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 Hugo Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 2280 to 2329 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Network Comparison Type
description
Value Type
red
network_comparison
green
285 RRM2B Subtracted ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Squared 32117 7937 40054
286 no value rna-binding protein. [refseq;acc:nm_019027] Measured 4069.83 1182.34 5252.17
transforming protein n-ras. [swissprot;acc:p01111] Rooted 108.65 8.3 100.35
CSRP2 Divided smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 51.8717 1.11965 46.3287
EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Measured 23316 1.20878 19288.8
NEDD9 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Ranked 224.633 1.1052 203.251
PBK t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Squared 6693.64 1.27956 8564.94
RPL30 Subtracted 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked 242.593 22.772 265.365
RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Squared 32056.4 7909.4 39965.8
287 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Measured 4069.83 1182.34 5252.17
KHDRBS3 Divided kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Squared 6693.64 1.27956 8564.94
PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Measured 23303.1 1.2087 19279.5
RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked 240.758 1.10517 266.079
SF3B1 Subtracted splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 225.217 22.758 202.459
SHCBP1 Divided likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Rooted 51.8714 1.11965 46.3281
TCP1 Subtracted t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 97.1967 8.1053 105.302
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Squared 28878.8 7904.7 36783.5
288 no value Divided 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Ranked 240.758 1.10517 266.078
Subtracted small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Rooted 55.8956 8.068 63.9636
CPSF3 Divided cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Measured 23422.4 1.20857 19380.3
CRK Subtracted proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Squared 28896.2 7870.8 36767
CSRP3 Divided lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Rooted 51.8789 1.11949 46.3416
KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Squared 6693.64 1.27956 8564.94
STX10 Subtracted syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked 234.691 22.751 257.442
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Measured 4069.83 1182.34 5252.17
289 no value Divided hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Ranked 272.781 1.10486 246.892
ABL2 Subtracted tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Squared 28896.2 7870.8 36767
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Measured 4069.83 1182.34 5252.17
KHDRBS2 Divided kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Squared 6693.64 1.27956 8564.94
LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Measured 4682.88 1.20571 5646.19
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted 57.4274 1.11899 64.2609
SNRPF Subtracted small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 55.8956 8.068 63.9636
STX6 syntaxin 6. [swissprot;acc:o43752] Ranked 234.673 22.741 257.414
290 no value Divided atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Rooted 75.6323 1.11788 67.6572
Subtracted proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Squared 28896.2 7870.8 36767
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Ranked 242.109 22.681 264.79
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Measured 4071.1 1180.65 5251.75
NCBP2 Divided 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Squared 15734.4 1.27916 20126.8
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Ranked 231.969 1.10428 210.064
TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Measured 4991.48 1.20487 6014.08
WAS Subtracted wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Rooted 66.1122 8.0316 74.1438
291 no value Divided ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 113.983 1.11771 101.979
AK2 Subtracted adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Ranked 241.509 22.654 264.163
CLEC3B Divided tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Squared 59016.1 1.27909 75486.9
CRK Subtracted proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Rooted 66.1064 8.001 74.1074
HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Squared 28896.2 7870.8 36767
NFYB Divided nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Ranked 251.679 1.10368 228.037
PLDN Subtracted pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Measured 5894.75 1178.9 7073.65
UBAC1 Divided putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 44490.5 1.20481 36927.5
292 no value Subtracted proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted 66.1064 8.001 74.1074

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/