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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


Navigation/Query Panel:
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expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 1751 to 1800 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.606896 0.150518 1224 HPCA NEURON SPECIFIC CALCIUM-BINDING PROTEIN HIPPOCALCIN (P23K) (CALCIUM- BINDING PROTEIN BDR-2). [SWISSPROT;Acc:P32076] 0.248012839
0.60766 0.168547 423 AAK1 ADAPTOR-ASSOCIATED KINASE 1. [RefSeq;Acc:NM_014911] 0.277370569
0.608346 0.15369 1064 BAG2 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-2. [SWISSPROT;Acc:O95816] 0.252635836
0.608459 0.194219 219 EIF3A EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 10 (EIF-3 THETA) (EIF3 P167) (EIF3 P180) (EIF3 P185) (EIF3A). [SWISSPROT;Acc:Q14152] 0.319198171
220 EIF3G EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 4 (EIF-3 DELTA) (EIF3 P44) (EIF-3 RNA-BINDING SUBUNIT) (EIF3 P42) (EIF3G). [SWISSPROT;Acc:O75821]
0.60884 0.183128 296 MAGI1 BAI1-ASSOCIATED PROTEIN 1; WW DOMAIN-CONTAINING PROTEIN 3; ATROPHIN-1 INTERACTING PROTEIN 3. [RefSeq;Acc:NM_004742] 0.300781815
0.609191 0.149037 1376 C14orf129 0.244647409
0.610067 0.170665 365 GRSF1 G-RICH SEQUENCE FACTOR-1 (GRSF-1). [SWISSPROT;Acc:Q12849] 0.279747962
0.611499 0.149203 1415 NUP43 NUCLEOPORIN NUP43 (P42). [SWISSPROT;Acc:Q8NFH3] 0.243995493
0.613112 0.176498 323 THOC7 0.287872363
0.614336 0.193648 230 no value JUN DIMERIZATION PROTEIN. [RefSeq;Acc:NM_130469] 0.315215127
231 FOS PROTO-ONCOGENE PROTEIN C-FOS (CELLULAR ONCOGENE FOS) (G0/G1 SWITCH REGULATORY PROTEIN 7). [SWISSPROT;Acc:P01100]
0.615511 0.0229678 3190 PPP1R14D "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 14D; PKC-DEPENDENT PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_017726]" 0.037315011
0.615573 0.137099 2273 no value "GLYCEROL KINASE, TESTIS SPECIFIC 2 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14410]" 0.222717696
0.616542 0.121488 2812 C9orf23 0.197047403
0.617604 0.217015 140 GABRA4 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-4 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P48169] 0.351382115
0.618161 0.154662 1149 OLA1 PUTATIVE GTP-BINDING PROTEIN PTD004 (PRO2455). [SWISSPROT;Acc:Q9NTK5] 0.250196955
0.618915 0.13384 2485 GPI GLUCOSE-6-PHOSPHATE ISOMERASE (EC 5.3.1.9) (GPI) (PHOSPHOGLUCOSE ISOMERASE) (PGI) (PHOSPHOHEXOSE ISOMERASE) (PHI) (NEUROLEUKIN) (NLK) (SPERM ANTIGEN-36) (SA-36). [SWISSPROT;Acc:P06744] 0.216249404
0.619267 0.159907 909 no value NEUROTRIMIN PRECURSOR (HNT). [SWISSPROT;Acc:Q9P121] 0.258219799
0.619508 0.130073 2652 NUMB NUMB PROTEIN HOMOLOG (H-NUMB) (PROTEIN S171). [SWISSPROT;Acc:P49757] 0.209961776
0.619812 0.038917 3169 no value RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464] 0.062788394
0.620608 0.155587 1121 SFRS8 "SPLICING FACTOR, ARGININE/SERINE-RICH 8 (SUPPRESSOR OF WHITE APRICOT PROTEIN HOMOLOG). [SWISSPROT;Acc:Q12872]" 0.250700926
0.620827 0.0228851 3193 CHMP4A PROTEIN HSPC134 (PROTEIN CDA04). [SWISSPROT;Acc:Q9BY43] 0.036862282
0.62131 0.218317 142 GABRA6 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-6 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q16445] 0.351381758
0.621928 0.263027 30 DR1 TATA-BINDING PROTEIN-ASSOCIATED PHOSPHOPROTEIN (DOWN-REGULATOR OF TRANSCRIPTION 1) (DR1 PROTEIN). [SWISSPROT;Acc:Q01658] 0.422921946
0.623248 0.161768 896 PRPF38B 0.259556388
0.623804 0.146293 1808 MED9 0.234517573
0.623964 0.156724 1101 LSM6 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6 (SM PROTEIN F). [SWISSPROT;Acc:Q9Y4Y8] 0.251174747
0.624522 0.219446 139 GABRE GAMMA-AMINOBUTYRIC-ACID RECEPTOR EPSILON SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P78334] 0.351382337
0.62496 0.12066 2838 SSR4 "TRANSLOCON-ASSOCIATED PROTEIN, DELTA SUBUNIT PRECURSOR (TRAP-DELTA) (SIGNAL SEQUENCE RECEPTOR DELTA SUBUNIT) (SSR-DELTA). [SWISSPROT;Acc:P51571]" 0.193068356
0.625183 0.162988 844 ADCY5 "ADENYLATE CYCLASE, TYPE V (EC 4.6.1.1) (ATP PYROPHOSPHATE-LYASE) (ADENYLYL CYCLASE) (FRAGMENT). [SWISSPROT;Acc:O95622]" 0.260704466
0.626348 0.157326 1100 ACLY ATP-CITRATE SYNTHASE (EC 2.3.3.8) (ATP-CITRATE (PRO-S-)-LYASE) (CITRATE CLEAVAGE ENZYME). [SWISSPROT;Acc:P53396] 0.251179855
0.62682 0.150184 1621 CYC1 "CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL PRECURSOR (CYTOCHROME C-1). [SWISSPROT;Acc:P08574]" 0.239596694
0.627474 0.124033 2809 ZBTB45 0.197670342
0.627636 0.154288 1299 ALAD DELTA-AMINOLEVULINIC ACID DEHYDRATASE (EC 4.2.1.24) (PORPHOBILINOGEN SYNTHASE) (ALADH). [SWISSPROT;Acc:P13716] 0.245824013
0.628094 0.1385 2347 no value 0.220508395
0.628521 0.166963 680 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 5 (EC 2.7.1.-) (MAPK/ERK KINASE KINASE 5) (MEK KINASE 5) (MEKK 5) (APOPTOSIS SIGNAL- REGULATING KINASE 1) (ASK-1). [SWISSPROT;Acc:Q99683] 0.265644266
0.629022 0.0313105 3179 CUL1 CULLIN HOMOLOG 1 (CUL-1). [SWISSPROT;Acc:Q13616] 0.049776478
3180 PSEN1 PRESENILIN 1 (PS-1) (S182 PROTEIN). [SWISSPROT;Acc:P49768]
0.629342 0.167849 670 USP30 0.266705543
0.629348 0.163652 884 SCRIB SCRIBBLE. [RefSeq;Acc:NM_015356] 0.260034194
0.629835 0.25896 54 AHCYL1 PUTATIVE ADENOSYLHOMOCYSTEINASE 2 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:O43865] 0.411155303
0.6302 0.173881 453 PTPN2 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 2 (EC 3.1.3.48) (T- CELL PROTEIN-TYROSINE PHOSPHATASE) (TCPTP). [SWISSPROT;Acc:P17706]" 0.275913996
0.634694 0.0559756 3119 C1orf14 0.088193051
0.635895 0.1722 565 PPP2R1A "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 65 KDA REGULATORY SUBUNIT A, ALPHA ISOFORM (PP2A, SUBUNIT A, PR65-ALPHA ISOFORM) (PP2A, SUBUNIT A, R1-ALPHA ISOFORM) (MEDIUM TUMOR ANTIGEN-ASSOCIATED 61 KDA PROTEIN). [SWISSPROT;Acc:P30153]" 0.270799424
0.636381 0.16564 865 DLG1 "PRESYNAPTIC PROTEIN SAP97 (SYNAPSE-ASSOCIATED PROTEIN 97) (DISCS, LARGE HOMOLOG 1) (HDLG). [SWISSPROT;Acc:Q12959]" 0.260284327
0.636394 0.168097 756 BIRC5 BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5 (APOPTOSIS INHIBITOR SURVIVIN) (APOPTOSIS INHIBITOR 4). [SWISSPROT;Acc:O15392] 0.264139825
0.636513 0.160828 1057 RPA2 REPLICATION PROTEIN A 32 KDA SUBUNIT (RP-A) (RF-A) (REPLICATION FACTOR-A PROTEIN 2). [SWISSPROT;Acc:P15927] 0.252670409
0.63684 0.170567 652 ZMIZ2 0.267833365
0.63809 0.176985 429 SALL1 SAL-LIKE PROTEIN 1 (ZINC FINGER PROTEIN SALL1) (SPALT-LIKE TRANSCRIPTION FACTOR 1) (HSAL1). [SWISSPROT;Acc:Q9NSC2] 0.277366829

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/