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 [...,...].
description Rank Gene expected measured final Hugo
Results: HTML CSV LaTeX Showing element 2408 to 2457 of 3206 in total
description
Rank
expected
measured
final
Hugo
PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-1 (HOMEOBOX PROTEIN PBX1) (HOMEOBOX PROTEIN PRL). [SWISSPROT;Acc:P40424] 1069 1.19272 0.301322 0.252634315 PBX1
PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-2 (HOMEOBOX PROTEIN PBX2) (G17 PROTEIN). [SWISSPROT;Acc:P40425] 1061 1.16629 0.294647 0.252636137 no value
PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-3 (HOMEOBOX PROTEIN PBX3). [SWISSPROT;Acc:P40426] 1063 1.12271 0.283637 0.252636032 PBX3
PRE-MRNA CLEAVAGE COMPLEX II PROTEIN CLP1. [SWISSPROT;Acc:Q92989] 1946 0.920283 0.212972 0.231420118 CLP1
PRE-MRNA CLEAVAGE COMPLEX II PROTEIN PCF11 (FRAGMENT). [SWISSPROT;Acc:O94913] 2479 1.15996 0.251152 0.216517811 PCF11
PRE-MRNA PROCESSING FACTOR 31 HOMOLOG; PRE-MRNA PROCESSING FACTOR 31 HOMOLOG (YEAST). [RefSeq;Acc:NM_015629] 319 1.77067 0.515195 0.290960484 PRPF31
PRE-MRNA SPLICING FACTOR PRP17 (HPRP17) (EH-BINDING PROTEIN 3) (EHB3). [SWISSPROT;Acc:O60508] 376 0.982579 0.274292 0.279155162 CDC40
PREFOLDIN SUBUNIT 1. [SWISSPROT;Acc:O60925] 661 0.480838 0.128438 0.267112832 PFDN1
PREFOLDIN SUBUNIT 2 (HSPC231). [SWISSPROT;Acc:Q9UHV9] 1789 0.643016 0.15115 0.235064135 PFDN2
PREFOLDIN SUBUNIT 3 (VON HIPPEL-LINDAU BINDING PROTEIN 1) (VHL BINDING PROTEIN-1) (VBP-1) (HIBBJ46). [SWISSPROT;Acc:Q15765] 1787 0.129981 0.0305539 0.235064356 VBP1
PREFOLDIN SUBUNIT 5 (C-MYC BINDING PROTEIN MM-1) (MYC MODULATOR 1). [SWISSPROT;Acc:Q99471] 2076 1.30706 0.299475 0.229121081 PFDN5
PREFOLDIN SUBUNIT 6 (PROTEIN KE2). [SWISSPROT;Acc:O15212] 2077 0.118824 0.027225 0.22912038 no value
PREIMPLANTATION PROTEIN 3; LIKELY ORTHOLOG OF PREIMPLANTATION PROTEIN 3. [RefSeq;Acc:NM_015387] 161 0.860216 0.297365 0.345686432 MOBKL3
PRESENILIN 1 (PS-1) (S182 PROTEIN). [SWISSPROT;Acc:P49768] 3180 0.629022 0.0313105 0.049776478 PSEN1
PRESENILIN 2 (PS-2) (STM-2) (E5-1) (AD3LP) (AD5). [SWISSPROT;Acc:P49810] 3183 0.517685 0.0257685 0.049776408 PSEN2
PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). [SWISSPROT;Acc:Q8TCT7] 1852 0.142049 0.0331615 0.233451133 no value
PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). [SWISSPROT;Acc:Q8TCT8] 1855 0.117865 0.0275157 0.233450982
PRESENILINS ASSOCIATED RHOMBOID-LIKE PROTEIN. [RefSeq;Acc:NM_018622] 1080 0.702909 0.177185 0.252073882 PARL
PRIP-INTERACTING PROTEIN PIPMT; PRIP-INTERACTING PROTEIN WITH METHYLTRANSFERASE DOMAIN. [RefSeq;Acc:NM_024831] 962 0.152962 0.0391646 0.25604137 TGS1
PROBABLE ATP-DEPENDENT 61 KDA NUCLEOLAR RNA HELICASE (DEAD-BOX PROTEIN 21). [SWISSPROT;Acc:Q9NY93] 1329 1.14368 0.280718 0.245451525 DDX56
PROBABLE ATP-DEPENDENT HELICASE DDX35 (DEAH-BOX PROTEIN 35). [SWISSPROT;Acc:Q9H5Z1] 2613 0.122212 0.0258274 0.211332766 DHX35
PROBABLE ATP-DEPENDENT RNA HELICASE DDX20 (DEAD-BOX PROTEIN 20) (DEAD- BOX PROTEIN DP 103) (COMPONENT OF GEMS 3) (GEMIN3). [SWISSPROT;Acc:Q9UHI6] 1478 0.378775 0.092033 0.242975381 DDX20
PROBABLE ATP-DEPENDENT RNA HELICASE P54 (ONCOGENE RCK) (DEAD-BOX PROTEIN 6). [SWISSPROT;Acc:P26196] 2865 4.24298 0.801671 0.188940556 DDX6
PROBABLE CALCIUM-TRANSPORTING ATPASE KIAA0703 (EC 3.6.3.8). [SWISSPROT;Acc:O75185] 1450 0.296552 0.0721789 0.243393739 ATP2C2
PROBABLE CATION-TRANSPORTING ATPASE 1 (EC 3.6.1.-). [SWISSPROT;Acc:Q9NQ11] 1189 0.123075 0.0305968 0.248602884 ATP13A2
PROBABLE RIBOSOME BIOGENESIS PROTEIN NEP1 (C2F PROTEIN). [SWISSPROT;Acc:Q92979] 1508 2.10953 0.511781 0.242604277 EMG1
PROBABLE RRNA PROCESSING PROTEIN EBP2 (EBNA1 BINDING PROTEIN 2) (NUCLEOLAR PROTEIN P40). [SWISSPROT;Acc:Q99848] 1345 1.10693 0.271421 0.245201594 EBNA1BP2
PROBABLE SERINE PROTEASE HTRA3 PRECURSOR (EC 3.4.21.-). [SWISSPROT;Acc:P83110] 2579 2.33696 0.498067 0.213126027 HTRA3
PROBABLE SERINE PROTEASE HTRA4 PRECURSOR (EC 3.4.21.-). [SWISSPROT;Acc:P83105] 2578 2.30709 0.491713 0.213131261 HTRA4
PROBABLE SERINE/THREONINE-PROTEIN KINASE KIAA0537 (EC 2.7.1.-). [SWISSPROT;Acc:O60285] 1004 0.54802 0.139695 0.25490858 NUAK1
PROGRAMMED CELL DEATH PROTEIN 5 (TFAR19 PROTEIN) (TF-1 CELL APOPTOSIS RELATED GENE-19 PROTEIN). [SWISSPROT;Acc:O14737] 1796 0.930463 0.218499 0.234828252 PDCD5
PROGRAMMED CELL DEATH PROTEIN 6 (PROBABLE CALCIUM-BINDING PROTEIN ALG- 2). [SWISSPROT;Acc:O75340] 114 0.506093 0.182783 0.361164845 PDCD6
PROHIBITIN. [SWISSPROT;Acc:P35232] 2403 1.22481 0.26817 0.218948245 PHB
PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) (CYCLIN). [SWISSPROT;Acc:P12004] 2722 3.65293 0.754507 0.206548442 PCNA
PROLIFERATING-CELL NUCLEOLAR ANTIGEN P120 (PROLIFERATION-ASSOCIATED NUCLEOLAR PROTEIN P120). [SWISSPROT;Acc:P46087] 1565 2.96197 0.714168 0.241112503 NOL1
PROLIFERATION-ASSOCIATED PROTEIN 2G4 (CELL CYCLE PROTEIN P38-2G4 HOMOLOG) (HG4-1). [SWISSPROT;Acc:Q9UQ80] 665 0.311645 0.083217 0.26702498 PA2G4
PROLINE SYNTHETASE CO-TRANSCRIBED BACTERIAL HOMOLOG PROTEIN. [SWISSPROT;Acc:O94903] 3171 0.74486 0.0439931 0.05906224 PROSC
PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 5 PRECURSOR (EC 3.4.21.-) (PROPROTEIN CONVERTASE PC5) (SUBTILISIN/KEXIN-LIKE PROTEASE PC5) (CONVERTASE PC5) (PC6) (HPC6). [SWISSPROT;Acc:Q92824] 3086 0.408247 0.0398596 0.09763599 PCSK5
PROTEASOME SUBUNIT ALPHA TYPE 1 (EC 3.4.25.1) (PROTEASOME COMPONENT C2) (MACROPAIN SUBUNIT C2) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C2) (PROTEASOME NU CHAIN) (30 KDA PROSOMAL PROTEIN) (PROS-30). [SWISSPROT;Acc:P25786] 1430 5.69292 1.38784 0.243783507 PSMA1
PROTEASOME SUBUNIT ALPHA TYPE 2 (EC 3.4.25.1) (PROTEASOME COMPONENT C3) (MACROPAIN SUBUNIT C3) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C3). [SWISSPROT;Acc:P25787] 1375 4.1775 1.02216 0.244682226 PSMA2
PROTEASOME SUBUNIT ALPHA TYPE 3 (EC 3.4.25.1) (PROTEASOME COMPONENT C8) (MACROPAIN SUBUNIT C8) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C8). [SWISSPROT;Acc:P25788] 1667 4.005 0.956289 0.238773783 PSMA3
PROTEASOME SUBUNIT ALPHA TYPE 4 (EC 3.4.25.1) (PROTEASOME COMPONENT C9) (MACROPAIN SUBUNIT C9) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C9) (PROTEASOME SUBUNIT L). [SWISSPROT;Acc:P25789] 1400 2.17049 0.529846 0.244113541 PSMA4
PROTEASOME SUBUNIT ALPHA TYPE 5 (EC 3.4.25.1) (PROTEASOME ZETA CHAIN) (MACROPAIN ZETA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX ZETA CHAIN). [SWISSPROT;Acc:P28066] 2946 1.38339 0.210608 0.152240511 PSMA5
PROTEASOME SUBUNIT ALPHA TYPE 6 (EC 3.4.25.1) (PROTEASOME IOTA CHAIN) (MACROPAIN IOTA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX IOTA CHAIN) (27 KDA PROSOMAL PROTEIN) (PROS-27) (P27K). [SWISSPROT;Acc:P34062] 1181 3.75112 0.93387 0.248957645 PSMA6
PROTEASOME SUBUNIT ALPHA TYPE 7 (EC 3.4.25.1) (PROTEASOME SUBUNIT RC6-1) (PROTEASOME SUBUNIT XAPC7). [SWISSPROT;Acc:O14818] 1826 3.47138 0.813157 0.234246035 PSMA7
PROTEASOME SUBUNIT ALPHA TYPE 7-LIKE (EC 3.4.25.1). [SWISSPROT;Acc:Q8TAA3] 1815 3.09996 0.726532 0.234368185 PSMA8
PROTEASOME SUBUNIT BETA TYPE 1 (EC 3.4.25.1) (PROTEASOME COMPONENT C5) (MACROPAIN SUBUNIT C5) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C5) (PROTEASOME GAMMA CHAIN). [SWISSPROT;Acc:P20618] 1150 3.08939 0.771753 0.249807567 PSMB1
PROTEASOME SUBUNIT BETA TYPE 10 PRECURSOR (EC 3.4.25.1) (PROTEASOME MECL-1) (MACROPAIN SUBUNIT MECL-1) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT MECL-1). [SWISSPROT;Acc:P40306] 1071 0.294313 0.0742909 0.252421402 CTRL
PROTEASOME SUBUNIT BETA TYPE 2 (EC 3.4.25.1) (PROTEASOME COMPONENT C7-I) (MACROPAIN SUBUNIT C7-I) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C7-I). [SWISSPROT;Acc:P49721] 1569 4.00866 0.966048 0.240990256 PSMB2
PROTEASOME SUBUNIT BETA TYPE 3 (EC 3.4.25.1) (PROTEASOME THETA CHAIN) (PROTEASOME CHAIN 13) (PROTEASOME COMPONENT C10-II). [SWISSPROT;Acc:P49720] 1157 3.13091 0.781534 0.249618801 PSMB3

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/