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.


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description Rank Gene measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 3206 in total
description
Rank
measured
expected
final
Hugo
SACCHAROMYCES CEREVISIAE NIP7P HOMOLOG. [RefSeq;Acc:NM_016101] 1330 0.455858 1.85732 0.245438589 NIP7
SAD1/UNC-84 PROTEIN-LIKE 1. [SWISSPROT;Acc:O94901] 222 0.240086 0.755227 0.317899122 UNC84A
SAL-LIKE PROTEIN 1 (ZINC FINGER PROTEIN SALL1) (SPALT-LIKE TRANSCRIPTION FACTOR 1) (HSAL1). [SWISSPROT;Acc:Q9NSC2] 429 0.176985 0.63809 0.277366829 SALL1
SAL-LIKE PROTEIN 2 (ZINC FINGER PROTEIN SALL2) (HSAL2). [SWISSPROT;Acc:Q9Y467] 414 0.13272 0.478487 0.277374307 SALL2
SAL-LIKE PROTEIN 3 (ZINC FINGER PROTEIN SALL3) (HSALL3). [SWISSPROT;Acc:Q9BXA9] 419 0.148125 0.534032 0.277371019 SALL3
SAL-LIKE PROTEIN 4 (ZINC FINGER PROTEIN SALL4). [SWISSPROT;Acc:Q9UJQ4] 415 0.135171 0.487324 0.277373985 SALL4
SALIVARY PROLINE-RICH PROTEIN PO (ALLELE K) [CONTAINS: PEPTIDE P-D] (FRAGMENT). [SWISSPROT;Acc:P10162] 1449 0.0770791 0.316634 0.243432796 PRB4
SARCOGLYCAN ZETA; ZETA-SARCOGLYCAN. [RefSeq;Acc:NM_139167] 1876 0.0628075 0.269823 0.232772966 SGCZ
SCRATCH; SCRATCH 1. [RefSeq;Acc:NM_031309] 1775 0.322861 1.36866 0.235895694 no value
SCRIBBLE. [RefSeq;Acc:NM_015356] 884 0.163652 0.629348 0.260034194 SCRIB
SCY1-LIKE 1; TELOMERASE REGULATION-ASSOCIATED PROTEIN; HT019 PROTEIN; TELOMERASE REGULATION-ASSOCIATED PROTEIN; N-TERMINAL KINASE-LIKE PROTEIN; TERATOMA-ASSOCIATED TYROSINE KINASE; N-TERMINAL KINASE-LIKE. [RefSeq;Acc:NM_020680] 2174 0.0350787 0.154573 0.226939375 SCYL1
SEC13-RELATED PROTEIN. [SWISSPROT;Acc:P55735] 1753 0.126518 0.534471 0.236716305 SEC13
SECRETED MODULAR CALCIUM-BINDING PROTEIN 1. [RefSeq;Acc:NM_022137] 659 0.0285187 0.106766 0.267114063 no value
SECRETED MODULAR CALCIUM-BINDING PROTEIN 2; SMOOTH MUSCLE ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_022138] 660 0.035822 0.134108 0.267113073 SMOC2
SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 1. [SWISSPROT;Acc:O15126] 2656 0.0466014 0.221972 0.209942695 SCAMP1
SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 2. [SWISSPROT;Acc:O15127] 2655 0.0366237 0.174446 0.209942905 SCAMP2
SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 3. [SWISSPROT;Acc:O14828] 2654 0.0359383 0.171181 0.209943276 SCAMP3
SECRETORY PATHWAY COMPONENT SEC31B-1. [RefSeq;Acc:NM_015490] 1752 0.107954 0.456048 0.236716311 SEC31B
SEDLIN. [SWISSPROT;Acc:O14582] 3025 0.0250043 0.209553 0.119322081 ZNF547
SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-1 (DISHEVELLED-1) (DSH HOMOLOG 1). [SWISSPROT;Acc:O14640] 761 0.217793 0.825859 0.26371693 DVL1
SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-2 (DISHEVELLED-2) (DSH HOMOLOG 2). [SWISSPROT;Acc:O14641] 762 0.223153 0.846393 0.263651755 DVL2
SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-3 (DISHEVELLED-3) (DSH HOMOLOG 3). [SWISSPROT;Acc:Q92997] 771 0.256243 0.973151 0.263312682 DVL3
SENESCENCE MARKER PROTEIN-30 (SMP-30) (REGUCALCIN) (RC). [SWISSPROT;Acc:Q15493] 1620 0.0724203 0.302259 0.239596836 RGN
SEPRASE (EC 3.4.21.-) (FIBROBLAST ACTIVATION PROTEIN ALPHA) (INTEGRAL MEMBRANE SERINE PROTEASE) (170-KDA MELANOMA MEMBRANE-BOUND GELATINASE). [SWISSPROT;Acc:Q12884] 2540 0.0377549 0.175918 0.214616469 FAP
SEPTIN 1 (LARP) (SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR- 24). [SWISSPROT;Acc:Q8WYJ6] 2963 0.0798252 0.547429 0.145818362 SEPT1
SEPTIN 10 ISOFORM 1. [RefSeq;Acc:NM_144710] 3022 0.106813 0.88182 0.121127895 SEPT10
SEPTIN 4 (PEANUT-LIKE PROTEIN 2) (BRAIN PROTEIN H5) (CELL DIVISION CONTROL-RELATED PROTEIN 2) (HCDCREL-2) (BRADEION BETA) (CE5B3 BETA) (CEREBRAL PROTEIN-7) (HUCEP-7). [SWISSPROT;Acc:O43236] 2989 0.16041 1.17491 0.136529607 SEPT4
SEPTIN 6. [SWISSPROT;Acc:Q14141] 3008 0.116797 0.952641 0.122603373 SEPT6
SEPTIN 7 (CDC10 PROTEIN HOMOLOG). [SWISSPROT;Acc:Q16181] 3009 0.09144 0.749104 0.122065828 SEPT7
SEPTIN-LIKE PROTEIN KIAA0202 (FRAGMENT). [SWISSPROT;Acc:Q92599] 3023 0.118014 0.986632 0.119612986 SEPT8
SEQUESTOSOME 1; UBIQUITIN-BINDING PROTEIN P62; PHOSPHOTYROSINE INDEPENDENT LIGAND FOR THE LCK SH2 DOMAIN P62. [RefSeq;Acc:NM_003900] 107 0.0692099 0.188735 0.366704109 SQSTM1
SERINE PALMITOYLTRANSFERASE 1 (EC 2.3.1.50) (LONG CHAIN BASE BIOSYNTHESIS PROTEIN 1) (LCB 1) (SERINE-PALMITOYL-COA TRANSFERASE 1) (SPT 1) (SPT1). [SWISSPROT;Acc:O15269] 2167 0.0595157 0.262124 0.227051701 SPTLC1
SERINE PALMITOYLTRANSFERASE 2 (EC 2.3.1.50) (LONG CHAIN BASE BIOSYNTHESIS PROTEIN 2) (LCB 2) (SERINE-PALMITOYL-COA TRANSFERASE 2) (SPT 2). [SWISSPROT;Acc:O15270] 2304 0.0524219 0.235868 0.222251005 SPTLC2
SERINE PROTEASE HTRA1 PRECURSOR (EC 3.4.21.-) (L56). [SWISSPROT;Acc:Q92743] 2586 0.574918 2.69828 0.213068325 HTRA1
SERINE RACEMASE (EC 5.1.1.-). [SWISSPROT;Acc:Q9GZT4] 1955 0.0573513 0.247999 0.231256174 SRR
SERINE--PYRUVATE AMINOTRANSFERASE (EC 2.6.1.51) (SPT) (ALANINE-- GLYOXYLATE AMINOTRANSFERASE) (EC 2.6.1.44) (AGT). [SWISSPROT;Acc:P21549] 2351 0.143655 0.651843 0.220382822 AGXT
SERINE/THREONINE KINASE 6 (EC 2.7.1.37) (SERINE/THREONINE KINASE 15) (AURORA/IPL1-RELATED KINASE 1) (AURORA-RELATED KINASE 1) (HARK1) (AURORA-A) (BREAST-TUMOR-AMPLIFIED KINASE). [SWISSPROT;Acc:O14965] 1255 0.0366317 0.148106 0.247334342 AURKA
SERINE/THREONINE PROTEIN KINASE 12 (EC 2.7.1.37) (AURORA- AND IPL1- LIKE MIDBODY-ASSOCIATED PROTEIN 1) (AIM-1) (AURORA/IPL1-RELATED KINASE 2) (AURORA-RELATED KINASE 2) (STK-1) (AURORA-B). [SWISSPROT;Acc:Q96GD4] 1257 0.0285544 0.115449 0.247333455 AURKB
SERINE/THREONINE PROTEIN KINASE 13 (EC 2.7.1.37) (AURORA/IPL1/EG2 PROTEIN 2) (AURORA/IPL1-RELATED KINASE 3) (AURORA-C). [SWISSPROT;Acc:Q9UQB9] 1254 0.0283804 0.114745 0.247334524 AURKC
SERINE/THREONINE PROTEIN KINASE 23 (EC 2.7.1.37) (MUSCLE-SPECIFIC SERINE KINASE 1) (MSSK-1). [SWISSPROT;Acc:Q9UPE1] 1342 0.0417611 0.170257 0.24528272 SRPK3
SERINE/THREONINE PROTEIN PHOSPHATASE 4 (EC 3.1.3.16) (PP4) (PROTEIN PHOSPHATASE X) (PP-X). [SWISSPROT;Acc:P33172] 1598 0.161804 0.67395 0.240083092 PPP4C
SERINE/THREONINE PROTEIN PHOSPHATASE 6 (EC 3.1.3.16) (PP6). [SWISSPROT;Acc:O00743] 2760 0.0987657 0.487402 0.202637043 PPP6C
SERINE/THREONINE PROTEIN PHOSPHATASE PP1-ALPHA 1 CATALYTIC SUBUNIT (EC 3.1.3.16) (PP-1A). [SWISSPROT;Acc:P08129] 2333 0.634044 2.86607 0.221224185 PPP1CA
SERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT (EC 3.1.3.16) (PP-1G). [SWISSPROT;Acc:P36873] 2393 0.518333 2.36093 0.219546111 PPP1CC
SERINE/THREONINE-PROTEIN KINASE DCAMKL1 (EC 2.7.1.-) (DOUBLECORTIN- LIKE AND CAM KINASE-LIKE 1). [SWISSPROT;Acc:O15075] 1432 0.408607 1.67671 0.24369569 DCLK1
SERINE/THREONINE-PROTEIN KINASE NEK1 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 1) (NY-REN-55 ANTIGEN). [SWISSPROT;Acc:Q96PY6] 1690 0.035086 0.147362 0.238093946 NEK1
SERINE/THREONINE-PROTEIN KINASE NEK2 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 2) (NIMA-LIKE PROTEIN KINASE 1) (HSPK 21). [SWISSPROT;Acc:P51955] 16 0.106175 0.22325 0.475587906 NEK2
SERINE/THREONINE-PROTEIN KINASE NEK3 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 3) (HSPK 36). [SWISSPROT;Acc:P51956] 1688 0.0267969 0.112547 0.238095196 NEK3
SERINE/THREONINE-PROTEIN KINASE PAK 1 (EC 2.7.1.-) (P21-ACTIVATED KINASE 1) (PAK-1) (P65-PAK) (ALPHA-PAK). [SWISSPROT;Acc:Q13153] 2184 0.0568471 0.250928 0.226547456 PAK1
SERINE/THREONINE-PROTEIN KINASE PAK 2 (EC 2.7.1.-) (P21-ACTIVATED KINASE 2) (PAK-2) (PAK65) (GAMMA-PAK) (S6/H4 KINASE). [SWISSPROT;Acc:Q13177] 2182 0.0463914 0.204773 0.226550375 PAK2

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/