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:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
expected Rank Gene description measured final Hugo
Results: HTML CSV LaTeX Showing element 1752 to 1801 of 3206 in total
expected
Rank
description
measured
final
Hugo
0.60766 423 ADAPTOR-ASSOCIATED KINASE 1. [RefSeq;Acc:NM_014911] 0.168547 0.277370569 AAK1
0.608346 1064 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-2. [SWISSPROT;Acc:O95816] 0.15369 0.252635836 BAG2
0.608459 219 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 10 (EIF-3 THETA) (EIF3 P167) (EIF3 P180) (EIF3 P185) (EIF3A). [SWISSPROT;Acc:Q14152] 0.194219 0.319198171 EIF3A
220 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 4 (EIF-3 DELTA) (EIF3 P44) (EIF-3 RNA-BINDING SUBUNIT) (EIF3 P42) (EIF3G). [SWISSPROT;Acc:O75821] EIF3G
0.60884 296 BAI1-ASSOCIATED PROTEIN 1; WW DOMAIN-CONTAINING PROTEIN 3; ATROPHIN-1 INTERACTING PROTEIN 3. [RefSeq;Acc:NM_004742] 0.183128 0.300781815 MAGI1
0.609191 1376 0.149037 0.244647409 C14orf129
0.610067 365 G-RICH SEQUENCE FACTOR-1 (GRSF-1). [SWISSPROT;Acc:Q12849] 0.170665 0.279747962 GRSF1
0.611499 1415 NUCLEOPORIN NUP43 (P42). [SWISSPROT;Acc:Q8NFH3] 0.149203 0.243995493 NUP43
0.613112 323 0.176498 0.287872363 THOC7
0.614336 230 JUN DIMERIZATION PROTEIN. [RefSeq;Acc:NM_130469] 0.193648 0.315215127 no value
231 PROTO-ONCOGENE PROTEIN C-FOS (CELLULAR ONCOGENE FOS) (G0/G1 SWITCH REGULATORY PROTEIN 7). [SWISSPROT;Acc:P01100] FOS
0.615511 3190 "PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 14D; PKC-DEPENDENT PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_017726]" 0.0229678 0.037315011 PPP1R14D
0.615573 2273 "GLYCEROL KINASE, TESTIS SPECIFIC 2 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14410]" 0.137099 0.222717696 no value
0.616542 2812 0.121488 0.197047403 C9orf23
0.617604 140 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-4 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P48169] 0.217015 0.351382115 GABRA4
0.618161 1149 PUTATIVE GTP-BINDING PROTEIN PTD004 (PRO2455). [SWISSPROT;Acc:Q9NTK5] 0.154662 0.250196955 OLA1
0.618915 2485 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] 0.13384 0.216249404 GPI
0.619267 909 NEUROTRIMIN PRECURSOR (HNT). [SWISSPROT;Acc:Q9P121] 0.159907 0.258219799 no value
0.619508 2652 NUMB PROTEIN HOMOLOG (H-NUMB) (PROTEIN S171). [SWISSPROT;Acc:P49757] 0.130073 0.209961776 NUMB
0.619812 3169 RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464] 0.038917 0.062788394 no value
0.620608 1121 "SPLICING FACTOR, ARGININE/SERINE-RICH 8 (SUPPRESSOR OF WHITE APRICOT PROTEIN HOMOLOG). [SWISSPROT;Acc:Q12872]" 0.155587 0.250700926 SFRS8
0.620827 3193 PROTEIN HSPC134 (PROTEIN CDA04). [SWISSPROT;Acc:Q9BY43] 0.0228851 0.036862282 CHMP4A
0.62131 142 GAMMA-AMINOBUTYRIC-ACID RECEPTOR ALPHA-6 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q16445] 0.218317 0.351381758 GABRA6
0.621928 30 TATA-BINDING PROTEIN-ASSOCIATED PHOSPHOPROTEIN (DOWN-REGULATOR OF TRANSCRIPTION 1) (DR1 PROTEIN). [SWISSPROT;Acc:Q01658] 0.263027 0.422921946 DR1
0.623248 896 0.161768 0.259556388 PRPF38B
0.623804 1808 0.146293 0.234517573 MED9
0.623964 1101 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6 (SM PROTEIN F). [SWISSPROT;Acc:Q9Y4Y8] 0.156724 0.251174747 LSM6
0.624522 139 GAMMA-AMINOBUTYRIC-ACID RECEPTOR EPSILON SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:P78334] 0.219446 0.351382337 GABRE
0.62496 2838 "TRANSLOCON-ASSOCIATED PROTEIN, DELTA SUBUNIT PRECURSOR (TRAP-DELTA) (SIGNAL SEQUENCE RECEPTOR DELTA SUBUNIT) (SSR-DELTA). [SWISSPROT;Acc:P51571]" 0.12066 0.193068356 SSR4
0.625183 844 "ADENYLATE CYCLASE, TYPE V (EC 4.6.1.1) (ATP PYROPHOSPHATE-LYASE) (ADENYLYL CYCLASE) (FRAGMENT). [SWISSPROT;Acc:O95622]" 0.162988 0.260704466 ADCY5
0.626348 1100 ATP-CITRATE SYNTHASE (EC 2.3.3.8) (ATP-CITRATE (PRO-S-)-LYASE) (CITRATE CLEAVAGE ENZYME). [SWISSPROT;Acc:P53396] 0.157326 0.251179855 ACLY
0.62682 1621 "CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL PRECURSOR (CYTOCHROME C-1). [SWISSPROT;Acc:P08574]" 0.150184 0.239596694 CYC1
0.627474 2809 0.124033 0.197670342 ZBTB45
0.627636 1299 DELTA-AMINOLEVULINIC ACID DEHYDRATASE (EC 4.2.1.24) (PORPHOBILINOGEN SYNTHASE) (ALADH). [SWISSPROT;Acc:P13716] 0.154288 0.245824013 ALAD
0.628094 2347 0.1385 0.220508395 no value
0.628521 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] 0.166963 0.265644266
0.629022 3179 CULLIN HOMOLOG 1 (CUL-1). [SWISSPROT;Acc:Q13616] 0.0313105 0.049776478 CUL1
3180 PRESENILIN 1 (PS-1) (S182 PROTEIN). [SWISSPROT;Acc:P49768] PSEN1
0.629342 670 0.167849 0.266705543 USP30
0.629348 884 SCRIBBLE. [RefSeq;Acc:NM_015356] 0.163652 0.260034194 SCRIB
0.629835 54 PUTATIVE ADENOSYLHOMOCYSTEINASE 2 (EC 3.3.1.1) (S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE) (ADOHCYASE). [SWISSPROT;Acc:O43865] 0.25896 0.411155303 AHCYL1
0.6302 453 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 2 (EC 3.1.3.48) (T- CELL PROTEIN-TYROSINE PHOSPHATASE) (TCPTP). [SWISSPROT;Acc:P17706]" 0.173881 0.275913996 PTPN2
0.634694 3119 0.0559756 0.088193051 C1orf14
0.635895 565 "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]" 0.1722 0.270799424 PPP2R1A
0.636381 865 "PRESYNAPTIC PROTEIN SAP97 (SYNAPSE-ASSOCIATED PROTEIN 97) (DISCS, LARGE HOMOLOG 1) (HDLG). [SWISSPROT;Acc:Q12959]" 0.16564 0.260284327 DLG1
0.636394 756 BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5 (APOPTOSIS INHIBITOR SURVIVIN) (APOPTOSIS INHIBITOR 4). [SWISSPROT;Acc:O15392] 0.168097 0.264139825 BIRC5
0.636513 1057 REPLICATION PROTEIN A 32 KDA SUBUNIT (RP-A) (RF-A) (REPLICATION FACTOR-A PROTEIN 2). [SWISSPROT;Acc:P15927] 0.160828 0.252670409 RPA2
0.63684 652 0.170567 0.267833365 ZMIZ2
0.63809 429 SAL-LIKE PROTEIN 1 (ZINC FINGER PROTEIN SALL1) (SPALT-LIKE TRANSCRIPTION FACTOR 1) (HSAL1). [SWISSPROT;Acc:Q9NSC2] 0.176985 0.277366829 SALL1
430 "CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 4; NOT4 (NEGATIVE REGULATOR OF TRANSCRIPTION 4, YEAST) HOMOLOG; CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT. [RefSeq;Acc:NM_013316]" CNOT4

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/