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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 423 to 472 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
212 CUL1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Divided 285.684 252.234 1.13261
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Subtracted 237.302 212.41 24.892
213 HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Divided 210.693 186.95 1.127
214 LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 191.644 170.192 1.12605
MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Subtracted 241.282 266.12 24.838
215 no value myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Divided 112 126 1.125
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Subtracted 237.292 212.457 24.835
216 MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Divided 112 126 1.125
SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Subtracted 226.471 201.769 24.702
217 MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Divided 112 126 1.125
RPL26 60s ribosomal protein l26. [swissprot;acc:q02877] Subtracted 242.326 267.008 24.682
218 MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Divided 112 126 1.125
RPL35 60s ribosomal protein l35. [swissprot;acc:p42766] Subtracted 242.333 266.999 24.666
219 no value 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 242.339 266.986 24.647
MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Divided 112 126 1.125
220 MRPL2 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Subtracted 242.339 266.986 24.647
MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 112 126 1.125
221 no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
EIF1B protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Subtracted 242.627 267.151 24.524
222 no value 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 242.153 266.673 24.52
MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Divided 112 126 1.125
223 MYH13 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
SRR serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Subtracted 242.153 266.673 24.52
224 RPL34 60s ribosomal protein l34. [swissprot;acc:p49207]
SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Divided 185.969 165.623 1.12285
225 SEC61A2 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Subtracted 242.153 266.673 24.52
SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Divided 226.471 201.769 1.12243
226 COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 239.991 269.238 1.12187
SEC61A1 protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Subtracted 242.153 266.673 24.52
227 METAP1 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] 244.126 268.604 24.478
THBS3 thrombospondin 3 precursor. [swissprot;acc:p49746] Divided 239.99 269.234 1.12186
228 METAP2 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Subtracted 244.126 268.604 24.478
SH2D3C sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Divided 226.411 202.088 1.12036
229 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 226.401 202.094 1.12028
RPL3L 60s ribosomal protein l3-like. [swissprot;acc:q92901] Subtracted 242.195 266.663 24.468
230 CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Divided 239.35 267.915 1.11934
EIF1 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Subtracted 242.694 267.017 24.323
231 SH2D3C sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 226.411 202.088
SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Divided 239.336 267.881 1.11927
232 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Subtracted 226.401 202.094 24.307
CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Divided 239.336 267.879 1.11926
233 no value 60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted 235.727 259.984 24.257
CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Divided 239.32 267.842 1.11918
234 CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 287.41 256.835 1.11905
RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] Subtracted 243.944 268.195 24.251
235 MRPS12 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
PAH phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Divided 227.357 254.15 1.11785
236 DUS1L pp3111 protein. [refseq;acc:nm_022156]
RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Subtracted 252.644 228.42 24.224

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/