 4.3286
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Squared 26312 30514.1 4202.1
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Measured 5248.07 5901.72 653.65
740 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] Ranked Divided 223.58 235.027 1.0512
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Rooted 53.1114 56.7251 1.06804
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Squared 22075.1 25775.1 1.16761
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Rooted Subtracted 95.094 90.7685 4.3255
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Squared 12326.4 16522.9 4196.5
syntaxin 7. [swissprot;acc:o15400] Measured 5580.97 6233.52 652.55
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Ranked 223.463 212.875 10.588
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Measured Divided 5768.32 6434.78 1.11554
741 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Rooted 53.1114 56.7251 1.06804
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Subtracted 65.3248 69.648 4.3232
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Measured Divided 5768.32 6434.78 1.11554
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Ranked 223.58 235.027 1.0512
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Squared 23894.7 27894.5 1.16739
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 12326.4 16522.9 4196.5
sipl protein. [refseq;acc:nm_018269] Measured 6522.94 7175.18 652.24
step ii splicing factor slu7. [refseq;acc:nm_006425] Ranked 223.463 212.875 10.588
742 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Measured 4864.66 5514.87 650.21
brain protein 44. [swissprot;acc:o95563] Ranked Divided 126.215 120.078 1.05111
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Squared Subtracted 12326.4 16522.9 4196.5
eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Measured Divided 4131.04 4607.9 1.11543
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Ranked Subtracted 226.003 215.541 10.462
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Squared Divided 31406.6 36662.8 1.16736
syntaxin 12. [refseq;acc:nm_177424] Rooted Subtracted 61.3557 65.66 4.3043
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Divided 67.0234 71.5506 1.06755
743 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Measured Subtracted 4864.66 5514.87 650.21
cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Squared Divided 31406.6 36662.8 1.16736
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Measured 4131.04 4607.9 1.11543
katanin p60 subunit a 1. [refseq;acc:nm_007044] Rooted 54.4988 51.0573 1.0674
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Ranked Subtracted 225.996 215.535 10.461
nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] Squared 32053.5 36239.4 4185.9
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Ranked Divided 126.215 120.078 1.05111
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Rooted Subtracted 50.3767 46.0753 4.3014
744 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Squared Divided 31406.6 36662.8 1.16736
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Measured Subtracted 9903.22 9253.79 649.43
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Divided 12515.4 11221.1 1.11535
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Ranked Subtracted 225.996 215.535 10.461
dynactin 4. [refseq;acc:nm_032486] Rooted Divided 55.2242 51.7372 1.0674
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Subtracted 61.0082 65.306 4.2978
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Squared 31586.9 35762.8 4175.9
septin 6. [swissprot;acc:q14141] Ranked Divided 126.604 120.463 1.05098
745 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Measured Subtracted 9899.79 9251.2 648.59
cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Squared Divided 31406.6 36662.8 1.16736
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Ranked Subtracted 225.989 215.53 10.459
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Squared 27084.5 31257.9 4173.4
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Rooted 61.0097 65.3071 4.2974

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/