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

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/